title: Sample4323


title: Sample4322

status: Public on Feb 01 2021

type: SRA

city: Houston

first: Hongjie

last: Li

state: TX

address: one Baylor Plaza

country: USA

institute: Baylor College of Medicine

description:
single cell or single nucleus
ORN_all.h5ad

library_source: transcriptomic

data_processing:
de-mutiplexd (bcl2fastq 2.19.0.316)
alignment (STAR 2.5.4)
gene count (HTseq 0.11.2, default settings except ‘‘-m  536 intersection-strict’)
normalization (gene counts were rescaled to counts per million reads (CPM), and log transformed to Log2(CPM+1) for processed data)
filtering (cells with fewer than 100,000 uniquely mapped reads were excluded, and cells with high expression of neuronal markers are retained for processed data)
Genome_build: Dmel r6.10
Supplementary_files_format_and_content: annotated .h5ad files of high-quality neurons

molecule: total RNA

organism: Drosophila melanogaster

source_name: FACS sorted olfactory receptor neurons

extract_protocol:
Modified SMART-seq2 (Li et al. 2017)
Modified SMART-seq2 (Li et al. 2017)

tag: number of cells


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title: E3 AF-15

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

organism: Homo sapiens

source_name: Amniotic fluid

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

extract_protocol: RNA samples were extracted from amniotic fluid using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

tag: age

value: 37 years

tag: Sex

value: Female

tag: histrogical diagnosis of placenta

value: non-Chorionitis


title: C3 AF-08

value: 36 years

value: Chorionitis


title: E1 AF-13

value: 38 years


title: E2 AF-14


title: Sample9


title: D2 AF-10

value: 26 years


title: D4 AF-12

value: 23 years


title: D1 AF-09

value: 35 years


title: Sample7


title: coronary artery, severe_diabetic, rep3

city: Boston

first: Stefan

last: Haemmig

state: MA

address: 77 Avenue Louis Pasteur, NRB-742

department: Medicine

institute: Brigham and Women Hospital / Harvard Medical School

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality (error rate < 0.05) at the end
After trimming, sequence reads shorter than 50 nucleotides were discarded
Remaining sequence reads were aligned to the Sus scrofa reference genome with CLC Genomics Server program
After mapping and total gene hit counts calculation using CLC Genomics workbench, the total gene hit counts table was used for downstream differential expression analysis using DESeq2
Genes with adjusted p-value < 0.1 and Log2Fold change >1 were called as differentially expressed genes for each comparison (please refer attached excel table for list of all the genes and associated Log2 fold changes).
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: xlsx, differential gene expression (DESeq2)

organism: Sus scrofa

source_name: coronary artery, severe_diabetic

growth_protocol: in vivo samples

extract_protocol:
Trizol RNA isolation
poly-A selection, fragmentation and random priming, frist and second-strad cDNA synthesis, end-repair, phosphorylation and A-tailing, adapter ligation, PCR amplifciation, sequencing

tag: breed

value: Yorkshire

tag: disease state

value: atherosclerosis = severe

value: diabetic status = yes

tag: tissue

value: coronary artery segments


title: coronary artery, severe_diabetic, rep4


title: coronary artery, severe_diabetic, rep2


title: coronary artery, moderate_diabetic, rep5

source_name: coronary artery, moderate_diabetic

value: atherosclerosis = moderate


title: coronary artery, moderate_diabetic, rep4


title: Sample3


title: B2 AF-04

value: Chorioamnionitis


title: A2 AF-02

value: 28 years


title: coronary artery, moderate_diabetic, rep6


title: B1 AF-03

value: 31 years


title: A1 AF-01

value: 37 years


title: coronary artery, moderate_diabetic, rep3


title: coronary artery, moderate_diabetic, rep2


title: B3 AF-05

value: Female


title: C2 AF-07

value: 39 years


title: C1 AF-06


title: coronary artery, severe_non_diabetic, rep5

source_name: coronary artery, severe_non_diabetic


title: coronary artery, moderate_diabetic, rep1


title: D3 AF-11

value: 30 years


title: coronary artery, severe_non_diabetic, rep4

value: diabetic status = no


title: coronary artery, severe_non_diabetic, rep1


title: coronary artery, severe_non_diabetic, rep2


title: coronary artery, moderate_non_diabetic, rep2

source_name: coronary artery, moderate_non_diabetic


title: coronary artery, severe_diabetic, rep1


title: coronary artery, moderate_non_diabetic, rep1


title: coronary artery, mild_non_diabetic, rep4

source_name: coronary artery, mild_non_diabetic

value: atherosclerosis = mild


title: coronary artery, mild_non_diabetic, rep3


title: coronary artery, moderate_non_diabetic, rep4


title: coronary artery, moderate_non_diabetic, rep3


title: FFC group liver 320_440

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: genomic

data_processing:
Raw sequencing reads were processed using cutadapt (V2.10), with more than 30% ‘N’s or quality value less than 20 in over 10% of the sequences were discarded for subsequent analysis
The clean reads were aligned to the pig reference genome (NCBI build Sscrofa11.1) by the bisulfite sequence MAPping program (BSMAP V2.73) with up to 4 mismatches and 2 continuous gaps.
Genome_build: NCBI build Sscrofa11.1
Supplementary_files_format_and_content: bed format; each file represents CHH/CHG/CG methylation level generated from BSMAP

molecule: genomic DNA

source_name: liver

growth_protocol: All the minipigs had free access to bedding material and fresh drinking water at all times. Before termination, the minipigs were fasted overnight and then euthanized by exsanguination in general of anaesthesia by a mixture of zolazepam, tiletamine, ketamine, xylazine and butorphanol as described by a previous study.

extract_protocol:
Genomic DNA was extracted from the liver tissue using the DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer’s instructions.
LHC-BS strategy

treatment_protocol: Samples from liver lobe (SM) were collected, snap frozen in liquid nitrogen and kept at -80 °C for subsequent analysis of the DNA methylation and expression studies.

tag: diet

value: FFC group


title: coronary artery, mild_non_diabetic, rep2


title: FFC group liver 319_875


title: coronary artery, mild_non_diabetic, rep1


title: FFC group liver 319_799


title: FFC group liver 319_798


title: FFC group liver 319_239


title: FFC group liver 221_538


title: FFC group liver 319_035


title: FFC group liver 319_389


title: FFC/SD group liver 319_869

value: FFC/SD group


title: FFC/SD group liver 319_797


title: FFC/SD group liver 319_810


title: FFC group liver 221_497


title: coronary artery, severe_non_diabetic, rep3


title: FFC/SD group liver 319_791


title: FFC/SD group liver 319_343


title: FFC/SD group liver 319_471


title: FFC/SD group liver 320_328


title: FFC/SD group liver 319_796


title: FFC/SD group liver 222_171


title: FFC/SD group liver 221_644


title: SD group liver 319_411

value: SD group


title: SD group liver 319_340


title: FFC/SD group liver 221_504


title: SD group liver 319_922


title: FFC/SD group liver 319_048


title: SD group liver 319_860


title: SD group liver 319_207


title: FFC group liver 221_510


title: SD group liver 319_778


title: SD group liver 319_427


title: LNCaP_TMF2_9_3

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to hg38 with STAR software then raw counts were computed with featureCounts for each gene in each sample.
Data normalization and selection of differentially expressed genes was performed according to DESeq2 methodology.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes  ENSEMBL id  and raw counts for each gene, in each sample

source_name: LNCaP cells

extract_protocol:
RNAeasy mini columns (from QIAGEN) following vendor instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate; derived from metastatic site:left supraclavicular lymph node

tag: shRNA


title: LNCaP_TMF2_4_3


title: LNCaP_TMF2_3_3


title: LNCaP_TMF2_9_2


title: LNCaP_TMF2_9_1


title: LNCaP_TMF2_4_2


title: LNCaP_TMF2_4_1


title: LNCaP_TMF2_3_2


title: LNCaP_TMF2_3_1


title: LNCaP_Scr_1

value: shScramble


title: LNCaP_Scr_2


title: LNCaP_L3_3


title: LNCaP_L3_1


title: LNCaP_L3_2


title: RNA-seq_MOLM-13_MPP8-KO-2_rep3

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human  reference (hg 38) genome by STAR.
Gene and repetitive element counts were quantified with featureCount. Repetitive elements annotated by Repeat Masker. Read counts of each repeat family were calculated by the summation of individual read counts from the same repeat family.
Differential gene-repeat expression analyses were performed using DEseq2.
Genome_build: hg38
Supplementary_files_format_and_content: text file of gene read count values

growth_protocol: Human leukemia cells MOLM-13 were cultured in RPMI-1640 medium containing 10% FBS and 1% penicillin/streptomycin. Cultures were incubated at 37°C in 5% CO2.

extract_protocol: For RNA-seq analysis using the illumina NextSeq500, 0.1-1 ug of total RNA was processed for library generation using the NEBNext® Ultra™ II Directional RNA Library Prep Kit following the manufacturer’s protocol.

tag: cell line

tag: cell type

value: human myeloid leukemia cell line

tag: genotype/variation

value: MPHOSPH8 (MPP8) KO


title: RNA-seq_MOLM-13_MPP8-KO-2_rep2


title: RNA-seq_MOLM-13_MPP8-KO-2_rep1


title: RNA-seq_MOLM-13_MPP8-KO-1_rep2


title: RNA-seq_MOLM-13_MPP8-KO-1_rep3


title: RNA-seq_MOLM-13_Control_rep1

value: control


title: ChIP-seq_MOLM-13-MPP8-KO_MPP8_16796_AP_rep3

data_processing:
ChIP-seq raw reads were aligned to the hg38 genome assembly using Bowtie2 with the default parameters
Bigwig files were generated by deepTools  bamCoverage with the parameters  of  --normalizeUsing RPGC --extendReads 200
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 1-10 ng of ChIP DNA was processed for library generation using the NEBNext Ultra II DNA Library Prep kit following the manufacturer’s protocol (New England Biolabs).

tag: chip antibody


title: RNA-seq_MOLM-13_Control_rep3


title: RNA-seq_MOLM-13_Control_rep2


title: ChIP-seq_MOLM-13-MPP8-KO_MPP8_16796_AP_rep2


title: ChIP-seq_MOLM-13_MPP8_16796_AP_rep2


title: ChIP-seq_MOLM-13-MPP8-KO_MPP8_16796_AP_rep1


title: RNA-seq_MOLM-13_MPP8-KO-1_rep1


title: ChIP-seq_MOLM-13_MPP8_16796_052_rep2


title: ChIP-seq_MOLM-13_MPP8_16796_AP_rep1


title: LNCaP_Scr_3


title: ChIP-seq_MOLM-13_MPP8_16796_051_rep1


title: ChIP-seq_MOLM-13_MPP8_16796_051_rep2


title: ChIP-seq_MOLM-13_MPP8_16796_052_rep1


title: ChIP-seq_MOLM-13_H3K9me3_rep1


title: ChIP-seq_MOLM-13_H3K9me3_rep2