title: 3 day-old WT dark-grown cotyledons exposed to light for three hours in the presence of ABA rep3

city: Cerdanyola del Vallès

first: Guiomar

last: Martín

state: Barcelona

address: Vall Moronta

country: Spain

institute: Centre for Research in Agricultural Genomics

data_processing:
Gene expression (GE) quantification is performed using vast-tools. vast-tools maps the first 50 nucleotides of the forward read (if longer and paired end) to a library with one reference transcript per gene, the *.1 transcript according to the TAIR 10 nomenclature or else that with the lowest suffix (33,602 genes in total). GE levels are provided using the cRPKM metric (corrected [for mappability] Reads Per Kilobasepair and Million mapped reads), as detailed in Labbé et al., Stem Cells 2012. cRPKM can be converted to TPMs applying the following formula: TPM = 10^6 * cRPKM/sum_all(cRPKM).
Assembly: Ensemble Plants v31
Supplementary files format and content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

organism: Arabidopsis thaliana

source_name: cotyledons

growth_protocol: Stratified seeds were irradiated with white light at 21 ºC for 3 hours to induce germination and then grown in darkness for 3 days before being exposed to white light (40 µmol·m-2·s-1) in the presence or absence of ABA (100 µM).

extract_protocol:
Total RNA (1 µg) was extracted from whole Arabidopsis seedlings using the innuPREP Plant RNA kit (Analytik Jena BioSolutions).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cotyledons

tag: cultivar

value: Columbia

value: 3 hours in white light in the presence of ABA (100uM)


title: cardiomyocyte,sham, replicate1-12, scRNAseq

status: Public on Aug 01 2024

type: SRA

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

description:
smartseq2
sham_1.xlsx

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: heart

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.

tag: cell type

value: cardiomyocyte

tag: tissue

value: heart

tag: strain

tag: age

value: 6-8 weeks old

tag: treatment

value: sham


title: WT_1

type: RNA

city: Shanghai

first: Shiliang

last: Cai

address: 800 Xiangyin Road

country: China

institute: Second Military Medical University

description: Gene expression in Hela cells transfected with  wild type preS

hyb_protocol: Sample hybridization was performed for 16 hours at 45°C according to standard protocol. Washing and staining was performed on Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip scanner 3000.

data_processing: The data were processed with Expression Console Software. Normalization was performed by the Signal Space Transformation-Robust multi-array average method (sst-RMA).

label: biotin

organism: Homo sapiens

source_name: WT,replicate 1

label_protocol: Labeling was performed according to manufacturer's standard protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HeLa cell lines expressing wild-type and mutant preS stably was constructed.

tag: cell line

value: HeLa


title: shKLF2_rep2

first: Qian

last: Bian

address: Jinzun Road No.115

department: Shanghai Institute of Precision Medicine, Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

description: shKLF2 RNA-seq replicate2

library_source: transcriptomic

data_processing:
For analyzing RNA-seq data of shControl and shKLF2 HemSCs, adaptor-trimmed sequencing data were aligned to human reference genome (hg38) with STAR (version 2.7.3a). Mapped reads were then counted with HTSeq (version 0.12.4) to generate counts of RNA-seq libraries, which were further normalized with DESeq2 (version 1.38.1).
Reads matching the forward primer sequence were selected from the total fastq files to ensure an overall high quality of the raw data. The primer sequences were then removed from selected reads, which were then mapped to mm10 reference genome with Bowtie2.
Adaptor sequences in CUT&Tag fastq files were trimmed with trim galore.
Differentially expressed genes (DEGs) were identified with cutoff P value<0.05 and |log2Foldchange|>1.
FPKM values of each sample were counted with rnanorm (https://github.com/genialis/RNAnorm).
Assembly: hg38
Supplementary files format and content: counts (mapped counts)
Supplementary files format and content: csv (FPKM)
Supplementary files format and content: csv (DEGs)

source_name: HemSCs

extract_protocol:
Proliferating regions of IH specimens were minced into pieces and digested with collagenase (Sigma-Aldrich) and Dispase (Gibco). After removal of red blood cells with RBC lysis buffer (Sangon), HemSCs were isolated from cell suspension by anti-CD133 magnetic beads (Miltenyi), and were cultured in vitro on fibronectin-coated (Corning) petri dishes or plates in Endothelial Cell Growth Medium-2 (EGM-2, Lonza, Cat#CC-3162) supplemented with 20% FBS (Gibco). HemSCs between passage 3 to passage 6 were used in this study.
Briefly,mRNA was captured from total RNA with VAHTS mRNA Capture Beads (Vazyme, Cat#N401) for fragmentation into short length nucleotides. First-strand cDNA synthesis was then performed with   1st Strand Enzyme Mix 2, followed by generation of second-strand cDNA with 2nd Strand Enzyme Super Mix. Double-stranded cDNA was then ligated with sequencing adapters, purified and amplified with PCR. After size selection, the RNA-seq libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode. Three biological replicates of RNA-seq libraries were prepared for shControl and shKLF2 HemSCs respectively.

tag: genotype

value: KLF2 Knockdown

value: HemSCs


title: Cell_7d_bio1_tech1

first: Huaxin

last: Song

address: Shanghai Jiao Tong University School of Medicine

description: Cell growth inhibition test.xlsx

library_source: genomic

data_processing:
Library strategy: DNA-seq
NGS data were processed with the ORFCall software developed by the Broad Institute and aligned to the TP53 reference sequence. The raw read counts were standardized to the fraction of counts at each codon position. Then, the reads of each p53 variant were normalized so that the average reads of 5 nonsense variants in different libraries will be equal.
Genome_build: TP53 CDS
Supplementary_files_format_and_content: Excel table includes normalized reads of each sample

molecule: genomic DNA

source_name: Myeloid malignant cell line

growth_protocol: U937 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (Moregate) and cultured in a humidified incubator at 32 or 37℃ under 5% CO2.

extract_protocol:
gDNA was purified from a minimum of 1 × 106 library cells using Blood Genomic DNA Mini Kit (CW2087, Cwbio). Three PCR reactions were performed for each gDNA sample to amplify the p53 region. Each reaction contained a total volume of 50 μL with 1 μg gDNA, 25 μL of VAHTS® HiFi Amplification Mix (N616-02, Vazyme) and 2.5 μL of each (5 μM) library amplification primer. The parameters for PCR were 95 °C for 3 min, 27 cycles of 98 °C for 20 s, 58 °C for 15 s, and 72 °C for 45 s, followed by one cycle of 72 °C for 5 min. Amplicons were separated from nonspecific fragments by electrophoresis on a 1% agarose gel, extracted from the gel and purified using a Wizard® SV Gel and PCR Clean-Up System (A9282, Promega).
Sequencing sample preparations reactions were performed using TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme), followed by sequenced on an Illumina Novaseq6000 (Illumina) using two reads, each 150 bases in length.

treatment_protocol: no treatment/0.6 μg/ml ATO/intraperitoneal injection with PBS daily/intraperitoneal injection with 5 mg/kg ATO daily/cell culture at 32 degrees Celsius

tag: experiment

value: cell growth inhibition test

value: no treatment


title: Sunitinib-Treated rep2 RNA-Seq

city: Chicago

first: Soroush

last: Tahmasebi

address: 909 S Wolcott, Chicago, IL 60607

country: USA

institute: University of Illinois

data_processing:
adapter AGATCGGAAGAGCACACGTCTGAA was removed with cutadapt version 1.18
Reads aligning to human rRNA were removed (aligned using bowtie 1.0.1)
Reads were aligned to the human GENCODE transcriptome version 25 (aligned using bowtie version 1.0.1)
Read counts were extracted from the CDS regions of principal transcript isoforms (principal isoforms were taken from the APPRIS database)
hg38
Genome_build: Matrix table with raw gene counts for every gene and every sample

source_name: iPSC-Ecs

extract_protocol:
RNA fragments of expected size were isolated after the ribosomal pellet was resolved by electrophoresis through a denaturing gel.
Gel extract footprints were reverse-transcribed and cloned into a cDNA library for RNA sequencing.Randomly fragmented total mRNA libraries were also prepared in parallel for each sample for RNA sequencing.

value: iPSC-EC

tag: molecule subtype

value: total RNA


title: Control rep1 Ribo-Seq

data_processing:
Library strategy: Ribo-seq
adapter AGATCGGAAGAGCACACGTCTGAA was removed with cutadapt version 1.18
Reads aligning to human rRNA were removed (aligned using bowtie 1.0.1)
Reads were aligned to the human GENCODE transcriptome version 25 (aligned using bowtie version 1.0.1)
Read counts were extracted from the CDS regions of principal transcript isoforms (principal isoforms were taken from the APPRIS database)
hg38
Genome_build: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

value: Ribosome Protected Fragments


title: 3 day-old WT dark-grown cotyledons exposed to light for three hours in the presence of ABA rep2


title: shControl_rep1

description: shControl RNA-seq replicate1

value: Control


title: THAP1_YY1-ChIP-seq R2

city: Tuebingen

first: Fubo

last: Cheng

address: Calwerstrasse 7

department: Institute of Medical Genetics and Applied Genomics

country: Germany

institute: University of Tuebingen

data_processing:
Base calling performed using Illumina bcl2fastq2 version 2.19.1
Reads qualities of ChIP-seq data in fastq files were assessed using QoRTs (v1.2.37)
ChIP-seq raw reads were aligned to the hg19 genome assembly using Bowtie. Only reads that uniquely mapped to the genome were used for further analysis.
ChIP-seq peaks were identified using MACS.
Assembly: hg19
Supplementary files format and content: Bigwig file

growth_protocol: SH-SY5Y cells were maintained in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum and 1% GlutaMAX at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Cells were crosslinked by 1% formaldehyde (ThermoFisher scientific) and sonicated in RIPA buffer (10mM Tris-HCl, 1mM EDTA, 0.5% sodium deoxycholate, 0.1% SDS, 1% NP-40, 1× Protease inhibitor cocktail (Roche), pH 8.0) to 200-500 bp. The sonicated lysate was subjected to immunoprecipitation with specific antibody. The immunoprecipitated DNA (at least 1ng) was purified and subjected to libraries generation.
ChIP-seq libraries were generated using NEBNext® Ultra™ II DNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions.

value: Neuroblastoma

tag: chip antibody


title: 3 day-old WT dark-grown cotyledons exposed to light for three hours in the presence of ABA rep1

value: cotyledons


title: cardiomyocyte,sham, replicate1-10, scRNAseq

description:
smartseq2
sham_1.xlsx


title: Vector

description: Gene expression in Hela cells transfected with Vector

source_name: Vector,replicate 1


title: Sunitinib-Treated rep1 RNA-Seq


title: THAP1_YY1-ChIP-seq R1


title: Control rep2 RNA-Seq


title: cardiomyocyte,sham, replicate1-9, scRNAseq

description:
smartseq2
sham_1.xlsx


title: WT_YY1_ChIP-seq_R2

value: Wild-type


title: cardiomyocyte,sham, replicate1-8, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 3 day-old WT dark-grown cotyledons exposed to light for three hours rep3

value: Columbia

value: 3 hours in white light


title: 3 day-old WT dark-grown cotyledons exposed to light for three hours rep2


title: Control rep1 RNA-Seq


title: WT_YY1_ChIP-seq_R1


title: cardiomyocyte,sham, replicate1-7, scRNAseq

description:
smartseq2
sham_1.xlsx

value: cardiomyocyte

value: heart


title: 3 day-old WT dark-grown cotyledons rep3

value: darkness


title: cardiomyocyte,sham, replicate1-6, scRNAseq

description:
smartseq2
sham_1.xlsx

value: 6-8 weeks old

value: sham


title: cardiomyocyte,sham, replicate1-11, scRNAseq

description:
smartseq2
sham_1.xlsx


title: 3 day-old WT dark-grown cotyledons exposed to light for three hours rep1


title: CSNK2A1_CTCF-ChIP-seq R2

value: CTCF


title: CSNK2A1_CTCF-ChIP-seq R1


title: 3 day-old WT dark-grown cotyledons rep2


title: 3 day-old WT dark-grown cotyledons rep1


title: cardiomyocyte,sham, replicate1-4, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,sham, replicate1-5, scRNAseq

description:
smartseq2
sham_1.xlsx


title: cardiomyocyte,sham, replicate1-2, scRNAseq

description:
smartseq2
sham_1.xlsx


title: WT_CTCF_ChIP-seq_R4


title: THAP1_CTCF-ChIP-seq R1


title: Fresh CD4+ cells, miR-23/24/27 KO

city: San Francisco

first: K. Mark

last: Ansel

state: CA

address: 513 Parnassus Ave. UCSF Box 0414

department: Microbiology & Immunology

institute: UCSF

description: Ago2 HITS-CLIP analysis of freshly isolated miR-23, 24, 27 KO CD4 T cells (not analyzed with DeepRNA-Reg)

data_processing:
Raw Fastqs were binned based on barcode using python bst and perl fastx_barcode_splitter.pl
barcodes and adapters were trimmed using parallel -j3 'cutadapt -e 0.2 -a GTGTCTTTACACAGCTACGGCGTCG -m 19 --cut 11
The fastq files were aligned to the mm10 genome using bowtie2 and samtools
For downstream use with dCLIP and DeepRNA-reg, miRNA reads (miRBase) were exluded using samtools
Assembly: mm10
Supplementary files format and content: BAM files containing aligned reads excluding those that align with mature miRNAs from miRBase

source_name: spleen and lymph nodes

growth_protocol: T cells from mouse spleens and lymph nodes were enriched by Dynabead-positive selection (Invitrogen). For Th2 culture, enriched CD4+ T cells were plated into culture wells precoated with goat anti-hamster IgG (1 μg/mL, Thermo) in high glucose DMEM with pyruvate and L-glutamine containing 1x MEM non-essential amino acids, 1x MEM vitamin solution, 1x aspartate - arginine -folic acid mixture, 1x penicillin and streptomycin, 1x HEPES, 1x L-glutamine, 2-mercapoethanol and 10% fetal bovine serum. Cells were activated with hamster anti-mouse CD3 (clone 2C11) and CD28 (clone 37.51) in the presence of IL-4 (500 U/mL) and anti-IFN-γ (clone XMG1.2) for 3 days to promote Th2 cell differentiation. Cells were then split into new dishes containing fresh media supplemented with recombinant IL-2 (20 U/mL, NCI Biological Resources Branch), IL-4, and anti-IFN-γ for each of the next 2 days.

extract_protocol:
Cells were lysed by resuspension in PXL buffer without SDS. Cell debris was pelleted and lysate was treated with magnetically bound AGO2 antibody (Wako).
Immunoprecipitation beads were treated to an on bead ligation of radiolabeled 3' linker RNA. RNA was removed from beads and run on a size selecting SDS-PAGE gel, and AGO2-RNA complexes were selected. RNA was gel extracted and treated with proteinase K, and treated with a 5' linker before reverse transription and used for cDNA amplification.

treatment_protocol: Cells were UV treated to crosslink RNA and protein prior to lysis.

value: spleen and lymph nodes

value: CD4+ T Cells

value: Mirc11;Mirc22 dKO


title: Fresh CD4+ cells, WT

description: Ago2 HITS-CLIP analysis of freshly isolated WT CD4 T cells (not analyzed with DeepRNA-Reg)

value: WT


title: cardiomyocyte,sham, replicate1-3, scRNAseq

description:
smartseq2
sham_1.xlsx


title: WT_CTCF_ChIP-seq_R3


title: Tumor Bearing for KPP C

city: Charleston

first: Benjamin

last: Pryce

address: 173 Ashley Ave

institute: Medical University of South Carolina

description: Total RNA extracted from muscle tissue, 100ng loaded onto the platform

hyb_protocol: No hyb

scan_protocol: No scan

data_processing: Each tumor model were isolated individually on nCounter platform. Background and Normalization to housekeeping genes was performed in nCounter software. Counts were extracted and converted to z-scores

label: no label

source_name: muscle tissue

label_protocol: No label

growth_protocol: All mouse experiments were approved the Medical University of South Carolina Institutional Animal Care and Use Committee under protocol IACUC-2021-01223. Animals were housed with littermates, up to 5 total mice/cage and given ad libitum access to a standard show diet and water. Due to sexual dimorphisms in cancer cachexia, only male mice were used in this study

extract_protocol: TA muscles were isolated from sacrificed mice and flash frozen

treatment_protocol: 1x10^6 C26, or 5x10^5 C-26 and LLC cells were injected into mice. Tamoxifen (1mg/10g) was injected IP into KPP mice to induce tumor formation

tag: tumor status

value: tumor bearing

tag: Sex

value: male


title: cardiomyocyte,sham, replicate1-1, scRNAseq

description:
smartseq2
sham_1.xlsx


title: Th2 cells, miR-23/24/27 KO

description: Ago2 HITS-CLIP analysis of miR-23, 24, 27 KO Th2 cells; Proceed data show DeepRNA-Reg predicted loci of enrichment in the miR-23, 24, 27 KO condition, relative to the WT condition

value: Th2 culture


title: WT_CTCF_ChIP-seq_R2

value: Neuroblastoma


title: Th2 cells, WT

description: Ago2 HITS-CLIP analysis of WT Th2 cells; Proceed data show DeepRNA-Reg predicted loci of enrichment in the WT condition, relative to miR-23, 24, 27 KO


title: Tumor Bearing for KPP A


title: THAP1_CTCF-ChIP-seq R2


title: Human_Ctrl siRNA_72h_Cy3_rep1

city: Xi`an

first: Rui

last: Ge

address: YAN TA WEST ROAD N0.277

department: Department of Dermatology

institute: First Affiliated Hospital，Xi’an Jiaotong University

description:
raw data file: A2058 ctrl vs. PARP1 72h.txt
A2058-Ctrl siRNA-72h(Cy3)

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v13 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by lowess normalization.

source_name: Ctrl siRNA transfected A2058 cells

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: A2058 cells were maintained in DMEM (Gibco; Thermo Fisher Scientific, Inc.) supplemented with 10% FBS (Invitrogen; Thermo Fisher Scientific, Inc.).

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: A2058 cells were transfected with PARP1 siRNA or control siRNA for 48 and 72 h using Lipofectamine 3000 (Invitrogen; Thermo Fisher Scientific, Inc.) following manufacturer's instructions.

tag: time point

value: day 5

tag: genotype/variation

value: Ctrl siRNA transfected


title: 810-plus-LPS-3

city: Hangzhou

first: Facai

last: Zhang

state: Zhejiang

address: 158 Shangtang Road

institute: Zhejiang Provincial People‘s Hospital

data_processing:
Genes were considered significantly differentially expressed if they had an adjusted P value <0.01.
Assembly: hg18
Supplementary files format and content: excel files included raw counts and FPKM value

source_name: Abdominal

growth_protocol: WT、TLR4-K730R and TLR4-K810R mouse peritoneal macrophages were obtained as previously described and subjected to treatment with LPS (100 ng/mL) for 6 hours. Subsequently, total RNA from the cells was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA, USA), following the manufacturer’s instructions. The RNA-seq analysis was performed by GENEWIZ, Inc., utilizing an Illumina sequencing platform.

extract_protocol:
total RNA from the cells was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA, USA)
The RNA-seq analysis was performed by GENEWIZ, Inc., utilizing an Illumina sequencing platform

value: Abdominal

value: macrophage

value: LPS


title: WT_CTCF_ChIP-seq_R1

value: Wild-type


title: Control for KPP C

value: non tumor bearing


title: KO_rep2

city: Ann Arbor

first: Shigeki

last: Iwase

address: 1241 E. Catherine St.

institute: University of Michigan

data_processing:
Read QC by FastQC
Read alignment by STAR
Transcript quantification by RSEM
Assembly: mm10
Supplementary files format and content: Count table were generaetd by RSEM, which is fed to Deseq2 for differential expression analysis

source_name: Cerebellum

extract_protocol:
Total RNA was isolated from fresh cerebellum tissue using the RNeasy mini kit (Qiagen, Valencia, CA). RNA concentration was measured on Epoch Microplate Spectrophotometer (BioTek Winooski, Vermont). RNA integrity assessment was performed on an Agilent Bioanalyzer 2100 using a Nano 6000 assay kit (Agilent Technologies, Santa Clara, CA). A RNA integrity number (RIN) > 7.2 was considered the minimum requirement for library preparation .
NEBNext Ultra II Directional RNA Library Prep Kit

value: Cerebellum


title: KO_rep1


title: Human_PARP1 siRNA_72h_Cy5_rep1

description:
raw data file: A2058 ctrl vs. PARP1 72h.txt
A2058-PARP1 siRNA-72h(Cy5)

source_name: PARP1 siRNA transfected A2058 cells

value: PARP1 siRNA transfected


title: 810-plus-LPS-2


title: Human_Ctrl siRNA_48h_Cy3_rep1

description:
raw data file: A2058 ctrl vs. PARP1 48h.txt
A2058-Ctrl siRNA-48h(Cy3)

value: day 4


title: SH_CSNK2A1_KO_C2

data_processing:
Read quality of RNA-seq data in fastq files was assessed using QoRTs (v1.2.37).
Reads were aligned to hg19 genome using HISAT2 (Version 2.2.1).
Normalized read counts for all genes were obtained using featureCount (v3.18.1).
Differential expression was determined in each of the pair-wise comparisons between experimental and control groups using DESeq (V1.22.1).
Assembly: hg19
Supplementary files format and content: Tabular files include raw counts for each sample.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (QIAGEN) following manufacturer’s protocol.
A total of 100ng total RNA was subjected to polyA enrichment and cDNA libraries preparation using NEBNext Ultra II Directional RNA library Preparation Kit for Illumina (NEB, E7760L).

value: CSNK2A1 KO


title: Control for KPP B


title: Human_PARP1 siRNA_48h_Cy5_rep1

description:
raw data file: A2058 ctrl vs. PARP1 48h.txt
A2058-PARP1 siRNA-48h(Cy5)


title: 810-plus-LPS-1


title: WT_rep3


title: SH_CSNK2A1_KO_C1


title: WT_rep2


title: SH_PAF1_KO_C1

value: PAF1 KO


title: SH_PAF1_KO_C2


title: Tumor Bearing for LLC C


title: Tumor Bearing for LLC B


title: WT_rep1

value: WT


title: 810-minus-LPS-2

value: control


title: Tumor Bearing for KPP B

value: tumor bearing

value: male


title: 810-minus-LPS-1


title: Tumor Bearing for LLC A


title: M_3

city: suzhou

first: Chenya

last: Wang

institute: Soochow University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/ , version:cutadapt-1.9).
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/ , version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/ , version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml , version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Ensembl release 101 (ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/).
Supplementary files format and content: MVSBlank_Gene_differential_expression.txt
Supplementary files format and content: MVSBlank_Transcript_differential_expression.txt

source_name: tumor tissue

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA libraries were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Balb/c mouse CT26 colon cancer model

value: tumor tissue

value: M@F.S treated


title: M_2


title: SH_CTCF_KO_C1

value: Neuroblastoma

value: CTCF KO


title: 730-plus-LPS-3

value: Abdominal

value: macrophage

value: LPS


title: M_1


title: 730-plus-LPS-2


title: DNAJB1-PRKACA expressing liver cancer H12 cells, 6

city: Madison

first: Sean

middle: M

last: Ronnekleiv-Kelly

state: Wisconsin

address: K3/705 CSC, 600 Highland Avenue

department: Surgery

institute: University of Wisconsin Madison School of Medicine and Public Health

data_processing:
Illumina bcl2fastq v2.20.0.422
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output
Differential expression estimation with edgeR v3.28.0, including read-count filtering with option filterByExpr
Assembly: GRCh38.p10 (NCBI:GCA_000001405.25)
Supplementary files format and content: Microsoft excel document of differential expression results

growth_protocol: Hepatoblastoma HepG2 cell line was obtained from ATCC. Cells were maintained in RPMI1640 culture medium supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin-glutamine at 37 °C and 5% CO2.

extract_protocol:
RNA Isolation was carried out using the RNeasy protocol according to the manufacturer’s recommendations. Quality was tested for an RNA integrity number (RIN) > 7.5 on the Agilent 2100 bioanalyzer.
A total of 300 ng of mRNA was enriched with poly-A selection and sequencing was performed on the Illumina NovaSeq 6000 platform.

treatment_protocol: To evaluate for transcriptomic differences between HepG2 and HepG2DNAJB1-PRKACA clones (H33 and H12 cells), bulk RNA-seq was performed on 6 biological replicates collected from each cell line.

value: hepatoblastoma


title: DNAJB1-PRKACA expressing liver cancer H12 cells, 5


title: KO_rep3

value: Cerebellum


title: Control for LLC B

value: non tumor bearing


title: Control for LLC A


title: 730-plus-LPS-1


title: Blank_3

value: untreated


title: DNAJB1-PRKACA expressing liver cancer H12 cells, 4


title: SH_CTCF_KO_C2


title: Blank_2


title: DNAJB1-PRKACA expressing liver cancer H12 cells, 3


title: Control for KPP A


title: Tumor Bearing for C26 C


title: Tumor Bearing for C26 B


title: CH27, NFYB, IP2

city: Milano

first: Diletta

last: Dolfini

state: MI

address: Via Celoria, 26

department: Bioscience

country: Italy

institute: University of Milan

description:
ChIP-seq reads were trimmed to get a final length of 35 bp
NFYB_CH27_ENCODEpipeline_mm10_fc_signal.bigwig
NFYB_CH27_ENCODEpipeline_mm10.bed

data_processing:
ChIP-seq reads were processed using the ENCODE pipeline 2.1.5, setting default peak caller and bowtie2 aligner.
Homo sapiens ChIP-seq reads were aligned to the hg38 v4 genome provided by ENCODE pipeline.
Mus musculus ChIP-seq reads were aligned to the mm10 v4 genome provided by ENCODE pipeline.
Supplementary files format and content: hg38, mm10
Supplementary files format and content: bigWig, bed narrowPeak (except for Input sample)

extract_protocol:
HeLa: material was processed for ChIP.
DNA libraries were prepared using the NEbNext ChIP-Seq Library kit and TruSeq sample prep (Illumina)

treatment_protocol: HeLa cells at 25-30% confluence were transfected with 50 nM siRNA using Lipofectamine 3000 Reagent (ThermoFisher).

value: Tumor

value: NFYB, IP


title: DNAJB1-PRKACA expressing liver cancer H12 cells, 2


title: 730-minus-LPS-1

value: control


title: WT-plus-LPS-3

value: WT


title: DNAJB1-PRKACA expressing liver cancer H12 cells, 1


title: WT-plus-LPS-2


title: Tumor Bearing for C26 A

value: tumor bearing

value: male


title: Control for C26 C


title: 730-minus-LPS-3


title: Control for LLC C


title: MEL, NFYB, IP, rep2

description:
ChIP-seq reads were trimmed to get a final length of 35 bp
NFYB_MEL_ENCODEpipeline_mm10_fc_signal.bigwig
NFYB_MEL_ENCODEpipeline_mm10.bed

source_name: MEL

value: MEL


title: WT-plus-LPS-1


title: DNAJB1-PRKACA expressing liver cancer H33 cells 5

extract_protocol:
RNA Isolation was carried out using the RNeasy protocol according to the manufacturer’s recommendations. Quality was tested for an RNA integrity number (RIN) > 7.5 on the Agilent 2100 bioanalyzer.
A total of 300 ng of mRNA was enriched with poly-A selection and sequencing was performed on the Illumina NovaSeq6000 platform.


title: DNAJB1-PRKACA expressing liver cancer H33 cells 6


title: Control for C26 B


title: Blank_1

value: Balb/c mouse CT26 colon cancer model

value: tumor tissue


title: 810-minus-LPS-3


title: Lint-O KD RNA-seq rep 2

city: Yayoi, Bunkyo-ku

first: Hitomi

last: Yamamoto-Matsuda

department: Dept. Biol. Sci.

institute: the University of Tokyo

data_processing:
Basecalls were performed by illumina Hiseq
RNA-seq reads were alighed to the dm6 genome assembly using HISAT2
only unique reads were extracted
reads are counted per genes by HTSeq
Differential expression analysis were done by edgeR, and FPKMs were caluculated
genome build: dm6
processed data files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila melanogaster

source_name: OSCs

growth_protocol: OSCs were cultured in Shields and Sang M3 Insect Medium(Sigma). The medium included extra-added 0.6 mg/ml glutathione, 10% FBS, 10mU/mL insulin and 10% fly extract(Saito et al., 2009)

extract_protocol:
RNAs were extracted according to NipponGene's instructions accompanying RNA extraction kit(311-07361).
Libraries were prepared according to Illumina's instructions accompanying Truseq Stranded mRNA Library Prep Kit(20020595). Poly-A selected mRNAs were brought to library preparation.

treatment_protocol: RNAi treated for 48 hours

value: cultured ovarian somatic cells [OSCs]

value: Lint-O KD


title: Control for C26 A


title: WT-minus-LPS-3

value: Abdominal

value: macrophage


title: CH27, input

description: ChIP-seq reads were trimmed to get a final length of 35 bp


title: Lint-O KD RNA-seq rep 1


title: DNAJB1-PRKACA expressing liver cancer H33 cells 4

value: hepatoblastoma


title: DNAJB1-PRKACA expressing liver cancer H33 cells 3


title: WT-minus-LPS-2


title: MEL, input


title: DNAJB1-PRKACA expressing liver cancer H33 cells 2


title: Lint-1 KD RNA-seq rep 2

value: Lint-1 KD


title: CH27, NFYB, IP1


title: 730-minus-LPS-2


title: WT-minus-LPS-1


title: D464T28_WT2

city: Paris

first: Kevin

last: De Azevedo

address: 12 rue Lhomond

country: France

institute: Institut Curie

data_processing:
Sample demultiplexing, alignment, UMI counting, and cell calling is performed using CellRanger v3.0.2 with default parameters
Doublets are predicted by running doubletdetection.py 50 times with a p-value threshold of 1E-7 at each iteration; a barcode is labeled as doublet if it is detected as such in at least 40 iterations
Gene-cell expression matrices imported with Seurat v3.0.0 for each sample separately. Expression values normalized and log-transformed (log((xij+1)/nj) where x is the UMI count of gene j in cell i and nj is the total UMI count for cell j); cells with <200 detected genes (UMI>0) and genes detected in <2 cells are filtered out
Filtered and normalized gene-cell expression matrices for the four samples are concatenated; gene expression is centered and scaled (z-score)
Gene expression dispersion computed with mean.var.plot method from Seurat v3.0.0; highly variable genes defined as those with average expression in [0.1,10] and scaled dispersion 1
PCA computed on the highly variable genes; the 20 top PCs are retained. Clustering on the 20 PCs using Waltman and van Eck algorithm using k=50 neighbors and resolution r=0.1
Genome_build: mm10
Supplementary_files_format_and_content: All-samples_cluster_renamed.rds.gz : RDS Seurat object with counts, metadata and clustering results
Supplementary_files_format_and_content: counts.tsv.gz : Raw counts for every cell in every sample
Supplementary_files_format_and_content: norm_counts.tsv.gz : Normalized counts for every cell in every sample
Supplementary_files_format_and_content: sc_metadata_progeria.tsv.gz : Cell-level metadata
Supplementary_files_format_and_content: Raw barcodes, features, and matrix from CellRanger
Supplementary_files_format_and_content: Filtered barcodes, features and matrix from CellRanger

source_name: Lung CD45+ cells

extract_protocol:
Live, CD45.2+ immune cells were sorted from the lungs of 2 WT vand 2 LmnaG609G/G609G mice at 15 weeks of age.
Approximately 9600 cells were processed using the Chromium Single Cell 3' Reagents Kits v3.1 and sequenced using 25,000 reads per cell (NovaSeq).

tag: phenotype

value: Wild-Type

value: lung

value: CD45.2+ immune cells

value: LmnaWT/WT

value: mixed B6 J/N

value: 15 weeks


title: DNAJB1-PRKACA expressing liver cancer H33 cells 1


title: Srebp1c, High fat diet, ZT18 HiSeq_rep2

city: MEXICO CITY

first: LORENA

last: AGUILAR ARNAL

address: TERCER CIRCUITO EXTERIOR, CU

department: BIOLOGIA CELULAR Y FISIOLOGIA

country: Mexico

institute: INSTITUTO DE INVESTIGACIONES BIOMEDICAS- UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO

data_processing:
Adapters and primer sequences were trimmed using Trim Galore,
files were aligned to mm9 mouse genome with bowtie2.
Assembly: mm9
Supplementary files format and content: Bam files
Library strategy: 4C-seq

source_name: liver

extract_protocol:
4C templates were prepared from 0.5-0.7 g of mouse  liver tissues homogenized in PBS 1X pH 7.4, filtered in 70 µm cell strainer and diluted to 30 ml with PBS. Cells were pelleted and crosslinked in 25 ml of DMEM with 1% of formaldehyde at room temperature under rotation for 15 minutes and immediately quenching the reaction with glycine at 0.125 M final concentration for 5 minutes at 4°C. Nuclear isolation was performed in NI buffer (10mM Tris HCl, 10mM NaCl, 0.2% NP-40) for 1 h at 4°C. For first restriction, selected six-cutter enzymes were EcoRI for Pparγ2 bait, and HindIII for Dbp, Pparα and Srebp1c baits. Ten million nuclei per sample were resuspended in 500 µl of 1X NEBbuffer 2.1 (New England BioLabs) containing 0.3% SDS and incubated 10 min at 60°C and 50 min at 37°C. Triton X100 was added at 1.8% v/v, incubated 1 h at 37°C, and 400U of restriction enzyme were added and incubated at 37°C overnight with agitation. First ligation was performed with 100U of T4 DNA ligase (ThermoScientific Cat. No. EL0011) with 5% polyethylenglicol in 7ml final volume, during 6h at 16°C. DNA crosslinking was reversed by adding 30 µl of 10 mg/ml proteinase K (EMD Millipore Cat. No. 124568) and incubating 6h at 65°C, followed by addition of 30 µl of 10 mg/ml RNAse A (Sigma Cat. No.R5000) and incubation 45 min at 37°C. DNA was purified with phenol/chloroform extraction and sodium acetate/ethanol precipitation. The purified DNA had a second restriction with 200U of Csp6I (New England BioLabs) in 500 µl reaction volume. Finally, a second round of ligation with 200U de T4 DNA ligase with 5% PEG in a 14 ml final volume was performed. Circular DNA was resuspended in molecular grade H2O. Efficiency of each reaction was evaluated by loading DNA in 0.8% agarose gel.
Libraries were prepared with a two-step PCR procedure. For each 4C template, eight reactions of 100-200 ng were amplified by PCR using high fidelity Hot Start Phusion II DNA polymerase (ThermoFisher, F549) and long-template specific-bait primers containing the NexteraXT overhang sequences (Pparγ2_EcorI: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGATTAGTTTTATCTCTATTTAACTTGA Pparγ2_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGATAGACTTGTTGAATAAATCACCT Dbp_HindIII: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAAACCTGTTCTGTGGTGGATAAGC Dbp_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCACTGGTTTTTGCCTGGAGGTC Pparα_HindIII: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCATCTCCAGGGTCTCAGTTTTGCA Pparα_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCATTTTCCTACCCTGGCCTGTA Srebp1c_HindIII: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATCTGTCCCTGTCCCTTGCTGG Srebp1c_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGCTGTCGGGGTAGCGTCTG), 2 min at 98°C, (15s at 98°C, 1 min at 48°C , 3 min at 72°C) x 30 cycles and a final extension of 7 min at 72°C. PCRs were pooled and for a second round of PCR using NexteraXT index kit. PCR products were size selected with 2% agarose gel to 200 bp-2kb, purified with gel purification kit (Qiagen) and fragment size distribution analyzed with bioanalyzer tapestation (Agilent).

value: liver

tag: time

tag: diet

value: High Fat

tag: gene


title: L(3)mbt KD RNA-seq rep 2

tag: cell type

value: L(3)mbt KD


title: Srebp1c, High fat diet, ZT18 HiSeq_rep1

tag: tissue


title: Control liver cancer cells 6

value: WT


title: Control liver cancer cells 5


title: Srebp1c, High fat diet, ZT6 HiSeq_rep2


title: D464T27_WT1

tag: strain

tag: age


title: D464T30_KI2

value: Progeria


title: L(3)mbt KD RNA-seq rep 1

value: cultured ovarian somatic cells [OSCs]

tag: treatment


title: EGFP KD RNA-seq rep 2

value: EGFP KD


title: Control liver cancer cells 4

tag: cell line

tag: genotype


title: Srebp1c, Control diet, ZT18 HiSeq_rep2

value: Control


title: Control liver cancer cells 3


title: D464T29_KI1


title: Srebp1c, High fat diet, ZT6 HiSeq_rep1


title: input genome rep 2

data_processing:
Basecalls were performed by illumina Hiseq
trim down the base to first 50 bp from 150 bp using seqkit
ChIP-seq reads were alighed to the dm6 genome assembly using bowtie2
only unique reads were extracted
dupicate reads were removed with picard tool
WIG files were generated using MACS14, peak files were generated using MACS2
genome build: dm6
processed data files format and content: wig files were generated using MACS14

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA-protein complexes were immunoprecipitated with antibody
Libraries were prepared according to illumina's instructions accompanying NEBNext Ultra 2 FS DNA Library Prep Kit (E7805). In the adaptor ligation step, the original adaptor reagent was diluted to 10 times. After adapter ligation DNA was purified with AMPure XP beads(Beckman Coulter) for size selection. Then DNA was PCR amplified with Illumina primers for 13~16 cycles and library fragments of ~325 bp (insert plus adaptor and PCR primer sequences) were purified with AMPure XP beads(Beckman Coulter). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.


title: Control liver cancer cells 2


title: Sample 1c_Wk8_Ctrl_noPTH_PF212

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Data was aligned to mouse genome mm10 (reference v3.0.0 provided by 10X Genomics) by CellRanger (version 3.1.0)
Data was also aligned to a reference file of exogenous sequences, including tdTomato (1431bp),  WPRE (Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element; 592bp) and GFP (720), by CellRanger (version 3.1.0)
The resulting matrix files were integrated and further processed on Seurat (version 3).
Dimension reduction including CCA, PCA, tSNE and UMAP were perforedm.
Clustering were performed, and differentially expressed genes between one cluster and another (or all remaining clusters) were performed. A further filtering of abs(log2(fold-change)) > 1/2 and FDR <0.05 was applied to ensure higher specificity and correct for multiple testing.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression file in mm10 or exogenous genes

growth_protocol: The mice grow under normal condition.

extract_protocol:
RNA extraction from disassociated cells was done according to standard 10X Genomics Protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were extracted with dispase collagenase and trysin for 1 hr

tag: strain/genotype

value: Col10a1Cre;Rosa26-Tdtomato;Irx3 +/Δ;Irx5 +/- (Irx3/5 heterozygous control)

value: 8 weeks

value: proximal and distal tibia


title: Sample 1d_Wk8_Ctrl_noPTH_PF212


title: Lint-1 KD RNA-seq rep 1

tag: chip antibody

value: Lint-1 KD


title: input genome rep 1


title: Control liver cancer cells 1

value: hepatoblastoma


title: Srebp1c, Control diet, ZT6 HiSeq_rep2


title: Sample 1a_Wk8_Ctrl_noPTH_PF212


title: Lint-O-ChIP-seq rep 2

value: Lint-O antibody


title: Srepb1c, Control diet, ZT6 HiSeq_rep1


title: Erythroid cells, ZnF4 edited, rep 2

city: Vellore

first: Mohankumar

last: Murugesan

state: Tamilnadu

address: Christian Medical College

department: Center for Stemcell Research

country: India

institute: CHRISTIAN MEDICAL COLLEGE AND HOSPITAL

data_processing:
The raw reads were filtered using Trimmomatic for quality scores and adapters
Filtered reads were aligned to the Human genome (hg38) using splice aware aligners like HISAT2 to quantify reads mapped to each transcript.
Total number of uniquely mapped reads were counted using feature counts.
The uniquely mapped reads were then subjected to differential gene expression using DeSeq2.
Assembly: hg18
Supplementary files format and content: .txt containing the RNA editing information

source_name: Blood

extract_protocol:
RNA was isolated using MACHEREY-NAGEL RNA isolation kit
TruSeq RNA Library Prep Kit v2, Illumina, library kits was used following the manufacturer"s instructions.

value: Blood

value: Erythroid cells

value: Primary cell

value: ZnF 4 altered

value: Study target, Erythroid differentiation


title: EG3,Plant tissue

city: sichuan

first: leming

last: zhou

address: chengdu

institute: Reference transcriptome

data_processing:
The software for QC is fastp (version 0.19.7) with the parameters fastp -g -q 5 -u 50 -n 15 -l 150.
hisat2  2.0.5  Default parameters Alignment   with reference genome
Sequencing error rates for individual base positions after QC are generally less than 1% and up to 6%
Fast and accurate comparison of Clean Reads with the reference genome using HISAT2 software to obtain information on the positioning of Reads on the reference genome
Supplementary files format and content:   Text file with labels including FPKM values, chromosome positions, etc. for each sample

organism: Juglans regia

source_name: branch

extract_protocol:
Total RNA was extracted by phenol-chloroform method, followed by removal of genomic DNA with DNase, RNase inhibitor and other reagents. 1.3 ug of total RNA was used to construct sequencing libraries.
The fragmented mRNA was used as a template and random oligonucleotides were used as primers to synthesize the first strand of cDNA in M-MuLV reverse transcriptase system, followed by degradation of RNA strands with RNaseH and synthesis of the second strand of cDNA with dNTPs under DNA polymerase I system. The purified double-stranded cDNA was end-repaired, A-tailed and ligated with sequencing connectors. cDNAs of about 250-300bp were screened with AMPure XP beads, PCR amplified and PCR products were purified again using AMPure XP beads to finally obtain libraries. The kit used for library construction is NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.

value: branch

value: inoculated with the walnut branch blight pathogen Phomopsis capsici


title: EGFP KD RNA-seq rep 1


title: Erythroid cells, ZnF4 edited, rep 1


title: Lint-O-ChIP-seq rep 1


title: EG2,Plant tissue


title: Ppara, High fat diet, ZT18 HiSeq_rep2

value: liver

value: High Fat

value: Ppara


title: Ppara, High fat diet, ZT18 HiSeq_rep1


title: L(3)mbt-ChIP-seq rep 2

value: cultured ovarian somatic cells [OSCs]

value: L(3)mbt antibody produced in our lab


title: EG1,Plant tissue


title: L(3)mbt-ChIP-seq rep 1


title: Erythroid cells, Binding site edited, rep 2

value: Binding site disrupted

value: Clinical target, Erythroid differentiation


title: CK3,Plant tissue

value: control


title: Srebp1c, Control diet, ZT18 HiSeq_rep1

value: Control


title: Ppara, High fat diet, ZT6 HiSeq_rep2


title: CK2,Plant tissue


title: Sample 1b_Wk8_Ctrl_noPTH_PF212

value: Col10a1Cre;Rosa26-Tdtomato;Irx3 +/Δ;Irx5 +/- (Irx3/5 heterozygous control)

value: 8 weeks

value: proximal and distal tibia


title: Erythroid cells, BCL11A Knockout edited, rep 2

value: Blood

value: Erythroid cells

value: Primary cell

value: BCL11A knockout

value: Positive control, Erythroid differentiation


title: Erythroid cells, Binding site edited, rep 1


title: KO_E12.5_Pit

city: Chiba

first: SAISHU

last: YOSHIDA

address: 2-2-1 Miyama, Funabashi-shi

department: Department of Biomolecular Science,

institute: Toho University

data_processing:
Cutadapt v1.9.1 was used to trim and filter reads, and clean data were aligned to the reference genome (ENSEMBLE, GRCm38.97) using the software HISAT 2 (v2.0.1).
Assembly: ENSEMBL, GRCm38.97
Supplementary files format and content: Relative gene expression was quantified and normalized in a FPKM format

extract_protocol:
Total cellular RNA was extracted with using RNeasy mini kit (QIAGEN) with DNase I treatment (QIAGEN).
stranded library preparation with polyA selection


title: Ppara, High fat diet, ZT6 HiSeq_rep1

value: liver


title: WT_E12.5_Pit

value: WT


title: Ppara, Control diet, ZT18 HiSeq_rep2

value: Ppara


title: Erythroid cells, BCL11A Knockout edited, rep 1


title: CK1,Plant tissue

value: branch


title: G_lamblia_BGS_rep3

city: Aurora

first: Neelanjan

last: Mukherjee

state: Colorado

address: Research Complex 1 South, 12801 E 17th Ave

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
ONT reads were basecalled using guppy. For Giardia lamblia we were using one replicate prepared in this study and two datasets from our previous paper (10.1261/rna.078793.121, GSE168675)
Poly(A) tail length was assesed using nanopolish and reads with poly(A) tail shorter than 15 nt (N. gruberi) or 30 nt (others) were discarded.
Alignment was performed using minimap2
Quantification was performed using featureCounts from Rsubread
Annotation of 3’UTRs, cleavage sites, poly(A) signals and auxiliary elements was done with custom scripts.
Assembly: Entamoeba_histolytica.JCVI-ESG2-1.0.dna_rm.toplevel.
Assembly: GiardiaDB-56_GintestinalisAssemblageAWB_Genome
Assembly: GiardiaDB-56_GintestinalisAssemblageBGS_Genome
Assembly: GiardiaDB-56_GmurisRobertsThomson_Genome
Assembly: Naegleria_gruberi_gca_000004985.V1.0.dna_rm.toplevel
Assembly: TrichDB-56_TvaginalisG3_Genome
Assembly: TrichDB-56_TfoetusK_Genome
Supplementary files format and content: Tab separated files with feature counts gene quantifications for every replicate in every organism together with genes coordinates.

organism: Giardia duodenalis

source_name: protist cells

growth_protocol: Giardia strains were grown in Keister’s modified TYI-S-33 medium, Trichomonas vaginalis and Tritrichomonas foetus were grown in trypticase-yeast extract maltose (TYM) medium, supplemented with 10% horse serum (Omega), 0.74% ammonium iron (II) sulfate hexahydrate (Sigma-Aldrich) and 1% penicillin-streptomycin (Sigma-Aldrich), and adjusted to pH 6.2. Entamoeba histolitica was grown in TYI-S-33 medium. All were grown axenically at 37ºC under anaerobic conditions. Naegleria gruberi was grown in M7 media in 26ºC.

extract_protocol:
RNA was extracted using TRIZOL reagent.
Nanopore libraries were prepared according to the direct RNA sequencing protocol from ONT (SQK-RNA002). Because the lengths of poly(A) tails were unknown when we initiated this study, total RNA was used in place of oligo(dT)-selected RNA. Libraries were sequenced on a FLO-MIN106 flow cell and minION sequencing device.
Oxford Nanopore Technology direct RNA sequencing

treatment_protocol: Giardia spp, E. histolitica, T. vaginalis and T. foetus were grown in log phase to no more than 80% confluence, detached by cooling on ice (E. histolytica and Giardia) or by vigorous shaking (others), and washed twice by centrifugation and resuspension in ice-cold PBS. The washed pellets were lysed in TRI Reagent (Zymo research) and RNA was extracted and purified using Direct-zol RNA Miniprep Kit (Zymo research) following the manufacturer’s instructions. Total RNA concentration and purity (A260/A280 ratio) were quantified using a NanoDropTM 1000 instrument (Thermo Fisher Scientific). RNA concentrations were >200 ng/µl and A260/A280 ratios >2.0 for all samples. Cell harvesting and RNA extraction were repeated for each parasite strain on three different three different days. Between 2X10^6 and 5X10^6 N. gruberi cells (on their 5th, 6th, or 7th passage after thawing liquid nitrogen stocks) were washed once in 2 mM Tris and spun down at 1500 RCF in a Beckman Coulter microfuge 20R at room temperature. The supernatant was aspirated, and the pellet was suspend in 1 ml TRIzol, vortexed, and promptly stored at -80 C until RNA extractions. The samples were lysed using FastPrep homogenizer with bead beating in TRIzol. Lysate was cleaned up using a Zymo kit with on column DNase treatment. Finally eluted in kit provided MQ water (40 ul). RNA integrity was vrified on Qubit.

tag: isolate

value: BGS

value: protist cells


title: cardiomyocyte,sham, replicate1-13, scRNAseq

city: Bunkyo-ku

first: Manami

last: Katoh

address: 7-3-1 Hongo

institute: The University of Tokyo

description:
smartseq2
sham_1.xlsx

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
Cardiomyocytes and noncardiomyocyte were isolated using Langendorff perfusion from the left ventricular free wall. Enzymatic dissociation using Langendorff perfusion was performed with 37 °C pre-warmed 35 mL enzyme solution (collagenase Type II 1 mg/mL (Worthington), protease type XIV 0.05 mg/mL (Sigma-Aldrich], NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, pH 7.4) at a rate of 3 mL/min. Enzymes were neutralized with fetal bovine serum (FBS) at a final concentration of 0.2%. Cell suspensions were filtered through a 100 μm nylon mesh cell strainer and centrifuged at 20 g for 3 min. The supernatant was discarded. To prevent hypercontraction, the cardiomyocytes were resuspended in medium (NaCl 130 mM, KCl 5.4 mM, MgCl2 0.5 mM, NaH2PO4 0.33 mM, D-glucose 22 mM, HEPES 25 mM, FBS 0.2%, pH 7.4) containing a low concentration of calcium (0.5 mM). Rod-shaped live cardiomyocytes (viability of cardiomyocytes was ≥70%) were collected immediately after isolation from two mice at each condition with a 0.2–2 μL pipette (sample volume, 0.5 μL) and incubated in lysis buffer.The supernatant was collected as non-cardiomyocytes and the cells were continued to lysis process according to the 10X protocol.
Sample 731-736,library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.  Other samples, single-cell cDNA libraries were generated using the Smart-seq2 protocol.  And the efficiency of reverse transcription was assessed by examining the cycle threshold (Ct) values of control genes (Tnnt2) from quantitative real-time polymerase chain reaction (qRT-PCR) using a CFX96 Real-Time PCR Detection System (Bio-Rad) and by examining the dis- tribution of the lengths of cDNA fragments using a LabChip GX (Perkin Elmer) and/or TapeStation 2200 (Agilent Technologies). The following primer sets were used for qRT-PCR: Tnnt2 mRNA forward, TCCTGGCAGA GAGGAGGAAG; Tnnt2 mRNA reverse, TGCAGGTCGA ACTTCTCAGC. A Ct value of 25 was set as the threshold.

value: cardiomyocyte

value: heart

value: 6-8 weeks old

value: sham


title: Ppara, Control diet, ZT18 HiSeq_rep1

value: Control


title: Erythroid cells, Control edited, rep 2

value: AAVS1 edited

value: Control edited, Erythroid differentiation


title: G_lamblia_BGS_rep2


title: WT_LLC_MPE2

city: hangzhou

first: min

last: zhang

address: hangzhou,xihu

institute: zhejiang university

data_processing:
Data filtering: The raw data was filtered with SOAPnuke (v1.4.0) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 5%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 20%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping： The clean data were mapped to the reference genome by HISAT (v2.1.0)
New transcript prediction:  StringTie ( v1.0.4 ) was used to reconstruct transcripts, and Cuffmerge was used to integrate the assembled transcripts. Cuffcompare was used to compare the integrated transcripts to a reference annotation. The transcripts with class code types u, i, o, j were selected as new transcripts. The protein-coding potential of new transcripts was predicted by CPC ( v0.9-r2 ).
Differential Gene Expression: Within-group differential gene analysis was performed using DESeq under the conditions of Fold Change ≥ 2 and Adjusted Pvalue ≤ 0.001（The specific situation shall be subject to the actual project）. PossionDis was performed between-group differential gene analysis under the conditions of Fold Change ≥ 2 and FDR ≤ 0.001. Using the pheatmap function on the differential gene set to draw a heatmap of differential gene clusters. According to the GO and KEGG annotation results and official classification, the differential ly expressed genes were functionally classified, and the phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) in R software was used for KEGG enrichment analysis, and the TermFinder package was used for GO Enrichment analysis (https://metacpan.org/pod/GO::TermFinder). With Qvalue ≤ 0.05 as the threshold, candidate genes that met this condition was defined as being significantly enriched.
Gene Annotation: Annotating assembled Unigene with functional databases (KEGG, GO), and predicting the transcription factors.
Assembly: The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5). The expression level of genes was calculated by RSEM (v1.2.8)
Supplementary files format and content: DEGs.txt is the count matrix

source_name: eosinophils

extract_protocol:
Total RNA from sorted eosinophils was extracted using the RNeasy Micro kit (QIAGEN, Cat#74004).Total RNA was used for the construction of sequencing libraries.
Qualified amplified cDNAs use transposon-based method for further library construction.

value: eosinophils


title: Erythroid cells, Control edited, rep 1

value: Blood

value: Erythroid cells

value: Primary cell


title: Ppara, Control diet, ZT6 HiSeq_rep2

value: liver


title: Ppara, Control diet, ZT6 HiSeq_rep1


title: WT_LLC_MPE1

value: WT


title: WT_LLC_BM2

source_name: bone marrow

value: bone marrow


title: G_lamblia_rep3

description:
Giardia lamblia BGS
g_lamblia_fc.tsv

value: WB clone C6


title: Pparg2, High fat diet, ZT18 HiSeq_rep2

value: High Fat


title: N_2

city: Hongo, Bunkyo-ku

first: Chikako

last: Shibata

data_processing:
The quality of the raw sequence reads was assessed with FastQC (Version0.11.7).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic software Version 0.38 (parameter- ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.)
Trimmed sequence reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0)
The result files of HISAT2 (.sam) were converte into .bam files with Samtools (Version 1.9).
Read count extraction and normalization were performed using featureCounts (Version 1.6.3) and transcripts per million (TPM).

source_name: HUVEC

extract_protocol:
Total RNAs were extracted using ISOGEN 2 Reagent (Nippon Gene). 1 ug of total RNA was used for the construction of sequencing libraries.
Library construction was performed at Rhelixa Corporation (Japan) using NEBNext® Ultra TM2 Directional RNA Library Prep Kit.

value: HUVEC

value: SELE overexpression

value: BxPC EV (CA19-9 negative)


title: WT_LLC_BM1


title: db_F_2

city: Tucson

first: Sakthivel

last: Sadayappan

state: AZ

address: 1656 E Mabel Street, Medical Research Building, Rm 315, Cellular and Molecular Medicine

department: Cellular and Molecular Medicine

institute: University of Arizona College of Medicine

data_processing:
The raw data containing reads of low quality, connector contamination and excessively high leveles of unknown base N were removed before data analysis. The clean reads thus generated were aligned to the reference genome using HISAT, mapped to reference genes using Bowtie2. The mapped genes were  subjected to differential expression analysis using DEseq2. The nondiabetic samples were grouped as control-2 and the diabetic samples were  grouped as case-2 for the DESeq2 analysis.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: The processed file is in Excel format and contains FPKM, TPM, read counts, log2fc, qvalue, p value for the respetive genes with their gene symbol, gene ID and other gene related informations.

source_name: Heart

growth_protocol: Male C57BL/KsJ-Lepr db/Lepr db diabetic (db/db) mice and their nondiabetic C57BL/WT mice were obtained from Jackson Laboratories (Bar Harbor, ME) and used for experiments in this work from 2 months of age. The animal facility had a controlled environment (20°C temperature, 60% humidity, and 12 hours of light/dark cycles), and mice were fedad libitumwith a standard diet.

extract_protocol:
Mice hearts were dissected at 6 months of age, followed by total RNA isolation using an RNA isolation kit (Qiagen, cat# 763134), according to the manufacturer’s instructions. Total RNA concentration and quality (A260/280 ratio ≥2.0) were evaluated using a Nanodrop spectrophotometer (ThermoFisher Scientific). The quality of total RNA was further measured using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
After Sample QC was by qubit and Agilent Bioanalyzer, a certain amount of RNA samples were denatured at suitable temperatures to open-up their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads followed by mRNA fragmentation and cDNA Synthesis. The double-stranded cDNA fragments were subjected to end-repair, the addition of a single ‘A’ nucleotide to the 3’ ends of the blunt fragments and ligated to adaptors before amplification.

tag: Sex

value: Female

value: Heart

tag: disease state

value: Diabetic

value: KsJ-Lepr db/Lepr db

value: 6 Months


title: db_M_1

value: Male


title: Pparg2, High fat diet, ZT18 HiSeq_rep1


title: P_3

value: BxPC EV (CA19-9 positive)


title: N_1


title: G_lamblia_rep2 (re-analysis)

description:
Giardia lamblia BGS
reanalysis of GSM5155604

value: protist cells


title: P_2


title: HCC-61

city: Chengdu

first: Ling

last: Bai

state: Sichuan

address: No.37 Guoxue Alley

department: Department of Laboratory Medicine

institute: West China Hospital, Sichuan University

data_processing:
GATK 3.7 best practices workflow
After removing terminal adaptor sequences and low-quality data, sequences were mapped to the reference human genome using the Burrows-Wheel Aligner (BWA) software.
Duplicate reads were removed with Gene Analysis Toolkit. MuTect2 algorithm was utilized to call single-nucleotide variants (SNVs) and somatic insertions/deletions (InDel).
GnomAD database was applied to filter germline mutations. Afterwards, mutated variant allele frequency (VAF) ≥0.01 was filtered.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw mutations for each sample
Library strategy: DNA-seq

source_name: Liver

extract_protocol:
Genomic DNA was extracted from the fresh HCC tumor tissues of individual patients with the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) according to the standard procedures. In brief, tissue samples (less than 10 mg) were digested overnight at 56°C with protein K and Buffer ALT. After extraction with Buffer AL and reprecipitation in ethanol (97%), nucleic acids were then rinsed with Buffer AW1 and Buffer AW2. After that, DNA was solubilized in Buffer AE and stored at -20°C.
DNA libraries for DNA-seq were prepared using The Human 1021 Gene Mutation Detection Kit (Gene+, Beijing, China) following manufacturer's protocols.

value: Liver

value: Hepatocellular Carcinoma

value: surgical resection


title: G_lamblia_rep1 (re-analysis)

description:
Giardia lamblia BGS
reanalysis of GSM5155603


title: Pparg2, High fat diet, ZT6 HiSeq_rep1

value: liver


title: HCC-60


title: db_F_1


title: P_1


title: N_3


title: G_lamblia_BGS_rep1

value: BGS


title: Pparg2, Control diet, ZT18 HiSeq_rep1

value: Control


title: WF_M_2

value: Non diabetic

value: WT


title: WT_F_1


title: C_1

value: HUVEC

value: SELE overexpression

value: PBS


title: Pparg2, Control diet, ZT6 HiSeq_rep2


title: HCC-58


title: Pparg2, High fat diet, ZT6 HiSeq_rep2

value: High Fat


title: SHG141 GSCs, rhPOSTN

city: Soochow

first: Hao

state: Jiangsu

address: 899 Pinghai Road

department: Department of Neurosurgery & Brain and Nerve Research Laboratory

institute: The First Affiliated Hospital of Soochow University

data_processing:
The mixed sequencing libraries of different samples were denatured with 0.1 M NaOH to generate single-stranded DNA, which was subsequently diluted to a concentration of 8 pM and amplified in situ via a reagent kit.
The ends of the generated fragments were sequenced for 150 cycles using a DNBSEQ-T7 sequencer.     The original sequencing data were subjected to quality control and comparison for statistical and quantitative analysis of gene and transcript expression.
Solexa pipeline version 1.8 (off-line base caller software, version 1.8) was adopted to perform image processing and base recognition.
FastOC software evaluates the sequencing quality of reads after removing adapters;     Genome version used in reads mapping is GenCode GRCh37.
The Ballgown R package was used to calculate expression differences between groups based on FPKM from genetic levels. Differentially expressed mRNAs (DEmRNAs) were determined by the Ballgown package under the conditions of fold change ≥1.5 and p value ≤ 0.05.
Assembly: hg37
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Glioblastoma

growth_protocol: The GSCs culture medium consisted of DMEM/F12 (Corning), B27 (Gibco), 20 ng ml-1 recombinant human epidermal growth factor and 20 ng/ml basic fibroblast growth factor. All cells were maintained at 37 ℃ and 5% CO2.

extract_protocol:
Total RNA was extracted and the concentration was measured by NanoDropND-1000. 1∼2 µg of total RNA was selected from each sample for RNA sequencing library construction.
1 ∼ 2 µg of total RNA was selected from each sample for sequencing library construction. Total RNA was first enriched for mRNA using NEB Next® Poly(A) mRNA Magnetic Isolation Module (or RiboZero Magnetic Gold Kit for rRNA removal). The processed RNA was used to construct the library using KAPA Stranded RNA-Seq Library Prep Kit (Roche).

treatment_protocol: glioblastoma stem cells treated with sh-Control, sh-POSTN or human recombinant POSTN

value: Glioblastoma

value: SHG141 GSCs

value: Human glioblastoma stem cells

value: rhPOSTN


title: Pparg2, Control diet, ZT6 HiSeq_rep1


title: HCC-57


title: mRNAs in M2-exo treated Caco-2 cells 3

city: Beijing

first: xinyuan

last: huang

address: Yongan Street 95

institute: Beijing Friendship Hospital affiliated Capital Medical University

description: gene_count.txt, gene_fpkm.txt

data_processing:
As for mRNA, the image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.Reference genome (GRCh38) and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 and paired-end clean reads were aligned to the reference genome using Hisat2. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.FeatureCounts was used to mRNA count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38
Supplementary files format and content: count and FPKM

source_name: Caco-2 cells

extract_protocol:
Caco-2 cells were cultured in Dulbecco's modified Eagle’s medium (DMEM) supplemented with 18% fetal bovine serum.THP-1 cells were cultured in RPIM 1640 medium supplemented with 10% fetal bovine serum. All cell lines were cultured at 37 °C with 5% CO2 and optimal humidity in a cell culture incubator.
Caco-2 cells were treated with PBS or M2-exo.

value: Caco-2 cells

value: stem cells

value: wild type


title: Dbp, High fat diet, ZT18 HiSeq_rep2

value: Dbp


title: HCC-56

value: Liver

value: Hepatocellular Carcinoma

value: surgical resection


title: SHG141 GSCs, PBS

last: Wang


title: HCC-55


title: mRNAs in M2-exo treated Caco-2 cells 1

description: gene_count.txt, gene_fpkm.txt


title: Dbp, High fat diet, ZT18 HiSeq_rep1

value: liver


title: HCC-54


title: mRNAs in untreated Caco-2 cells 3

description: gene_count.txt, gene_fpkm.txt


title: SHG143 GSCs, sh-POSTN

value: SHG143 GSCs

value: sh-POSTN


title: HCC-59


title: H1975_OR_3

city: Tianjin

first: Jing

last: Zhou

address: Huanhuxi Street

department: Department of Thoracic Oncology

institute: Tianjin Medical University Cancer Institute & Hospital

data_processing:
The transcriptome sequencing and analysis were conducted by GenePlus Co., Ltd. (Jiangsu, China).
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In 1 this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Then the clean reads were mapped to reference genome using GRCh37.
Genes differentially expressed between groups were identified using the DESeq R package. A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Assembly: GRCH37
Supplementary files format and content: Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: lung adenocarcinoma

growth_protocol: H1975 and H1975 OR cells were cultured in RPMI-1640 medium supplemented with 10% FBS.

extract_protocol:
Cells were washed twice with pre-chilled PBS, and then total RNAs were harvested using Trizol reagent (Takara, Japan).
RNA libraries for RNA-seq were prepared using GenePlus mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: H1975 cells were treated under normal conditions. H1975 OR cells were treated with 1 μM osimertinib.

value: lung adenocarcinoma

value: Lung cancer cell

value: Osimertinib resistance cell

value: 1 μmol osimertinib stimulated culture


title: Dbp, High fat diet, ZT6 HiSeq_rep2

value: High Fat


title: HCC-52


title: Dbp, High fat diet, ZT6 HiSeq_rep1


title: H1975_OR_2


title: Dbp, Control diet, ZT18 HiSeq_rep2

value: Control


title: mRNAs in untreated Caco-2 cells 1

description: gene_count.txt, gene_fpkm.txt

data_processing:
As for mRNA, the image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.Reference genome (GRCh38) and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 and paired-end clean reads were aligned to the reference genome using Hisat2. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.FeatureCounts was used to mRNA count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: miRBase22.0
Supplementary files format and content: count and FPKM


title: H1975_OR_1


title: mRNAs in untreated Caco-2 cells 2

description: gene_count.txt, gene_fpkm.txt


title: HCC-46


title: Dbp, Control diet, ZT18 HiSeq_rep1


title: HCC-45


title: H1975_3

value: parental cell


title: SHG143 GSCs, sh-Control

value: Glioblastoma

value: Human glioblastoma stem cells

value: WT

value: sh-Control


title: Dbp, Control diet, ZT6 HiSeq_rep2

value: Dbp


title: HCC-43

value: Liver

value: Hepatocellular Carcinoma


title: H1975_2


title: Dbp, Control diet, ZT6 HiSeq_rep1

value: liver


title: Day25b

city: Melbourne

first: Jacky

middle: Yisheng

last: Li

state: Victoria

address: 50 Flemington Rd

department: Cellular Biology

country: Australia

institute: MCRI

description:
ML221790
features + barcodes + counts matrix

data_processing:
Assembly: hg38
Matrix barcode feature files

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

treatment_protocol: The dataset descrips a continous event of differentiation, with no compaision of results of special treatments. Formulation of the basal differentiation medium is as previously described (Motazedian et al. 2020) added with the differentiation factors on different days.  Sample of day6, day12, day15, day19 and day25a/b were collected and sequenced.

value: human embryonic stem cell derivatives


title: microRNA in M2-exo

data_processing:
Processed reads of length at 18 to 35 nt for animals or 18-30 nt for plants were then mapped to their reference genome and analyzed using the bowtie package. To identify conserved miRNAs, the predicted miRNA hairpins were compared against miRNA precursor sequences from miRBase22.0 using mirDeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. MirDeep2's quantifier.pl were used to obtain the miRNA counts, and custom scripts were used to obtain base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively. miRNA expression levels were estimated by TPM (transcript per million):Normalization formula: Normalized expression = mapped read count/Total reads* 1000000.
Assembly: miRBase22.0
Supplementary files format and content: count and FPKM

source_name: THP-1 cells

value: THP-1 cells

value: stem cells

value: wild type


title: Day25a

description:
ML221789
features + barcodes + counts matrix


title: H1975_1

value: lung adenocarcinoma

value: Lung cancer cell


title: HCC-47

value: surgical resection


title: Tumour-5

city: Nanjing

first: Zhen

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

data_processing:
After library quality validation, raw data for each sRNA library were generated on the Illumina HiSeq 2500 platform.
The clean reads were obtained after data filtration. Precursor and mature miRNA sequences were obtained from miRBase v21.
To annotate miRNA, clean reads were mapped to known mouse miRNA precursor sequences by using bowtie and only candidates with no more than 1 mismatch and 2 shifts were counted as miRNA matches.
Differential analysis was performed using DESeq2.
Significance was set at uncorrected P < 0.05 for broad pattern identification. A fold-change threshold was set at > 2. Volcano plot was generated using the ggplot2 R package and heatmap were generated using the pheatmap R package.
Assembly: miRBase v21
Supplementary files format and content: expr.txt: Tab-delimited text file includes normalized miRNAs counts of each sample.

source_name: lung

extract_protocol:
Total RNA was extracted from mouse tissues with TRIzol Reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
All sRNA library construction and deep sequencing were performed by Novogene (Beijing, China). sRNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA).

treatment_protocol: For KRASG12D activation in mouse lungs, six-week-old KRASLSL-G12D/+ mice were first anaesthetized with ketamine (100 mg/kg) and xylazine (10 mg/kg), and then, 5 × 10^6 plaque-forming units of Adeno-Cre were diluted with PBS to obtain a final volume of 50 μL and given through intratracheal administration.

value: lung

value: Adeno-Cre treatment

value: male

value: 5 month


title: HCC-40


city: shenyang

first: jun

address: liaoning

institute: Shenyang Agricultural University

description: maize degradome sequencing were performed on maize inbred lines.

data_processing:
Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
The degradome reads were matched to transcriptome to generate the degradome density file. In addition, the targeted mRNA sequences of the miRNAs were predicted using TargetFinder software (http://targetfinder.org/). The overlapped mRNAs of the predicted target mRNAs and the mRNAs in degradome density file were considered as the target genes of the miRNAs.
Assembly: ftp://ftp.ensemblgenomes.org/pub/release-45/plants/fasta/zea_mays/dna/
Supplementary files format and content: excel,expression profiles
Library strategy: Degradome sequencing

organism: Zea mays

source_name: maize

growth_protocol: The maize (Zea mays L.) inbred lines were grown in growth chambers (28 oC, 16 h day and 22 oC, 8 h night cycles).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Poly(A) RNA is purified from plant total RNA(20ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Because of the 3′ cleavage product of the mRNA contains a 5′-monophosphate，the 5' adapters were ligated to the 5' end of the 3′ cleavage product of the mRNA by the RNA ligase. The next step is reverse transcription to make the first strand of cDNA with a 3′-adapter random primer. and size selection was performed with AMPureXP beads.Then the cDNA were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 15cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 200-400 bp. At last, we performed the 50bp single-end sequencing on an Illumina Hiseq 2500 (LC Bio, China) following the vendor's recommended protocol.

treatment_protocol: The crude extracts of maize leaves tissue infected with SCMV were prepared by mixing 0.01M phosphate buffer solution (0.01 M KH2PO4: 0.01 M Na2HPO4 = 49: 51 (V/V), pH 7.0) at a ratio of 1:10 (W/V).The crude extracts were inoculated on the second leaves of six-day-old Chang7-2 and Mo17 maize seedlings, and buffer-inoculated plants were used as control.

value: seedlings


title: Day19

description:
ML221788
features + barcodes + counts matrix


title: Tumour-4


title: Tumour-3


title: HCC-39


title: Eye-antennal disc, Eyeless-Gal4 Dam-Jra Replicate 2 (Set 1)

first: Kieran

last: Harvey

address: 305 Grattan Street

department: Research

institute: Peter MacCallum Cancer Centre

description:
DamIDcounts.csv
jra_peaks
jra_peaks_filtered.bed
jra_peaks_filtered.togene
Jun2

data_processing:
DamID alignment: Subread and featureCounts DamID analysis: process with EdgeR in R for differentially methylated GATC motifs DamID analysis: generate peaks from adjacent mehtylated sites, find closest gene with Bedtools
Assembly: dm6
Supplementary files format and content: sd_peaks_filtered.togene contains DamID signficantly methylated Sd peaks and the closest gene within 5kbp in BED format
Supplementary files format and content: yki_peaks_filtered.togene contains DamID signficantly methylated Sd peaks and the closest gene within 5kbp in BED format
Supplementary files format and content: jun_peaks_filtered.togene contains DamID signficantly methylated Sd peaks and the closest gene within 5kbp in BED format
Supplementary files format and content: DamIDcounts.csv contains a list of GATC features/'tags' and the raw counts for all replicates
Library strategy: DamID-seq

source_name: Eye-antennal disc

growth_protocol: Crosses producing larvae with the indicated genotype were allowed to lay eggs o/n at 25°C. Eggs were transferred to the non-permissive temperature (18°C) for 4 days. To restrict expression of the TaDa transgenes to a defined period, larvae were transferred to the permissive temperature (29°C) 24 hours before dissection.

extract_protocol:
Eye-antennal discs were treated with protK, RNase A followed by phenol chloroform DNA extraction. DNA was ethanol precipitated, washed and dissolved, followed by DpnI digestion, DamID adaptors ligation, DpnII digestion and PCR amplification. MePCR product was sonicated using a Covaris S2 device to generate fragments of 100-500bp, with an average of 300bp. DNA was purified using Agencourt AMPure beads purification.
Illumina sequencing libraries were prepared using KAPA Hyper prep kit (Kapa Biosystems) and 300ng starting material. Five to seven cycles of PCR were performed.

value: Eye-antennal disc

value: Eyeless-Gal4 Gal80ts UAS-Dam-Jra


title: microRNA in M0-exo


title: HCC-38

value: Liver


title: Day12

description:
ML221786
features + barcodes + counts matrix


title: Pparg2, Control diet, ZT18 HiSeq_rep2

city: MEXICO CITY

first: LORENA

address: TERCER CIRCUITO EXTERIOR, CU

institute: INSTITUTO DE INVESTIGACIONES BIOMEDICAS- UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO

data_processing:
Adapters and primer sequences were trimmed using Trim Galore,
files were aligned to mm9 mouse genome with bowtie2.
Assembly: mm9
Supplementary files format and content: Bam files
Library strategy: 4C-seq

source_name: liver

extract_protocol:
4C templates were prepared from 0.5-0.7 g of mouse  liver tissues homogenized in PBS 1X pH 7.4, filtered in 70 µm cell strainer and diluted to 30 ml with PBS. Cells were pelleted and crosslinked in 25 ml of DMEM with 1% of formaldehyde at room temperature under rotation for 15 minutes and immediately quenching the reaction with glycine at 0.125 M final concentration for 5 minutes at 4°C. Nuclear isolation was performed in NI buffer (10mM Tris HCl, 10mM NaCl, 0.2% NP-40) for 1 h at 4°C. For first restriction, selected six-cutter enzymes were EcoRI for Pparγ2 bait, and HindIII for Dbp, Pparα and Srebp1c baits. Ten million nuclei per sample were resuspended in 500 µl of 1X NEBbuffer 2.1 (New England BioLabs) containing 0.3% SDS and incubated 10 min at 60°C and 50 min at 37°C. Triton X100 was added at 1.8% v/v, incubated 1 h at 37°C, and 400U of restriction enzyme were added and incubated at 37°C overnight with agitation. First ligation was performed with 100U of T4 DNA ligase (ThermoScientific Cat. No. EL0011) with 5% polyethylenglicol in 7ml final volume, during 6h at 16°C. DNA crosslinking was reversed by adding 30 µl of 10 mg/ml proteinase K (EMD Millipore Cat. No. 124568) and incubating 6h at 65°C, followed by addition of 30 µl of 10 mg/ml RNAse A (Sigma Cat. No.R5000) and incubation 45 min at 37°C. DNA was purified with phenol/chloroform extraction and sodium acetate/ethanol precipitation. The purified DNA had a second restriction with 200U of Csp6I (New England BioLabs) in 500 µl reaction volume. Finally, a second round of ligation with 200U de T4 DNA ligase with 5% PEG in a 14 ml final volume was performed. Circular DNA was resuspended in molecular grade H2O. Efficiency of each reaction was evaluated by loading DNA in 0.8% agarose gel.
Libraries were prepared with a two-step PCR procedure. For each 4C template, eight reactions of 100-200 ng were amplified by PCR using high fidelity Hot Start Phusion II DNA polymerase (ThermoFisher, F549) and long-template specific-bait primers containing the NexteraXT overhang sequences (Pparγ2_EcorI: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGGATTAGTTTTATCTCTATTTAACTTGA Pparγ2_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGATAGACTTGTTGAATAAATCACCT Dbp_HindIII: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAAACCTGTTCTGTGGTGGATAAGC Dbp_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCACTGGTTTTTGCCTGGAGGTC Pparα_HindIII: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCATCTCCAGGGTCTCAGTTTTGCA Pparα_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGCCATTTTCCTACCCTGGCCTGTA Srebp1c_HindIII: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATCTGTCCCTGTCCCTTGCTGG Srebp1c_Csp6I: GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGCTGTCGGGGTAGCGTCTG), 2 min at 98°C, (15s at 98°C, 1 min at 48°C , 3 min at 72°C) x 30 cycles and a final extension of 7 min at 72°C. PCRs were pooled and for a second round of PCR using NexteraXT index kit. PCR products were size selected with 2% agarose gel to 200 bp-2kb, purified with gel purification kit (Qiagen) and fragment size distribution analyzed with bioanalyzer tapestation (Agilent).

value: Control


title: HCC-36

value: Hepatocellular Carcinoma


title: mRNAs in M2-exo treated Caco-2 cells 2

description: gene_count.txt, gene_fpkm.txt

value: Caco-2 cells


title: Day6

description:
ML221785
features + barcodes + counts matrix

value: human embryonic stem cell derivatives


title: Tumour-1


title: HCC-41


title: Eye-antennal disc, Eyeless-Gal4 Dam Replicate 3 (Set 3)

description:
DamIDcounts.csv
Dam9

value: Eyeless-Gal4 Gal80ts UAS-Dam


title: HCC-28


title: Eye-antennal disc, Eyeless-Gal4 Dam Replicate 2 (Set 3)

description:
DamIDcounts.csv
Dam8


title: HCC-19


title: HCC-16


title: Eye-antennal disc, Eyeless-Gal4 Dam Replicate 1 (Set 3)

description:
DamIDcounts.csv
Dam7


title: Normal-4

value: Without Adeno-Cre treatment


title: A549, transfected with siDROSHA [DROSHA]

first: Changhui

last: Ge

email: chge502@163.com, chge88@sina.com

address: 27 Taiping Rd., Haidian Dist.

department: Department of Experimental Hematology and Biochemistry

institute: Beijing institute of Radiation Medicine

data_processing:
Cluster was generated by cBot with the library diluted to 10pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo_sapiens.GRCm38 V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: A549 epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit(Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.

treatment_protocol: RNase L, ANG, Dicer, Drosha, AGO2, and RNase T2 were knocked down by siRNA transfection in A549 cells, respectively, and these cells were harvested 48 h after siRNA transfection.

value: epithelial cell

value: Drosha knockdown

value: transfected with siDROSHA


title: Normal-3

value: lung


title: Eye-antennal disc, Eyeless-Gal4 Yki-Dam Replicate 3 (Set 2)

description:
DamIDcounts.csv
yki_peaks
yki_peaks_filtered.bed
yki_peaks_filtered.togene
Yki3

value: Eyeless-Gal4 Gal80ts UAS-Yki-Dam


title: A549, transfected with siRNaseL [RnaseL]

value: AGO2 knockdown

value: transfected with siRnaseL


title: Eye-antennal disc, Eyeless-Gal4 Dam-Jra Replicate 3 (Set 1)

description:
DamIDcounts.csv
jra_peaks
jra_peaks_filtered.bed
jra_peaks_filtered.togene
Jun3


title: A549, transfected with siDICER3 [DICER3]

value: Dicer knockdown

value: transfected with siDICER3


title: Normal-2

value: male

value: 5 month


title: Eye-antennal disc, Eyeless-Gal4 Dam-Jra Replicate 1 (Set 1)

description:
DamIDcounts.csv
jra_peaks
jra_peaks_filtered.bed
jra_peaks_filtered.togene
Jun1

value: Eye-antennal disc

value: Eyeless-Gal4 Gal80ts UAS-Dam-Jra


title: Tumour-2

value: Adeno-Cre treatment


title: A549, transfected with siRnaseT2 [RnaseT2]

value: RNaseT2 knockdown

value: transfected with siRnaseT2


title: A549, transfected with siANG [ANG]

value: ANG knockdown

value: transfected with siANG


title: Normal-5

value: Without Adeno-Cre treatment


title: Normal-1


title: Eye-antennal disc, Eyeless-Gal4 Yki-Dam Replicate 1 (Set 2)

description:
DamIDcounts.csv
yki_peaks
yki_peaks_filtered.bed
yki_peaks_filtered.togene
Yki1


title: Eye-antennal disc, Eyeless-Gal4 Dam Replicate 3 (Set 2)

description:
DamIDcounts.csv
Dam3

value: Eyeless-Gal4 Gal80ts UAS-Dam


title: A549, transfected with siAgo2 [Ago2]

value: epithelial cell

value: RNaseL knockdown

value: transfected with siAgo


title: HCC-32

value: Liver

value: Hepatocellular Carcinoma

value: surgical resection


title: HCC-33


title: A549,transfected with control siRNA [mock]

value: WT

value: transfected with control siRNA


title: Wild Type, time 3, replicate 3 [RNA-seq]

city: Barcelona

first: Elias

last: Bechara

address: Dr Aiguader 88

institute: CRG

data_processing:
Basecalling with Illumina bcl2fastq version 2.17.1.14
STAR v2.5.3a mapping to Mus musculus Gencode version M14 (mm10) with –quantMode geneCounts option to get raw counts per gene and per sample
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Text files: raw counts per gene obtained by STAR mapper’s –quantMode GeneCounts parameter (4th column: reverse stranded protocol)

source_name: Wild Type, time 3

extract_protocol:
In order to perform the RNA-sequencing, total RNA was extracted with the Maxwell 16 LEV simplyRNA Cells Kit (AS1270, Promega) according to manufacturer’s instructions from WT, Sam68-/- and QKI -/-  EBs in three biological replicates. DNA-free RNA was then quantified using the Nanodrop and quality checked with the Bioanalizer
rRNA depletion and library preparation was done with the TruSeq stranded total RNA Library prer Human/Mouse/Rat (20020596, Illumina). The sequencing was performed using 2x125bp paired-ends reads on a HiSeq 2500 sequencer with HiSeq v4 chemistry.

tag: cell line background

value: mouse embryonic stem cells

tag: knock-out

value: Wild Type

tag: time point


title: Wild Type, time 10, replicate 3 [RNA-seq]

source_name: Wild Type, time 10


title: Day15

description:
ML221787
features + barcodes + counts matrix

value: human embryonic stem cell derivatives

tag: time


title: Eye-antennal disc, Eyeless-Gal4 Dam Replicate 2 (Set 2)

description:
DamIDcounts.csv
Dam2

value: Eye-antennal disc


title: HCC-31


title: HCC-35


title: A549, normal cell [NC]

value: no treatment


title: Wild Type, time 0, replicate 3 [RNA-seq]

source_name: Wild Type, time 0


title: Eye-antennal disc, Eyeless-Gal4 Dam Replicate 1 (Set 2)

description:
DamIDcounts.csv
Dam1


title: Eye-antennal disc, Eyeless-Gal4 Yki-Dam Replicate 2 (Set 2)

description:
DamIDcounts.csv
yki_peaks
yki_peaks_filtered.bed
yki_peaks_filtered.togene
Yki2

value: Eyeless-Gal4 Gal80ts UAS-Yki-Dam


title: C48_3

first: wen

middle: wen

last: xue

address: 22 Han Kou Road, Nanjing

department: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: cell line

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium containing 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37C.

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

treatment_protocol: The cells were incubated for 24 hours in the absence or presence of 1 μM Loonamycin A.

value: cell line

value: Triple negative breast cancer

value: Loonamycin A,1 μM,24 h


title: Wild Type, time 3, replicate 2 [RNA-seq]


title: Eye-antennal disc, Eyeless-Gal4 Dam-Sd Replicate 3 (Set 1)

description:
DamIDcounts.csv
sd_peaks
sd_peaks_filtered.bed
sd_peaks_filtered.togene
Sd3

value: Eyeless-Gal4 Gal80ts UAS-Dam-Sd


title: HCC-29


title: HCC-34


title: C48_2


title: Wild Type, time 10, replicate 2 [RNA-seq]


title: Eye-antennal disc, Eyeless-Gal4 Dam-Sd Replicate 2 (Set 1)

description:
DamIDcounts.csv
sd_peaks
sd_peaks_filtered.bed
sd_peaks_filtered.togene
Sd2


title: HCC-24


title: Wild Type, time 0, replicate 2 [RNA-seq]