title: Uninduced_hepatocyte_6_2b38

description:
Single cell mRNA
Uninduced


title: P18MC.1H3

status: Public on Apr 23 2019

type: SRA

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

library_source: transcriptomic

data_processing:
Demultiplexed FASTQ files were aligned to the mouse genome (mm10 build) using STAR version 2.5.2 (Dobin et al., 2013) with default options.
Reads aligned to each gene were counted using featureCounts version 1.5.1 (Liao et al., 2014)
Filtered out cells outside the limits of median ± 4 * median absolute deviations for both reads number and genes detected; and excluded cells with more than 10% of reads aligning to mitochondrial genes
Further downstream processing was performed using Seurat (version 2.3.1 (Butler et al., 2018)) and Monocle2 (version 2.6.4 (Qiu et al., 2017a, 2017b; Trapnell et al., 2014))
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files of raw count data
Supplementary_files_format_and_content: tab-delimited text files of normalised count data (log normalised, scaled by 10000)

molecule: polyA RNA

organism: Mus musculus

source_name: Cortex

growth_protocol: APPswe/PS1dE9 (APP/PS1) were crossed with a C57Bl/6-Apoenull breeder to obtain homozygous APP/PS1-Apoenull mice [Hudry et. al., submited)]. APP/PS1-Apoe(null) mice, along with parental APP/PS1 mice and the respective control strains C57Bl/6 and C57Bl/6-Apoe(null), were transferred from the Hyman lab to the De Strooper lab, and housed for at least 1 month before being used for experiments.

extract_protocol:
The dissection and microglia isolation steps were carried out on ice or at +4°C. Cortex and hippocampus were dissected and finely chopped, and transferred to a tuve containing ice-cold Hibernate A medium without phenol red. Single cell suspension prepared using the Adult Brain Dissociation kit. Single live microglia cells (CD11b+/DAPI-) were sorted using BD FACSAria III
Single cell retrotranscription and preparation of sequencing libraries was performed using a modified SmartSeq2 protocol (Picelli et al., 2013, 2014; Trombetta et al., 2014). We used 5’-biotinylated primers throughout the protocol

tag: genotype

tag: ngene

tag: nreads

tag: age

tag: Sex

value: M

tag: plateplus

tag: plate

tag: lane


title: P18MC.1H4


title: P18MC.2A11


title: P18MC.1H11


title: P18MC.1H10


title: Uninduced_hepatocyte_6_2b3

city: Providence

first: Nicola

last: Neretti

state: RI

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry

country: USA

institute: Brown University

description:
Single cell mRNA
Uninduced

data_processing:
(Smart-seq2 time course experiment):Paired-end reads were quality trimmed using Trim galore and subsequently aligned to the human reference genome, hg19, and ERCC spike-in sequences using HISAT2. Cells that have less than 200,000 hg19 aligned reads, and a ratio of ERCC RNA spike-in control aligned reads to total aligned reads that is greater than 0.5 were filtered out. 232 IMR90 cells (100 growing cells, 41 day 2 cells, 43 day 4 cells and 48 senescent cells) passed this first filtering step. Subsequently, hg19 aligned reads were randomly downsampled to 200,000 reads. Genes were quantified using HTSeq-Count[25]. Cells that have more than 80,000 total gene counts and at least 500 genes with at least one count were used for downstream analysis. 224 IMR90 cells (100 Growing cells, 41 Day2 cells, 42 Day4 cells and 41 senescent cells) passed this second filtering step. Downstream analyses were done on the 224 cells as indicated in the sample description field
(10x Co-culture experiment): Cell Ranger 2.0.1 was used to align 10x Chromium RNA-seq reads  to hg19, TurboGFP and  puromycin sequence from pGIPZ and neomycin sequence from pLNCX2-ER-ras_neo, using the default parameters, and to generate gene-cell matrices. The data were subsequently processed using Seurat 2.3.0 to generate t-SNE plots and three clusters were identified using sparcl 1.0.3 (https://cran.r-project.org/web/packages/sparcl/index.html).
(Smart-seq2 hepatocyte): Paired-end reads were quality trimmed using Trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and subsequently aligned to the mouse reference genome mm10 and ERCC spike-in sequences using HISAT2. The mm10 aligned reads were randomly downsampled to 50,000 and cells that have less than 50,000 reads were removed. 75 single cells from the induced and uninduced hepatocyte passed this filter. Subsequently, cells that have less than 20,000 gene count and less than 500 genes with at least one read detected were removed. 43 single cells from the induced hepatocytes and 21 cells from the uninduced hepatocytes were retained. Lastly, cells with the log-transformed number of expressed genes and library size of 3 median absolute deviation below the median value were removed [19]. 39 single cells from the induced hepatocytes and 19 cells from the uninduced hepatocytes passed these filters.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: csv file contains FPKM values (Time_course_FPKM.csv) and tab-delimited files contain counts from HTSeq after downsampling (Hepatocyte_downsampled_Htseq.txt and Time_course_downsampled_HTSeq)
Supplementary_files_format_and_content: Mdm2_deleted_hepatocyte_HTSeq.txt: counts from HTSeq for cells that passed the filter (Induced_hepatocyte)
Supplementary_files_format_and_content: timecourse_HTSeq.txt: counts from HTSeq for cells that passed the filter
Supplementary_files_format_and_content: timecourse_FPKM.csv: FPKM for cells that passed the filter
Supplementary_files_format_and_content: Growing_Sen_10x_count.txt contains UMI counts from 10x dataset and Growing_Sen_10x_metadata.txt contains the metadata for the UMI counts

molecule: total RNA

source_name: colony N4 C57/Bl6J  background

extract_protocol:
Single-cell RNA-seq was performed using Smart-seq2 or 10x chromium as indicated by each experiemnt
Smart-seq2 or 10x Genomics 3' expression protocol

treatment_protocol: (Smart-seq2 Time course experiment): ER:RasG12V -expressing cells were induced into senescence for 7 days with 4-hydroxytamoxifen (4-OHT) and were isolated as single cells using FACS. Single cells that were not induced with 4-OHT were used as control. Single cells were also collected at another two time points, day 2 and day 4, before they became fully senescent on day 7. (10x Co-culture experiment): GFP cells are co-cultured with ER:Ras expressing cells and were induced into senescence with 4-OHT. Single cell 3' gene expression was generated using 10x Genomics Chromium.  (Smart-seq2 Hepatocyte experiment): Ex vivo primary hepatocytes were isolated using a modified retrograde perfusion technique as previously described[27]. Briefly, following perfusion with Perfusion Medium (Gibco) for 5 min, and Liver Digest Medium (Gibco) for 10 min, the liver was excised and the capsule disrupted to yield a cell suspension that was collected in Williams' E Medium supplemented with 2% FCS. Hepatocytes were purified by pelleting through a 40% (v:v) percoll gradient prior to FACS analysis.

tag: background strain

tag: tissue

value: Hepatocyte

tag: protocol used


title: Uninduced_hepatocyte_6_2b95

description:
Single cell mRNA
Uninduced


title: Uninduced_hepatocyte_6_2b28

description:
Single cell mRNA
Uninduced


title: P18MC.1H2


title: Uninduced_hepatocyte_6_2b27

description:
Single cell mRNA
Uninduced


title: P18MC.1H12


title: Uninduced_hepatocyte_6_2b2

description:
Single cell mRNA
Uninduced


title: P18MC.1H1


title: Uninduced_hepatocyte_6_2b15

description:
Single cell mRNA
Uninduced


title: P18MC.1G9


title: P18MC.1G7


title: Uninduced_hepatocyte_6_2b12

description:
Single cell mRNA
Uninduced


title: P18MC.1G8


title: Uninduced_hepatocyte_6_2b14

description:
Single cell mRNA
Uninduced


title: Uninduced_hepatocyte_6_2b11

description:
Single cell mRNA
Uninduced


title: P18MC.1G3


title: Uninduced_hepatocyte_6_2b1

description:
Single cell mRNA
Uninduced


title: Induced_hepatocyte_6_1c96

description:
Single cell mRNA
Not included in downstream analysis


title: P18MC.1G4


title: P18MC.1G5


title: Uninduced_hepatocyte_6_2b19

description:
Single cell mRNA
Uninduced


title: Induced_hepatocyte_6_1c93


title: Induced_hepatocyte_6_1c9


title: P18MC.1G12


title: Induced_hepatocyte_6_1c92


title: P18MC.1F9


title: Induced_hepatocyte_6_1c94


title: Induced_hepatocyte_6_1c95


title: P18MC.1G2


title: P18MC.1G11


title: P18MC.1G1


title: Induced_hepatocyte_6_1c90


title: Induced_hepatocyte_6_1c91


title: P18MC.1G10


title: P18MC.1F3


title: P18MC.1F2


title: Induced_hepatocyte_6_1c88


title: P18MC.1G6


title: P18MC.1F8


title: Induced_hepatocyte_6_1c87


title: Induced_hepatocyte_6_1c89


title: Induced_hepatocyte_6_1c82


title: P18MC.1F12


title: P18MC.1F11


title: Induced_hepatocyte_6_1c8


title: Induced_hepatocyte_6_1c85


title: Induced_hepatocyte_6_1c81


title: Induced_hepatocyte_6_1c84


title: P18MC.1F10


title: P18MC.1F7


title: P18MC.1F6


title: P18MC.1F5


title: Induced_hepatocyte_6_1c80


title: P18MC.1E8


title: Induced_hepatocyte_6_1c79


title: P18MC.1F1


title: Induced_hepatocyte_6_1c78


title: Induced_hepatocyte_6_1c86


title: P18MC.1E9


title: P18MC.1E7


title: P18MC.1F4


title: Induced_hepatocyte_6_1c83


title: P18MC.1E6


title: Induced_hepatocyte_6_1c76


title: Induced_hepatocyte_6_1c75


title: P18MC.1E5


title: Induced_hepatocyte_6_1c74


title: Induced_hepatocyte_6_1c73


title: Induced_hepatocyte_6_1c77


title: P18MC.1E2


title: P18MC.1E3


title: P18MC.1E4


title: Induced_hepatocyte_6_1c72


title: Induced_hepatocyte_6_1c71


title: Induced_hepatocyte_6_1c7


title: Induced_hepatocyte_6_1c69


title: Induced_hepatocyte_6_1c68


title: P18MC.1E11


title: P18MC.1D9


title: Induced_hepatocyte_6_1c64


title: P18MC.1E10


title: Induced_hepatocyte_6_1c65


title: P18MC.1E12


title: Induced_hepatocyte_6_1c63


title: P18MC.1D7


title: P18MC.1D8


title: P18MC.1D2


title: Induced_hepatocyte_6_1c62


title: Induced_hepatocyte_6_1c56


title: P18MC.1D5


title: P18MC.1D4


title: Induced_hepatocyte_6_1c59


title: Induced_hepatocyte_6_1c60


title: Induced_hepatocyte_6_1c6


title: P18MC.1D3


title: P18MC.1D10


title: P18MC.1D11


title: P18MC.1D1


title: Induced_hepatocyte_6_1c54


title: P18MC.1C8


title: P18MC.1C6


title: Induced_hepatocyte_6_1c51


title: P18MC.1C9


title: Induced_hepatocyte_6_1c5


title: P18MC.1C7


title: P18MC.1D12


title: Induced_hepatocyte_6_1c66


title: Induced_hepatocyte_6_1c50


title: P18MC.1D6


title: Induced_hepatocyte_6_1c49


title: P18MC.1E1


title: P18MC.1C4


title: Induced_hepatocyte_6_1c55


title: Induced_hepatocyte_6_1c58


title: Induced_hepatocyte_6_1c48


title: P18MC.1C5


title: P18MC.1C3


title: Induced_hepatocyte_6_1c46


title: Induced_hepatocyte_6_1c44


title: P18MC.1C12


title: Induced_hepatocyte_6_1c52


title: P18MC.1C11


title: P18MC.1C2


title: Induced_hepatocyte_6_1c47


title: P18MC.1C1


title: Induced_hepatocyte_6_1c53


title: Induced_hepatocyte_6_1c42


title: P18MC.1B9


title: Induced_hepatocyte_6_1c41


title: Induced_hepatocyte_6_1c38


title: Induced_hepatocyte_6_1c39


title: P18MC.1B7


title: P18MC.1B8


title: P18MC.1B6


title: Induced_hepatocyte_6_1c36


title: P18MC.1B5


title: Induced_hepatocyte_6_1c34


title: P18MC.1B3


title: Induced_hepatocyte_6_1c35


title: Induced_hepatocyte_6_1c33


title: P18MC.1B4


title: P18MC.1B2


title: P18MC.1B12


title: P18MC.1B11


title: P18MC.1C10


title: Induced_hepatocyte_6_1c30


title: Induced_hepatocyte_6_1c31


title: Induced_hepatocyte_6_1c3


title: Induced_hepatocyte_6_1c43


title: Induced_hepatocyte_6_1c29


title: P18MC.1B1


title: P18MC.1B10


title: Induced_hepatocyte_6_1c27


title: Induced_hepatocyte_6_1c28


title: P18MC.1A9


title: P18MC.1A6


title: Induced_hepatocyte_6_1c24


title: P18MC.1A5


title: Induced_hepatocyte_6_1c22


title: P18MC.1A4


title: Induced_hepatocyte_6_1c23


title: Induced_hepatocyte_6_1c21


title: P18MC.1A3


title: P18MC.1A2


title: Induced_hepatocyte_6_1c20


title: P18MC.1A12


title: Induced_hepatocyte_6_1c19


title: Induced_hepatocyte_6_1c17


title: P18MC.1A10


title: Induced_hepatocyte_6_1c18


title: P18MC.1A11


title: P18MC.1A8


title: Induced_hepatocyte_6_1c16


title: P18MC.1A1


title: Induced_hepatocyte_6_1c13


title: D18MC.2H9


title: P18MC.1A7


title: Induced_hepatocyte_6_1c45


title: Induced_hepatocyte_6_1c26


title: Induced_hepatocyte_6_1c1


title: D18MC.2H8


title: Induced_hepatocyte_6_1c14


title: D18MC.2H6


title: D18MC.2H7


title: D18MC.2H3


title: Induced_hepatocyte_6_1c12


title: Induced_hepatocyte_6_1b95


title: D18MC.2H4


title: D18MC.2H5


title: D18MC.2H2


title: Induced_hepatocyte_6_1c11


title: Induced_hepatocyte_6_1b92


title: Induced_hepatocyte_6_1c25


title: D18MC.2H11


title: Induced_hepatocyte_6_1b94


title: D18MC.2H12


title: D18MC.2H10


title: D18MC.2H1


title: Induced_hepatocyte_6_1b91


title: Induced_hepatocyte_6_1b88


title: D18MC.2G8


title: Induced_hepatocyte_6_1b89


title: D18MC.2G9


title: Induced_hepatocyte_6_1c10


title: D18MC.2G7


title: Induced_hepatocyte_6_1b86


title: Induced_hepatocyte_6_1b87


title: D18MC.2G5


title: Induced_hepatocyte_6_1b83


title: Induced_hepatocyte_6_1b84


title: D18MC.2G6


title: Induced_hepatocyte_6_1b96


title: Induced_hepatocyte_6_1b8


title: Induced_hepatocyte_6_1b82


title: D18MC.2G4


title: D18MC.2G3


title: D18MC.2G2


title: D18MC.2G12


title: Induced_hepatocyte_6_1b81


title: D18MC.2G1


title: D18MC.2G11


title: Induced_hepatocyte_6_1b80


title: D18MC.2G10


title: Induced_hepatocyte_6_1b75


title: Induced_hepatocyte_6_1b74


title: D18MC.2F9


title: Induced_hepatocyte_6_1b73


title: D18MC.2F8


title: D18MC.2F7


title: D18MC.2F6


title: Induced_hepatocyte_6_1b71


title: D18MC.2F4


title: Induced_hepatocyte_6_1b7


title: Induced_hepatocyte_6_1b70


title: Induced_hepatocyte_6_1b69


title: D18MC.2F3


title: D18MC.2F5


title: D18MC.2F2


title: Induced_hepatocyte_6_1b68


title: Induced_hepatocyte_6_1b66


title: Induced_hepatocyte_6_1b65


title: D18MC.2F12


title: Induced_hepatocyte_6_1b63


title: D18MC.2F11


title: Induced_hepatocyte_6_1b78


title: Induced_hepatocyte_6_1b6


title: D18MC.2F1


title: D18MC.2F10


title: D18MC.2E9


title: D18MC.2E8


title: Induced_hepatocyte_6_1b59


title: Induced_hepatocyte_6_1b60


title: D18MC.2E7


title: D18MC.2E6


title: Induced_hepatocyte_6_1b72


title: Induced_hepatocyte_6_1b58


title: Induced_hepatocyte_6_1b57


title: Induced_hepatocyte_6_1b56


title: D18MC.2E4


title: D18MC.2E3


title: D18MC.2E5


title: Induced_hepatocyte_6_1b54


title: Induced_hepatocyte_6_1b50


title: Induced_hepatocyte_6_1b47


title: D18MC.2E2


title: D18MC.2E11


title: Induced_hepatocyte_6_1b48


title: D18MC.2E12


title: D18MC.2E10


title: Induced_hepatocyte_6_1b46


title: Induced_hepatocyte_6_1b45


title: D18MC.2E1


title: D18MC.2D9


title: Induced_hepatocyte_6_1b44


title: Induced_hepatocyte_6_1b43


title: D18MC.2D8


title: D18MC.2D7


title: D18MC.2D6


title: Induced_hepatocyte_6_1b41


title: Induced_hepatocyte_6_1b40


title: D18MC.2D5


title: Induced_hepatocyte_6_1b38


title: TMEV-infected Neuro-2a cells_MOI=10_8h_3

type: RNA

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

country: Japan

institute: Kindai University Faculty of Medicine

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the LSU Core Facility and Kindai University Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: Raw data were processed with an R package Affy for RMA normalization.  Data analysis and statistical evaluations were performed with R and Microsoft Excel.

label: biotin

source_name: Mouse neuroblastoma cell line

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were collected using trypsin treatment and frozen in liquid nitrogen.

extract_protocol: Total RNA was isolated from collected cells using RNeasy Mini Kit (QIAGEN), according to the manufacturer’s instructions.  DNase treatment was conducted during RNA extraction.

treatment_protocol: TMEV was diluted with plaquing diluent.  Cells were washed with PBS and incubated in 500 ul of plaquing diluent containing virus for 1 hour.  After 1 hour incubation, cells were washed with PBS 5 times and incubated in the medium for 7 hours.

tag: cell line

tag: cell type

value: Mouse neuroblastoma cell line


title: TMEV-infected Neuro-2a cells_MOI=10_8h_1


title: TMEV-infected Neuro-2a cells_MOI=10_8h_2


title: TMEV-infected Neuro-2a cells_MOI=10_8h_4


title: Mock-infected Neuro-2a cells_8h_4


title: Mock-infected Neuro-2a cells_8h_2


title: Induced_hepatocyte_6_1b42


title: Induced_hepatocyte_6_1b36


title: HL-1 cells incubated with UV-irradiated TMEV_MOI=10_8h_2

source_name: Mouse myocardial cell line

value: Mouse myocardial cell line


title: TMEV-infected Neuro-2a cells_MOI=10_8h_5


title: Mock-infected Neuro-2a cells_8h_5


title: Mock-infected Neuro-2a cells_8h_3


title: Mock-infected Neuro-2a cells_8h_1


title: TMEV-infected HL-1 cells_MOI=10_8h_3


title: HL-1 cells incubated with UV-irradiated TMEV_MOI=10_8h_1


title: Induced_hepatocyte_6_1b55


title: Induced_hepatocyte_6_1b34


title: D18MC.2D2


title: TMEV-infected HL-1 cells_MOI=10_8h_2


title: TMEV-infected HL-1 cells_MOI=1_8h_1


title: D18MC.2D4


title: D18MC.2D12


title: TMEV-infected HL-1 cells_MOI=10_8h_1


title: TMEV-infected HL-1 cells_MOI=1_8h_3


title: Mock-infected HL-1 cells_8h_3


title: D18MC.2D3


title: Induced_hepatocyte_6_1b32


title: Induced_hepatocyte_6_1b33


title: D18MC.2D11


title: D18MC.2D1


title: H3K27ac_ChIPSeq_Differentiation

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

country: Sweden

institute: Karolinska Institutet

description: ChIP-seq of H3K27ac in control differentiating oli-neu

library_source: genomic

data_processing:
Raw reads were mapped to the mouse genome (GRCm38/mm10) with Bowtie 2.1.0. Uniquely mapped reads (17 and 19.5 million for proliferation and differentiation chromatin samples) were then processed with SAMTools for format conversion and removal of PCR duplicates. Broad peaks corresponding to H3K27ac enrichment were called using MACS 2.0.10, with q-value cutoff at 5*10-2. H3K27ac peaks were filtered against blacklisted genomic regions prone to artifacts (ENCODE Project Consortium, 2012) with BEDTools and annotated to the nearest Transcription Start Site with PeakAnalyzer.
Genome_build: mm10
Supplementary_files_format_and_content: H3K27ac Proliferanting and Differentiating Oli-neu signal wiggle (.bedGraph) files, normalized and dedup.  Broak peaks bed files for H3K27ac Proliferating and Differentiating.

molecule: genomic DNA

source_name: oli-neu

growth_protocol: Oli-neu cells were grown in poly-L-lysine coated dishes and expanded in proliferation media consisting of DMEM ((life tec 41965062), N2 supplement, Pen/Strep Glu (life tec 10378016), T3 (sigma T6397) 340ng/ml, L-thyroxine (sigma 89430) 400 ng/ml, bFGF 10ng/ml and Pdgf-BB 1ng/ml.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.

treatment_protocol: For Oli-neu differentiation, media without growth factors was added for 1 day in vitro and in the presence of 1μM of erb inhibitor (PD174265, St Cruz, ref sc-204170).

value: oli-neu cells

value: embryonic derived oligodendrocyte progenitor cells

tag: strain

tag: chip antibody

value: H3K27ac (Millipore, 17-683)


title: TMEV-infected HL-1 cells_MOI=1_8h_2


title: D18MC.2D10


title: Mock-infected HL-1 cells_8h_2


title: Induced_hepatocyte_6_1b31


title: Input tumor cells 2

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

data_processing:
Paired-end reads were mapped to M. musculus genome assembly mm10. We used Bowtie v1.1.2 with “-m 1” parameter setting.
Mapped eads were extended to 200bp prior to calculating genome-wide coverage
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files with genome-wide fragment coverage

source_name: tumor cells

growth_protocol: Embryonic acinar cells and adult acinar cells from C57Bl6/J wildtype mice were freshly isolated by collagen-digestion and directly used for DNA extraction. Adult acinar cells were additionally cultivated in 3D-collagen for 7 days, undergoing acinar-to-ductal metaplasia. Low-passage tumor cells, isolated from a conditional mutant Kras-driven pancreatic cancer mouse model, were grown in standard medium.

extract_protocol:
After formalin fixation, fragmented DNA was precipitated with specific antibodies, reverse-crosslinked and extracted with a PCR purification kit from Qiagen according to the manufacture´s instructions.
NEBNext Ultra DNA Library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: Acinar-to-ductal metaplasia was additionally treated with 50 ng/ml Tgf-alpha.

value: C57Bl6/J wildtype

value: tumor cells

value: Input


title: Induced_hepatocyte_6_1b29


title: H3K27ac_ChIPSeq_Proliferation

description: ChIP-seq of H3K27ac in proliferating oli-neu


title: H2AK119ub tumor cells

value: H2AK119ub (Cell Signaling, 8240)


title: Mock-infected HL-1 cells_8h_4


title: D18MC.2C9


title: H3K27me3 tumor cells

value: H3K27me3 (Abcam, ab6002)


title: Input acinar-to-ductal-metaplasia 2

source_name: acinar-to-ductal metaplasia

value: acinar-to-ductal metaplasia


title: Mock-infected HL-1 cells_4h_2


title: Induced_hepatocyte_6_1b25


title: Mock-infected HL-1 cells_8h_5


title: Mock-infected HL-1 cells_8h_1


title: TMEV-infected HL-1 cells_MOI=10_4h_1


title: TMEV-infected HL-1 cells_MOI=10_4h_2


title: D18MC.2C8


title: D18MC.2C5


title: H3K27me3 acinar-to-ductal-metaplasia


title: H2AK119ub adult acinar cells

source_name: adult acinar cells

value: adult acinar cells


title: Input embryonic acinar cells 2

source_name: embryonic acinar cells

value: embryonic acinar cells


title: H3K27me3 adult acinar cells


title: Induced_hepatocyte_6_1b21


title: Induced_hepatocyte_6_1b24


title: Induced_hepatocyte_6_1b23


title: D18MC.2C4


title: D18MC.2C7


title: D18MC.2C6


title: Induced_hepatocyte_6_1b22


title: H3K4me3 tumor cells

value: H3K4me3 (Cell Signaling, 9751)


title: H3K27me3 embryonic acinar cells


title: Input adult acinar cells 2


title: Induced_hepatocyte_6_1b28


title: H2AK119ub acinar-to-ductal-metaplasia


title: Input acinar-to-ductal-metaplasia 1


title: D18MC.2C3


title: Input tumor cells 1


title: H3K4me3 acinar-to-ductal-metaplasia


title: Induced_hepatocyte_6_1b17


title: D18MC.2C2


title: Induced_hepatocyte_6_1b19


title: Input embryonic acinar cells 1


title: Input adult acinar cells 1


title: H3K4me3 adult acinar cells


title: D18MC.2C12


title: H2AK119ub embryonic acinar cells


title: Induced_hepatocyte_6_1b12


title: D18MC.2C11


title: H3K4me3 embryonic acinar cells


title: Induced_hepatocyte_6_1b1


title: Induced_hepatocyte_6_1b10


title: Induced_hepatocyte_6_1b11


title: D18MC.2C1


title: Induced_hepatocyte_6_1b20


title: D18MC.2B9


title: D18MC.2B8


title: Induced_hepatocyte_6_1b13


title: Induced_hepatocyte_6_1b52

description:
Single cell mRNA
Mdm2+


title: D18MC.2B7


title: Induced_hepatocyte_6_1b2

description:
Single cell mRNA
Mdm2+


title: D18MC.2C10


title: D18MC.2B6


title: Induced_hepatocyte_6_1c70

description:
Single cell mRNA
Mdm2+


title: D18MC.2B5


title: Mock-infected HL-1 cells_4h_1


title: Induced_hepatocyte_6_1c57

description:
Single cell mRNA
Mdm2+


title: Control_TemporalCortex_Sample1338_TechRep1

city: Grand Rapids

first: Erin

middle: Catherine

last: McKay

state: MI

address: 400 Monroe Ave NW

department: TSMM

institute: Michigan State University

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_1_4.txt
temporal cortex
temporal cortex sample 1338 technical replicate #1

hyb_protocol: For each sample, 300 ng of labelled, linearly amplified cRNA was digested and hybridized for 17 hrs on Agilent Human 8x60k v2 microarrays

scan_protocol: Slides were scanned on an Agilent C Microarray Scanner using the G3 microarray format with the resolution set to 3µm.

data_processing: Data was extracted via Agilent Feature Extraction Software (v 10.7.3.1). Extracted data was imported into R via limma where data was background subtracted, normalized between arrays, and log2 transformed.

organism: Homo sapiens

label_protocol: Agilent’s Low Input QuickAmp Labeling Kit was used with 100 ng total RNA/sample to generate cRNA labelled with Cy3 and Cy5 dyes

extract_protocol: RNA was extracted from the samples using the mirVana miRNA isolation kit (Ambion).

tag: patient diagnosis

value: Control

value: Brain

tag: brain region

value: temporal cortex

tag: subject id

tag: pmi

value: Male


title: Control_TemporalCortex_Sample915_TechRep2

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_1_3.txt
temporal cortex
temporal cortex sample 915 technical replicate #2

value: Female


title: D18MC.2B4

tag: genotype

tag: ngene

tag: nreads

value: M


title: Control_FrontalCortex_Sample1338_TechRep2

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_1_4.txt
frontal cortex
frontal cortex sample 1338 technical replicate #2

value: frontal cortex

tag: Sex

tag: age


title: Control_TemporalCortex_Sample915_TechRep1

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_1_4.txt
temporal cortex
temporal cortex sample 915 technical replicate #1


title: Control_FrontalCortex_Sample978_TechRep2

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_2_4.txt
frontal cortex
frontal cortex sample 978 technical replicate #2


title: Control_FrontalCortex_Sample978_TechRep1

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_2_3.txt
frontal cortex
frontal cortex sample 978 technical replicate #1


title: Control_FrontalCortex_Sample1338_TechRep1

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_1_3.txt
frontal cortex
frontal cortex sample 1338 technical replicate #1


title: Control_TemporalCortex_Sample1338_TechRep2

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_1_3.txt
temporal cortex
temporal cortex sample 1338 technical replicate #2


title: Control_FrontalCortex_Sample915_TechRep2

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_1_4.txt
frontal cortex
frontal cortex sample 915 technical replicate #2


title: Control_FrontalCortex_Sample915_TechRep1

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_1_3.txt
frontal cortex
frontal cortex sample 915 technical replicate #1


title: Control_TemporalCortex_Sample978_TechRep1

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_2_4.txt
temporal cortex
temporal cortex sample 978 technical replicate #1


title: Control_TemporalCortex_Sample732_TechRep1

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_2_4.txt
temporal cortex
temporal cortex sample 732 technical replicate #3


title: Control_TemporalCortex_Sample732_TechRep2

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_2_3.txt
temporal cortex
temporal cortex sample 732 technical replicate #4


title: Control_TemporalCortex_Sample978_TechRep2

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_2_3.txt
temporal cortex
temporal cortex sample 978 technical replicate #2


title: Induced_hepatocyte_6_1c4

description:
Single cell mRNA
Mdm2+

value: Hepatocyte


title: D18MC.2B3

tag: plateplus

tag: plate

tag: lane


title: Induced_hepatocyte_6_1c15

description:
Single cell mRNA
Mdm2+

tag: background strain

tag: tissue

tag: protocol used


title: Control_FrontalCortex_Sample732_TechRep2

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_2_4.txt
frontal cortex
temporal cortex sample 732 technical replicate #2


title: Control_FrontalCortex_Sample732_TechRep1

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_2_3.txt
frontal cortex
temporal cortex sample 732 technical replicate #1


title: Induced_hepatocyte_6_1b93

description:
Single cell mRNA
Mdm2+


title: D18MC.2B2


title: Control_TemporalCortex_Sample729_TechRep2

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_2_1.txt
temporal cortex
frontal cortex sample 729 technical replicate #4


title: D18MC.2B12


title: Induced_hepatocyte_6_1b9

description:
Single cell mRNA
Mdm2+


title: Induced_hepatocyte_6_1b85

description:
Single cell mRNA
Mdm2+


title: Control_FrontalCortex_Sample729_TechRep2

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_2_2.txt
frontal cortex
frontal cortex sample 729 technical replicate #2


title: D18MC.2B11


title: Control_TemporalCortex_Sample729_TechRep1

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_2_2.txt
temporal cortex
frontal cortex sample 729 technical replicate #3


title: Induced_hepatocyte_6_1b77

description:
Single cell mRNA
Mdm2+


title: Induced_hepatocyte_6_1b76

description:
Single cell mRNA
Mdm2+


title: D18MC.2B10


title: D18MC.2A9


title: D18MC.2B1


title: Control_FrontalCortex_Sample566_TechRep2

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_1_4.txt
frontal cortex
frontal cortex sample 566 technical replicate #2


title: Control_FrontalCortex_Sample566_TechRep1

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_1_3.txt
frontal cortex
frontal cortex sample 566 technical replicate #1


title: Control_TemporalCortex_Sample382_TechRep1

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_2_4.txt
temporal cortex
temporal cortex sample 382 technical replicate #1


title: Induced_hepatocyte_6_1b64

description:
Single cell mRNA
Mdm2+


title: Control_TemporalCortex_Sample566_TechRep1

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_1_4.txt
temporal cortex
temporal cortex sample 566 technical replicate #1


title: Control_FrontalCortex_Sample729_TechRep1

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_2_1.txt
frontal cortex
frontal cortex sample 729 technical replicate #1


title: Induced_hepatocyte_6_1b5

description:
Single cell mRNA
Mdm2+


title: Control_FrontalCortex_Sample382_TechRep2

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_2_4.txt
frontal cortex
frontal cortex sample 382 technical replicate #2


title: Control_FrontalCortex_Sample382_TechRep1

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_2_3.txt
frontal cortex
frontal cortex sample 382 technical replicate #1


title: Control_FrontalCortex_Sample110_TechRep2

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_2_4.txt
frontal cortex
frontal cortex sample 110 technical replicate #2


title: D18MC.2A6


title: Control_TemporalCortex_Sample566_TechRep2

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_1_3.txt
temporal cortex
temporal cortex sample 566 technical replicate #2


title: Control_FrontalCortex_Sample110_TechRep1

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_2_3.txt
frontal cortex
frontal cortex sample 110 technical replicate #1


title: Control_TemporalCortex_Sample110_TechRep1

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_2_4.txt
temporal cortex
temporal cortex sample 110 technical replicate #1


title: Control_TemporalCortex_Sample100_TechRep2

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_2_1.txt
temporal cortex
temporal cortex sample 100 technical replicate #2


title: Control_TemporalCortex_Sample110_TechRep2

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_2_3.txt
temporal cortex
temporal cortex sample 110 technical replicate #2


title: D18MC.2A8


title: Control_FrontalCortex_Sample100_TechRep1

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_2_1.txt
frontal cortex
frontal cortex sample 100 technical replicate #1


title: D18MC.2A7


title: Induced_hepatocyte_6_1b53

description:
Single cell mRNA
Mdm2+


title: Control_TemporalCortex_Sample382_TechRep2

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_2_3.txt
temporal cortex
temporal cortex sample 382 technical replicate #2


title: Induced_hepatocyte_6_1b4

description:
Single cell mRNA
Mdm2+


title: 2.5HIP-PLG

city: Aurora

first: Braxton

middle: L

last: Jamison

state: CO

address: 12800 East 19th Avenue Mail Stop 8333

department: Department of Immunology and Microbiology

institute: University of Colorado School of Medicine

description: CD4+ BDC-2.5 Teff cells from 2.5HIP-PLG treated mice

data_processing:
BBMap (Version 38.32). Used to remove adapter sequences (BBDuk).
RSEM (Version 1.3.1). Used to align reads (STAR) and to compile expected counts
Genome_build: GRCm38.6_r94
Supplementary_files_format_and_content: tab-delimited text file includes compiled expected counts

source_name: isolated CD4+ BDC-2.5 Teff cells

extract_protocol:
RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using Universal Plus mRNA Library Kit (NuGen Technologies)

treatment_protocol: NOD.scid mice were injected intravenously (i.v.) with 1.75 mgs of 2.5HIP-PLG nanoparticles one day after i.v. adoptive transfer of activated BDC-2.5 T cells.

tag: strain

tag: treatment

tag: cell type

value: CD4+ BDC-2.5 Teff cells


title: Untreated

description: CD4+ BDC-2.5 Teff cells from control mice

value: Untreated


title: Induced_hepatocyte_6_1b30

description:
Single cell mRNA
Mdm2+


title: Z25_R

city: Shanghai

first: Denghui

last: Liu

state: Shanghai

address: ShengLi Building, 320 Yueyang Road

country: China

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

description: Z.FilterProteinCoding.Counts.Normalized.FPKM.txt

data_processing:
Reads quality were first checked by "Fastqc"
And then clean reads were mapped to the reference genome by HISAT
Uniquely mapped reads were utilized to calculate the counts of each gene by HTSeq
Reads counts matrix was then normalized to library size by DESeq2 with default parameters, and normalized reads were then used to calculate the FPKM
Genome_build: GRCz10
Supplementary_files_format_and_content: Contains the expression level of all samples, measured by FPKM

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
The samples were lysed and performed single cell-based PCR for further amplification. Then DNA libraries were prepared for sequencing.
The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.

value: zebrafish embryos

tag: region

value: Right

tag: layer


title: Z25_N

value: Neuro


title: D18MC.2A4


title: D18MC.2A3


title: Induced_hepatocyte_6_1b27

description:
Single cell mRNA
Mdm2+


title: D18MC.2A2


title: Control_TemporalCortex_Sample90_TechRep2

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_1_3.txt
temporal cortex
temporal cortex sample 90 technical replicate #2

tag: patient diagnosis

tag: brain region

tag: subject id

tag: pmi


title: Z25_L

value: Left


title: Induced_hepatocyte_6_1b18

description:
Single cell mRNA
Mdm2+


title: Control_FrontalCortex_Sample90_TechRep2

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_1_4.txt
frontal cortex
frontal cortex sample 90 technical replicate #2

tag: Sex


title: Induced_hepatocyte_6_1b51

description:
Single cell mRNA
Mdm2+


title: D18MC.2A5

tag: genotype

tag: ngene

tag: nreads

tag: age


title: Z25_CVP

value: CVP


title: D18MC.2A12

tag: plateplus

tag: plate

tag: lane


title: Induced_hepatocyte_6_1b16

description:
Single cell mRNA
Mdm2+

tag: background strain

tag: tissue

tag: protocol used


title: Control_FrontalCortex_Sample100_TechRep2

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_2_2.txt
frontal cortex
frontal cortex sample 100 technical replicate #2


title: D18MC.2A11


title: Z25_CV

tag: region

value: CV


title: D18MC.2A10


title: Induced_hepatocyte_6_1b15

description:
Single cell mRNA
Mdm2+


title: D18MC.2A1


title: Z22_R

tag: layer


title: Induced_hepatocyte_6_1b39

description:
Single cell mRNA
Mdm2-


title: Induced_hepatocyte_6_1b14

description:
Single cell mRNA
Mdm2+


title: D18MC.1H9


title: Z22_L


title: D18MC.1H8


title: Control_TemporalCortex_Sample90_TechRep1

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_1_4.txt
temporal cortex
temporal cortex sample 90 technical replicate #1

tag: patient diagnosis


title: Control_FrontalCortex_Sample57_TechRep2

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_1_2.txt
frontal cortex
frontal cortex sample 57 technical replicate #2

tag: brain region


title: Z22_N


title: Control_TemporalCortex_Sample57_TechRep2

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_1_1.txt
temporal cortex
temporal cortex sample 57 technical replicate #2

tag: subject id


title: Induced_hepatocyte_6_1c67

description:
Single cell mRNA
Mdm2-


title: Control_TemporalCortex_Sample57_TechRep1

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_1_2.txt
temporal cortex
temporal cortex sample 57 technical replicate #1

tag: pmi


title: AD_TemporalCortex_Sample1337_TechRep2

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_1_1.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 1337 technical replicate #2

value: Alzheimer's disease

tag: Sex


title: Control_FrontalCortex_Sample90_TechRep1

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_1_3.txt
frontal cortex
frontal cortex sample 90 technical replicate #1

value: Control


title: Control_FrontalCortex_Sample57_TechRep1

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_1_1.txt
frontal cortex
frontal cortex sample 57 technical replicate #1

value: Brain


title: Induced_hepatocyte_6_1c61

description:
Single cell mRNA
Mdm2-


title: D18MC.1H7

tag: genotype


title: Z22_CV


title: Induced_hepatocyte_6_1c37

description:
Single cell mRNA
Mdm2-


title: Z22_CA

value: CA


title: AD_FrontalCortex_Sample1337_TechRep2

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_1_2.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 1337 technical replicate #2


title: Induced_hepatocyte_6_1c32

description:
Single cell mRNA
Mdm2-


title: Z25_CA


title: D18MC.1H6

tag: ngene


title: D18MC.1H4

tag: nreads


title: Control_TemporalCortex_Sample100_TechRep1

description:
raw data file:
Counts_JB_141101_253949435349_S01_GE2_107_Sep09_2_2.txt
temporal cortex
temporal cortex sample 100 technical replicate #1

value: temporal cortex

tag: age


title: Induced_hepatocyte_6_1c40

description:
Single cell mRNA
Mdm2-


title: AD_TemporalCortex_Sample1181_TechRep1

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_2_2.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 1181 technical replicate #1

value: Female


title: Induced_hepatocyte_6_1c2

description:
Single cell mRNA
Mdm2-


title: Z19_R


title: AD_TemporalCortex_Sample1337_TechRep1

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_1_2.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 1337 technical replicate #1


title: Z19_L


title: AD_FrontalCortex_Sample1337_TechRep1

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_1_1.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 1337 technical replicate #1


title: Z22_CVP


title: D18MC.1H2

value: M

tag: plateplus


title: D18MC.1H12

tag: plate


title: Z19_CVP


title: Z19_N


title: D18MC.1H3

tag: lane


title: Z19_CV


title: Induced_hepatocyte_6_1b90

description:
Single cell mRNA
Mdm2-

tag: background strain


title: Induced_hepatocyte_6_1b79

description:
Single cell mRNA
Mdm2-

tag: tissue


title: AD_FrontalCortex_Sample1181_TechRep2

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_2_2.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 1181 technical replicate #2

value: frontal cortex


title: AD_FrontalCortex_Sample1181_TechRep1

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_2_1.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 1181 technical replicate #1


title: AD_TemporalCortex_Sample1181_TechRep2

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_2_1.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 1181 technical replicate #2


title: Induced_hepatocyte_6_1b67

description:
Single cell mRNA
Mdm2-

value: Hepatocyte

tag: protocol used


title: D18MC.1H5


title: D18MC.1H10


title: D18MC.1H1


title: Induced_hepatocyte_6_1b49

description:
Single cell mRNA
Mdm2-


title: D18MC.1H11


title: Induced_hepatocyte_6_1b62

description:
Single cell mRNA
Mdm2-


title: D18MC.1G8


title: Z10_L

description: Z.FilterProteinCoding.Counts.Normalized.FPKM.txt

tag: region


title: Induced_hepatocyte_6_1b61

description:
Single cell mRNA
Mdm2-


title: Z19_CA

tag: layer


title: AD_TemporalCortex_Sample958_TechRep2

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_2_1.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 958 technical replicate #2

tag: patient diagnosis


title: AD_FrontalCortex_Sample958_TechRep2

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_2_2.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 958 technical replicate #2

tag: brain region


title: Z10_CVP


title: AD_TemporalCortex_Sample958_TechRep1

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_2_2.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 958 technical replicate #1

tag: subject id


title: Z10_R


title: Z10_N


title: D18MC.1G9


title: Induced_hepatocyte_6_1b37

description:
Single cell mRNA
Mdm2-


title: Z6_R


title: Induced_hepatocyte_6_1b3

description:
Single cell mRNA
Mdm2-


title: D18MC.1G7


title: D18MC.1G4


title: D18MC.1G5


title: Induced_hepatocyte_6_1b35

description:
Single cell mRNA
Mdm2-


title: D18MC.1G6


title: Z6_L


title: Z10_CV


title: D18MC.1G3


title: AD_FrontalCortex_Sample958_TechRep1

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_2_1.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 958 technical replicate #1

tag: pmi


title: AD_TemporalCortex_Sample850_TechRep2

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_2_3.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 850 technical replicate #2

tag: Sex

value: Male


title: Z10_CA


title: Induced_hepatocyte_6_1b26

description:
Single cell mRNA
Mdm2-


title: AD_TemporalCortex_Sample895_TechRep1

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_1_2.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 895 technical replicate #1


title: yTC2R43

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: TRAMP-C2 tumor from young mouse (R43).

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.66.3 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4.
Sequencing reads were mapped to the mm10 mouse genome using TopHat v2.0.12.
Mean and standard deviation of fragment size were calculated with picard-tools v2.7.1.
Gene level abundance was quantitated from the filtered mouse alignments in R using the Genomic Alignments Bioconductor package v1.6.3 using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_processed_data.txt: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: TRAMP-C2 tumor from young mouse (R43)

growth_protocol: One million TRAMP-C2 cells were orthotopically injected into the dorsolateral prostate of immune-competent syngeneic young (4 month-old; n=20) C57BL/6 mice. Thirty to forty-five days post-injection, mice were sacrificed and prostate tumors were harvested.

extract_protocol:
Tumors from young and aged mice were homogenized in Qiagen RLT buffer, and RNA was isolated using the RNeasy extraction kit (Qiagen, Valencia, CA). RNA concentration, purity, and integrity were assessed by NanoDrop (Thermo Fisher Scientific Inc) and Agilent Bioanalyzer.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 generating 50 bp paired end reads.

tag: strain/background

tag: gender

value: male

tag: age of host

value: 4 months old

tag: cell line

tag: cell type

value: epithelial prostate adenocarcinoma


title: oTC2R50

description: TRAMP-C2 tumor from aged mouse (R50).

source_name: TRAMP-C2 tumor from aged mouse (R50)

growth_protocol: One million TRAMP-C2 cells were orthotopically injected into the dorsolateral prostate of immune-competent syngeneic aged (20-24 month-old; n=19) C57BL/6 mice. Thirty to forty-five days post-injection, mice were sacrificed and prostate tumors were harvested.

value: 20-24 months old


title: yTC2R40

description: TRAMP-C2 tumor from young mouse (R40).

source_name: TRAMP-C2 tumor from young mouse (R40)


title: AD_FrontalCortex_Sample895_TechRep2

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_1_2.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 895 technical replicate #2

tag: age


title: D18MC.1G11

tag: genotype

tag: ngene

tag: nreads

tag: plateplus

tag: plate

tag: lane


title: Z6_CA

tag: tissue

value: zebrafish embryos

tag: region

tag: layer


title: D18MC.1G10


title: AD_TemporalCortex_Sample895_TechRep2

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_1_1.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 895 technical replicate #2

tag: patient diagnosis

tag: brain region

tag: subject id

tag: pmi


title: Z6_N

value: Neuro


title: yTC2R37

description: TRAMP-C2 tumor from young mouse (R37).

source_name: TRAMP-C2 tumor from young mouse (R37)

tag: strain/background

tag: gender

tag: age of host


title: oTC2R47

description: TRAMP-C2 tumor from aged mouse (R47).

source_name: TRAMP-C2 tumor from aged mouse (R47)

tag: cell line

tag: cell type


title: yTC2R36

description: TRAMP-C2 tumor from young mouse (R36).

source_name: TRAMP-C2 tumor from young mouse (R36)


title: D18MC.1G2

source_name: Cortex

tag: genotype

tag: ngene

tag: age

tag: Sex


title: Z6_CVP

value: CVP


title: AD_FrontalCortex_Sample850_TechRep1

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_2_3.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 850 technical replicate #1

value: Alzheimer's disease


title: AD_TemporalCortex_Sample765_TechRep1

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_2_2.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 765 technical replicate #1


title: AD_FrontalCortex_Sample895_TechRep1

description:
raw data file:
Counts_JB_141121_253949435348_S01_GE2_107_Sep09_1_1.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 895 technical replicate #1


title: D18MC.1G12

tag: nreads

tag: plateplus

tag: plate

tag: lane


title: AD_TemporalCortex_Sample765_TechRep2

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_2_1.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 765 technical replicate #2

tag: patient diagnosis

tag: tissue


title: AD_TemporalCortex_Sample850_TechRep1

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_2_4.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 850 technical replicate #1

tag: brain region

tag: subject id


title: AD_FrontalCortex_Sample850_TechRep2

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_2_4.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 850 technical replicate #2

tag: pmi


title: oTC2R51

description: TRAMP-C2 tumor from aged mouse (R51).

source_name: TRAMP-C2 tumor from aged mouse (R51)

tag: strain/background

tag: gender


title: oTC2R46

description: TRAMP-C2 tumor from aged mouse (R46).

source_name: TRAMP-C2 tumor from aged mouse (R46)

tag: age of host

tag: cell line


title: Z6_CV

tag: region

value: CV

tag: layer


title: D18MC.1F9

tag: genotype

tag: ngene

tag: age


title: Z1_N


title: D18MC.1G1

tag: nreads

tag: Sex

tag: plateplus


title: Z1_R

value: Right


title: Z1_L

value: Left


title: Z1_CVP


title: Post-Larval Hypoxic Oil 3

city: Florence

first: Elizabeth

middle: R.

last: Jones

state: SC

address: 4822 E. Palmetto St.

department: Biology

institute: Francis Marion University

data_processing:
Bases called using Illumina CASAVA software
Read quality assessed using Illumina FastQC software; adpater trimming performed using Trimomatic software
Reads were aligned to C. variegatus genome using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany).
Gene expression (Transcripts per million --TPM) calculated using CLC Genomics Workbench 10.1.1 (Qiagen, Hilden, Germany)
Genome_build: C. variegatus genome (NCBI genome ID 13078)
Supplementary_files_format_and_content: CSV text files including TPM expression values

organism: Cyprinodon variegatus

source_name: whole body, n=10

growth_protocol: Animals were maintained  in 30 ppt artificial sea water at 30 °C for duration of experiment.

extract_protocol:
Qiagen RNEasy, according to manufacturer's protocol
Illumina TruSeq Stranded mRNA kit to construct polyA libraries

treatment_protocol: C. variegatus from three life stages (embryonic, post-hatch, or post larval) were subjected to oil exposure (12.5% HEWAF) under normoxic (≥ 5 mg/L oxygen) or hypoxic ( ≤ 2 mg/L oxygen) conditions for 48 hours.

value: whole body

value: 6 days post hatch

tag: oil concentration

tag: oxygen concentration

value: ≤ 2 mg/L


title: D18MC.1F7

value: M

tag: plate

tag: lane


title: Post-Larval Hypoxic Oil 2

tag: tissue


title: D18MC.1F6


title: Post-Larval Hypoxic Oil 1


title: Z1_CA

value: CA


title: Z1_CV


title: D18MC.1F5


title: D18MC.1F4


title: Post-Larval Hypoxic Control 2

value: 0 tPAH29


title: D18MC.1F3


title: D18MC.1F8


title: Post-Larval Hypoxic Control 1


title: D18MC.1F2


title: M17_N

description: M.FilterProteinCoding.AllCounts.Normalized.FPKM.txt


title: M17_L


title: Post-Larval Normoxic Oil 3

value: ≥ 5 mg/L


title: AD_FrontalCortex_Sample765_TechRep1

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_2_1.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 765 technical replicate #1

tag: patient diagnosis

value: Brain

tag: brain region

value: frontal cortex

tag: subject id

tag: pmi

value: Female


title: AD_TemporalCortex_Sample754_TechRep4

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_2_1.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 754 technical replicate #4

value: temporal cortex


title: AD_TemporalCortex_Sample754_TechRep3

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_2_2.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 754 technical replicate #3


title: AD_FrontalCortex_Sample765_TechRep2

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_2_2.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 765 technical replicate #2


title: AD_TemporalCortex_Sample754_TechRep1

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_1_4.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 754 technical replicate #1


title: M17_CVP

value: zebrafish embryos

tag: region


title: Post-Larval Normoxic Oil 2


title: Post-Larval Hypoxic Control 3


title: M17_R

tag: layer


title: Post-Larval Normoxic Oil 1


title: Post-Larval Normoxic Control 3


title: D18MC.1F10

tag: genotype


title: M15_R


title: AD_FrontalCortex_Sample754_TechRep2

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_1_4.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 754 technical replicate #2


title: D18MC.1F12

tag: ngene


title: AD_FrontalCortex_Sample754_TechRep4

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_2_2.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 754 technical replicate #4

tag: age


title: AD_FrontalCortex_Sample754_TechRep1

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_1_3.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 754 technical replicate #1


title: D18MC.1F1

tag: nreads


title: AD_FrontalCortex_Sample754_TechRep3

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_2_1.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 754 technical replicate #3

tag: Sex


title: D18MC.1E9

tag: plateplus


title: D18MC.1F11


title: Post-Larval Normoxic Control 1

tag: oil concentration


title: AD_TemporalCortex_Sample754_TechRep2

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_1_3.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 754 technical replicate #2


title: D18MC.1E8


title: M17_CV


title: M17_CA


title: D18MC.1E7


title: M15_L


title: M15_CVP

value: CVP


title: Post-Hatch Hypoxic Oil 2

value: 2.5 days post hatch

tag: oxygen concentration


title: D18MC.1E6

tag: plate


title: AD_TemporalCortex_Sample544_TechRep1

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_1_2.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 544 technical replicate #1

value: Alzheimer's disease

value: Male


title: Post-Larval Normoxic Control 2


title: D18MC.1E5

tag: lane


title: Post-Hatch Hypoxic Oil 1

tag: tissue


title: M15_CA


title: M15_CV

value: CV


title: M15_N

value: Neuro


title: Post-Hatch Hypoxic Control 3

value: whole body


title: Post-Hatch Hypoxic Oil 3

value: ≤ 2 mg/L


title: D18MC.1E4

value: M


title: M12_R

value: Right


title: Post-Hatch Hypoxic Control 2

value: 0 tPAH29


title: M12_N


title: AD_TemporalCortex_Sample544_TechRep2

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_1_1.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 544 technical replicate #2

tag: patient diagnosis


title: Post-Hatch Hypoxic Control 1


title: AD_TemporalCortex_Sample418_TechRep1

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_1_4.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 418 technical replicate #1

tag: brain region


title: AD_FrontalCortex_Sample544_TechRep2

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_1_2.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 544 technical replicate #2

tag: subject id


title: AD_FrontalCortex_Sample544_TechRep1

description:
raw data file:
Counts_JB_141121_253949435346_S01_GE2_107_Sep09_1_1.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 544 technical replicate #1

tag: pmi


title: M12_L

tag: region

value: Left


title: AD_FrontalCortex_Sample418_TechRep2

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_1_4.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 418 technical replicate #2

value: Brain


title: D18MC.1E2


title: Post-Hatch Normoxic Oil 3

value: ≥ 5 mg/L


title: D18MC.1E3


title: D18MC.1E12


title: M12_CVP

description: M.FilterProteinCoding.AllCounts.Normalized.FPKM.txt

tag: layer


title: AD_TemporalCortex_Sample413_TechRep2

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_1_1.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 413 technical replicate #2

value: Female


title: D18MC.1E11

tag: genotype


title: M12_CV


title: D18MC.1E10

tag: ngene


title: AD_TemporalCortex_Sample413_TechRep1

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_1_2.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 413 technical replicate #1

value: temporal cortex

tag: age


title: AD_FrontalCortex_Sample418_TechRep1

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_1_3.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 418 technical replicate #1

value: frontal cortex


title: AD_TemporalCortex_Sample418_TechRep2

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_1_3.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 418 technical replicate #2


title: M12_CA

value: zebrafish embryos

value: CA


title: AD_TemporalCortex_Sample326_TechRep2

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_1_3.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 326 technical replicate #2

value: Alzheimer's disease


title: Post-Hatch Normoxic Control 3

value: 2.5 days post hatch


title: Post-Hatch Normoxic Oil 1


title: M8_R


title: D18MC.1E1

tag: nreads


title: AD_FrontalCortex_Sample413_TechRep2

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_1_2.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 413 technical replicate #2

tag: Sex


title: D18MC.1D9

tag: plateplus


title: M8_L


title: Embryonic Hypoxic Oil 3

value: 60 h post fertilization

tag: oil concentration


title: Post-Hatch Normoxic Oil 2

tag: oxygen concentration


title: Post-Hatch Normoxic Control 1


title: M8_N

value: Neuro


title: M8_CVP

value: CVP


title: AD_FrontalCortex_Sample413_TechRep1

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_1_1.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 413 technical replicate #1


title: Post-Hatch Normoxic Control 2

value: whole body


title: AD_TemporalCortex_Sample326_TechRep1

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_1_4.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 326 technical replicate #1


title: M8_CA


title: D18MC.1D4

value: M

tag: plate


title: AD_FrontalCortex_Sample326_TechRep1

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_1_3.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 326 technical replicate #1


title: D18MC.1D7

tag: lane


title: M8_CV

tag: tissue

value: CV


title: Embryonic Hypoxic Oil 2

value: ≤ 2 mg/L


title: D18MC.1D5


title: AD_FrontalCortex_Sample326_TechRep2

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_1_4.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 326 technical replicate #2

tag: patient diagnosis


title: Emryonic Hypoxic Control 3

value: 0 tPAH29


title: Emryonic Hypoxic Control 1


title: M6_R

value: Right


title: AD_TemporalCortex_Sample279_TechRep4

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_1_1.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 279 technical replicate #4

value: Brain

tag: brain region


title: Embryonic Hypoxic Oil 1


title: D18MC.1D8


title: AD_FrontalCortex_Sample279_TechRep4

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_1_2.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 279 technical replicate #4

tag: subject id

value: Female


title: D18MC.1D6


title: Embryonic Normoxic Oil 3

value: ≥ 5 mg/L


title: D18MC.1D12


title: AD_TemporalCortex_Sample279_TechRep3

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_1_2.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 279 technical replicate #3

value: temporal cortex

tag: pmi


title: AD_TemporalCortex_Sample279_TechRep1

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_1_2.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 279 technical replicate #1


title: AD_TemporalCortex_Sample279_TechRep2

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_1_1.txt
AD temporal cortex
Alzheimer's disease temporal cortex sample 279 technical replicate #2


title: AD_FrontalCortex_Sample279_TechRep3

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_1_1.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 279 technical replicate #3

value: frontal cortex


title: Emryonic Hypoxic Control 2


title: D18MC.1D2


title: D18MC.1D3


title: M6_L

description: M.FilterProteinCoding.AllCounts.Normalized.FPKM.txt

value: zebrafish embryos

tag: region

value: Left


title: AD_FrontalCortex_Sample279_TechRep1

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_1_1.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 279 technical replicate #1

value: Alzheimer's disease


title: M6_N

tag: layer


title: Embryonic Normoxic Oil 1

value: 60 h post fertilization


title: M6_CA

value: CA


title: Embryonic Normoxic Oil 2


title: M6_CV


title: D18MC.1D11

tag: genotype


title: M2_R


title: D18MC.1C9

tag: ngene


title: D18MC.1D10

tag: age


title: Embryonic Normoxic Control 2


title: M6_CVP

value: CVP


title: Embryonic Normoxic Control 3

value: whole body


title: M2_N

value: Neuro


title: D18MC.1D1

tag: nreads

value: M


title: AD_FrontalCortex_Sample279_TechRep2

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_1_2.txt
AD frontal cortex
Alzheimer's disease frontal cortex sample 279 technical replicate #2

tag: Sex


title: Embryonic Normoxic Control 1


title: VaD_TemporalCortex_Sample1396_TechRep2

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_2_3.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 1396 technical replicate #2

value: Vascular dementia

value: Male


title: VaD_TemporalCortex_Sample1396_TechRep1

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_2_4.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 1396 technical replicate #1


title: D18MC.1C8

tag: plateplus


title: M2_L


title: VaD_FrontalCortex_Sample1396_TechRep2

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_2_4.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 1396 technical replicate #2


title: 38Liver

city: University Park

first: William

middle: J.

last: Horton

state: PA

address: 324 Henning Bldg

department: Animal Science

institute: Pennsylvania State University

data_processing:
Raw reads were trimmed for quality and adapter sequence using Trimmomatic
Trimmed reads were mapped to our de novo transcriptome using bowtie2
Finally, expression was quantified (both for counts and FPKM) using eXpress
Genome_build: sparrow_heart_transps.fasta & sparrow_liver_transps.fasta
Supplementary_files_format_and_content: tab delimited output for each sample from eXpress,  including raw counts and FPKM by transcript

organism: Zonotrichia albicollis

source_name: Liver

extract_protocol:
Tissues were dissected and preserved in RNALater and stored at -20 until all samples collected. Total RNA extracted with Qiagen RNeasy Mini kit according to manufacturers protocol, with DNA digestion on columns.
Libraries prepared with Illumina TruSeq Total RNA Library Prep Kit with RiboZero Gold acording to manufacturers protocols and sequenced on an Illumina Hi Seq 2500 @ 100bp, single end reads

tag: time

tag: migratory status

value: Non-Migratory


title: D18MC.1C7

tag: plate


title: M2_CVP


title: 37Liver


title: VaD_FrontalCortex_Sample1396_TechRep1

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_2_3.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 1396 technical replicate #1

value: Brain


title: VaD_TemporalCortex_Sample1370_TechRep2

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_2_1.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 1370 technical replicate #2

value: Female


title: D18MC.1C6

tag: lane


title: 35Liver


title: D18MC.1C5


title: M2_CV

tag: tissue

value: CV


title: 33Liver


title: M2_CA


title: D18MC.1C4


title: 30Liver


title: D18MC.1C3


title: D18MC.1C2


title: 29Liver


title: VaD_FrontalCortex_Sample1370_TechRep1

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_2_1.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 1370 technical replicate #1

tag: patient diagnosis


title: VaD_FrontalCortex_Sample1370_TechRep2

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_2_2.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 1370 technical replicate #2

tag: brain region


title: VaD_TemporalCortex_Sample1063_TechRep2

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_1_3.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 1063 technical replicate #2

value: temporal cortex

tag: subject id


title: 27Liver

value: Migratory


title: D18MC.1C11


title: 26Liver


title: VaD_TemporalCortex_Sample1370_TechRep1

description:
raw data file:
Counts_JB_141125_253949435728_S01_GE2_107_Sep09_2_2.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 1370 technical replicate #1

tag: pmi


title: 25Liver


title: D18MC.1C10


title: HCT116_sh-PNO1_rep2

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: Gene expression data from HCT116 cells tranduced with lentivirus encoding PNO1 sh-RNA

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip PrimeView Human gene expression array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip  scanner 3000

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Colorectal cancer cells, transduced with lentivirus encoding sh-PNO1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Trizol (Thermo Fisher Scientific) extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell line

tag: shRNA

value: PNO1 shRNA


title: VaD_FrontalCortex_Sample1063_TechRep2

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_1_4.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 1063 technical replicate #2

value: frontal cortex


title: VaD_TemporalCortex_Sample1063_TechRep1

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_1_4.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 1063 technical replicate #1


title: HCT116_sh-PNO1_rep3


title: 24Liver


title: HCT116_sh-PNO1_rep1


title: VaD_FrontalCortex_Sample1063_TechRep1

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_1_3.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 1063 technical replicate #1


title: D18MC.1B9

tag: genotype


title: VaD_TemporalCortex_Sample981_TechRep1

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_1_2.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 981 technical replicate #1


title: D18MC.1C12

tag: ngene


title: VaD_TemporalCortex_Sample981_TechRep2

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_1_1.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 981 technical replicate #2

tag: age


title: 28Liver


title: HCT116_sh-Ctrl-1_rep3

description: Gene expression data from HCT116 cells tranduced with lentivirus encoding Control sh-RNA

source_name: Colorectal cancer cells, transduced with lentivirus encoding sh-Ctrl

value: Control shRNA


title: HCT116_sh-Ctrl-1_rep2


title: HCT116_sh-Ctrl-1_rep1


title: 22Liver


title: VaD_FrontalCortex_Sample981_TechRep1

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_1_1.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 981 technical replicate #1


title: bi262FLlate_01

city: Madison

first: Wesley

middle: w.

last: Morovic

state: WI

address: 3329 Agriculture Dr.

department: Genomics & Microbiome Science

institute: DuPont Nutrition & Health

description:
A600= 1.0+
raw_rnaseq_counts.tsv
Bi26_2'FL_fullcomps.gff

data_processing:
Paired-end reads were imported and mapped to the B. longum subsp. infantis Bi-26 genome (SAMN10380491) using the “Geneious for RNA” Mapper with default settings in Geneious v. 11.0.4
Transcript levels in the resulting assemblies were calculated using the “Calculate Expression Levels” function, which enabled the comparison of replicates and experiments using the “Compare Expression Levels” with the DESeq2 method and parametric fit type.
The assemblies were exported as BAM files and imported into ArrayStar v. 1.2 (DNAStar, Madison, WI), processed using QSeq, and normalized by reads per kilobase of transcript per million mapped reads (RPKM).
Regression analyses of the RNA data were made in ArrayStar software using the Student’s t-test with FDR correction. Statistical analyses between sets of samples were analyzed using DESeq2 method as above. Differences in expression were considered significant if the Absolute Confidence (-Log10 adjusted p-value) was +1.00, and the Log2 ratio was at + 1.00, representing p < 0.05 and a > 2x fold change, respectively, after normalization.
Genome_build: RJJM00000000
Supplementary_files_format_and_content: .bam sequence alignment using Geneious v. 11.0.4

organism: Bifidobacterium longum subsp. infantis

source_name: Bacterial culture

growth_protocol: Samples grown anerobicall in modified Bifidobacterium media 58 (mBM58) at 38°C. mBM58 from Deutsche Sammlung von Microorganismen und Zellculturen; [casein peptone, tryptic digest 10 g/L, yeast extract 5 g/L, meat extract 5 g/L,  K2HPO4 3 g/L,  ascorbic acid 10 g/L, and cysteine-HCl 0.5 g/L; pH 6.8].

extract_protocol:
After each sample reached its desired A600 range, cells were centrifuged for 10 min. at 4,063 x g. The supernatant was removed and 1 mL of TRIzol (p/n: 15596026, Thermo) was added. The pellet was re-suspended by vortexing and the tubes were immediately frozen at -80°C. The cell pellets were later thawed, transferred to a Lysing Matrix B 2mL tube (p/n: 116911050, MPBio, Santa Ana, CA), and disrupted using a Mini-Beadbeater. The lysate was subjected to a chloroform organic extraction and followed by purification using RNeasy Mini Kit (p/n: 74104, Qiagen, Hilden, Germany).
Quality checks and quantifications of the isolated RNA were carried out on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Ribosomal RNA was removed prior to library construction using Ribo-Zero rRNA Removal Kit Gram-Positive Bacteria (p/n: MRZGP126, Illumina). Stranded cDNA libraries were prepared using TruSeq Stranded mRNA Kit (p/n: 20020594, Illumina), quantitated by Agilent TapeStation, pooled quimolarly, and sequenced on one flowcell lane for 75 cycles using paired-end 75 basepair sequencing on Illumina 2500 HiSeq Rapid Cluster Kit v. 2 (p/n: PE-402-4002, Illumina) and HiSeq Rapid SBS Kit v. 2 (p/n: FC-402-4021, Illumina).

treatment_protocol: Carbon source

tag: strain

tag: carbon source

tag: growth phase

value: Late-log


title: D18MC.1B8

tag: nreads

tag: Sex

tag: plateplus


title: bi262FLmid_02

description:
A600= 0.5-0.9
raw_rnaseq_counts.tsv
Bi26_2'FL_fullcomps.gff

value: Mid-log


title: VaD_TemporalCortex_Sample745_TechRep2

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_1_1.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 745 technical replicate #2


title: D18MC.1B7

tag: plate

tag: lane


title: 16Liver

tag: time

tag: migratory status


title: D18MC.1B6


title: 14Liver


title: VaD_FrontalCortex_Sample981_TechRep2

description:
raw data file:
Counts_JB_141125_253949435727_S01_GE2_107_Sep09_1_2.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 981 technical replicate #2

tag: patient diagnosis

tag: tissue

tag: brain region

tag: subject id


title: bi262FLearly_02

description:
A600= 0.2
raw_rnaseq_counts.tsv
Bi26_2'FL_fullcomps.gff

value: Early


title: VaD_TemporalCortex_Sample745_TechRep1

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_1_2.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 745 technical replicate #1

tag: pmi


title: VaD_FrontalCortex_Sample745_TechRep2

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_1_2.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 745 technical replicate #2


title: 12Liver


title: D18MC.1B5

tag: genotype

tag: ngene


title: 11Liver


title: 19Liver


title: 8Liver


title: bi26laclate_01

tag: strain

value: Lactose


title: D18MC.1B3

tag: age


title: D18MC.1B4


title: VaD_FrontalCortex_Sample745_TechRep1

description:
raw data file:
Counts_JB_141121_253949435347_S01_GE2_107_Sep09_1_1.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 745 technical replicate #1


title: VaD_TemporalCortex_Sample488_TechRep2

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_2_3.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 488 technical replicate #2


title: VaD_FrontalCortex_Sample488_TechRep2

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_2_4.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 488 technical replicate #2


title: bi26lacmid_02

tag: carbon source

tag: growth phase


title: bi262FLmid_01


title: 5Liver


title: D18MC.1B2

tag: nreads

tag: Sex


title: D18MC.1C1

tag: plateplus

tag: plate


title: bi26lacmid_01


title: D18MC.1B12

tag: lane


title: 2Liver

tag: time

tag: migratory status


title: bi262FLearly_01


title: bi26laclate_02


title: D18MC.1B11


title: VaD_TemporalCortex_Sample488_TechRep1

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_2_4.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 488 technical replicate #1

tag: patient diagnosis

tag: tissue


title: bi262FLlate_02


title: VaD_TemporalCortex_Sample444_TechRep2

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_2_1.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 444 technical replicate #2

tag: brain region

tag: subject id


title: bi26lacearly_02


title: D18MC.1B10

tag: genotype


title: D18MC.1B1

tag: ngene


title: 3 mpf kidney-NC rep2

extract_protocol:
The total RNA of sorted cells was isolated by QIAGEN RNeasy Mini Kit (Cat. No. 74104).
The mRNA sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina.

value: zebrafish kidney

tag: cell type

value: double negative cells

tag: Stage

value: 3 mpf


title: bi26lacearly_01

tag: strain

tag: carbon source


title: 37Heart

source_name: Heart


title: 3 mpf kidney-NC rep1


title: 3 mpf kidney-HSPC rep2

value: hematopoietic stem and progenitor cells


title: 33Heart

value: Non-Migratory


title: 30Heart


title: 35Heart


title: D18MC.1A9

tag: nreads

tag: age

value: M


title: VaD_TemporalCortex_Sample444_TechRep1

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_2_2.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 444 technical replicate #1

value: Vascular dementia

value: Brain

tag: pmi

tag: Sex

value: Female


title: VaD_FrontalCortex_Sample444_TechRep1

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_2_1.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 444 technical replicate #1


title: D18MC.1A7

tag: plateplus

tag: plate

tag: lane


title: D18MC.1A8


title: 38Heart

tag: time

tag: migratory status


title: 29Heart


title: D18MC.1A6


title: VaD_TemporalCortex_Sample381_TechRep3

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_1_4.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 381 technical replicate #3

tag: patient diagnosis

tag: tissue

tag: brain region

value: temporal cortex

value: Male


title: 4 dpf CHT-NC rep2

value: zebrafish embryos

value: 4 dpf


title: VaD_FrontalCortex_Sample488_TechRep1

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_2_3.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 488 technical replicate #1

value: frontal cortex

tag: subject id


title: 28Heart


title: VaD_TemporalCortex_Sample381_TechRep2

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_2_1.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 381 technical replicate #2


title: D18MC.1A5

tag: genotype

tag: ngene


title: 4 dpf CHT-NC rep1

tag: cell type

tag: Stage


title: VaD_TemporalCortex_Sample381_TechRep4

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_1_3.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 381 technical replicate #4


title: 27Heart

value: Migratory


title: D18MC.1A4

tag: nreads


title: VaD_TemporalCortex_Sample381_TechRep1

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_2_2.txt
VaD temporal cortex
Vascular dementia temporal cortex sample 381 technical replicate #1

tag: age


title: 4 dpf CHT-HSPC rep2


title: VaD_FrontalCortex_Sample444_TechRep2

description:
raw data file:
Counts_JB_141101_253949435351_S01_GE2_107_Sep09_2_2.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 444 technical replicate #2

tag: pmi


title: 26Heart


title: 4 dpf CHT-HSPC rep1


title: 3 mpf kidney-HSPC rep1


title: 25Heart


title: D18MC.1A2

tag: Sex


title: VaD_FrontalCortex_Sample381_TechRep4

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_1_4.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 381 technical replicate #4


title: D18MC.1A12

tag: plateplus


title: D18MC.1A3

tag: plate


title: VaD_FrontalCortex_Sample381_TechRep3

description:
raw data file:
Counts_JB_141203_253949435729_S01_GE2_107_Sep09_1_3.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 381 technical replicate #3


title: TMP195 1

first: Timothy

last: McKinsey

department: Division of Cardiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
FastQ files were aligned to RN6 using the ROPHAT2/Cufflinks pipline
Geometric method was used for normalization
Genes that had an expression greater than 1 were selected for future analysis
Significant differences were computed using a Mann-Whitney U test and corrected for multple comparisons. Gnes that had a p value of less than 0.05 were considered significant
Genome_build: RN6

organism: Rattus norvegicus

source_name: Left ventricule

growth_protocol: NRVMs were cultured in serum-free, nutridoma-supplemented DMEM

extract_protocol:
Total RNA was prepared using the Rneasy Plus Mini Kit (Qiagen)
Libraries were prepared using the Ovation® RNA-Seq SYSTEMS 1-16

treatment_protocol: NRVMs were treated with 3 μM TMP195 or DMSO for 48 hours before harvesting

value: neonatal primary cells

tag: treatment

value: 3 μM TMP195


title: VaD_FrontalCortex_Sample381_TechRep1

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_2_1.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 381 technical replicate #1


title: TMP195 2


title: 22Heart

tag: time


title: Vehicle 2

value: DMSO


title: VaD_FrontalCortex_Sample381_TechRep2

description:
raw data file:
Counts_JB_141101_253949435350_S01_GE2_107_Sep09_2_2.txt
VaD frontal cortex
Vascular dementia frontal cortex sample 381 technical replicate #2


title: 3 dpf CHT-NC rep2

source_name: zebrafish embryos

value: double negative cells

value: 3 dpf


title: D18MC.1A11

tag: lane


title: 19Heart

tag: migratory status


title: 24Heart


title: 4 dpf CHT-EC rep1

tag: tissue

value: endothelial cells


title: D18MC.1A10


title: 16Heart


title: Vehicle 1


title: 3 dpf CHT-NC rep1


title: D18MC.1A1


title: 4 dpf CHT-EC rep2


title: 14Heart


title: 3 dpf CHT-HSPC rep1

value: hematopoietic stem and progenitor cells


title: 12Heart


title: stage8, rep1

city: Berlin

first: Dijun

last: Chen

address: Philippstr. 13 (House 22)

department: Plant Cell and Molecular Biology

institute: Humboldt University

data_processing:
Reads were mapped to the A.thaliana genome (TAIR10) using Bowtie (version 1.1.2) with parameters “--threads 8 -n 2 -m 10 -k 1 --best --chunkmbs 256 -q”.
Redundant reads were removed using Picard tools (v2.60; http://broadinstitute.github.io/picard/). Peak-calling was performed using MACS2 (version 2.1.0). Duplicated reads were not considered (--keep-dup=1) during peak calling in order to achieve a better specificity
The “--mfold” parameter was set as “2-20” to build the model.
Peaks across replicates with an IDR ≤ 0.1 (https://sites.google.com/site/anshulkundaje/projects/idr) were retained.
Wiggle tracks were generated by DeepTools with the command “bamCoverage”; read coverage was normalized to 1x sequencing depth (also known as reads per genomic content, RPGC).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: Plants were grown in a phytotron growth chamber under long day conditions (22 °C daytime, 20°C at night).

extract_protocol:
Chromatin immunoprecipitation for H3K27ac modification was performed according to a published protocol with minor modifications (Kaufmann et al 2010; doi:10.1038/nprot.2009.244).
ChIP-seq libraries as well as control libraries that were based on “input” DNA were prepared using ThruPLEX DNA-seq kit (RUBICON GENOMICS, USA) following the manufacturer.

treatment_protocol: Inflorescences were treated with DEX- induction solution (2 μM Dexamethasone, 0.01% (v/v) ethanol, and 0.01% Silwet L-77) daily or 0.01% (v/v) ethanol, and 0.01% Silwet L-77 as control

tag: background ecotype

value: Ler

value: inflorescence

tag: developmental stage

value: stage 7-8 of flower development

tag: antibody

value: Anti-H3K27ac (Milipore Merck; catalog number:07-360; lot number 2322526)


title: 8Heart

value: Non-Migratory


title: HuRAKO2

city: Jinan

first: Wencheng

last: Zhang

state: Shandong

address: Wenhua Xi Road No.44

department: cardiology

institute: Qilu hospital

data_processing:
Off-Line Base Caller software, version 1 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRC38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of gene/transcript model per Million mapped fragments(FPKM) were got according to ballgown calculation.
Genome_build: GRCm38
Supplementary_files_format_and_content: excel files include FPKM values for each Sample

source_name: epididymal adipose tissue

extract_protocol:
epididymal adipose tissue were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: High-fat diet feeding for 16 weeks from the eight-week age

tag: strain

value: white adipose tissue

tag: genotype/variation


title: HuRAKO3


title: HuRAKO1


title: stage4, rep1

tag: genotype

value: stage 4-5 of flower development


title: stage4, rep2


title: stage2, rep2

value: stage 2 of flower development


title: 52 hpf CHT-NC rep2

value: zebrafish embryos

tag: cell type

tag: Stage

value: 52 hpf


title: 5Heart

value: Migratory


title: stage2, rep1


title: CTR2


title: 3 dpf CHT-HSPC rep2


title: 52 hpf CHT-NC rep1


title: CTR1


title: 3 dpf CHT-EC rep1


title: 36 hpf  NC rep2

value: 36 hpf


title: stage0, rep2

value: inflorescence meristem


title: shKdm5b_MNase_ESC

city: Detroit

first: Benjamin

last: Kidder

address: 4100 John R St

department: Oncology

institute: Wayne State University

description: MNase digested DNA

data_processing:
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
Danpos dpos function was used to generate wig files and nucleosome position difference files.
Genome_build: mm9
Supplementary_files_format_and_content: wig

growth_protocol: shLuc and shKdm5b ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
Cells were crosslinked with formaldehyde and subsequently treated with MNase. Mononucleosome sized fragments of MNase-digested DNA was subjected to library preparation.
MNase-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of custom Illumina adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: shRNA

value: ES cell


title: GFP-NoContact-B

description:
Ribo-depleted total RNA
Transwell_HTSeqCount.txt

data_processing:
Reads were aligned to the human reference genome, hg19, using HISAT2 v2.0.1beta
Reads mapping to annotated genes were quantified using HTSeq-0.6.1
Differential gene expression was determined using DESeq2 v1.22.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

growth_protocol: ER:Ras cells were co-cultured with GFP cells in a twelve well plate (GFP contact) and GFP cells on their own in the transwell of the same well (GFP no contact).

extract_protocol: Libraries were prepared from total-RNA sample using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina with the NEBNext rRNA Depletion kit

tag: cell line

tag: condition

value: GFP cells on their own


title: stage8, rep2


title: stage0, rep1


title: GFP-NoContact-C


title: 36 hpf  NC rep1

value: double negative cells


title: 11Heart


title: shLuc_MNase_ESC

description: MNase digested DNA


title: 36 hpf  HSPC rep2

value: hematopoietic stem and progenitor cells


title: GFP-NoContact-A


title: 3 dpf CHT-EC rep2

value: endothelial cells

value: 3 dpf


title: CTR3


title: negative control, rep2

description: Processed data available on GSM3092473.

value: Ler

value: inflorescence

value: stage 4 of flower development

value: none (input)


title: 36 hpf EC rep2


title: negative control, rep1


title: 36 hpf  HSPC rep1


title: GFP-Contact-B

value: ER:Ras cells were co-cultured with GFP cells


title: S3: Bisulfite_seq-sperm

city: Greensboro

first: Ramji

middle: Kumar

last: Bhandari

state: NC

address: 321 McIver St

institute: University of North Carolina Greensboro

data_processing: Bismark (Version: v0.19.0) was used to map bisulfite sequencing reads onto medaka genome (Ensembl release-89) with default parameters (Krueger and Andrews, 2011). To guarantee getting the most accurate mapping result, we only retained the reads being mapped on unique position of genome. The utility “bismark_methylation_extractor” wrapped in Bismark was used to extract methylation levels on each site.

organism: Oryzias latipes

growth_protocol: The medaka strain Hd-rR was used and maintained under standard conditions

extract_protocol:
Genomic DNA  from each sample was extracted using ZR-Duet™ DNA/RNA MiniPrep Plus kit (Zymo Research, D7003) according to the manufacturer’s instruction.
Whole genome bisulfite sequencing (WGBS) libraries were prepared with NEBNext® Ultra™ II FS DNA Library Prep Kit (NEB, E7805S) according to the manufacturer’s user manual.

value: Hd-rR

value: sperm


title: GFP-Contact-A

first: Nicola

last: Neretti

institute: Brown University


title: 36 hpf EC rep1

value: zebrafish embryos


title: S4: Bisulfite_seq-sperm


title: S2: Bisulfite_seq-sperm


title: 2Heart

value: Non-Migratory


title: aIFNAR1 treated_2

status: Public on Apr 22 2019

city: Chicago

first: Pablo

last: Penaloza-Macmaster

state: Illinois

address: 303 E. Chicago Avenue

department: Microbiology-Immunology

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to mm10 using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with read counts per gene

source_name: DbGP33+ CD8 T

growth_protocol: splenocytes were harvested in R10

extract_protocol:
Spleen cells were MACS sorted to isolate CD8 T cells by negative selection (STEMCELL kit). Then, DbGP33+ cells were FACS-sorted and resuspended in Trizol. RNA extraction was performed using the Agecourt RNA extraction kit as per the manufacter instructions, and extracted RNA was delivered to the NUSeq Core at Northwestern University in downtown Chicago.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LCMV mixed with 100 ug of IgG control (MOPC-21) or 100 ug aIFNAR (MAR1-5A3). Injections were intramuscularly (50uL per quadriceps)

tag: agent

value: 100 ug aIFNAR (MAR1-5A3)

value: DbGP33+ CD8 T


title: aIFNAR1 treated_5


title: IgG treated_2

value: IgG control


title: IgG treated_4


title: IgG treated_3


title: pUC57 AIRN G3

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

data_processing:
Pacbio reads were pre-processed into raw ccs reads using Pacbio SMRT Link v6.0 (default parameters).
Raw CCS reads were mapped using bismark v0.20.0 with the following parameters: -q --score-min L,0,-0.8 --rdg 2,1 --rfg 2,1 --ignore-quals.
Peaks were called using a sliding window algorithm with the following parameters: minimum cytosine conversion threshold of 55% and peak length of 30bp.
Genome_build: pUC57
Supplementary_files_format_and_content: bed files were generated using sliding window algorithm; Each row represents the coordinates of an R-loop peak in a specific read (read names are specified in column 4)

organism: Escherichia coli

source_name: bacterial cells

extract_protocol:
The plasmids were purified using the NucleoBond® XtraMidi kit (Macherey-Nagel) according to the manufacturer’s recommendations. DNA was transcribed in vitro using T3 RNA polymerase and was then treated with sodium bisulfite at non-denaturing condition using Zymo Lightning bisulfite modification kit.
Library was constructed using Pacific Biosciences protocol.

treatment_protocol: Airn and the Airn G-stretch mutant were synthesized (GeneCust) and cloned into pUC57. sum3 was amplified from genomic DNA using the forward primer Xba_sum3 FW that contains the sequence of the T3 promoter and the reverse primer Bam_sum3 RV and cloned into the pUC57 plasmid using standard protocols.


title: RB886_L4_160816_TGACCA

city: Haifa

first: Ayelet

last: Lamm

address: Technion st

country: Israel

institute: Technion

data_processing:
Filter sequences with irrelevant barcodes
Split relevant sequences by barcode
Remove the linker from each sequence. Trim additional 3 bases.
Merge identical reads.
Sequences were aligned to gene transcripts using Bowtie, aloowing multiple alignments.
DEseq package in R (http://www.r-project.org) was used from the data obtained from bowtie to identify differentially expressed genes.
Genome_build: WS220/ce10

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: worms were grown at 20°C on enriched NGM with OP50 as food

extract_protocol:
Synchronized Embryos or L4 larval worms were washed several times to avoid contamination with bacteria, snap-freezed at liquid nitrogen, and grinded to powder in a liquid nitrogen -prechilled mortar and pestle. High-molecular weight and Low-molecular weight RNA fractions were isolated using miRVana miRNA isolation kit Applied Biosystems (Ambion).
libraries were prepared from the high molecular weight fraction by means of SMARTer® Stranded RNA-Seq Kit (Clontech Laboratories) after ribosomal depletion by Ribozero kit (Epicenter)

treatment_protocol: Embryos were isolated from gravid N2 adults by treatment with sodium hypochlorite solution. To obtain synchronized L4 worms, embryos were incubated in M9 media without food at 20 °C for 24h. Hutched synchronized L1 were grown until they reached L4 larval stage.

tag: bio replicate no


title: RB886_E_15_12_16_TTAGGC

value: Embryo


title: pUC57 AIRN WT

value: wild-type


title: aIFNAR1 treated_3


title: IgG treated_1


title: RB886_embryo_110916_CGATGT


title: RB886_E_11_9_16_ACAGTG


title: RB886_L4_20_9_16_TGACCA


title: GFP-Contact-C

city: Providence

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry


title: N2_L4_AYYA_TTAGGC


title: N2_L4_220816_ATCACG


title: aIFNAR1 treated_4


title: N2_embryo_111216_TAGCTT


title: N2_E_15_9_16_CGATGT


title: N2_E_15_12_16_CGATGT


title: aIFNAR1 treated_1


title: RB886_L4_Ayya_GCCAAT


title: BB3_L4_10_10_16_ACTTGA


title: BB3_L4_Ayya_CTTGTA


title: N2_L4_18_9_16_ATCACG


title: BB2_L4_230816_CAGATC


title: BB2_L4_221216_ACAGTG


title: BB3_embryo_011216_TAGCTT


title: BB3_embryo_230816_ACAGTG


title: BB19_L4_6_10_16_TAGCTT


title: BB2_embryo_070916_TTAGGC


title: BB2_L4_Ayya_ATCACG


title: BB3_E_19_12_16_GATCAG


title: BB3_L4_160816_GATCAG


title: BB2_E_18_12_16_CAGATC


title: N2_embryo_230816_ATCACG


title: BB19_embryo_310816_TTAGGC


title: BB19_L4_Ayya_GGCTAC


title: TKO

city: Suzhou

first: Xing

last: Fang

state: Jiangsu

address: 708 Renmin Rd

department: Institute for Cardiovascular Science

institute: Soochow University

data_processing:
Basecalls were performed using CASAVA software.
Raw data (raw reads) of fastq format were further processed including removing reads containing adapter, reads containing ploy-N and low quality reads from raw data to obtain a clean data (clean reads).
Index of the reference genome was built and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The reads numbers mapped to each gene were counted by FeatureCounts v1.5.0-p3. Finally, FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene names and FPKM values for each Sample

source_name: hESC derived cells

growth_protocol: Human embryonic stem cell line H1 was routinely maintained in PSCeasy® medium (Cellapy, China) on Matrigel-coated plates (Corning, USA) and passaged every 4 days using 0.5 mM EDTA.

extract_protocol:
Total RNAs were isolated using a TRIzol Reagent® (Sigma-Aldrich, USA) from cells derived from both th MIR148A-TKO and wild-type (WT) hESCs on day 4 of cardiac differentiation. A total amount of 3 µg RNAs per sample was subjected to library preparation and RNA sequencing on an Illumina Hiseq platform (Illumina, USA)
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: hESCs were grown to about 85% confluence and subsequently differentiated for 4 days following the small-molecule-based monolayer method described previously (Cell Stem Cell. 2015 Jul 2;17(1):89-100).

value: hESC-differentiated cells on day 4

value: Day 4 of Cardiac differentiation

value: triple knockout of MIR148A family members


title: CTR

value: wild type