title: DAY9_S3

description: Clec9a-tdTomato+ CD45+ MHC-II+

source_name: mouse embryonic fibroblast

value: mouse embryonic fibroblast

value: Clec9aCre/WT Rosa26stopflox-tdTomato/WT


title: 54-12 T4 r1

status: Public on Dec 07 2018

type: SRA

city: London

first: Christopher

middle: Raja Socrates

last: Banerji

address: New Hunts House

department: Randall Division of Cell and Molecular Biophysics

country: United Kingdom

institute: King's College London

library_source: transcriptomic

data_processing:
Raw reads were trimmed using trim-galore, utilising cutadapt14 (v0.4.0) to remove the Illumina Sequencing Adapter (AGATCGGAAGAGC) at the 3' end. Additionally, 12 bases were also trimmed from the 5' end of the reads since they showed a biased distribution. Reads were mapped to the human transcriptome using the human genome sequence GRCh38 and v82 gene annotations downloaded from Ensembl. Mapping was performed using tophat 15 (v2.1.0) and bowtie 16 (v1.1.0), enabling the fr-firststrand option of tophat to restrict mapping to the sense strand of the transcript. Reads were assigned to genes using the featureCounts program 17 (v1.5.0), counting fragments and ignoring multi-mapping reads, and restricted to the sense strand.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read count files for each batch
Supplementary_files_format_and_content: 12_16_gene_counts.csv
Supplementary_files_format_and_content: 54a5_a10_2_gene_counts.csv
Supplementary_files_format_and_content: 5412_546_gene_counts.csv

molecule: total RNA

organism: Homo sapiens

source_name: Immortalised Human Myoblasts

growth_protocol: Myoblasts were plated at 312,000 cells per well in 12 well plates and cultured for 48 hours in cultured in Skeletal Muscle Cell Growth Medium (Promocel) supplemented with 20% foetal bovine serum, 50ug/ml Fetuin (bovine), 10ng/ml Epidermal Growth Factor (recombinant human), 1ng/ml Basic Fibroblast Growth Factor (recombinant human), 10ug/ml Insulin (recombinant human), 0.4ug/ml Dexamethasone and 50 ug/ml Gentamycin, at 37oC under 5% CO2. Confluent cells were washed with PBS and induced to differentiate in DMEM gluatamax supplemented with 1/1000 insulin + 1/1000 gentamycin at 37oC under 5% CO2.

extract_protocol:
RNA was isolated at 8 time points: T1: 0 mins (confluent proliferating myoblasts); T2: 440 mins (54-6 alignment), T3: 530 mins (54-12 alignment), T4: 1355 mins (54-6 initiation of fusion), T5: 1505 mins (54-12 initiation of fusion), T6: 1860 mins (54-6 myotube formation), T7: 2165 mins (54-12 myotube formation) and T8: 5040 mins (myotube maturation) using miRNeasy kit (Qiagen, Manchester, UK) including DNase digestion from each cell line in triplicate. RNA quality/concentration were checked by LabChip Bioanalyzer (RIN>8.0) and Nanodrop.
RNA-seq libraries were prepared using the Agilent sureselect stranded RNAseq protocol, which allows polyA selection but was modified to work with ribodepletion. Libraries were sequenced on an Illumina HiSeq2500.

tag: pathology

value: FSHD

tag: gender

value: M

tag: batch


title: DAY9_S2

city: Cantanhede

first: Andreia

last: Gomes

address: Parque Tecnológico de Cantanhede, Núcleo 4, lote 8

department: CNC

country: Portugal

institute: Universidade de Coimbra

description: Clec9a-tdTomato+ CD45+ MHC-II+

data_processing:
bcl2fastq2 v2.20 was used to convert BCL files generated by Illumina NextSeq to standard FASTQ file formats
Alignment to GRCm38.p5 was done using STAR v2.5.3a with default settings except for the following ones: --sjdbOverhang 74 --quantMode GeneCounts.
The resulting gene counts were further processed and normalised using DESeq2 R package v1.20.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: raw counts

organism: Mus musculus

growth_protocol: MEFs were cultured in gelatin-coated plates in DMEM+10%FBS. After co-transduction with lentiviral particles encoding PU.1, IRF8, and BATF3 and M2RTTA, MEFs were cultured in the presence of Doxycycline (1 µg/mL) – day 0.

extract_protocol:
Total RNA was extracted with TRIzol. cDNA was generated with the SMARTSeq v4 Ultra low input RNA kit (Takara).
Library preparation was performed using the Nextera XT DNA library preparation kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Cells were sorted by FACS.

tag: cell type

tag: genotype


title: 54-12 T3 r3


title: scRNA_seq_FoxD3_Citrine_33

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

data_processing:
ChIP-seq, Biotin-ChIP-seq, and ATAC-seq reads were trimmed for quality using sickle (v 1.33) and mapped using bowtie (v.1.0.0). Smoothened bigWig files were generated using a enhanced Perl script courtesy of Jim Hughes.
RNA-seq reads were mapped using STAR (v.2.4.2a)
Genome_build: danRer10

organism: Danio rerio

source_name: Citrine reporter expressing cells from 5-6ss embryos

extract_protocol:
FACS sorted cells were washed with PBS and stored at -80C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit (AM1931), checked on Bioanalyser, samples with RIN >7 were used to prepare cDNA using Takara Clontech SmartSeq2 V4 kit (634889).
Sequencing libraries were prepared using Illumina Nextera XT library preparation kit (FC-131-1024).
For scRNA.seq, individual cells were collected by FACS, cDNA was obtained and sequencing libraries as previously described (Picelli et al., 2014). Libraries were sequenced using 50 bp single end reads for 96 cells. 4x10E7 dilution of ERCC spike in control was used.

tag: strain

tag: tissue

tag: assay

value: scRNA-seq

value: FACS


title: 54-12 T3 r2


title: 54-12 T6 r1


title: scRNA_seq_FoxD3_Citrine_30

value: Citrine reporter expressing cells from 5-6ss embryos


title: DAY9_S1

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: DAY8_S3

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: DAY8_S2

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: scRNA_seq_FoxD3_Citrine_29


title: 54-12 T3 r1


title: scRNA_seq_FoxD3_Citrine_28


title: DAY8_S1

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: 54-12 T2 r3


title: 54-12 T2 r2


title: scRNA_seq_FoxD3_Citrine_27


title: DAY7_S3

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: 54-12 T2 r1


title: DAY7_S2

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: DAY7_S1

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: scRNA_seq_FoxD3_Citrine_31


title: scRNA_seq_FoxD3_Citrine_25


title: scRNA_seq_FoxD3_Citrine_32


title: scRNA_seq_FoxD3_Citrine_26


title: shRNA SENCR #1

city: Rochester

first: Joseph

middle: M

last: Miano

state: NY

address: 601 Elmwood Avenue

country: USA

institute: University of Rochester

data_processing:
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
subread-1.5.0p3, featurecounts, "-s 2 -t exon -g gene_name"
Genome_build: GRCh38.p7 + Gencode-25 Annotation
Supplementary_files_format_and_content: Text file containing raw read counts per sample

source_name: HUVEC

growth_protocol: HUVEC were grown at passage 2-4 in Medium 200 supplemented with LSGS (low serum/growth supplement) from ThermoFisher.

extract_protocol:
Standard TriZol reagent was used to isolate total RNA from each sample
TruSeq Stranded mRNA

treatment_protocol: At 80% confluency, cells were transduced with lentivirus carrying GFP and either a short hairpin RNA to SENCR or a scrambled sequence control.

value: umbilical cord endothelial cells

tag: lentivirus

value: shRNA SENCR


title: Scrambled shRNA #3

value: scambled shRNA


title: shRNA SENCR #2


title: DAY5_S4

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: scRNA_seq_FoxD3_Citrine_24


title: Scrambled shRNA #2


title: scRNA_seq_FoxD3_Citrine_21


title: shRNA SENCR #3


title: scRNA_seq_FoxD3_Citrine_23


title: DAY5_S2

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: scRNA_seq_FoxD3_Citrine_22


title: scRNA_seq_FoxD3_Citrine_20


title: scRNA_seq_FoxD3_Citrine_19


title: Scrambled shRNA #1


title: MEF_S4

description: unsorted cells


title: MEF_S5

description: unsorted cells


title: MEF_S3

description: unsorted cells


title: scRNA_seq_FoxD3_Citrine_17


title: MEF_S2

description: unsorted cells


title: scRNA_seq_FoxD3_Citrine_16


title: MEF_S1

description: unsorted cells


title: DAY5_S3

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: scRNA_seq_FoxD3_Citrine_15


title: scRNA_seq_FoxD3_Citrine_13


title: DAY5_S1

description: Clec9a-tdTomato+ CD45+ MHC-II+


title: wt H3K36me2_ChIPSeq

city: Nanjing

first: jingjing

last: chen

address: 101 Longmian Road

country: China

institute: Nanjing Medical University

library_source: genomic

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (default settings).
Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Genome_build: mm10
Supplementary_files_format_and_content: The resulting histograms (genomic “signal maps”) were stored in bigWig files.

molecule: genomic DNA

source_name: Germinal center B cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

value: Germinal center B cells from spleens

tag: age


title: scRNA_seq_FoxD3_Citrine_14


title: scRNA_seq_FoxD3_Citrine_10


title: scRNA_seq_FoxD3_Citrine_12


title: scRNA_seq_FoxD3_Citrine_8


title: ko H3K36me2_ChIPSeq


title: scRNA_seq_FoxD3_Citrine_7


title: input DNA


title: scRNA_seq_FoxD3_Citrine_11


title: scRNA_seq_FoxD3_Citrine_6


title: scRNA_seq_FoxD3_Citrine_5


title: scRNA_seq_FoxD3_Citrine_9


title: scRNA_seq_FoxD3_Citrine_18


title: C32 Organoid 4

city: Parkville

first: Luke

last: Zappia

address: 50 Flemington Road

country: Australia

institute: Murdoch Childrens Research Institute

description:
GSM3149442
org4_counts.csv.gz, org4_matrix.mtx.gz, org4_barcodes.tsv, org4_genes.tsv

data_processing:
The 10x Genomics Cell Ranger pipeline (v1.3.1) was used to align, filter and de-duplicate reads before counting those overlapping genes to produce count matrices for each sample.
Count matrics from batch 1 (organoids 1, 2 and 3) were combined using cellranger aggr with no normalisation. Organoid 4 was processed in a separate batch and is provided in separate files. The resulting datasets consist of matrix files (org_matrix.mtx, org4_matrix.mtx) containing the UMI count values, barcode files (org_matrix.tsv, org4_matrix.tsv) containing the detected cell barcodes and genes files (org_genes.tsv, org4_genes.tsv) containing the ENSEMBL ids of the detected genes. These have been converted to dense matrices in CSV format (org_counts.csv, org4_counts.csv).
Genome_build: hg38
Supplementary_files_format_and_content: Cell Ranger output files and CSV files containing raw count matrices.

source_name: C32 human embryonic stem cell

growth_protocol: Kidney organoids were made according to a published protocol (Takasata et al., Generation of kidney organoids from human pluripotent stem cells, Nature protocols 2016, PMID:27560173.

extract_protocol:
Human kidney organoids were dissected into ice cold PBS then digested over 15 minutes at 37C in Trypsin with manual dissociation via pippetting through a P1000 tip every 5 minutes. Following dissociation, cells were passed through a 30 micron filter and stored on ice in APEL media.
Chromium Single Cell Library kit V2
Illumina HiSeq HT chemistry- 100bp paired end sequencing

value: ES-derived kidney organoid

tag: day of differentiation


title: scRNA_seq_FoxD3_Citrine_4


title: scRNA_seq_FoxD3_Citrine_3


title: C32 Organoid 3

description:
GSM2914999
org_counts.csv.gz, org_matrix.mtx.gz, org_barcodes.tsv, org_genes.tsv


title: C32 Organoid 2

description:
GSM2914998
org_counts.csv.gz, org_matrix.mtx.gz, org_barcodes.tsv, org_genes.tsv


title: C32 Organoid 1

description:
GSM2914997
org_counts.csv.gz, org_matrix.mtx.gz, org_barcodes.tsv, org_genes.tsv


title: scRNA_seq_FoxD3_Citrine_2


title: scRNA_seq_FoxD3_Citrine_1


title: BiotinChIP_BirA_input

source_name: Cells expressing Citrine and Cherry reporter from 5-6ss embryos

extract_protocol:
FACS sorted cells were washed with PBS and stored at -80C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit (AM1931), checked on Bioanalyser, samples with RIN >7 were used to prepare cDNA using Takara Clontech SmartSeq2 V4 kit (634889).
Sequencing libraries were prepared using Illumina Nextera XT library preparation kit (FC-131-1024).
Foxd3 Biotin-ChIP was performed on 320 5-6ss whole embryos (128,000 cells of interest). Embryos were manually dechorionated, cells were dissociated with 20 strokes using pestle A in isotonic nuclei extraction buffer (NEB: 0.5% NP40, 0.25% Triton X, 10 mM Tris-HCl (pH 7.5), 3 mM CaCl2, 0.25 M sucrose, 1mM DTT, 0.2 mM PMSF, 1X Proteinase inhibitor (PI) ) in a glass homogeniser and cross-linked using 1% formaldehyde at room temperature for 10 min. Fixation was quenched with 125 mM of glycine for 5min. Cross-linker was washed-out by 3x pellet washes with 1x PBS (with 1X PI, 1 mM DTT and 0.2 mM PMSF) centrifuging at 2000 x g for 4min at 4C. Pellets were re-suspended in NEB. Cell nuclei were expulsed with 20 strokes using pestle B in a glass homogeniser, pelleted and washed with 1 xPBS (with 1X PI, 1 mM DTT and 0.2 mM PMSF). Nuclei were lysed in SDS lysis buffer (0.7% SDS, 10mM EDTA, 50 mM Tris-HCl (pH 7.5), 1x PI). Cross-linked chromatin was sonicated at 12A 10x (10s ON 30s OFF) followed by 8A 4x (30s ON 30s OFF). Sheared chromatin samples were pre-cleared in pre-blocked Protein G beads (Dynabeads Protein G, Life Technologies) for 1 hour at 4C. 1/20 of biotinChIP was collected as an input fraction and stored at -80C. Pre-cleared chromatin samples were incubated on pre-blocked streptavidin beads (Dynabeads M-280 streptavidin beads, Life Technologies) o/n at 4C. Beads were washed with SDS Wash Buffer (2% SDS, 10mM Tris-HCl (pH 7.5), 1 mM EDTA) at room temperature, followed by 4x RIPA washes (50 mM Hepes-KOH (pH 8.0), 500 mM LiCl, 1mM EDTA, 1% NP40, 0.7% Na-Deoxycholate, 1x PI) and 1x Na-Cl TE wash (1x TE, 50mM NaCl) at 4C. Chromatin was eluted from the beads with SDS ChIP elution buffer (50 mM Tris-HCl (pH 7.5), 10 mM EDTA, 1% SDS). Cross-linking was reversed o/n at 70C in the thermomixer at 1300 rpm. Cellular RNA was digested with RNAse A (0.2 g/ml) at 37C for 1 hour, and cellular protein with Proteinase K (0.4 mg/ml) at 55C for 2 hours. Chromatin samples were separated from the streptavidin beads. Input and ChIP DNA was extracted using a standard phenol-chloroform extraction method. Libraries were prepared using MicropPlex Library Preparation kit (Diagenode) and sequenced using NextSeq 500/550 High Output Kit v2 (75 cycles) on NextSeq 500 sequencing system.

value: Biotin ChIP-seq


title: BiotinChIP_BirA

value: Cells expressing Citrine and Cherry reporter from 5-6ss embryos


title: BiotinChIP_FoxD3_input


title: BiotinChIP_FoxD3_ChIP


title: ChIPseq_H3K27ac_NCC5-6ss_Cit_input

extract_protocol:
FACS sorted cells were washed with PBS and stored at -80C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit (AM1931), checked on Bioanalyser, samples with RIN >7 were used to prepare cDNA using Takara Clontech SmartSeq2 V4 kit (634889).
Sequencing libraries were prepared using Illumina Nextera XT library preparation kit (FC-131-1024).
For histone ChIP, FACS sorted cells were cross-linked with 1% formaldehyde and sonicated to 300-800bp fragments. Preblocked Protein A Dynabeads were incubated with antibody (Abcam Ab4729). Sonicated DNA-protein complexes were applied to beads, IgG antibody (Millipore 12-370) was used as control and an input sample was taken. Samples were washed, cross-links were reversed, immunoprecipitated DNA was eluted, purified and libraries prepared using amplification protocol for small cell numbers (Adli and Bernstein, 2011). H3K27Ac ChIP libraries were sequences using 50bp paired end reads using Illumina Hiseq2500 platform.

value: ChIP-seq


title: ChIPseq_H3K27ac_NCC5-6ss_Citrine-Cherry

source_name: Citrine reporter and Cherry reporter expressing cells from 14-16ss embryos


title: RNA-seq ko2

data_processing:
Illumina Casava1.8 software was used for basecalling.
The raw reads were filtered by removing reads containing adapter, poly-N and low quality reads for subsequent analysis.
The reference genome and gene model annotation files were downloaded directly from the genome website. The reference genome index was built using Bowtie(v2.2.9), and paired-end clean reads were aligned to the reference genome using TopHat(v2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol:
Germinal center B cells from wt/ko spleens were sorted by BD Aria II then extracted in 1ml Tizol.
The sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep Kit for Illumina(Vazyme,NR601) following manufacturer's recommdendations.


title: Mino_karo_2

type: RNA

city: Oslo

first: Thea

middle: Kristin

last: Vatsveen

address: Ullernschauseen 70

department: Cancer Research

country: Norway

institute: Oslo University Hospital

hyb_protocol: microarray study performed at core facility of Ullevaal hospotital, Oslo University Hospital, Norway

data_processing:
The Robust Multichip Analysis (RMA) algorithm was applied for generation of signal values and normalization.
Gene set enrichment analysis was performed using the GSEA software v.3.0. combining both cell line data against predicted gene sets (Hallmark datasets) downloaded from the MSigDB collection. A thousand permutations were performed to test against control and karonudib treated cells. Gene sets with false discovery rate (FDR) q values < 0.1 were regarded as significantly enriched gene sets.

label: biotin

source_name: Mantle Cell lymphoma cell line

extract_protocol: Total RNA was isolated (MiRNeasy, Qiagen, Hilden, Germany) after 12 h treatment with karonudib (0.5 µM).

tag: cell line

value: Mino

value: Mantle Cell lymphoma cell line

tag: treatment

value: karonudib treated


title: BL_41_1_ctrl

scan_protocol: microarray study performed at core facility of Ullevaal hospotital, Oslo University Hospital, Norway

source_name: Burkitts Lymphoma cell line

value: Burkitts Lymphoma cell line

value: ctrl


title: ChIPseq_H3K27ac_NCC5-6ss_Citrine


title: ChIPseq_H3K27ac_NCC5-6ss_CitChe_input

value: Citrine reporter and Cherry reporter expressing cells from 14-16ss embryos


title: RNA-seq wt2


title: RNA-seq ko1


title: Mino_karo_1

label_protocol: microarray study performed at core facility of Ullevaal hospotital, Oslo University Hospital, Norway


title: BL-41_karo_2


title: BL-41_Ctrl_2


title: Mino_2 ctrl


title: RNA-seq wt1


title: BL_41_Karo_1


title: MCF7_siCtrl_Rep4

city: York

first: Andrew

middle: Nicholas

last: Holding

address: Wentwork Way

department: Biology

institute: University of York

data_processing:
Alignment with Bowtie2.
DAC Blacklisted.
Peaks called with MACS2.
Full R Markdown available at https://github.com/andrewholding/VULCANSupplementary
Genome_build: GRChr38
Supplementary_files_format_and_content: *_peaks.broadPeak
Supplementary_files_format_and_content: *_peaks.narrowPeak

growth_protocol: Cells were grown in DMEM with phenol red, FBS and glutamate.

extract_protocol:
Cells were cross-linked with 1% Formaldehyde, DNA was sheared using ultrasound and IP was overnight at 4C.
ThruPLEX

treatment_protocol: siGRHL2 or siCTRL was transfected with RNAmax.

value: Breast cancer cell line

tag: sirna

value: siCtrl

tag: chip-antibody

value: anti-H3K27ac (abcam ab4729)


title: MCF7_siCtrl_Rep3


title: MG tumor, biological replicate 6

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
DKFZ_1215_MG
Gene expression array data derived from murine MG (Myc/Gfi1) medulloblastoma tumor.

hyb_protocol: As recommended by Affymetrix.

scan_protocol: As recommended by Affymetrix.

data_processing: Microarray gene expression data for n=7 MG tumors and n=5 NSC samples were obtained using the GeneChip Mouse Genome 430 2.0 Array from Affymetrix. The raw data were preprocessed using the RMA algorithm that includes background correction, normalization and calculation of expression steps. The resulting expression values were in log base 2 scale.

source_name: MG tumor

label_protocol: As recommended by Affymetrix.

growth_protocol: Mouse cerebellar stem cells (isolated from cerebella at P5-P7) were purified by sorting cells that expressed prominin-1 (detected with antibody 13A4) and lacked the lineage markers O4, polysialated (PSA)-NCAM (Chemicon) and TAPA-1 (eBioscience). Prominin+lin− cells were sorted into Neurobasal medium with B27 supplement (NB-B27, Invitrogen) containing 10 mg ml−1 BSA (Sigma), washed and resuspended in NB-B27 with appropriate growth factors.

extract_protocol: To isolate NSCs, Prominin1+, Lineage-negative (lin-) cells were FACS-sorted from cerebella of 5-7-day-old WT mice. Tumor cells were isolated by enzymatic dissociation of cerebella from adult tumor-bearing mice. All cells were snap-frozen in liquid nitrogen. RNA was isolated using the RNAqueous kit (Ambion), and was labeled and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

value: MG (Myc/Gfi1) medulloblastoma tumor


title: MCF7_siCtrl_Rep1


title: MG tumor, biological replicate 5

description:
DKFZ_1214_MG
Gene expression array data derived from murine MG (Myc/Gfi1) medulloblastoma tumor.


title: T47D_siCtrl_Rep1


title: hel 293 1

city: Toronto

first: Yasin

last: Mamatjan

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

hyb_protocol: 5.5 micrograms of cRNA were hybridized for 16 hr at 45 degrees Celcius on the Affymetrix Human Gene 2.0 ST array platform. Gene chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix CEL files were loaded and analyzed using Partek® Genomics Suite™ version 6.6. Quantile Normalization and RMA Background Correction were perfromed using this package.

source_name: HEK293 cells control cells

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocols.

growth_protocol: not applicable

extract_protocol: Extraction of RNA was performed using the Qiagen RNeasy extraction kit as per the manufacturer's protocol

treatment_protocol: not applicable

value: Human embryonic kidney cells


title: MCF7_input


title: Mino_1 ctrl


title: u87 1

source_name: U87 control cells

value: Glioblastoma cell line


title: MG tumor, biological replicate 4

description:
DKFZ_1213_MG
Gene expression array data derived from murine MG (Myc/Gfi1) medulloblastoma tumor.


title: hel 293 2

source_name: HEK293 cells transfected with CIC


title: T47D_siGRHL2_Rep2


title: T47D_siCtrl_Rep4


title: T47D_siCtrl_Rep3


title: T47D_siCtrl_Rep2


title: T47D_siGRHL2_Rep3


title: MG tumor, biological replicate 2

description:
DKFZ_1211_MG
Gene expression array data derived from murine MG (Myc/Gfi1) medulloblastoma tumor.


title: T47D_siGRHL2_Rep4


title: u87 2

source_name: U87 cells transfected with CIC


title: MG tumor, biological replicate 3

description:
DKFZ_1212_MG
Gene expression array data derived from murine MG (Myc/Gfi1) medulloblastoma tumor.


title: MG tumor, biological replicate 7

description:
DKFZ_1216_MG
Gene expression array data derived from murine MG (Myc/Gfi1) medulloblastoma tumor.


title: MCF7_siGRHL2_Rep2


title: MCF7_siCtrl_Rep2


title: T47D_siGRHL2_Rep1


title: MCF7_siGRHL2_Rep1


title: MCF7_siGRHL2_Rep3


title: T47D_input


title: MG tumor, biological replicate 1

description:
DKFZ_1210_MG
Gene expression array data derived from murine MG (Myc/Gfi1) medulloblastoma tumor.


title: MCF7_siGRHL2_Rep4


title: Cit_8ss_RNAseq

description: 1 transgenic allele: Gt(foxd3-Citrine)ct110a

data_processing:
ChIP-seq and ATAC-seq reads were mapped using bowtie (v.1.0.0)
ChIP-seq and ATAC-seq: duplicates were removed using MarkDuplicates (picard-tools/1.83)
Input reads were normalised to the same number of ChIP reads by random down-sampling using samtools/1.1
ChIP peak calling was performed using Homer (v.4.7) findPeaks script using -size 200-minDist 1500 parameters.
ATAC-seq: All samples were randomly down-sampled to the lowest-read containing sample (10,443,726) using samtools/1.1.
ATAC-seq: control tripilactes were merged and experimental triplicate BAM files were merged and sorted using samtools/1.1
ATAC-seq:k-means clustering of ATAC-seq signal was carried out using SeqMINER software as described (Ye et al., 2011), using 3.1 enhancer cluster ATAC-seq peaks and all pulled foxd3 Biotin-ChIP peaks as references for clustering.
RNA-seq reads were mapped using STAR (v.2.4.2a)
Genome_build: danRer10

extract_protocol: Illumina Nextera XT library preparation kit

value: Embryo

tag: development stage

value: 8 somites

value: Neural crest (foxd3 cells)

value: Dissociations and FACS

tag: amplification

value: RNA-seq


title: Cit_cherry_8ss_RNAseq

description: 2 transgenic alleles: Gt(foxd3-Citrine)ct110a x Gt(foxd3-Cherry)ct110R

value: Illumina Nextera XT library preparation kit


title: RNAseq_NCC5-6ss_Citrine-Cherry_2

source_name: Citrine reporter and Cherry reporter expressing cells from 5-6ss embryos

extract_protocol:
FACS sorted cells were washed with PBS and stored at -80C in lysis buffer. RNA was extracted using Ambion RNAqueous Micro Total RNA isolation kit (AM1931), checked on Bioanalyser, samples with RIN >7 were used to prepare cDNA using Takara Clontech SmartSeq2 V4 kit (634889).
Sequencing libraries were prepared using Illumina Nextera XT library preparation kit (FC-131-1024).
RNA pools extracted using RNAqueous Micro Scale Total RNA Isolation Kit. Non-directional sequencing libraries after polyA-selection of RNA transcripts (NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEB) were built using NEBnext Ultra RNA library kit for Illumina (NEB). Following ribodepletion using Ribo-ZeroTM Magnetic Kit (Epicentre), directional RNA-seq libraries were constructed using Stranded RNA-Seq Library Preparation Kit (KAPABiosystems).

value: FACS


title: RNAseq_NCC5-6ss_Citrine-Cherry_1

value: Citrine reporter and Cherry reporter expressing cells from 5-6ss embryos


title: RNAseq_NCC5-6ss_Citrine_2

value: Citrine reporter expressing cells from 5-6ss embryos


title: BOPCASQRSC3

city: Copenhagen

first: Bo

middle: Torben

last: Porse

address: Ole Maaløes Vej 5, 4.

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
For differential gene expression analysis, reads were mapped to human genome (hg19) using STAR (default parameters) (Dobin et al., 2013). Expression levels for GENCODE gene annotations (v19) were quantified using featureCounts (Liao et al., 2013). Differential gene expression analysis between shRBM25 and shScr was performed using DESeq2 (Love et al., 2014) at a FDR of < 0.05.
For alternative splicing analysis of transcripts, a computational pipeline involving following steps was used: a) Mapping of RNA-seq data to human genome (hg19) using TopHat v. 2.0.135, b) Transcript quantification using Cufflinks v. 2.2.16, c) The resulting full-length transcripts were annotated with classes of alternative splicing using the Bioconductor package spliceR7 with default settings.
bedGraph files were generated using bedtools. Signal is normalized to TPM. bedGraph files were converted to bigWig format using bedGraphToBigWig tool.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bw: bigWig files

source_name: U937 cells

growth_protocol: U937 cells were grown in RPMI-1640, GlutaMAXTM supplement medium containing 10% FCS and 1% Penicillin/Streptomycin.

extract_protocol:
RNA was extracted from 1 x 10^6 cells using the AllPrep DNA/RNA Mini kit (Qiagen).
For RNA-seq library generation, 1 mg RNA was fragmented, size selected (350-500 bp), reverse transcribed according to the TruSeq RNA Library Prep Kit V2 sample preparation guide (Illumina). The libraries were analyzed by Qbit and Agilent Bioanalyzer High sensitivity assay (Agilent) and pooled in equimolar amounts. Multiplexed samples were sequenced on an Illumina HiSeq 2000 system.

value: Myeloid leukemic cell line

tag: variation/genotype

value: WT


title: RNAseq_NCC5-6ss_Citrine_1

value: 75% Epiboly


title: BOPCASQRSC2


title: NH2PSL2

city: Jinan

first: Yuebin

last: Jia

address: 88 Cultural east road

institute: Shandong University

data_processing:
The RNA was purified by electrophoresis through a TBE-urea polyacrylamide gel. The gel regions harboring 18-30 nt fragments were excised and the RNA recovered. The resulting population of sRNAs was 5' and 3' RNA adapter-ligated using T4 RNA ligase, and amplified for 18 PCR cycles
The amplicons were purified and sequenced using an Illumina/Solexa Genome Analyzer (Beijing Genomics Institute, Shenzhen, China).
Raw reads were trimmed by removing low-quality and adaptor sequences, then aligned to the A. thaliana genome using SOAP2 software.
Transcript frequency was calculated using the reads per kilobase per million reads method. Differentially transcribed genes were identified using a method modified from Audic and Claverie (1997). Significance was based on the P value and the false discovery rate (FDR) (Audic and Claverie, 1997).
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited .txt  files include RPKM values for each Sample, and the log2 value of ratio of Group1-Expression to Group2-Expression.

organism: Arabidopsis thaliana

growth_protocol: Seedlings were grown on 1/2 MS  with or without PS-SO3H or PS-NH2 nanoplastics treatment for 10 days,  the leaf and root were extracted for RNA sequencing.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA, USA).
First strand cDNA was generated using reverse transcriptase and random primers. The constructed cDNA libraries was qualified and quantified with Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, and then sequenced via Illumina HiSeqTM 2000 or other sequencer when necessary at the Beijing Genomics Institute, Shenzhen, China.

treatment_protocol: PS-SO3H (50 μg/ml), PS-NH2 (50 μg/ml)

value: 10-day-old seedlings

value: leaf

value: wild type

value: PS-NH2 nanoplastics


title: PSR2

source_name: PS

value: root

value: PS-SO3H nanoplastics


title: BOPCASQRSC1


title: BOPCASQR332

value: RBM25 KD


title: BOPCASQR331


title: MSR2

source_name: MS

value: control


title: PSL1


title: BOPCASQR333


title: PSR1


title: PSL2


title: NH2PSL1


title: P14-3

city: Xiamen

last: Miao

state: Fujian

address: 668 Jimei Road

department: School of Medicine and School of Biomedical Sciences

institute: Huaqiao University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using MapSpliceprogram(v2.1.8) with parameters(-s22-p12--ins6--del6--non-canonical)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: excel files include RPKM values for each Sample

source_name: Cerebral cortex

extract_protocol:
The RNAs for RNA-seq from three P14 mouse cerebral cortices, were extracted by TRIzol (Invitrogen, USA) according to manufacturer’s instructions.Ribosome RNA (rRNA) was removed from the total RNA
RNA libraries were prepared for sequencing using standard Proton Sequencing process protocols


title: P14-2


title: P14-1


title: NH2PSR2


title: MSL2


title: NH2PSR1


title: MSR1


title: MSL1


title: WT V3

city: Birmingham

first: Daniel

middle: James

last: Gibbs

state: West Midlands

address: Edgbaston

department: School of Biosicences

institute: The University of Birmingham

description: WTCvsWTV.xlsx

data_processing:
150 bp reads (75x2 per fragment) were generated in fastq format, and aligned to the Arabidopsis genome (TAIR10)
Reads were analysed using Kallisto (https://pachterlab.github.io/kallisto/about)
The R- Package DSeq2 (https://bioconductor.org/ packages/release/bioc/html/ DESeq2.html) was subsequently used to compare pairs of samples and generate the final set of excel spreadsheets showing fold change differences
Genome_build: TAIR10
Supplementary_files_format_and_content: .xlxs

source_name: seedling

extract_protocol:
RNA was extracted from seedlings using an RNEasy plant mini kit (Qiagen; 74904) and converted to cDNA with Superscript II Reverse transcriptase (Invitrogen; 18064-014) using OligodT primers
The library was prepared using the Illumina TruSeq mRNA kit (polyA selection), before being analysed using the Qubit and the bioanalyser HS DNA chip. Samples were pooled and sequenced on the HiSeq 4000

tag: ecotype

value: 4 week vernalized

value: seedling


title: WT V2

description: WTCvsWTV.xlsx


title: WT C2

description: WTCvsWTV.xlsx

value: non-vernalized


title: WT V1

description: WTCvsWTV.xlsx


title: WI38-vector

status: Public on Dec 06 2018

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Demultiplexing using Illumina's BaseSpace platform
Sequenced reads were mapped to hg19 using STAR 2.5
Read counts are obtained using STAR's quantification tool
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: Human Fibroblasts WI38

growth_protocol: Cells were grown in DMEM culture media supplemented with 10% FBS

extract_protocol: RNA was extracted using Rneasy kit (Qiagen)

treatment_protocol: Cells were transduced with lentiviral vectors

tag: cell

value: cultured cell populations

value: lungs


title: WT C1

description: WTCvsWTV.xlsx


title: WT C3

description: WTCvsWTV.xlsx


title: WI38-K9-sh-2


title: WI38-CTRL-sh


title: WI38-K9-sh-1


title: liver-specific knockout of Nemo [NemoLPC-KO], biological replicate 1

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0001

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

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

source_name: Nemo cre+

label_protocol: Fragmented, biotinylated cDNAs were prepared from 300 ng total RNA using  the Affymetrix WT Plus Reagent Kit according to the manufacturers instructions.

growth_protocol: Hepatocytes isolated from 12 week old male mice

extract_protocol: Qiagen RNAeasy kit

tag: gender

value: male

value: 12 weeks old

value: liver-specific KO of Nemo

tag: cell type

value: hepatocyte


title: Wildtype, biological replicate 2

source_name: Nemo cre-

tag: genotype

value: Wildtype


title: VSMC_Input (chip-seq)

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

data_processing:
Basecalls performed using bcl2fastq version v2.18.0.12
For RNA-seq analysis, the reads were aligned to genomes of mm9 by subread (R version 1.24.2). Uniq reads were kept and assigned to in-build refseq gene annotation of rsubread using featureCounts. Differential analysis was conducted with limma
For ChIP-seq, reads were mapped by subread and called peaks with MACS2 (2.1.1). All factor peaks were called using narrow mode of MACS2.
bigWig files were produced by HOMER (4.8.3)
For RIP-seq,reads were aligned to genomes of mm9 by subread (R version 1.24.2) and assigned to in-build refseq gene annotation using featureCounts. Then raw read numbers were normalized against the median of enrichment ratios for all expressed genes, with the reads depth of a transcript d > 10. Gaussian mixture modeling was performed on enrichment ratios for all the filtered RIP signals.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig, read intensity of samples
Supplementary_files_format_and_content: txt,raw counts of RNA-seq
Supplementary_files_format_and_content: xlsx,log fold change of RNA-seq; enrichment ratios of RIP-seq

growth_protocol: For isolation of primary mouse vascular smooth muscle cells, six-week C57BL/6 mice were sacrificed, and aorta were removed to PBS containing heparin sodium (1000 units in 50 ml PBS). After removing the surrounding adipose tissues and para-aortic lymph nodes, aorta were chopped into small pieces and digested with Aorta Dissociation Enzyme stock solution (125 mg/ml Collagenase type I in high glucose DMEM) for 3-4 hour at 37°C. After incubation, the digested aorta were rigorously pipetted up and down for several times, and then filtered through a 70-μm cell strainer into 15ml tubes. Then, isolated cells were spun down (100 rpm, 10 minutes, 4°C), and seeded into 0.1% gelatin-coated plates in high-glucose DMEM containing 20% FBS.Isolated mouse VSMCs were maintained in 10% FBS/DMEM, and P4-P8 cells were used in our study unless otherwise specified.

extract_protocol:
[RNA-Seq] Total RNA was extracted from cells using the GeneJet RNA Purification Kit (Thermo Scientific) 4 days after infection. One µg of RNA was used for generation of sequencing library using the TruSeq RNA Library Prep Kit V2 (Illumina) according to the manufacturer’s instructions.
[ChIP-Seq] Mouse VSMCs were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop fixation. Cells were harvested, and DNA was fragmented to 300–500 bp by sonication with Covaris S220 sonicator. Immunoprecipitation was performed with antibodies conjugated to Dynabeads Protein G beads (Life Technology). ChIP DNA was eluted, reverse cross-linked, extracted by phenol/chloroform, and precipitated.
[RIP-Seq] RNA immunoprecipitation (RIP) was carried out using the Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore) according to manufacturer’s instructions. Eluted RNA was precipitated, quantified, and subjected to RT-qPCR or library generation for sequencing. RNA sequencing libraries were prepared with the TruSeqTM RNA Sample Preparation Kit (Illumina).

tag: strain

value: primary vascular smooth muscle cell

tag: passages

tag: chip antibody


title: VSMC_RIP10_Thoc5 (rip-seq)

tag: rip antibody

value: Thoc5 (Bethyl, cat#A302-119A)


title: Wildtype, biological replicate 1

tag: age


title: VSMC_Thoc5 (chip-seq)


title: CXCR6 knockout, biological replicate 3

source_name: Nemo_CXCR6 cre-

value: CXCR6 KO


title: liver-specific knockout of Nemo [NemoLPC-KO], biological replicate 2


title: CXCR6 knockout, biological replicate 1


title: VSMC_RIP3_Thoc5 (rip-seq)


title: VSMC_RIP10_Thoc2 (rip-seq)

value: Thoc2 (Abcam, cat#ab129485)


title: VSMC_RIP10_Input (rip-seq)


title: VSMC_RIP3_Input (rip-seq)


title: VSMC_RIP3_Thoc2 (rip-seq)


title: liver-specific knockout of Nemo [NemoLPC-KO] and CXCR6 knockout, biological replicate 3

source_name: Nemo_CXCR6 cre+

value: liver-specific KO of Nemo and CXCR6 KO


title: VSMC_shThoc5_2 (rna-seq)

description:
RNAseq_shNT_shThoc5_logFC.xlsx
RNAseq_genecountsraw.txt
shthoc5_773_2

value: Thoc5 silencing


title: liver-specific knockout of Nemo [NemoLPC-KO] and CXCR6 knockout, biological replicate 2


title: liver-specific knockout of Nemo [NemoLPC-KO], biological replicate 3


title: liver-specific knockout of Nemo [NemoLPC-KO] and CXCR6 knockout, biological replicate 1


title: VSMC_shThoc5_1 (rna-seq)

description:
RNAseq_shNT_shThoc5_logFC.xlsx
RNAseq_genecountsraw.txt
shthoc5_773_1


title: CXCR6 knockout, biological replicate 2


title: WI38-KLF9

tag: tissue


title: VSMC_shNT_1 (rna-seq)

description:
RNAseq_shNT_shThoc5_logFC.xlsx
RNAseq_genecountsraw.txt
shnt_1

tag: treatment

value: control


title: VSMC_shNT_2 (rna-seq)

description:
RNAseq_shNT_shThoc5_logFC.xlsx
RNAseq_genecountsraw.txt
shnt_2


title: SQ-80007_S29_E1-50

city: Seattle

first: Allen

last: Institute

state: WA

address: 615 Westlake Ave N

institute: The Allen Institute for Brain Science

description:
controls_exon_counts.csv.gz
controls_exon_counts.csv.gz

data_processing:
50-base pair paired-end reads were aligned to GRCm38 (mm10) using a RefSeq annotation gff file retrieved from NCBI on 01/18/2016 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/all/). Sequence alignment was performed using STAR v2.5.3 (Dobin et al., 2013) in twopassMode. PCR duplicates were masked and removed using STAR option “bamRemoveDuplicates”. Only uniquely aligned reads were used for gene quantification. Gene counts were computed using the R GenomicAlignments package (Lawrence et al., 2013) sumarizeOverlaps function using “IntersectionNotEmpty”.
Reads that did not map to the genome were then aligned to synthetic constructs (i.e. ERCC) sequences and the E.coli genome (version ASM584v2). Quantification was performed using summerizeOverlaps from the R package GenomicAlignments [38].
Single nucleus quality control criteria: >500,000 genome-mapped reads, >75% reads aligned, and >50% unique reads. Single cell quality control criteria: >200,000 transcriptome mapped reads and >1000 genes detected (counts > 0).
Genome_build: mm10

source_name: Control: 10pg Takara Control Total RNA

growth_protocol: All procedures were approved by the Institutional Animal Care and Use Committee at the Allen Institute for Brain Science (Protocol no. 1511). Animals were provided food and water ad libitum and were maintained on a regular 12-h day/night cycle. Mice were housed at no more than 5 adults per cage, with various enrichment materials added, including nesting materials, gnawing materials, and plastic shelters. Nutritional and foraging enrichment was provided in the form of foods such as sunflower seeds and sucrose pellets. Mice were maintained on the C57BL/6J background.

extract_protocol:
Tissue samples were obtained from adult male and female transgenic mice carrying a Cre transgene and a Cre-reporter transgene. After euthanasia, the brain was rapidly dissected and mounted for coronal slice preparation on a Compresstome VF-300 vibrating microtome (Precisionary Instruments) and sectioned at  250 μm intervals.     For whole cell dissociation, 2 mg/ml of pronase in ACSF solution was added to dissected tissues and enzymatic digestion was carried out at room temperature. After digestion,The tissue was triturated and the cell suspension was incubated on ice in preparation for fluorescence-activated cell sorting (FACS). Live cells were sorted by excluding DAPI positive events and debris, and gating to include red fluorescent events (tdTomato-positive cells). Single cells were collected into strip tubes containing 11.5μl of collection buffer (SMART-Seq v4 lysis buffer), RNase Inhibitor, and ERCCs (External RNA Controls Consortium, MIX1 at a final dilution of 1x10-8) and tubes were then stored at -80°C.    For nuclei isolation, dissected tissues were placed into a homogenization buffer (10mM Tris pH 8.0, 250mM sucrose, 25mM KCl, 5mM MgCl2, 0.1% Triton-X 100, 0.5% RNase inhibitor, 1X protease inhibitor, and 0.1mM DTT). Tissues were placed into a 1ml dounce homogenizer and homogenized using 10 strokes of the loose dounce pestle followed by 10 strokes of the tight pestle to liberate nuclei . Mouse anti-NeuN antibody (EMD Millipore, MAB377, Clone A60) was added to the nuclei at a final dilution of 1:1000 and nuclei suspensions were incubated at 4°C for 30 minutes, followed by incubation in secondary antibody (goat anti-mouse IgG (H+L), Alexa Fluor 594 conjugated, ThermoFisher Scientific, 1:5000) for 30 minutes at 4°C and staining with DAPI. Single nuclei were captured by gating on DAPI-positive events, excluding debris and doublets, and then gating on Alexa Fluor 594 (NeuN) signal. Strip tubes containing FACS isolated single nuclei were then frozen at -80°C.
The SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech #634894) was used per the manufacturer’s instructions for reverse transcription of single cell RNA and subsequent cDNA synthesis. Mouse whole cells were subjected to 18 PCR cycles after the reverse transcription step, whereas mouse nuclei were subjected to 21 PCR cycles.     Sequencing libraries were prepared using NexteraXT (Illumina, FC-131-1096) with NexteraXT Index Kit V2 Set A (FC-131-2001). NexteraXT libraries were prepared at 0.5x volume, but otherwise followed the manufacturer’s instructions.

value: Pass

tag: molecule

value: ControlTotalRNA


title: SQ-80007_S30_E1-50


title: SQ-80006_S22_E1-50

description:
controls_exon_counts.csv.gz
controls_exon_counts.csv.gz
GSM3189895

value: Fail


title: SQ-80008_S38_E1-50


title: SQ-80005_S14_E1-50


title: SQ-80005_S13_E1-50


title: SQ-80006_S21_E1-50


title: SQ-80003_S94_E1-50


title: SQ-80004_S06_E1-50


title: SQ-80003_S93_E1-50


title: SQ-80001_S22_E1-50


title: SQ-80002_S86_E1-50


title: SQ-80001_S21_E1-50


title: SQ-80008_S37_E1-50


title: LS-15543_S61_E1-50


title: LS-15542_S54_E1-50


title: LS-15545_S78_E1-50


title: LS-15542_S53_E1-50


title: LS-15544_S69_E1-50


title: LS-15545_S77_E1-50


title: LS-15543_S62_E1-50


title: SQ-80004_S05_E1-50


title: LS-15541_S45_E1-50


title: LS-15539_S30_E1-50


title: LS-15539_S29_E1-50


title: SQ-80002_S85_E1-50


title: LS-15538_S21_E1-50


title: US-1250275_E2_S85

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz

source_name: Primary Visual Cortex (VISp)

value: F

value: VISp

value: RFP-positive

value: Glutamatergic

value: Cells


title: US-1250275_E2_S90


title: LS-15538_S22_E1-50


title: LS-15544_S70_E1-50


title: US-1250275_E2_S79


title: US-1250275_E2_S73


title: US-1250275_E2_S72

value: M


title: US-1250275_E2_S74


title: US-1250275_E2_S64


title: US-1250275_E2_S61


title: LS-15541_S46_E1-50


title: US-1250275_E2_S29


title: US-1250275_E2_S45


title: US-1250275_E2_S40


title: US-1250275_E2_S31


title: US-1250275_E2_S26


title: US-1250275_E2_S16


title: US-1250275_E2_S04


title: US-1250275_E2_S08


title: US-1250273_E2_S74


title: US-1250273_E2_S66


title: US-1250273_E2_S67


title: US-1250275_E2_S05


title: US-1250273_E2_S62


title: US-1250273_E2_S49


title: US-1250273_E2_S57


title: US-1250273_E2_S40


title: US-1250273_E2_S55


title: US-1250275_E2_S84


title: US-1250275_E2_S82


title: US-1250273_E2_S33


title: US-1250273_E2_S24


title: US-1250273_E2_S23


title: US-1250273_E2_S22


title: US-1250275_E2_S25


title: US-1250273_E2_S13


title: US-1250273_E2_S04


title: US-1250273_E2_S03


title: US-1250273_E2_S06


title: US-1250273_E2_S02


title: SM-DAIFD_S61_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189960

value: SM-DAIFD


title: SQ-80001_S04_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189980

value: GABAergic


title: SM-DAIFF_S66_E1-50

value: SM-DAIFF


title: SM-DAIFF_S71_E1-50


title: US-1250273_E1_S37

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189947


title: US-1250273_E2_S01


title: SM-DAIFD_S42_E1-50


title: PANC-1 cells treatment with Ginsenoside Rg3 RNA-seq

city: Suzhou

first: Meng-Dan

last: Xu

address: Shizi Street

institute: the First Affiliated Hospital of Soochow University

description: Sample 2

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.2.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: PANC-1 cells

growth_protocol: PANC-1 cells were maintained in Dulbecco’s modified essential medium (DMEM; Gibco, Grand Island, NY, USA). Medium was supplemented with 10% fetal calf serum (FBS; Gibco), 100 U/mL penicillin, and 100 mg/mL streptomycin at 37C in a 5% CO2 incubator with a humidified atmosphere. The cells were passaged every 2–3 days to maintain exponential growth.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA sample was purified using an RNeasy Mini Column (Qiagen, CA, USA) and the RNA quality was assessed via 1.0% agarose gel electrophoresis.
Ion  Proton Sequencing Protocol

treatment_protocol: PANC-1 cells were treatment with  50μM tamoxifen and 200μM Rg3 for 24h seperately.

value: Pancreas

tag: cell line

tag: agent

value: Ginsenoside Rg3


title: PANC-1 cells treatment with tamoxifen RNA-seq

description: Sample 3

value: tamoxifen


title: PANC-1 cells RNA-seq

description: Sample 1


title: SM-D9EQK_S86_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189935

value: GFP-positive (RFP unknown)


title: SM-D9EPX_S01_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189904


title: SM-D9EQK_S88_E1-50


title: SM-D9EPX_S07_E1-50


title: US-1250273_E2_S16


title: SM-D9EQL_S79_E1-50


title: SM-D9EQI_S84_E1-50


title: US-1250273_E2_S21


title: SM-D9EPN_S50_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189954


title: SM-D9EPN_S53_E1-50


title: SM-D9EPN_S57_E1-50


title: SM-D9EPN_S54_E1-50


title: US-1250273_E2_S07


title: SM-D9EP8_S78_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189976


title: SM-D9EP8_S75_E1-50


title: SM-DAIFD_S58_E1-50


title: SM-D9EP8_S66_E1-50


title: SM-D9EP8_S69_E1-50


title: SM-D9EP8_S70_E1-50


title: SM-D9EP8_S63_E1-50


title: SM-D9EP8_S58_E1-50


title: SM-D9EP5_S46_E1-50


title: SM-D9EP5_S33_E1-50


title: SM-D9EOT_S30_E1-50


title: SM-D9EOT_S31_E1-50


title: SM-D9EOT_S26_E1-50


title: SM-D9EOT_S14_E1-50


title: SM-D9EOT_S13_E1-50


title: SM-D9EOT_S12_E1-50


title: SM-D9EOS_S30_E1-50


title: SM-D9EOS_S21_E1-50


title: SM-D9D8J_S94_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189952


title: SM-D9EOT_S07_E1-50


title: SM-D9EOT_S04_E1-50


title: SM-D9CZL_S06_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189953


title: SM-D9CZK_S23_E1-50


title: SM-D9CZL_S05_E1-50


title: SM-D9CZM_S84_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189906


title: SM-D9EOT_S09_E1-50


title: SM-D9CZK_S21_E1-50


title: SM-D9EP5_S61_E1-50


title: SM-D9CZK_S11_E1-50


title: SM-D9CZF_S34_E1-50


title: SM-D9CZF_S35_E1-50


title: SM-D9CZF_S27_E1-50


title: SM-D9CZF_S26_E1-50


title: SM-D9CZF_S25_E1-50


title: SM-D9CZF_S22_E1-50


title: SM-D9CZF_S19_E1-50


title: SM-D9D8J_S95_E1-50


title: SM-D9E66_S95_E1-50


title: SM-D9CZE_S38_E1-50


title: SM-D9CZF_S16_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189905


title: SM-D9CZE_S31_E1-50


title: SM-D9CZE_S33_E1-50


title: SM-D9CZE_S24_E1-50


title: SM-D9CZE_S25_E1-50


title: SM-D9CZE_S20_E1-50


title: SM-D9CZE_S21_E1-50


title: SM-D9CZE_S22_E1-50


title: SM-D9CZF_S39_E1-50


title: SM-D9CZ6_S64_E1-50


title: SM-D9CZE_S12_E1-50


title: SM-D9CZE_S18_E1-50


title: SM-D9CZ6_S52_E1-50


title: SM-D9CZF_S30_E1-50


title: SM-D9CZ6_S96_E1-50


title: SM-D9CZ6_S53_E1-50


title: SM-D9CZ6_S40_E1-50


title: SM-D9CZ6_S31_E1-50


title: SM-D9CZ6_S28_E1-50


title: SM-D9CZ6_S47_E1-50


title: SM-D9CYV_S63_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189949


title: SM-D9CYT_S03_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189977

value: GFP-positive


title: SM-D9CYB_S45_E1-50

value: Pass


title: SM-D9CYB_S27_E1-50


title: SM-D9CY7_S63_E1-50


title: SM-D9CY7_S78_E1-50


title: SM-D9CY7_S71_E1-50


title: LS-15913_S55_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189931


title: LS-15920_S35_E1-50


title: SM-D9CZ6_S66_E1-50


title: SM-D9CZE_S10_E1-50


title: LS-15912_S67_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189903


title: LS-15912_S53_E1-50


title: LS-15912_S57_E1-50


title: LS-15912_S59_E1-50


title: LS-15577_S52_E1-50


title: LS-15911_S28_E1-50


title: LS-15911_S32_E1-50


title: LS-15580_S23_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189971


title: LS-15577_S27_E1-50


title: LS-15577_S33_E1-50


title: LS-15577_S25_E1-50


title: LS-15576_S49_E1-50


title: LS-15577_S04_E1-50


title: LS-15552_S51_E1-50


title: LS-15546_S20_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189944


title: LS-15546_S38_E1-50


title: LS-15546_S14_E1-50


title: LS-15546_S46_E1-50


title: LS-15546_S02_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189943


title: LS-15912_S90_E1-50


title: LS-15544_S29_E1-50


title: LS-15521_S93_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189912


title: LS-15515_S23_E1-50


title: LS-15545_S96_E1-50


title: LS-15542_S45_E1-50


title: LS-15544_S32_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189947


title: LS-15515_S16_E1-50


title: LS-15390_S94_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189936


title: LS-15576_S50_E1-50


title: LS-15514_S06_E1-50


title: LS-15382_S56_E1-50


title: LS-15576_S53_E1-50


title: LS-15382_S51_E1-50


title: LS-15382_S23_E1-50


title: LS-15382_S38_E1-50


title: LS-15382_S17_E1-50


title: LS-15382_S33_E1-50


title: LS-15381_S54_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189958


title: LS-15507_S48_E2-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz


title: LS-15382_S53_E1-50


title: LS-15396_S89_E1-50


title: LS-15381_S25_E1-50


title: LS-15371_S19_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189957


title: LS-15366_S39_E1-50


title: LS-15366_S43_E1-50


title: LS-15367_S82_E1-50


title: LS-15379_S60_E1-50


title: LS-15366_S25_E1-50


title: LS-15366_S16_E1-50


title: LS-15365_S56_E1-50


title: LS-15365_S54_E1-50


title: LS-15366_S37_E1-50


title: LS-15366_S08_E1-50


title: LS-15365_S42_E1-50


title: LS-15365_S53_E1-50


title: LS-15365_S32_E1-50


title: LS-15366_S42_E1-50


title: LS-15365_S20_E1-50


title: LS-15365_S08_E1-50


title: LS-15364_S41_E1-50


title: LS-15364_S28_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189946


title: LS-15364_S11_E1-50


title: LS-15364_S12_E1-50


title: LS-15364_S20_E1-50


title: LS-15364_S14_E1-50


title: LS-15364_S33_E1-50


title: LS-15364_S96_E1-50


title: LS-15363_S04_E1-50


title: LS-15362_S15_E1-50


title: LS-15363_S07_E1-50


title: LS-15362_S92_E1-50


title: LS-15363_S20_E1-50


title: LS-15362_S25_E1-50


title: LS-15363_S06_E1-50


title: LS-15363_S26_E1-50


title: LS-15365_S29_E1-50


title: LS-15361_S94_E1-50


title: LS-15365_S05_E1-50


title: LS-15361_S96_E1-50


title: LS-15360_S23_E1-50


title: LS-15360_S29_E1-50


title: LS-15360_S30_E1-50


title: LS-15361_S60_E1-50


title: LS-15360_S22_E1-50


title: LS-15363_S29_E1-50


title: LS-15360_S16_E1-50


title: LS-15360_S10_E1-50


title: LS-15360_S17_E1-50


title: LS-15360_S04_E1-50


title: LS-15359_S38_E1-50


title: LS-15359_S31_E1-50


title: LS-15359_S29_E1-50


title: LS-15360_S14_E1-50


title: LS-15359_S21_E1-50


title: LS-15359_S08_E1-50


title: LS-15359_S05_E1-50


title: LS-15359_S35_E1-50


title: LS-15352_S59_E1-50


title: LS-15353_S18_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189969


title: LS-15361_S72_E1-50


title: LS-15360_S15_E1-50


title: LS-15352_S33_E1-50


title: LS-15352_S15_E1-50


title: LS-15351_S65_E1-50


title: LS-15359_S25_E1-50


title: LS-15352_S43_E1-50


title: LS-15351_S54_E1-50


title: LS-15351_S51_E1-50


title: LS-15351_S35_E1-50


title: LS-15351_S22_E1-50


title: LS-15350_S22_E1-50


title: LS-15350_S19_E1-50


title: LS-15350_S36_E1-50


title: LS-15350_S17_E1-50


title: LS-15350_S07_E1-50


title: LS-15349_S56_E1-50


title: LS-15349_S46_E1-50


title: LS-15346_S93_E1-50


title: LS-15346_S80_E1-50


title: LS-15346_S90_E1-50


title: LS-15343_S11_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189952


title: LS-15343_S06_E1-50


title: LS-15346_S86_E1-50


title: LS-15343_S08_E1-50


title: LS-15342_S92_E1-50


title: LS-15342_S89_E1-50


title: LS-15346_S78_E1-50


title: LS-15342_S93_E1-50


title: LS-15341_S91_E1-50


title: LS-15341_S90_E1-50


title: LS-15343_S03_E1-50


title: LS-15342_S96_E1-50


title: LS-15350_S90_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189932


title: LS-15341_S88_E1-50


title: LS-15341_S82_E1-50


title: LS-15351_S39_E1-50


title: LS-15341_S86_E1-50


title: LS-15341_S83_E1-50


title: LS-15095_S10_E1-50


title: LS-15095_S04_E1-50


title: LS-15095_S08_E1-50


title: LS-15305_S95_E1-50


title: LS-15090_S34_E1-50


title: LS-15083_S07_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189956


title: LS-15082_S16_E1-50


title: LS-15082_S08_E1-50


title: LS-15082_S13_E1-50


title: LS-15082_S05_E1-50


title: LS-15080_S70_E1-50


title: LS-15080_S63_E1-50


title: LS-15072_S91_E1-50


title: LS-15072_S76_E1-50


title: LS-15070_S11_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189968


title: LS-15095_S01_E1-50


title: LS-15068_S45_E1-50


title: LS-15070_S77_E1-50


title: LS-15069_S05_E1-50


title: LS-15062_S73_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189921


title: LS-15074_S12_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189911


title: LS-15059_S54_E1-50


title: LS-15061_S82_E1-50


title: LS-15070_S73_E1-50


title: LS-15069_S14_E1-50


title: LS-15068_S31_E1-50


title: LS-15059_S42_E1-50


title: LS-15058_S64_E1-50


title: LS-15083_S03_E1-50


title: LS-15082_S83_E1-50


title: LS-15058_S24_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189967


title: LS-15052_S31_E1-50


title: LS-15052_S27_E1-50


title: LS-15081_S88_E1-50


title: LS-15052_S67_E1-50


title: LS-15052_S19_E1-50


title: LS-15052_S24_E1-50


title: LS-15069_S35_E1-50


title: LS-15075_S44_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189963


title: LS-15052_S18_E1-50


title: LS-15050_S50_E1-50


title: LS-15050_S49_E1-50


title: LS-15050_S32_E1-50


title: LS-15050_S39_E1-50


title: LS-15049_S79_E1-50


title: LS-15050_S40_E1-50


title: LS-15046_S89_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189970


title: LS-15046_S96_E1-50


title: LS-15048_S10_E1-50


title: LS-15046_S56_E1-50


title: LS-15050_S27_E1-50


title: LS-15046_S21_E1-50


title: LS-15046_S26_E1-50


title: LS-15046_S30_E1-50


title: LS-15044_S71_E1-50


title: LS-15044_S25_E1-50


title: LS-15043_S32_E1-50


title: LS-15069_S32_E1-50


title: LS-15042_S95_E1-50


title: LS-15042_S91_E1-50


title: LS-15052_S05_E1-50


title: LS-15042_S42_E1-50


title: LS-15041_S63_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189966


title: LS-15042_S09_E1-50


title: LS-15041_S66_E1-50


title: LS-15042_S29_E1-50


title: LS-15042_S49_E1-50


title: LS-15041_S08_E1-50


title: LS-15032_S67_E1-50


title: LS-15032_S68_E1-50


title: LS-15033_S18_E1-50


title: LS-15038_S10_E1-50


title: LS-15032_S63_E1-50


title: LS-15041_S04_E1-50


title: LS-15041_S17_E1-50


title: LS-15032_S58_E1-50


title: LS-15032_S62_E1-50


title: LS-15032_S52_E1-50


title: LS-15032_S56_E1-50


title: LS-15032_S51_E1-50


title: LS-15032_S59_E1-50


title: LS-15038_S19_E1-50


title: LS-15041_S70_E1-50


title: LS-15032_S16_E1-50


title: LS-15041_S54_E1-50


title: LS-15052_S03_E1-50


title: LS-15031_S36_E1-50


title: LS-15032_S09_E1-50


title: LS-15031_S73_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189920


title: LS-15041_S09_E1-50


title: LS-15031_S31_E1-50


title: LS-15029_S71_E1-50


title: LS-15031_S35_E1-50


title: LS-15025_S08_E1-50


title: LS-15025_S59_E1-50


title: LS-15025_S07_E1-50


title: LS-15025_S44_E1-50


title: LS-15025_S69_E1-50


title: LS-15038_S21_E1-50


title: LS-15032_S15_E1-50


title: LS-15024_S39_E1-50


title: LS-15024_S33_E1-50


title: LS-15021_S93_E1-50


title: LS-15021_S89_E1-50


title: LS-15024_S37_E1-50


title: LS-15041_S02_E1-50


title: LS-15024_S34_E1-50


title: LS-15024_S08_E1-50


title: LS-15021_S73_E1-50


title: LS-15021_S96_E1-50


title: LS-15021_S87_E1-50


title: LS-15029_S96_E1-50


title: LS-15021_S67_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189965


title: LS-15021_S61_E1-50


title: LS-15021_S60_E1-50


title: LS-15021_S88_E1-50


title: LS-15021_S55_E1-50


title: LS-15021_S59_E1-50


title: LS-15021_S56_E1-50


title: LS-15021_S51_E1-50


title: LS-15021_S54_E1-50


title: LS-15025_S57_E1-50


title: LS-15025_S70_E1-50


title: LS-15021_S50_E1-50


title: LS-15021_S49_E1-50


title: LS-15021_S39_E1-50


title: LS-15021_S35_E1-50


title: LS-15021_S33_E1-50


title: LS-15020_S55_E1-50


title: LS-15020_S15_E1-50


title: LS-15020_S09_E1-50


title: LS-15020_S12_E1-50


title: LS-15020_S26_E1-50


title: LS-15020_S01_E1-50


title: LS-15016_S96_E1-50


title: LS-15016_S87_E1-50


title: LS-15016_S83_E1-50


title: LS-15016_S90_E1-50


title: LS-15016_S86_E1-50


title: LS-15016_S91_E1-50


title: LS-15016_S57_E1-50


title: LS-15015_S47_E1-50


title: LS-15016_S26_E1-50


title: LS-15015_S20_E1-50


title: LS-15020_S02_E1-50


title: LS-15011_S20_E1-50


title: LS-15011_S87_E1-50


title: LS-15010_S69_E1-50


title: LS-15010_S62_E1-50


title: LS-15016_S71_E1-50


title: LS-15010_S56_E1-50


title: LS-15020_S08_E1-50


title: LS-15010_S55_E1-50


title: LS-15020_S05_E1-50


title: LS-15010_S38_E1-50


title: LS-15010_S26_E1-50


title: LS-15010_S32_E1-50


title: LS-15010_S25_E1-50


title: LS-15010_S27_E1-50


title: LS-15010_S11_E1-50


title: LS-15011_S10_E1-50


title: LS-15009_S90_E1-50


title: LS-15009_S62_E1-50


title: LS-15010_S03_E1-50


title: LS-15008_S46_E1-50

description:
cells_exon_counts.csv.gz
cells_exon_counts.csv.gz
GSM3189962


title: LS-15008_S08_E1-50


title: LS-15007_S73_E1-50


title: LS-15010_S57_E1-50


title: LS-15007_S72_E1-50


title: LS-15007_S80_E1-50


title: LS-15007_S45_E1-50


title: LS-15008_S03_E1-50


title: LS-15007_S63_E1-50


title: LS-15007_S66_E1-50


title: LS-15003_S42_E1-50


title: LS-15006_S26_E1-50


title: LS-15003_S39_E1-50


title: LS-15002_S61_E1-50


title: LS-15003_S56_E1-50


title: LS-15003_S55_E1-50


title: LS-15002_S46_E1-50


title: LS-15010_S01_E1-50


title: LS-15001_S38_E1-50


title: LS-15001_S33_E1-50


title: LS-15002_S41_E1-50


title: LS-15000_S30_E1-50


title: LS-14696_S74_E1-50


title: LS-14696_S72_E1-50


title: LS-14696_S75_E1-50


title: LS-15008_S69_E1-50


title: LS-14696_S70_E1-50


title: LS-14696_S58_E1-50


title: LS-15007_S52_E1-50


title: LS-14696_S12_E1-50


title: LS-14692_S42_E1-50


title: LS-14692_S12_E1-50


title: LS-14690_S17_E1-50


title: SQ-80005_S95_E1-50

description:
nuclei_exon_counts.csv.gz
nuclei_exon_counts.csv.gz

value: NeuN-positive

value: Nuclei


title: SQ-80005_S96_E1-50

value: F


title: SQ-80005_S93_E1-50

value: VISp


title: SQ-80005_S94_E1-50


title: SQ-80005_S90_E1-50


title: SQ-80005_S92_E1-50


title: SQ-80005_S91_E1-50


title: SQ-80005_S89_E1-50


title: SQ-80005_S87_E1-50


title: SQ-80005_S88_E1-50


title: SQ-80005_S82_E1-50


title: SQ-80005_S80_E1-50


title: SQ-80005_S78_E1-50


title: SQ-80005_S76_E1-50


title: SQ-80005_S79_E1-50


title: LS-14696_S69_E1-50

value: RFP-positive


title: SQ-80005_S74_E1-50

value: Glutamatergic


title: SQ-80005_S71_E1-50


title: SQ-80005_S77_E1-50


title: SQ-80005_S72_E1-50


title: SQ-80005_S69_E1-50


title: SQ-80005_S70_E1-50


title: SQ-80005_S67_E1-50


title: SQ-80005_S68_E1-50

value: Fail


title: SQ-80005_S66_E1-50


title: SQ-80005_S64_E1-50


title: SQ-80005_S62_E1-50


title: SQ-80005_S60_E1-50


title: SQ-80005_S59_E1-50


title: SQ-80005_S63_E1-50


title: SQ-80005_S81_E1-50


title: SQ-80005_S58_E1-50


title: SQ-80005_S56_E1-50


title: SQ-80005_S52_E1-50


title: SQ-80005_S55_E1-50


title: SQ-80005_S75_E1-50


title: SQ-80005_S50_E1-50


title: SQ-80005_S49_E1-50


title: SQ-80005_S53_E1-50


title: SQ-80005_S61_E1-50


title: SQ-80005_S51_E1-50


title: SQ-80005_S45_E1-50


title: SQ-80005_S48_E1-50


title: SQ-80005_S44_E1-50


title: SQ-80005_S43_E1-50


title: SQ-80005_S42_E1-50


title: LS-15543_S96_E1-50


title: LS-15543_S94_E1-50


title: LS-15543_S92_E1-50


title: LS-15543_S89_E1-50


title: LS-15543_S88_E1-50


title: LS-15543_S91_E1-50


title: LS-15543_S90_E1-50


title: SQ-80005_S57_E1-50


title: LS-15543_S87_E1-50


title: LS-15543_S86_E1-50


title: LS-15543_S85_E1-50


title: LS-15543_S83_E1-50


title: LS-15543_S84_E1-50


title: LS-15543_S82_E1-50


title: LS-15543_S81_E1-50


title: SQ-80005_S47_E1-50


title: LS-15543_S80_E1-50


title: LS-15543_S78_E1-50


title: LS-15543_S79_E1-50


title: SQ-80005_S41_E1-50


title: LS-15543_S76_E1-50


title: LS-15543_S75_E1-50


title: LS-15543_S74_E1-50


title: LS-15543_S95_E1-50


title: LS-15543_S70_E1-50


title: LS-15543_S71_E1-50


title: LS-15543_S77_E1-50


title: LS-15543_S73_E1-50


title: LS-15543_S68_E1-50


title: LS-15543_S69_E1-50


title: LS-15543_S67_E1-50


title: LS-15543_S66_E1-50


title: LS-15543_S56_E1-50


title: LS-15543_S65_E1-50


title: LS-15543_S55_E1-50


title: LS-15543_S53_E1-50


title: LS-15543_S52_E1-50


title: LS-15543_S51_E1-50


title: LS-15543_S54_E1-50


title: LS-15543_S50_E1-50


title: LS-15543_S48_E1-50


title: LS-15543_S47_E1-50


title: LS-15543_S49_E1-50


title: LS-15543_S45_E1-50


title: LS-15543_S43_E1-50


title: LS-15543_S42_E1-50


title: LS-15543_S72_E1-50


title: LS-15543_S41_E1-50


title: LS-15543_S40_E1-50


title: LS-15543_S36_E1-50


title: LS-15543_S38_E1-50


title: LS-15543_S37_E1-50


title: LS-15543_S35_E1-50


title: LS-15543_S34_E1-50


title: LS-15543_S32_E1-50


title: LS-15543_S31_E1-50


title: LS-15543_S33_E1-50


title: LS-15543_S30_E1-50


title: LS-15543_S46_E1-50


title: LS-15543_S28_E1-50


title: LS-15543_S29_E1-50


title: Tumor Pat75

city: Seoul

first: Sang-Won

last: Lee

address: 145 Anam-ro Seongbuk-gu

department: Chemistry

country: South Korea

institute: korea University

data_processing:
Read alignment, MapSplice-v2.1.8, -p 8 --qual-scale phred33 --bam --fusion
Expression calculation, rsem-1.2.15, --estimate-rspd -p 8 --no-bam-output --bam --paired-end
Normalization, /ubu/src/perl/quartile_norm.pl, -c 5 -q 75 -t 1000
Genome_build: Homo_sapiens.GRCh37.75.dna.fa
Supplementary_files_format_and_content: Tab delimited file containing quartile normalized expread count values for 34,908 genes

source_name: Gastric

extract_protocol:
1 μg of DNase I-treated total RNA using TruSeq kit (Illumina)
Poly(A)+ RNA was isolated using AMPure XP beads (Beckman Coulter, Brea, CA) and fragmented using an Ambion Fragmentation Reagents kit (Thermo Fisher Scientific). Complementary DNA (cDNA) synthesis, end repair, A-base addition, and ligation of the Illumina-indexed adapters were performed according to Illumina protocols

value: gastric cancer

tag: subject id

tag: histology

value: Diffuse

tag: msi

value: MSS/MSI-L

tag: ebv

value: Negative


title: Tumor Pat76


title: Tumor Pat78


title: Tumor Pat74


title: Tumor Pat80


title: Tumor Pat77


title: Tumor Pat79


title: Tumor Pat73


title: LS-15543_S27_E1-50


title: Tumor Pat72


title: Tumor Pat71


title: PANC-1 cells treated with okadaic acid

description: [OA](normalized)

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

scan_protocol: Differentially expressed genes were screened using Agilent 44K human whole-genome oligonucleotide microarrays.

data_processing:
Hierarchical clustering of samples was done by average linkage algorithm using TIGR MultiExperiment Viewer (The Institute for Genomic Research, Rockville, MD, USA).
The selection criterion was defined as a more than 2-fold difference in the level of expression (difference in up-regulated expression more than 2-fold, and difference in down-regulated expression less than 0.5-fold).

label_protocol: Sample preparation and processing procedure were performed as described in detail in the Agilent GeneChip Expression Analysis Manual (Santa Clara, CA).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: PANC-1 cells treated with 20μM cantharidin (CAN) or okadaic acid (OA) for 24h seperately

value: 20μM okadaic acid (OA)


title: LS-15543_S25_E1-50


title: PANC-1 cells treated with cantharidin

description: [CAN](normalized)

value: 20μM cantharidin (CAN)


title: Tumor Pat69


title: LS-15543_S23_E1-50


title: LS-15543_S22_E1-50


title: Tumor Pat70


title: Tumor Pat68


title: LS-15543_S24_E1-50


title: LS-15543_S26_E1-50


title: PANC-1 cells control

description: [CONTROL](normalized)

value: none (control)


title: Tumor Pat67


title: Tumor Pat66


title: LS-15543_S20_E1-50


title: LS-15543_S19_E1-50


title: LS-15543_S18_E1-50


title: LS-15543_S17_E1-50


title: LS-15543_S15_E1-50


title: LS-15543_S14_E1-50


title: Tumor Pat63


title: Tumor Pat61

value: Intestinal


title: LS-15543_S13_E1-50


title: Tumor Pat62


title: LS-15543_S11_E1-50


title: LS-15543_S10_E1-50


title: Tumor Pat60


title: Tumor Pat59

value: Mixed

value: MSI-H

value: EBV


title: LS-15543_S09_E1-50

value: NeuN-positive

value: Pass

value: Nuclei


title: LS-15543_S21_E1-50

value: F

value: VISp


title: LS-15543_S06_E1-50

value: Glutamatergic


title: LS-15543_S07_E1-50


title: LS-15543_S08_E1-50


title: LS-15543_S05_E1-50


title: Tumor Pat55

value: gastric cancer


title: Tumor Pat57

value: Diffuse


title: Tumor Pat56


title: Tumor Pat54

value: MSS/MSI-L


title: LS-15543_S03_E1-50


title: Tumor Pat65

value: Negative


title: LS-15543_S02_E1-50


title: Tumor Pat53


title: Tumor Pat64


title: Tumor Pat52


title: LS-15543_S01_E1-50


title: Tumor Pat51


title: Tumor Pat50


title: Tumor Pat58


title: Tumor Pat49


title: LS-15541_S94_E1-50


title: LS-15541_S93_E1-50

value: GABAergic


title: LS-15541_S95_E1-50


title: Tumor Pat47


title: LS-15541_S89_E1-50


title: Tumor Pat48


title: Tumor Pat45


title: LS-15541_S90_E1-50


title: Tumor Pat46


title: Tumor Pat44


title: Tumor Pat43


title: LS-15541_S88_E1-50


title: Tumor Pat42


title: LS-15541_S87_E1-50


title: LS-15541_S86_E1-50


title: Tumor Pat41


title: LS-15541_S83_E1-50


title: Tumor Pat38


title: Tumor Pat37


title: LS-15541_S82_E1-50


title: Tumor Pat39


title: LS-15541_S80_E1-50


title: LS-15541_S84_E1-50


title: LS-15541_S91_E1-50


title: Tumor Pat40


title: LS-15541_S81_E1-50


title: LS-15541_S79_E1-50


title: Tumor Pat35


title: LS-15541_S78_E1-50


title: LS-15541_S85_E1-50


title: Tumor Pat33


title: LS-15541_S76_E1-50


title: LS-15541_S74_E1-50


title: Tumor Pat34


title: Tumor Pat30


title: LS-15541_S73_E1-50


title: Tumor Pat32


title: Tumor Pat31


title: LS-15541_S71_E1-50


title: Tumor Pat29


title: LS-15541_S72_E1-50


title: Tumor Pat28


title: Tumor Pat27


title: LS-15541_S70_E1-50


title: LS-15541_S68_E1-50


title: Tumor Pat26


title: LS-15541_S69_E1-50


title: Tumor Pat36


title: Tumor Pat25


title: Tumor Pat24


title: LS-15541_S65_E1-50


title: LS-15541_S77_E1-50


title: Tumor Pat23


title: LS-15541_S64_E1-50


title: Tumor Pat19


title: Tumor Pat20


title: Tumor Pat22


title: LS-15541_S62_E1-50


title: Tumor Pat18


title: Tumor Pat17


title: Tumor Pat15


title: LS-15541_S59_E1-50


title: LS-15541_S57_E1-50


title: LS-15541_S56_E1-50


title: LS-15541_S58_E1-50


title: LS-15541_S60_E1-50


title: Tumor Pat14


title: Tumor Pat13


title: LS-15541_S67_E1-50


title: LS-15541_S66_E1-50


title: LS-15541_S53_E1-50


title: Tumor Pat12


title: Tumor Pat10


title: LS-15541_S54_E1-50


title: Tumor Pat11


title: LS-15541_S51_E1-50


title: LS-15541_S52_E1-50


title: Tumor Pat9


title: Tumor Pat21


title: LS-15541_S50_E1-50


title: Tumor Pat8


title: Tumor Pat16


title: LS-15541_S49_E1-50


title: Tumor Pat7


title: Tumor Pat6


title: LS-15541_S38_E1-50


title: Tumor Pat5


title: LS-15541_S37_E1-50


title: Tumor Pat3


title: Tumor Pat2


title: LS-15541_S63_E1-50


title: adjacent Pat80

value: normal stomach


title: Tumor Pat1


title: LS-15541_S33_E1-50


title: LS-15541_S34_E1-50


title: LS-15541_S32_E1-50


title: adjacent Pat79


title: LS-15541_S31_E1-50


title: LS-15541_S30_E1-50


title: LS-15541_S55_E1-50


title: adjacent Pat77


title: adjacent Pat75


title: LS-15541_S28_E1-50


title: LS-15541_S27_E1-50


title: adjacent Pat76


title: Tumor Pat4


title: LS-15541_S26_E1-50


title: adjacent Pat73


title: LS-15541_S25_E1-50


title: adjacent Pat74


title: LS-15541_S23_E1-50


title: LS-15541_S24_E1-50


title: LS-15541_S36_E1-50


title: adjacent Pat70


title: LS-15541_S22_E1-50


title: adjacent Pat71


title: LS-15541_S20_E1-50


title: LS-15541_S29_E1-50


title: LS-15541_S19_E1-50


title: LS-15541_S21_E1-50


title: adjacent Pat69


title: LS-15541_S18_E1-50


title: adjacent Pat68


title: adjacent Pat65


title: adjacent Pat78


title: adjacent Pat66


title: adjacent Pat63


title: LS-15541_S15_E1-50


title: adjacent Pat67


title: adjacent Pat64


title: LS-15541_S16_E1-50


title: LS-15541_S14_E1-50


title: adjacent Pat62


title: adjacent Pat61


title: LS-15541_S17_E1-50


title: LS-15541_S13_E1-50


title: adjacent Pat60


title: LS-15541_S12_E1-50


title: LS-15541_S11_E1-50


title: adjacent Pat59


title: adjacent Pat58


title: LS-15541_S10_E1-50


title: adjacent Pat57


title: LS-15541_S09_E1-50


title: adjacent Pat56


title: LS-15541_S08_E1-50


title: LS-15541_S07_E1-50


title: LS-15541_S06_E1-50


title: adjacent Pat54


title: LS-15541_S05_E1-50


title: adjacent Pat55


title: adjacent Pat53


title: adjacent Pat52


title: LS-15541_S04_E1-50


title: LS-15541_S03_E1-50


title: LS-15541_S02_E1-50


title: adjacent Pat50


title: adjacent Pat51


title: LS-15541_S01_E1-50


title: adjacent Pat48


title: adjacent Pat47


title: LS-15539_S95_E1-50


title: LS-15539_S94_E1-50


title: LS-15539_S93_E1-50


title: adjacent Pat44


title: LS-15539_S92_E1-50


title: adjacent Pat43


title: adjacent Pat42


title: LS-15539_S91_E1-50


title: adjacent Pat41


title: LS-15539_S90_E1-50


title: LS-15539_S86_E1-50


title: LS-15539_S87_E1-50


title: adjacent Pat39


title: LS-15539_S85_E1-50


title: LS-15539_S88_E1-50


title: adjacent Pat38


title: adjacent Pat49


title: adjacent Pat40


title: LS-15539_S83_E1-50


title: adjacent Pat36


title: adjacent Pat46


title: adjacent Pat37


title: LS-15539_S96_E1-50


title: adjacent Pat35


title: LS-15539_S84_E1-50


title: adjacent Pat45


title: adjacent Pat34


title: LS-15539_S81_E1-50


title: adjacent Pat33


title: adjacent Pat32


title: LS-15539_S78_E1-50


title: adjacent Pat30


title: LS-15539_S77_E1-50


title: adjacent Pat31


title: LS-15541_S40_E1-50


title: adjacent Pat28


title: LS-15539_S76_E1-50


title: LS-15539_S75_E1-50


title: adjacent Pat27


title: LS-15539_S82_E1-50


title: LS-15539_S74_E1-50


title: adjacent Pat29


title: adjacent Pat23


title: LS-15539_S72_E1-50


title: LS-15539_S71_E1-50


title: LS-15539_S70_E1-50


title: adjacent Pat26


title: adjacent Pat25


title: adjacent Pat24


title: LS-15539_S69_E1-50


title: LS-15539_S68_E1-50


title: adjacent Pat21


title: LS-15539_S79_E1-50


title: LS-15539_S67_E1-50


title: adjacent Pat22


title: adjacent Pat72


title: LS-15539_S66_E1-50


title: adjacent Pat19


title: adjacent Pat18


title: LS-15539_S65_E1-50


title: LS-15539_S73_E1-50


title: adjacent Pat17


title: LS-15539_S64_E1-50


title: adjacent Pat15


title: LS-15539_S62_E1-50


title: LS-15539_S63_E1-50


title: adjacent Pat14


title: LS-15539_S60_E1-50


title: LS-15539_S59_E1-50


title: adjacent Pat20


title: LS-15539_S58_E1-50


title: adjacent Pat11


title: LS-15539_S56_E1-50


title: adjacent Pat13


title: adjacent Pat9


title: LS-15539_S55_E1-50


title: adjacent Pat12


title: adjacent Pat7


title: LS-15539_S57_E1-50


title: adjacent Pat6


title: adjacent Pat10


title: adjacent Pat8


title: LS-15539_S52_E1-50


title: adjacent Pat5


title: LS-15539_S51_E1-50


title: adjacent Pat16


title: adjacent Pat4


title: LS-15539_S61_E1-50


title: LS-15539_S49_E1-50


title: adjacent Pat2


title: adjacent Pat3


title: LS-15539_S48_E1-50


title: LS-15539_S47_E1-50


title: adjacent Pat1


title: LS-15539_S45_E1-50


title: LS-15539_S43_E1-50


title: LS-15539_S44_E1-50


title: LS-15539_S54_E1-50


title: LS-15541_S35_E1-50


title: LS-15539_S41_E1-50


title: LS-15539_S39_E1-50


title: normal-10-lcc17322

city: Buffalo

first: Jie

address: Elm and Carlton Streets

department: Department of Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

description: miRNA

data_processing:
The 3’ adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) in the reads was trimmed by cutadapt (version 1.12). Only the reads with at least 6 nt perfect match against the adapter sequences and longer than 15 nt were kept for the downstream analysis.
The trimmed reads were aligned to human reference genome (hg19) by bwa (version 0.7.15) with no mismatches allowed.
The miRNA profiling pipeline developed by the British Columbia Genome Sciences Centre was implemented to quantify miRNA expression.  TCGA-formatted miRNA quantification data were generated including expression levels for the known pre-miRNAs and mature miRNAs for all samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: normal tissue

extract_protocol: The small RNA libraries were prepared using the New England Biolabs (NEB) NEBNext Multiplex Small RNA library prep set (Catalog #E7300). Briefly, small RNA molecules were hybridized to adapters and used for preparation of first strand cDNA synthesis. RNA molecules were removed chemically and PCR-specific barcodes were added to generate double stranded molecules. Templates were purified using Blue Pippen gel cartridges with optimally library sizes around 150 bp in length.

value: normal breast tissue

tag: race

value: African American


title: 19268

description: miRNA

source_name: breast tumor tissue

value: breast tumor

tag: er

value: Positive


title: normal-12-lcc27086

description: miRNA

value: Caucasian


title: 17411

description: miRNA


title: LS-15539_S40_E1-50

value: NeuN-positive


title: normal-8-lcc13694

description: miRNA


title: normal-11-lcc21258

description: miRNA


title: 14944

description: miRNA


title: LS-15539_S50_E1-50

value: Pass


title: 18268

description: miRNA


title: LS-15539_S37_E1-50

value: Nuclei


title: LS-15539_S38_E1-50

value: F


title: LS-15539_S36_E1-50

value: VISp


title: 13913

description: miRNA


title: 14051

description: miRNA


title: LS-15539_S35_E1-50

value: Glutamatergic


title: 9048

description: miRNA


title: normal-7-lcc17644

description: miRNA


title: LS-15539_S42_E1-50


title: normal-6-lcc18618

description: miRNA


title: LS-15539_S24_E1-50


title: LS-15539_S23_E1-50


title: normal-4-lcc28105

description: miRNA


title: 20376

description: miRNA


title: LS-15539_S22_E1-50


title: LS-15539_S21_E1-50


title: 19011

description: miRNA


title: 14677

description: miRNA


title: 14308

description: miRNA


title: 17271

description: miRNA


title: 18534

description: miRNA


title: 14496

description: miRNA


title: LS-15539_S18_E1-50


title: LS-15539_S15_E1-50


title: LS-15539_S19_E1-50


title: 18313

description: miRNA


title: LS-15539_S20_E1-50


title: 11326

description: miRNA


title: 18986

description: miRNA


title: LS-15539_S13_E1-50


title: LS-15539_S16_E1-50


title: LS-15539_S34_E1-50


title: LS-15539_S17_E1-50


title: LS-15539_S14_E1-50

value: NeuN-negative


title: 18800

description: miRNA


title: 12694

description: miRNA


title: LS-15539_S80_E1-50


title: 18475

description: miRNA


title: LS-15539_S33_E1-50


title: 17812

description: miRNA


title: LS-15539_S09_E1-50


title: 17614

description: miRNA


title: LS-15539_S11_E1-50


title: LS-15539_S12_E1-50


title: 17098

description: miRNA


title: LS-15539_S04_E1-50


title: 17074

description: miRNA


title: LS-15539_S03_E1-50


title: 11119

description: miRNA


title: LS-15071_S96_E1-50

value: M


title: 13240

description: miRNA


title: LS-15539_S02_E1-50


title: LS-15539_S01_E1-50


title: normal-5

description: miRNA


title: LS-15071_S95_E1-50


title: LS-15071_S94_E1-50


title: normal-1

description: miRNA


title: LS-15539_S06_E1-50


title: LS-15539_S07_E1-50


title: ZT24_seedling_9

city: Cambridge

first: James

last: Locke

address: Bateman St

institute: SLCU

data_processing:
The raw reads were analysed in house. We first assessed the quality of reads using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014), before being aligned to the TAIR10 transcriptome using Tophat (Trapnell et al., 2009). The potential optical duplicates resulted from library preparation were removed using the Picard tools (http://sourceforge.net/p/picard/wiki/Main_Page/#q-how-should-i-cite-picard-in-my-manuscript). For each gene, raw reads and TPM (Transcripts Per Million) (Wagner et al., 2012) were computed. Samples with at least 4 million reads were used for further analysis, which is between 14 and 16 samples per time-point. In order to be able to compare time-points, a total of 14 samples per time-points were used.
Genome_build: TAIR10

source_name: seedlings

growth_protocol: Col-0 WT Arabidopsis seeds were sterilised, stratified for 3 days at 4°C in dark and transferred for germination on solid 1X Murashige and Skoog (MS) media at 22°C in long days for 24 hours. Using a binocular microscope, seeds that were at the same stage of germination were transferred into a new plate containing solid 1X MS media. In total, 16 seeds were transferred into each of the 12 individual plates. Seedlings were grown at 22°C with 12 hours of light and 12 hours of dark. After 7 days of growth, seedlings were harvested individually into a 96-well plate and flash-frozen in dry ice. Sixteen seedlings were harvested individually and flash-frozen in dry ice at each time point, every two hours over a 24 hours period. ZT2 to ZT12 corresponding to time-points harvested during the day, and ZT14 to ZT0 to time-points harvested during the night, ZT124 and ZT0 being respectively harvested just a few minutes after dusk and dawn

extract_protocol:
Total RNA was isolated from one grinded seedling using the MagMAX-96 Total RNA Isolation kit (Ambion, AM1830), following the manufacturer’s instructions. RNA quality and integrity was assessed on the Agilent 2200 TapeStation.
Library preparation was performed using the TruSeq Stranded mRNA library preparation kit a (Illumina, RS-122-2101), following manufacturer’s instruction, for 1 ug of high integrity total RNA (RIN>8) into which 2 ul of diluted 1:100e ERCC RNA Spike-In Mix (ThermoFisher, cat 4456740) was added. The libraries were sequenced on a NextSeq500 at the Sainsbuty Laboratory, Cambridge University (Cambridge, UK), using paired-end sequencing of 75 bp in length.

tag: ecotype

value: Col0 WT

value: seedlings

tag: time point

tag: individual seedling


title: ZT24_seedling_7


title: LS-15071_S93_E1-50


title: LS-15071_S92_E1-50


title: 19282

description: miRNA

value: Negative


title: ZT24_seedling_6


title: 17982

description: miRNA


title: LS-15071_S91_E1-50


title: ZT24_seedling_5


title: 13558

description: miRNA


title: ZT24_seedling_4


title: 14302

description: miRNA


title: ZT24_seedling_2


title: LS-15071_S87_E1-50


title: 9038

description: miRNA


title: 17453

description: miRNA


title: normal-2

description: miRNA


title: ZT24_seedling_15


title: ZT24_seedling_16


title: LS-15071_S86_E1-50


title: LS-15071_S85_E1-50


title: 16823

description: miRNA


title: ZT24_seedling_8


title: ZT24_seedling_14


title: 12151

description: miRNA


title: ZT24_seedling_12


title: LS-15071_S84_E1-50


title: ZT22_seedling_9


title: 18612

description: miRNA


title: 18033

description: miRNA


title: 17506

description: miRNA


title: ZT24_seedling_1


title: ZT22_seedling_5


title: ZT22_seedling_8


title: LS-15071_S82_E1-50


title: LS-15071_S83_E1-50


title: LS-15071_S81_E1-50


title: ZT22_seedling_3


title: 16722

description: miRNA


title: ZT22_seedling_2


title: ZT22_seedling_16


title: 16296

description: miRNA


title: ZT24_seedling_13


title: LS-15071_S80_E1-50


title: ZT22_seedling_14


title: LS-15071_S79_E1-50


title: ZT22_seedling_13


title: 14738

description: miRNA


title: ZT22_seedling_11


title: ZT22_seedling_10


title: LS-15071_S78_E1-50


title: ZT24_seedling_10


title: ZT22_seedling_4


title: LS-15071_S77_E1-50

value: GABAergic


title: LS-15071_S76_E1-50


title: 14535

description: miRNA


title: 14128

description: miRNA


title: ZT20_seedling_8


title: LS-15071_S75_E1-50


title: 14045

description: miRNA


title: ZT22_seedling_1


title: ZT22_seedling_15


title: ZT20_seedling_5


title: ZT20_seedling_4


title: 16172

description: miRNA


title: 8785

description: miRNA


title: 10820

description: miRNA


title: ZT20_seedling_16


title: ZT22_seedling_12


title: ZT20_seedling_9


title: ZT20_seedling_15


title: 18367

description: miRNA


title: ZT20_seedling_11


title: LS-15071_S72_E1-50


title: ZT20_seedling_1


title: 17469

description: miRNA


title: LS-15071_S73_E1-50


title: 16053

description: miRNA


title: LS-15071_S70_E1-50


title: LS-15071_S68_E1-50


title: LS-15071_S69_E1-50


title: ZT18_seedling_9


title: ZT20_seedling_14


title: ZT18_seedling_5


title: LS-15071_S67_E1-50


title: 15980

description: miRNA


title: ZT18_seedling_7


title: ZT18_seedling_2


title: LS-15071_S71_E1-50


title: ZT18_seedling_16


title: 15362

description: miRNA


title: LS-15071_S66_E1-50


title: LS-15071_S65_E1-50


title: ZT18_seedling_3


title: ZT18_seedling_15


title: ZT18_seedling_14


title: LS-15071_S64_E1-50


title: 14843

description: miRNA


title: 14994

description: miRNA


title: LS-15071_S63_E1-50


title: 14503

description: miRNA


title: ZT18_seedling_12


title: ZT18_seedling_11


title: ZT18_seedling_10


title: LS-15071_S62_E1-50


title: ZT16_seedling_9


title: LS-15071_S61_E1-50


title: ZT18_seedling_1


title: ZT16_seedling_7


title: ZT18_seedling_13


title: 12777

description: miRNA


title: ZT16_seedling_6


title: LS-15071_S60_E1-50


title: ZT16_seedling_5


title: ZT16_seedling_4


title: 9648

description: miRNA


title: LS-15071_S59_E1-50


title: LS-15071_S58_E1-50


title: 13014

description: miRNA


title: LS-15071_S57_E1-50


title: ZT16_seedling_16


title: ZT16_seedling_15


title: ZT16_seedling_2


title: SUDHL6_GSK591_96H_R3

city: New York

first: Tharu

last: Fernando

address: 413 East 69th St BB1462

department: Medicine, Heme-Onc

institute: Weill Cornell Medical College

description:
PolyA RNA
processed data file: SUDHL6_GSK591_96H_counts.txt
processed data: TopTags_SUDHL6_GSK591_96hr.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads that passed filter were aligned to hg19 using STAR (Dobin et al., 2012).
Gene expression values were calculated by counting how many reads map uniquely to the union of all gene exons using HTseq-count.
Differentially expressed genes were identified with the edgeR package (Robinson et al., 2010). Genes with a logCPM < -3 and FDR < 0.05 were considered differentially expressed.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Read counts that map uniquely to the union of all gene exons using HTseq-count and topTags output from EdgeR is provided as .txt files.

source_name: SUDHL6 cells

growth_protocol: Cells were grown in RPMI 1640 medium with 10% FBS, 10 mM Hepes, 2 mM glutamine, and pen/strep.

extract_protocol:
Total RNA was harvested using the Trizol (Life Technologies).
Genomic DNA was eliminated with DNase treatment, and mRNA was isolated using two rounds of poly-T oligo attached magnetics beads. Sequencing libraries were generated with the Illumina TruSeq RNA sample prep kit.

treatment_protocol: Cells were treated with vehicle (0.01%DMSO) or 200nM GSK591 for 24 h or 96 h.

tag: time of treatment


title: LS-15071_S56_E1-50


title: LS-15071_S55_E1-50


title: ZT16_seedling_14


title: ZT16_seedling_1


title: ZT16_seedling_13


title: ZT16_seedling_11


title: ZT16_seedling_10


title: ZT14_seedling_9


title: ZT14_seedling_8


title: SUDHL6_VEH_96H_R3

value: Vehicle (0.01% DMSO)


title: SUDHL6_VEH_96H_R1


title: SUDHL6_GSK591_96H_R1


title: SUDHL6_VEH_96H_R2


title: SUDHL6_GSK591_96H_R2


title: ZT14_seedling_7


title: ZT20_seedling_7


title: ZT14_seedling_6


title: SUDHL6_GSK591_24H_R3

description:
PolyA RNA
processed data file: SUDHL6_GSK591_24H_counts.txt
processed data: TopTags_SUDHL6_GSK591_24hr.txt


title: ZT14_seedling_4


title: LS-15071_S53_E1-50


title: SUDHL6_GSK591_24H_R2


title: ZT16_seedling_3


title: ZT14_seedling_2


title: LS-15071_S51_E1-50


title: LS-15071_S54_E1-50


title: LS-15071_S50_E1-50


title: ZT14_seedling_16


title: LS-15071_S52_E1-50


title: SUDHL6_GSK591_24H_R1


title: ZT14_seedling_14


title: LS-15071_S49_E1-50


title: ZT14_seedling_13


title: ZT14_seedling_12


title: SUDHL6_VEH_24H_R3


title: ZT14_seedling_11


title: SUDHL6_VEH_24H_R2


title: ZT14_seedling_5


title: LS-15071_S48_E1-50


title: ZT14_seedling_1


title: ZT20_seedling_3


title: SUDHL6_VEH_24H_R1


title: ZT12_seedling_9


title: ZT12_seedling_8


title: ZT14_seedling_15


title: ZT12_seedling_7


title: ZT12_seedling_6


title: LS-15071_S46_E1-50


title: LS-15071_S47_E1-50


title: ZT12_seedling_2


title: ZT12_seedling_5


title: LS-15071_S45_E1-50


title: ZT12_seedling_16


title: LS-15071_S44_E1-50


title: ZT12_seedling_15


title: ZT12_seedling_14


title: ZT12_seedling_13


title: LS-15071_S43_E1-50


title: LS-15071_S42_E1-50


title: ZT12_seedling_11


title: ZT12_seedling_12


title: ZT20_seedling_13


title: ZT12_seedling_10


title: ZT20_seedling_10


title: ZT12_seedling_1


title: ZT10_seedling_9


title: ZT10_seedling_8


title: 191-AD

first: Ariel

last: Israel

address: 1425 Madison Avenue

department: Department of Dermatology

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from blood

hyb_protocol: Encore Biotin Module (Nugen) and Ambion

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GC-RMA (using gcrma package from R/Bioconductor)

label_protocol: Encore Biotin Module (Nugen) and Ambion

extract_protocol: Cells lysed in RLT with Beta-2-mercaptoethanol, RNA was extracted using RNeasy-Micro kit (QIAGEN, Valencia, CA).

tag: group

value: AD

value: blood

tag: gender

tag: agegroup

value: pediatric


title: 204-CB

description: Gene expression data from blood

value: Normal

tag: tissue


title: LS-15071_S40_E1-50

value: NeuN-positive

tag: molecule


title: LS-15071_S41_E1-50

value: Pass


title: 199-CB

description: Gene expression data from blood


title: 149-AD

description: Gene expression data from blood


title: 205-AD

description: Gene expression data from blood


title: 126-AD

description: Gene expression data from blood


title: ZT10_seedling_7


title: 107-CB

description: Gene expression data from blood


title: 105-AD

description: Gene expression data from blood

value: unknown


title: ZT10_seedling_3


title: ZT10_seedling_6


title: ZT10_seedling_5


title: LS-15071_S38_E1-50

value: Nuclei


title: ZT10_seedling_16


title: ZT10_seedling_2


title: LS-15071_S37_E1-50

value: VISp


title: LS-15071_S36_E1-50

value: Glutamatergic


title: ZT10_seedling_14


title: ZT10_seedling_4


title: ZT10_seedling_11


title: LS-15071_S39_E1-50


title: 099-AD

description: Gene expression data from blood


title: 097-AD

description: Gene expression data from blood


title: ZT10_seedling_10


title: ZT20_seedling_12


title: 098-AD

description: Gene expression data from blood


title: ZT10_seedling_1


title: LS-15071_S33_E1-50


title: 093-CB

description: Gene expression data from blood

value: F


title: ZT8_seedling_7


title: LS-15071_S35_E1-50

value: M


title: LS-15071_S32_E1-50


title: 096-AD

description: Gene expression data from blood


title: ZT8_seedling_6

value: Col0 WT


title: ZT8_seedling_5

value: seedlings


title: ZT10_seedling_13


title: 089-AD

description: Gene expression data from blood


title: ZT8_seedling_2


title: ZT8_seedling_4


title: LS-15071_S30_E1-50


title: LS-15071_S29_E1-50


title: ZT8_seedling_14


title: ZT8_seedling_16


title: ZT8_seedling_9


title: 088-AD

description: Gene expression data from blood


title: ZT8_seedling_13


title: 18664

description: miRNA

value: breast tumor

value: African American

value: Positive


title: ZT8_seedling_3


title: 084-AD

description: Gene expression data from blood

value: AD


title: LS-15071_S28_E1-50


title: 081-AD

description: Gene expression data from blood

value: blood


title: ZT8_seedling_12


title: LS-15071_S31_E1-50


title: 085-AD

description: Gene expression data from blood

value: pediatric


title: LS-15071_S27_E1-50

value: GABAergic


title: ZT8_seedling_10


title: ZT6_seedling_8


title: LS-15071_S26_E1-50

value: NeuN-positive


title: ZT8_seedling_11


title: ZT6_seedling_6


title: LS-15071_S24_E1-50

value: Pass


title: LS-15071_S23_E1-50


title: ZT6_seedling_7


title: 074-CB

description: Gene expression data from blood

value: Normal


title: ZT6_seedling_4


title: ZT6_seedling_3


title: ZT6_seedling_2


title: ZT6_seedling_5


title: ZT6_seedling_16


title: ZT6_seedling_9


title: LS-15071_S22_E1-50

value: NeuN-negative

value: Nuclei


title: LS-15071_S25_E1-50

value: VISp

value: Glutamatergic


title: LS-15071_S21_E1-50

value: M


title: ZT8_seedling_1

value: Col0 WT


title: 070-CB

description: Gene expression data from blood

value: F


title: 071-CB

description: Gene expression data from blood


title: 069-CB

description: Gene expression data from blood


title: 068-AD

description: Gene expression data from blood


title: 060-AD

description: Gene expression data from blood


title: ZT6_seedling_15

value: seedlings


title: LS-15071_S19_E1-50


title: ZT6_seedling_11


title: LS-15071_S20_E1-50


title: ZT6_seedling_10


title: LS-15071_S17_E1-50


title: ZT6_seedling_14


title: ZT6_seedling_1


title: ZT4_seedling_7


title: ZT4_seedling_8


title: ZT4_seedling_6


title: ZT4_seedling_9


title: 065-CB

description: Gene expression data from blood


title: 055-CB

description: Gene expression data from blood


title: 059-AD

description: Gene expression data from blood


title: ZT4_seedling_3


title: ZT4_seedling_5


title: ZT4_seedling_4


title: ZT4_seedling_2


title: ZT4_seedling_16


title: LS-15071_S08_E1-50


title: ZT4_seedling_15


title: LS-15071_S06_E1-50


title: LS-15071_S05_E1-50


title: ZT4_seedling_14


title: ZT4_seedling_13


title: LS-15071_S18_E1-50


title: ZT4_seedling_1


title: 052-CB

description: Gene expression data from blood


title: 048-CB

description: Gene expression data from blood


title: 050-CB

description: Gene expression data from blood


title: LS-15071_S07_E1-50


title: LS-15071_S03_E1-50


title: ZT2_seedling_6


title: 046-CB

description: Gene expression data from blood


title: ZT2_seedling_8


title: 044-CB

description: Gene expression data from blood


title: ZT2_seedling_5


title: LS-15071_S02_E1-50