title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G11_AD004_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G11_AD002_indexed

status: Public on Aug 25 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PIR

tag: Sex

value: male

tag: age

tag: strain


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G10_AD008_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G10_AD010_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G10_AD012_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G11_AD012_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G10_AD006_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G11_AD008_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G2_AD001_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G11_AD007_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G12_AD008_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G10_AD004_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F9_AD007_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F9_AD012_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G10_AD002_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F8_AD008_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F8_AD010_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F8_AD012_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F7_AD008_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F9_AD004_indexed


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title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F8_AD002_indexed


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title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F7_AD006_indexed


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title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F8_AD001_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F7_AD001_indexed


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title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F11_AD002_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_G10_AD001_indexed


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title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E8_AD010_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E8_AD006_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E8_AD001_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E7_AD010_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E7_AD007_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E7_AD012_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F11_AD007_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_F11_AD001_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E8_AD002_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E7_AD004_indexed


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title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E6_AD007_indexed


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title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E5_AD006_indexed


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title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E8_AD008_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E4_AD006_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E3_AD008_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E4_AD010_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E5_AD008_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E5_AD004_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E4_AD008_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E4_AD012_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E4_AD004_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E5_AD002_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E5_AD007_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E4_AD007_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E3_AD004_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E4_AD002_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E3_AD010_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E2_AD010_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E3_AD007_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E3_AD001_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E2_AD007_indexed


title: 180405_CEMBA_mm_P56_P63_4F_CEMBA180329_4F_1_CEMBA180329_4F_2_E3_AD002_indexed


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title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C11_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C11_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C11_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C11_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C10_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C10_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C10_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B9_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B9_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C10_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C2_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B9_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C2_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B9_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C10_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B9_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B9_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B9_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_C10_AD004_indexed


title: Li13649: CkoWt190

city: Calgary

first: Carol

last: Huang

state: AB

address: 3330 Hospital Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

library_source: transcriptomic

data_processing:
Libraries were sequenced on the Illumina NextSeq 550 System
Sequences obtained were aligned to the mouse transcriptome with Kallisto 0.42.4
Transcript counts were normalized as FPKM
Gene counts were generated but adding the transcript counts per gene
Genome_build: NCBI RefSeq transcript database (2017 version)
Supplementary_files_format_and_content: Abundance tables by transcript and gene

molecule: total RNA

source_name: maternal islet cells

extract_protocol:
After distention with collagenase P (0.66mg/ml in Hank’s Balanced Salt Solution, 2.5ml/pancreas) the pancreas was removed, agitated at 37 degrees celcius for 15 min and then islets were hand-picked. Total RNA was isolated with RNeasy Mini Kit (Qiagen) from 100–200 islets/mouse.
Library preparation was completed with NEBNext®Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina by the UCDNA Services, Cumming School of Medicine, University of Calgary

tag: knock-out tisse

value: pancreatic beta cells

tag: pregnancy stage

value: 15 days

tag: tissue

value: maternal islet cells


title: Li13650: CkoWt236


title: Li13651: CkoWt285


title: Li13655: Prlr950

value: all tissues


title: Li13652: CkoWt294


title: Li13656: Prlr951


title: Human_con_skin

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 500 Newton Road

department: Dermatology

institute: University of Iowa

data_processing:
Basecalls were converted into FASTQs using the Illumina bcl2fastq software by the University of Iowa Genomics Division
10x data was processed with the Cell Ranger pipeline, version 3.1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited tsv files for genes and cell barcodes, mtx single-cell expression matrix, csv of CDR3 contig sequences

molecule: polyA RNA

organism: Homo sapiens

source_name: Skin

extract_protocol:
CD45+ immune cell populations were flow sorted in parallel. Single-cell suspensions were processed with the Chromium Single Cell 5-prime Library & Gel Bead Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin

tag: condition

value: control


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B8_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B8_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B8_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B9_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B7_AD008_indexed


title: Li13653: Prlr943


title: CD34+ differentiation Day12-2

city: bethesda

first: Xiang

last: Guo

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to hg38 and mm10  whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.22.1
Genome_build: hg38 , mm10
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each Sample ...

source_name: human CD34+ cells

growth_protocol: Primary CD34+ umbilical cord cells were obtained from Lonza (cat. 2C-101) and were cultured as described (Wilber et al., 2010). Control C57BL/6J and Eto2 KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E8.5 and E12.5 control and knockout mice.

extract_protocol:
Total RNA was isolated using the Purelink RNA Mini Kit and PicoPure RNA isolation kit.
RNA sequencing libraries were generating from 1 ug total RNA from mouse E8.5 yolk sac/E12.5 fetal liver cells,  or 10 ng total RNA from CD34+ cord blood cells, respectively, using the Illumina TruSeq Stranded mRNA Library Preparation kit (20020594) following manufacturer’s protocol.

tag: cell type

value: CD34+ cells

tag: differentiation day

value: day 12

tag: genotype

value: WT


title: CD34+ differentiation Day8-1

value: day 8


title: CD34+ differentiation Day12-1


title: CD34+ differentiation Day10-1

value: day 10


title: CD34+ differentiation Day10-2


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B7_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B8_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B7_AD010_indexed


title: CD34+ differentiation Day8-2


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B7_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B5_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B8_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B5_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B7_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B4_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B8_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B4_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B4_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B5_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B4_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B5_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B4_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B3_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B3_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B4_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B2_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B3_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B3_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B3_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B7_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B3_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B2_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B2_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B7_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B5_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B2_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B5_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B2_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B2_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B2_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B1_AD012_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B2_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B1_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B1_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B1_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B12_AD007_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B1_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B1_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B12_AD004_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B12_AD006_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B1_AD001_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B12_AD012_indexed


title: NS2-corr2 iPSC-CMs d71 A

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Demultiplexing of the intensity files using bcl2fastq v2.20.0.422. Quality check was done via fastqc (v. 0.11.5, Babraham Bioinformatics)
Read alignment was performed using STAR aligner (v2.5.2a)
Read counting was performed using featureCounts (v1.5.0-p1)
Differential expression analysis was run using DESeq2 R package (version 1.24.0)
Genome_build: hg38 gene version 96
Supplementary_files_format_and_content: tab-delimited text files with raw read count for each gene in each sample

source_name: cardiomyocytes

growth_protocol: Human iPSC lines were maintained on Matrigel-coated (growth factor reduced, BD Biosciences) plates, passaged every 4-6 days with Versene solution (Thermo Fisher Scientific) and cultured in StemMACS iPS-Brew XF medium (Miltenyi Biotech) supplemented with 2 µM Thiazovivin (Merck Millipore) for 24 hr after passaging with daily medium change. Cell cultures were incubated in a humidiﬁed incubator with 5% CO¬2 and 21% O¬2 at 37°C. Directed differentiation of iPSCs into iPSC-CMs was initiated at confluence of 80-90% in Matrigel-coated plates with cardio differentiation medium composed of RPMI 1640 with Glutamax and HEPES (Thermo Fisher Scientific), 0.5 mg/ml human recombinant albumin (Sigma-Aldrich) and 0.2 mg/ml L-ascorbic acid 2-phosphate (Sigma-Aldrich) and sequential treatment with 4 µM CHIR99021 (Merck Millipore) for 48 h and 5 µM IWP2 (Merck Millipore) for further 48 h. Medium was changed to cardio culture medium composed of RPMI 1640 with Glutamax and HEPES and 2% B27 (Thermo Fisher Scientific) at day 8 with medium change every other day. Differentiated cultures around day 15 were digested with collagenase B (Worthington Biochemical) or 0.25% Trypsin/EDTA (Thermo Fisher Scientific) and replated at lower density (1:2-1:3) in Matrigel-coated plates. Metabolic selection of iPSC-CMs was performed using cardio selection medium composed of RPMI 1640 without glucose (Thermo Fisher Scientific), 0.5 mg/ml human recombinant albumin, 0.2 mg/ml L-ascorbic acid 2-phosphate and 4 mM lactate (Sigma-Aldrich) for 5 days. The iPSC-CMs were cultured in cardio culture medium at least to day 60 for further maturation.

extract_protocol:
Total RNA of iPSC-CM cultures was isolated using the SV Total RNA Isolation System (Promega) according to the manufacturer’s instructions.
RNA-seq libraries were performed using a modified non strand-specific, massively-parallel cDNA sequencing (RNA-Seq) protocol from Illumina starting with 200 ng RNA. The TruSeq RNA Library Preparation Kit v2, Set A (48 samples, 12 indexes; Illumina) was used. Quality and integrity of RNA was determined with the Fragment Analyzer (Agilent) (RIN > 8). The size of final cDNA libraries was determined by using the dsDNA 905 Reagent Kit (Agilent) exhibiting a sizing of 260 bp in average. Libraries were pooled and sequenced on an Illumina HiSeq 4000 (Illumina) generating 50 bp single-end reads (30-40 Mio reads/sample).

value: iPSC-derived cardiomyocytes

tag: cell line

value: isHOCMx2-corr33-A (UMGi031-A-1.33-A)

tag: maturity


title: NS2-corr1 iPSC-CMs d74 B

value: isHOCMx2-corr02-A (UMGi031-A-1.02-A)


title: NS2-corr1 iPSC-CMs d64 A


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B12_AD010_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B12_AD001_indexed


title: NS1-corr2 iPSC-CMs d60 B

value: isHOCMx1-corr34 (UMGi030-A-1.34)


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B11_AD007_indexed

value: PIR


title: NS1-corr2 iPSC-CMs d62 A


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B11_AD001_indexed

value: male


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B11_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B12_AD002_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B1_AD002_indexed


title: NS1-corr1 iPSC-CMs d60 B

value: isHOCMx1-corr4 (UMGi030-A-1.4)


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B12_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B11_AD004_indexed


title: NS2-1 iPSC-CMs d61 A

value: isHOCMx2.3 (UMGi031-A.3)


title: NS2-1 iPSC-CMs d61 B


title: NS1-1 iPSC-CMs d63 A


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B10_AD008_indexed


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B11_AD010_indexed


title: NS1-1 iPSC-CMs d60 B


title: 180408_CEMBA_mm_P56_P63_3E_CEMBA180326_3E_3_CEMBA180326_3E_4_B10_AD007_indexed


title: NS2-2 iPSC-CMs d60 #2

data_processing:
Demultiplexing of the intensity files using bcl2fastq version 2.17.1.14. Quality check was done via fastqc (v. 0.11.5, Babraham Bioinformatics)
Read alignment was performed using STAR aligner (v2.5.2a)
Read counting was performed using featureCounts (v1.5.0-p1)
Differential expression analysis was run using DESeq2 R package (version 1.24.0)
Genome_build: hg38 gene version 96
Supplementary_files_format_and_content: tab-delimited text files with raw read count for each gene in each sample

growth_protocol: Human iPSC lines were maintained on Matrigel-coated (growth factor reduced, BD Biosciences) plates, passaged every 4-6 days with Versene solution (Thermo Fisher Scientific) and cultured in StemMACS iPS-Brew XF medium (Miltenyi Biotech) supplemented with 2 µM Thiazovivin (Merck Millipore) for 24 hr after passaging with daily medium change. Cell cultures were incubated in a humidiﬁed incubator with 5% CO¬2 and 21% O¬2 at 37°C. Directed differentiation of iPSCs into iPSC-CMs was initiated at confluence of 80-90% in Matrigel-coated plates with cardio differentiation medium composed of RPMI 1640 with Glutamax and HEPES (Thermo Fisher Scientific), 0.5 mg/ml human recombinant albumin (Sigma-Aldrich) and 0.2 mg/ml L-ascorbic acid 2-phosphate (Sigma-Aldrich) and sequential treatment with 4 µM CHIR99021 (Merck Millipore) for 48 h and 5 µM IWP2 (Merck Millipore) for further 48 h. Medium was changed to cardio culture medium composed of RPMI 1640 with Glutamax and HEPES and 2% B27 (Thermo Fisher Scientific) at day 8 with medium change every other day. Differentiated cultures around day 15 were digested with collagenase B (Worthington Biochemical) or 0.25% Trypsin/EDTA (Thermo Fisher Scientific) and replated at lower density (1:2-1:3) in Matrigel-coated plates. Metabolic selection of iPSC-CMs was performed using cardio selection medium composed of RPMI 1640 without glucose (Thermo Fisher Scientific), 0.5 mg/ml human recombinant albumin, 0.2 mg/ml L-ascorbic acid 2-phosphate and 4 mM lactate (Sigma-Aldrich) for 5 days. The iPSC-CMs were cultured in cardio culture medium to day 60 for further maturation.

value: isHOCMx2.8 (UMGi031-A.8)