title: PIT_P5-PIT_P6-C10-AD007


title: PIT_P5-PIT_P6-C10-AD006

status: Public on Feb 23 2021

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/6 Male, brain dissected in P56

extract_protocol:
The snmC-seq2 protocol was applied to individual nuclei isolated from pituitary pooled from 30 adult male C57BL/6 mice
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: tissue

value: Pituitary

tag: age

tag: strain

tag: Sex

value: male


title: PIT_P7-PIT_P8-H6-AD012


title: PIT_P7-PIT_P8-E6-AD007


title: PIT_P3-PIT_P4-H6-AD004


title: PIT_P1-PIT_P2-B11-AD004


title: PIT_P5-PIT_P6-E9-AD006


title: PIT_P3-PIT_P4-H2-AD012


title: PIT_P3-PIT_P4-E5-AD008


title: PIT_P1-PIT_P2-E9-AD006


title: PIT_P7-PIT_P8-H3-AD002


title: PIT_P1-PIT_P2-E10-AD007


title: PIT_P7-PIT_P8-H2-AD004


title: PIT_P3-PIT_P4-A7-AD008


title: PIT_P5-PIT_P6-E1-AD001


title: PIT_P1-PIT_P2-D5-AD004


title: PIT_P7-PIT_P8-C6-AD002


title: PIT_P5-PIT_P6-E2-AD004


title: PIT_P3-PIT_P4-G5-AD004


title: PIT_P3-PIT_P4-F10-AD002


title: PIT_P7-PIT_P8-C5-AD012


title: PIT_P5-PIT_P6-A1-AD001


title: PIT_P7-PIT_P8-D7-AD006


title: PIT_P7-PIT_P8-A6-AD002


title: PIT_P7-PIT_P8-H12-AD002


title: PIT_P5-PIT_P6-B8-AD012


title: PIT_P7-PIT_P8-G5-AD006


title: PIT_P5-PIT_P6-H9-AD012


title: PIT_P3-PIT_P4-H5-AD007


title: PIT_P7-PIT_P8-G7-AD012


title: PIT_P1-PIT_P2-G7-AD006


title: PIT_P1-PIT_P2-C12-AD004


title: PIT_P1-PIT_P2-F12-AD002


title: PIT_P5-PIT_P6-H3-AD002


title: PIT_P1-PIT_P2-C3-AD008


title: PIT_P5-PIT_P6-H7-AD004


title: PIT_P5-PIT_P6-D8-AD007


title: PIT_P3-PIT_P4-D11-AD004


title: PIT_P1-PIT_P2-E1-AD006


title: PIT_P1-PIT_P2-B8-AD010


title: PIT_P1-PIT_P2-F4-AD008


title: PIT_P5-PIT_P6-H12-AD007


title: PIT_P5-PIT_P6-C11-AD002


title: PIT_P1-PIT_P2-G3-AD007


title: PIT_P3-PIT_P4-D4-AD006


title: PIT_P1-PIT_P2-B11-AD006


title: PIT_P7-PIT_P8-D1-AD012


title: PIT_P7-PIT_P8-H3-AD012


title: PIT_P1-PIT_P2-A8-AD007


title: PIT_P7-PIT_P8-A5-AD007


title: PIT_P3-PIT_P4-B6-AD001


title: PIT_P5-PIT_P6-F8-AD004


title: PIT_P5-PIT_P6-H2-AD006


title: PIT_P3-PIT_P4-A3-AD010


title: PIT_P3-PIT_P4-E11-AD001


title: PIT_P3-PIT_P4-H4-AD002


title: PIT_P5-PIT_P6-E10-AD007


title: PIT_P7-PIT_P8-G4-AD004


title: PIT_P5-PIT_P6-D2-AD008


title: PIT_P5-PIT_P6-G5-AD004


title: PIT_P3-PIT_P4-H12-AD007


title: PIT_P5-PIT_P6-B10-AD007


title: PIT_P3-PIT_P4-A8-AD006


title: PIT_P7-PIT_P8-B9-AD007


title: PIT_P5-PIT_P6-E1-AD004


title: PIT_P1-PIT_P2-B7-AD006


title: PIT_P3-PIT_P4-F4-AD001


title: PIT_P1-PIT_P2-D2-AD010


title: PIT_P7-PIT_P8-E10-AD008


title: PIT_P3-PIT_P4-F12-AD007


title: PIT_P1-PIT_P2-B8-AD004


title: PIT_P5-PIT_P6-F12-AD006


title: PIT_P7-PIT_P8-H5-AD006


title: PIT_P3-PIT_P4-D1-AD002


title: PIT_P5-PIT_P6-B12-AD008


title: PIT_P7-PIT_P8-F2-AD010


title: PIT_P1-PIT_P2-F1-AD012


title: PIT_P5-PIT_P6-E5-AD002


title: PIT_P3-PIT_P4-H5-AD004


title: PIT_P7-PIT_P8-F8-AD002


title: PIT_P5-PIT_P6-H1-AD006


title: PIT_P3-PIT_P4-F12-AD002


title: PIT_P1-PIT_P2-H12-AD001


title: PIT_P7-PIT_P8-A2-AD008


title: PIT_P5-PIT_P6-E8-AD007


title: PIT_P1-PIT_P2-G5-AD010


title: PIT_P3-PIT_P4-A2-AD008


title: PIT_P5-PIT_P6-A1-AD012


title: PIT_P7-PIT_P8-G10-AD010


title: PIT_P1-PIT_P2-E6-AD012


title: PIT_P7-PIT_P8-C4-AD002


title: PIT_P3-PIT_P4-B5-AD008


title: PIT_P1-PIT_P2-H12-AD010


title: PIT_P5-PIT_P6-B11-AD001


title: PIT_P1-PIT_P2-C6-AD007


title: PIT_P3-PIT_P4-A11-AD012


title: PIT_P5-PIT_P6-C3-AD008


title: PIT_P5-PIT_P6-G2-AD002


title: PIT_P3-PIT_P4-C2-AD010


title: PIT_P1-PIT_P2-H12-AD002


title: PIT_P7-PIT_P8-D8-AD006


title: PIT_P1-PIT_P2-A3-AD012


title: PIT_P3-PIT_P4-G6-AD001


title: PIT_P7-PIT_P8-D2-AD004


title: PIT_P5-PIT_P6-G4-AD006


title: PIT_P7-PIT_P8-D5-AD007


title: PIT_P5-PIT_P6-B6-AD008


title: PIT_P3-PIT_P4-E4-AD008


title: PIT_P3-PIT_P4-D12-AD012


title: PIT_P7-PIT_P8-A2-AD002


title: PIT_P3-PIT_P4-D3-AD010


title: PIT_P7-PIT_P8-D5-AD012


title: PIT_P1-PIT_P2-E6-AD010


title: PIT_P7-PIT_P8-A8-AD004


title: PIT_P1-PIT_P2-H1-AD010


title: PIT_P7-PIT_P8-B11-AD002


title: PIT_P5-PIT_P6-D3-AD010


title: PIT_P3-PIT_P4-C3-AD012


title: PIT_P7-PIT_P8-F4-AD002


title: PIT_P3-PIT_P4-A8-AD004


title: PIT_P3-PIT_P4-F2-AD001


title: PIT_P5-PIT_P6-B5-AD002


title: PIT_P5-PIT_P6-D4-AD004


title: PIT_P3-PIT_P4-D6-AD006


title: PIT_P5-PIT_P6-C2-AD007


title: PIT_P5-PIT_P6-C1-AD006


title: PIT_P1-PIT_P2-B6-AD006


title: PIT_P3-PIT_P4-B8-AD012


title: PIT_P5-PIT_P6-F4-AD004


title: PIT_P5-PIT_P6-A5-AD006


title: PIT_P7-PIT_P8-F1-AD006


title: PIT_P7-PIT_P8-H1-AD004


title: PIT_P3-PIT_P4-A6-AD010


title: PIT_P7-PIT_P8-C9-AD008


title: PIT_P5-PIT_P6-E11-AD001


title: PIT_P7-PIT_P8-A1-AD008


title: PIT_P7-PIT_P8-E5-AD006


title: PIT_P7-PIT_P8-E6-AD002


title: PIT_P3-PIT_P4-B8-AD008


title: PIT_P3-PIT_P4-C11-AD012


title: PIT_P5-PIT_P6-F10-AD004


title: PIT_P7-PIT_P8-H10-AD006


title: PIT_P5-PIT_P6-F7-AD007


title: PIT_P5-PIT_P6-F2-AD008


title: PIT_P1-PIT_P2-A11-AD002


title: PIT_P7-PIT_P8-C4-AD004


title: PIT_P5-PIT_P6-C9-AD004


title: PIT_P5-PIT_P6-D3-AD007


title: PIT_P5-PIT_P6-G11-AD008


title: PIT_P1-PIT_P2-G10-AD008


title: PIT_P7-PIT_P8-C7-AD002


title: PIT_P5-PIT_P6-F4-AD006


title: PIT_P3-PIT_P4-H6-AD007


title: PIT_P1-PIT_P2-B9-AD002


title: PIT_P7-PIT_P8-C9-AD004


title: PIT_P5-PIT_P6-B6-AD012


title: PIT_P7-PIT_P8-D12-AD004


title: PIT_P5-PIT_P6-C4-AD002


title: PIT_P3-PIT_P4-B9-AD001


title: PIT_P5-PIT_P6-G2-AD008


title: PIT_P5-PIT_P6-B3-AD010


title: PIT_P3-PIT_P4-A7-AD002


title: PIT_P5-PIT_P6-E7-AD001


title: PIT_P1-PIT_P2-F10-AD006


title: PIT_P1-PIT_P2-H1-AD007


title: PIT_P7-PIT_P8-C10-AD012


title: PIT_P1-PIT_P2-C10-AD007


title: PIT_P1-PIT_P2-E6-AD002


title: PIT_P1-PIT_P2-E12-AD012


title: PIT_P7-PIT_P8-B3-AD001


title: PIT_P1-PIT_P2-C2-AD006


title: PIT_P5-PIT_P6-C1-AD010


title: PIT_P1-PIT_P2-G3-AD008


title: PIT_P3-PIT_P4-E4-AD010


title: PIT_P7-PIT_P8-G7-AD010


title: PIT_P3-PIT_P4-F12-AD008


title: PIT_P3-PIT_P4-F9-AD001


title: PIT_P3-PIT_P4-H8-AD010


title: PIT_P3-PIT_P4-B1-AD007


title: PIT_P3-PIT_P4-C6-AD001


title: PIT_P1-PIT_P2-C10-AD004


title: PIT_P7-PIT_P8-C1-AD012


title: PIT_P3-PIT_P4-G10-AD002


title: PIT_P7-PIT_P8-C10-AD002


title: PIT_P7-PIT_P8-F3-AD006


title: PIT_P1-PIT_P2-F12-AD010


title: PIT_P7-PIT_P8-D10-AD001


title: PIT_P1-PIT_P2-D6-AD001


title: PIT_P5-PIT_P6-G8-AD007


title: PIT_P7-PIT_P8-H8-AD002


title: PIT_P7-PIT_P8-E10-AD007


title: PIT_P3-PIT_P4-G10-AD004


title: PIT_P1-PIT_P2-C11-AD004


title: PIT_P5-PIT_P6-F11-AD008


title: PIT_P5-PIT_P6-G11-AD007


title: PIT_P5-PIT_P6-A7-AD004


title: PIT_P5-PIT_P6-F6-AD008


title: PIT_P1-PIT_P2-E12-AD008


title: PIT_P7-PIT_P8-A3-AD002


title: PIT_P5-PIT_P6-A12-AD012


title: PIT_P1-PIT_P2-H2-AD006


title: PIT_P5-PIT_P6-E10-AD004


title: PIT_P3-PIT_P4-H8-AD012


title: PIT_P1-PIT_P2-F1-AD008


title: PIT_P5-PIT_P6-F8-AD012


title: PIT_P3-PIT_P4-D7-AD001


title: PIT_P5-PIT_P6-G5-AD007


title: PIT_P1-PIT_P2-C3-AD012


title: PIT_P1-PIT_P2-E4-AD006


title: PIT_P7-PIT_P8-B7-AD002


title: PIT_P7-PIT_P8-B10-AD006


title: PIT_P7-PIT_P8-B2-AD008


title: PIT_P1-PIT_P2-C2-AD001


title: PIT_P1-PIT_P2-C2-AD002


title: PIT_P1-PIT_P2-E3-AD012


title: PIT_P1-PIT_P2-A2-AD001


title: PIT_P1-PIT_P2-D12-AD007


title: PIT_P7-PIT_P8-E7-AD006


title: PIT_P5-PIT_P6-A1-AD008


title: PIT_P7-PIT_P8-H9-AD010


title: PIT_P7-PIT_P8-C11-AD010


title: PIT_P5-PIT_P6-F1-AD010


title: PIT_P1-PIT_P2-G11-AD004


title: PIT_P3-PIT_P4-C6-AD012


title: PIT_P1-PIT_P2-B7-AD004


title: PIT_P3-PIT_P4-B5-AD004


title: PIT_P1-PIT_P2-H7-AD002


title: PIT_P1-PIT_P2-H3-AD006


title: PIT_P1-PIT_P2-G5-AD002


title: PIT_P1-PIT_P2-A12-AD007


title: PIT_P1-PIT_P2-F8-AD010


title: PIT_P1-PIT_P2-D3-AD007


title: PIT_P3-PIT_P4-B9-AD012


title: PIT_P3-PIT_P4-H11-AD001


title: PIT_P7-PIT_P8-G3-AD006


title: PIT_P1-PIT_P2-E4-AD004


title: PIT_P7-PIT_P8-G11-AD006


title: PIT_P5-PIT_P6-H9-AD010


title: PIT_P7-PIT_P8-D11-AD004


title: PIT_P1-PIT_P2-D5-AD010


title: PIT_P5-PIT_P6-H7-AD010


title: PIT_P1-PIT_P2-E7-AD007


title: PIT_P5-PIT_P6-A5-AD004


title: PIT_P3-PIT_P4-G10-AD007


title: PIT_P3-PIT_P4-A10-AD007


title: PIT_P5-PIT_P6-E10-AD010


title: PIT_P5-PIT_P6-F2-AD001


title: PIT_P7-PIT_P8-H12-AD001


title: PIT_P5-PIT_P6-A8-AD001


title: PIT_P7-PIT_P8-B9-AD010


title: PIT_P5-PIT_P6-B8-AD001


title: PIT_P5-PIT_P6-E12-AD007


title: PIT_P7-PIT_P8-F2-AD004


title: PIT_P7-PIT_P8-H7-AD012


title: PIT_P7-PIT_P8-D10-AD010


title: PIT_P5-PIT_P6-E8-AD004


title: PIT_P1-PIT_P2-B9-AD010


title: PIT_P5-PIT_P6-C6-AD012


title: PIT_P5-PIT_P6-H1-AD001


title: PIT_P7-PIT_P8-B1-AD001


title: PIT_P1-PIT_P2-A4-AD006


title: PIT_P1-PIT_P2-B8-AD001


title: PIT_P5-PIT_P6-H6-AD002


title: PIT_P7-PIT_P8-H4-AD001


title: PIT_P1-PIT_P2-A12-AD010


title: PIT_P7-PIT_P8-F9-AD008


title: PIT_P7-PIT_P8-D4-AD001


title: PIT_P5-PIT_P6-C3-AD010


title: PIT_P7-PIT_P8-A10-AD002


title: PIT_P3-PIT_P4-C4-AD002


title: PIT_P3-PIT_P4-A6-AD004


title: PIT_P1-PIT_P2-G11-AD007


title: PIT_P3-PIT_P4-C10-AD004


title: PIT_P5-PIT_P6-B1-AD012


title: PIT_P1-PIT_P2-F7-AD012


title: PIT_P3-PIT_P4-D5-AD012


title: PIT_P7-PIT_P8-B8-AD001


title: PIT_P3-PIT_P4-D12-AD001


title: PIT_P7-PIT_P8-D12-AD001


title: PIT_P7-PIT_P8-B3-AD007


title: PIT_P5-PIT_P6-E5-AD006


title: PIT_P5-PIT_P6-A2-AD002


title: PIT_P7-PIT_P8-E4-AD007


title: PIT_P1-PIT_P2-B7-AD008


title: PIT_P1-PIT_P2-D9-AD008


title: PIT_P5-PIT_P6-E8-AD002


title: PIT_P7-PIT_P8-D2-AD001


title: PIT_P5-PIT_P6-C8-AD012


title: PIT_P3-PIT_P4-C1-AD002


title: PIT_P7-PIT_P8-H9-AD001


title: PIT_P1-PIT_P2-G3-AD012


title: PIT_P3-PIT_P4-F12-AD004


title: PIT_P7-PIT_P8-D5-AD010


title: PIT_P3-PIT_P4-E10-AD012


title: PIT_P5-PIT_P6-D10-AD012


title: PIT_P1-PIT_P2-H9-AD004


title: PIT_P7-PIT_P8-A9-AD008


title: PIT_P5-PIT_P6-C9-AD007


title: PIT_P7-PIT_P8-B4-AD004


title: PIT_P5-PIT_P6-B12-AD012


title: PIT_P7-PIT_P8-H11-AD007


title: PIT_P1-PIT_P2-F9-AD004


title: PIT_P7-PIT_P8-F1-AD012


title: PIT_P1-PIT_P2-A5-AD007


title: PIT_P1-PIT_P2-H4-AD007


title: PIT_P1-PIT_P2-C7-AD008


title: PIT_P7-PIT_P8-A2-AD010


title: PIT_P1-PIT_P2-A4-AD004


title: PIT_P5-PIT_P6-D6-AD010


title: PIT_P3-PIT_P4-F8-AD006


title: PIT_P1-PIT_P2-F8-AD004


title: PIT_P1-PIT_P2-B1-AD006


title: PIT_P5-PIT_P6-D10-AD004


title: PIT_P1-PIT_P2-C2-AD004


title: PIT_P3-PIT_P4-D1-AD008


title: PIT_P7-PIT_P8-F8-AD007


title: PIT_P7-PIT_P8-G12-AD006


title: PIT_P7-PIT_P8-B12-AD001


title: PIT_P1-PIT_P2-A12-AD012


title: PIT_P7-PIT_P8-A11-AD012


title: PIT_P5-PIT_P6-A3-AD007


title: PIT_P5-PIT_P6-B9-AD006


title: PIT_P3-PIT_P4-A1-AD012


title: PIT_P7-PIT_P8-H7-AD007


title: PIT_P7-PIT_P8-G11-AD001


title: PIT_P3-PIT_P4-D7-AD008


title: PIT_P5-PIT_P6-D10-AD007


title: PIT_P3-PIT_P4-C12-AD006


title: PIT_P3-PIT_P4-B3-AD010


title: PIT_P5-PIT_P6-A9-AD010


title: PIT_P1-PIT_P2-B6-AD010


title: PIT_P7-PIT_P8-B4-AD007


title: PIT_P3-PIT_P4-H3-AD004


title: PIT_P5-PIT_P6-B2-AD006


title: PIT_P5-PIT_P6-F5-AD007


title: PIT_P5-PIT_P6-G7-AD010


title: PIT_P3-PIT_P4-H3-AD002


title: PIT_P1-PIT_P2-B2-AD004


title: PIT_P1-PIT_P2-B2-AD006


title: PIT_P1-PIT_P2-A10-AD007


title: PIT_P1-PIT_P2-H11-AD006


title: PIT_P1-PIT_P2-E1-AD004


title: PIT_P7-PIT_P8-F7-AD007


title: PIT_P5-PIT_P6-B7-AD012


title: PIT_P7-PIT_P8-C1-AD001


title: PIT_P3-PIT_P4-C5-AD004


title: PIT_P1-PIT_P2-H9-AD001


title: PIT_P5-PIT_P6-D2-AD007


title: PIT_P5-PIT_P6-G9-AD001


title: PIT_P1-PIT_P2-B6-AD004


title: PIT_P3-PIT_P4-G8-AD002


title: PIT_P1-PIT_P2-G8-AD002


title: PIT_P7-PIT_P8-A12-AD010


title: PIT_P1-PIT_P2-E3-AD001


title: PIT_P3-PIT_P4-F3-AD002


title: PIT_P5-PIT_P6-D3-AD001


title: PIT_P1-PIT_P2-B5-AD004


title: PIT_P1-PIT_P2-G1-AD007


title: PIT_P5-PIT_P6-E11-AD010


title: PIT_P1-PIT_P2-A7-AD012


title: PIT_P3-PIT_P4-A11-AD010


title: PIT_P3-PIT_P4-A2-AD001


title: PIT_P1-PIT_P2-H4-AD001


title: PIT_P7-PIT_P8-B2-AD001


title: PIT_P3-PIT_P4-G3-AD012


title: PIT_P3-PIT_P4-D12-AD008


title: PIT_P3-PIT_P4-A12-AD004


title: PIT_P7-PIT_P8-H9-AD007


title: PIT_P5-PIT_P6-F9-AD004


title: PIT_P1-PIT_P2-D7-AD006


title: PIT_P5-PIT_P6-E12-AD010


title: PIT_P7-PIT_P8-F7-AD002


title: PIT_P7-PIT_P8-A7-AD001


title: PIT_P5-PIT_P6-A3-AD001


title: PIT_P5-PIT_P6-E2-AD010


title: PIT_P3-PIT_P4-G5-AD001


title: PIT_P3-PIT_P4-B3-AD007


title: PIT_P5-PIT_P6-H8-AD008


title: PIT_P3-PIT_P4-A2-AD002


title: PIT_P1-PIT_P2-G2-AD012


title: PIT_P3-PIT_P4-H7-AD007


title: PIT_P5-PIT_P6-E7-AD002


title: PIT_P7-PIT_P8-B2-AD007


title: PIT_P7-PIT_P8-E3-AD007


title: PIT_P5-PIT_P6-F2-AD012


title: PIT_P7-PIT_P8-F5-AD010


title: PIT_P3-PIT_P4-D6-AD010


title: PIT_P7-PIT_P8-D10-AD006


title: PIT_P5-PIT_P6-B1-AD002


title: PIT_P3-PIT_P4-A9-AD001


title: PIT_P5-PIT_P6-B5-AD010


title: PIT_P7-PIT_P8-D9-AD004


title: PIT_P1-PIT_P2-G12-AD004


title: PIT_P5-PIT_P6-C5-AD007


title: PIT_P7-PIT_P8-E8-AD012


title: PIT_P1-PIT_P2-D11-AD001


title: PIT_P1-PIT_P2-A6-AD008


title: PIT_P7-PIT_P8-H9-AD004


title: PIT_P5-PIT_P6-F5-AD010


title: PIT_P5-PIT_P6-B3-AD002


title: PIT_P5-PIT_P6-B1-AD006


title: PIT_P3-PIT_P4-B6-AD002


title: PIT_P1-PIT_P2-C6-AD002


title: PIT_P3-PIT_P4-G5-AD012


title: PIT_P7-PIT_P8-H1-AD012


title: PIT_P3-PIT_P4-B9-AD002


title: PIT_P1-PIT_P2-D1-AD012


title: PIT_P7-PIT_P8-H8-AD001


title: PIT_P3-PIT_P4-B4-AD008


title: PIT_P3-PIT_P4-D3-AD008


title: PIT_P5-PIT_P6-C4-AD006


title: PIT_P1-PIT_P2-F9-AD010


title: PIT_P5-PIT_P6-G4-AD007


title: PIT_P5-PIT_P6-B3-AD008


title: PIT_P7-PIT_P8-G8-AD012


title: PIT_P7-PIT_P8-B10-AD002


title: PIT_P7-PIT_P8-C1-AD006


title: PIT_P7-PIT_P8-D11-AD010


title: PIT_P5-PIT_P6-G5-AD002


title: PIT_P1-PIT_P2-D6-AD007


title: PIT_P5-PIT_P6-F1-AD004


title: PIT_P5-PIT_P6-C8-AD010


title: PIT_P1-PIT_P2-F12-AD001


title: PIT_P7-PIT_P8-G8-AD010


title: PIT_P7-PIT_P8-G5-AD008


title: PIT_P5-PIT_P6-B10-AD001


title: PIT_P3-PIT_P4-H8-AD007


title: PIT_P7-PIT_P8-B5-AD012


title: PIT_P5-PIT_P6-E11-AD008


title: PIT_P1-PIT_P2-D11-AD008


title: PIT_P7-PIT_P8-E4-AD010


title: PIT_P3-PIT_P4-D4-AD004


title: PIT_P3-PIT_P4-D1-AD006


title: PIT_P3-PIT_P4-H5-AD010


title: PIT_P7-PIT_P8-G6-AD002


title: PIT_P1-PIT_P2-E11-AD008


title: PIT_P5-PIT_P6-E2-AD001


title: PIT_P1-PIT_P2-G9-AD012


title: PIT_P7-PIT_P8-A10-AD004


title: PIT_P7-PIT_P8-A1-AD001


title: PIT_P5-PIT_P6-G12-AD008


title: PIT_P7-PIT_P8-A12-AD004


title: PIT_P5-PIT_P6-G1-AD008


title: PIT_P7-PIT_P8-H8-AD012


title: PIT_P7-PIT_P8-A10-AD001


title: PIT_P7-PIT_P8-F7-AD004


title: PIT_P1-PIT_P2-H11-AD004


title: PIT_P5-PIT_P6-A2-AD010


title: PIT_P1-PIT_P2-B11-AD007


title: PIT_P5-PIT_P6-C4-AD007


title: PIT_P1-PIT_P2-F10-AD008


title: PIT_P7-PIT_P8-B9-AD004


title: PIT_P3-PIT_P4-H11-AD008


title: PIT_P5-PIT_P6-G11-AD010


title: PIT_P5-PIT_P6-E6-AD006


title: PIT_P1-PIT_P2-B9-AD012


title: PIT_P7-PIT_P8-B4-AD006


title: PIT_P5-PIT_P6-E4-AD004


title: PIT_P3-PIT_P4-B10-AD010


title: PIT_P1-PIT_P2-D6-AD008


title: PIT_P3-PIT_P4-F4-AD002


title: PIT_P1-PIT_P2-B4-AD006


title: PIT_P7-PIT_P8-F7-AD006


title: PIT_P7-PIT_P8-E11-AD008


title: PIT_P7-PIT_P8-A6-AD006


title: PIT_P7-PIT_P8-A3-AD008


title: PIT_P1-PIT_P2-G5-AD012


title: PIT_P5-PIT_P6-H3-AD001


title: PIT_P3-PIT_P4-C5-AD012


title: PIT_P1-PIT_P2-A1-AD002


title: PIT_P5-PIT_P6-B11-AD007


title: PIT_P7-PIT_P8-A5-AD008


title: PIT_P1-PIT_P2-F6-AD008


title: PIT_P5-PIT_P6-G11-AD004


title: PIT_P1-PIT_P2-F4-AD006


title: PIT_P7-PIT_P8-D10-AD012


title: PIT_P5-PIT_P6-D6-AD001


title: PIT_P1-PIT_P2-C4-AD004


title: PIT_P3-PIT_P4-E7-AD004


title: PIT_P5-PIT_P6-B10-AD008


title: PIT_P1-PIT_P2-B4-AD004


title: PIT_P3-PIT_P4-H2-AD008


title: PIT_P5-PIT_P6-E7-AD010


title: PIT_P7-PIT_P8-F7-AD008


title: PIT_P7-PIT_P8-F5-AD008


title: PIT_P5-PIT_P6-B1-AD008


title: PIT_P3-PIT_P4-H5-AD012


title: PIT_P5-PIT_P6-F12-AD001


title: PIT_P7-PIT_P8-B1-AD007


title: PIT_P1-PIT_P2-A11-AD006


title: PIT_P1-PIT_P2-E11-AD007


title: PIT_P7-PIT_P8-C12-AD012


title: PIT_P7-PIT_P8-G9-AD004


title: PIT_P1-PIT_P2-E2-AD006


title: PIT_P7-PIT_P8-C4-AD006


title: PIT_P3-PIT_P4-H2-AD010


title: PIT_P5-PIT_P6-B4-AD008


title: PIT_P7-PIT_P8-A12-AD001


title: PIT_P3-PIT_P4-D6-AD001


title: PIT_P5-PIT_P6-H7-AD008


title: PIT_P1-PIT_P2-E3-AD010


title: PIT_P5-PIT_P6-F7-AD002


title: PIT_P5-PIT_P6-G8-AD012


title: PIT_P1-PIT_P2-G8-AD010


title: PIT_P3-PIT_P4-D10-AD006


title: PIT_P3-PIT_P4-D6-AD002


title: PIT_P3-PIT_P4-A6-AD002


title: PIT_P3-PIT_P4-H4-AD012


title: PIT_P7-PIT_P8-F3-AD004


title: PIT_P7-PIT_P8-B8-AD007


title: PIT_P1-PIT_P2-C4-AD001


title: PIT_P5-PIT_P6-E8-AD012


title: PIT_P1-PIT_P2-B10-AD012


title: PIT_P5-PIT_P6-E3-AD012


title: PIT_P3-PIT_P4-C3-AD004


title: PIT_P1-PIT_P2-D11-AD002


title: PIT_P1-PIT_P2-A6-AD007


title: PIT_P3-PIT_P4-H2-AD006


title: PIT_P1-PIT_P2-D4-AD010


title: PIT_P5-PIT_P6-E12-AD001


title: PIT_P7-PIT_P8-G6-AD007


title: PIT_P1-PIT_P2-A8-AD008


title: PIT_P5-PIT_P6-C9-AD010


title: PIT_P5-PIT_P6-D4-AD006


title: PIT_P5-PIT_P6-G4-AD004


title: PIT_P5-PIT_P6-D7-AD002


title: PIT_P3-PIT_P4-B2-AD007


title: PIT_P5-PIT_P6-F4-AD007


title: PIT_P3-PIT_P4-D9-AD001


title: PIT_P5-PIT_P6-F8-AD006


title: PIT_P7-PIT_P8-H10-AD010


title: PIT_P3-PIT_P4-D12-AD004


title: PIT_P7-PIT_P8-C8-AD001


title: PIT_P1-PIT_P2-D3-AD010


title: PIT_P7-PIT_P8-F10-AD012


title: PIT_P7-PIT_P8-B3-AD002


title: PIT_P1-PIT_P2-H3-AD008


title: PIT_P7-PIT_P8-E2-AD007


title: PIT_P7-PIT_P8-E8-AD008


title: PIT_P1-PIT_P2-H9-AD006


title: PIT_P3-PIT_P4-G5-AD010


title: PIT_P1-PIT_P2-E12-AD006


title: PIT_P5-PIT_P6-C4-AD008


title: PIT_P5-PIT_P6-H3-AD008


title: PIT_P5-PIT_P6-C8-AD004


title: PIT_P7-PIT_P8-E6-AD001


title: PIT_P7-PIT_P8-H9-AD002


title: PIT_P1-PIT_P2-D9-AD010


title: PIT_P5-PIT_P6-A7-AD007


title: PIT_P1-PIT_P2-B8-AD007


title: PIT_P5-PIT_P6-D8-AD001


title: PIT_P5-PIT_P6-B2-AD001


title: PIT_P7-PIT_P8-F4-AD007


title: PIT_P5-PIT_P6-G1-AD006


title: PIT_P1-PIT_P2-C8-AD012


title: PIT_P1-PIT_P2-A3-AD007


title: PIT_P5-PIT_P6-H10-AD001


title: PIT_P3-PIT_P4-D5-AD004


title: PIT_P1-PIT_P2-C7-AD001


title: PIT_P5-PIT_P6-F8-AD010


title: PIT_P1-PIT_P2-E5-AD012


title: PIT_P5-PIT_P6-H5-AD001


title: PIT_P1-PIT_P2-G6-AD001


title: PIT_P1-PIT_P2-H6-AD004


title: PIT_P5-PIT_P6-B8-AD004


title: PIT_P1-PIT_P2-F9-AD001


title: PIT_P1-PIT_P2-F5-AD012


title: PIT_P3-PIT_P4-B4-AD006


title: PIT_P5-PIT_P6-F12-AD004


title: PIT_P3-PIT_P4-H12-AD004


title: PIT_P3-PIT_P4-D7-AD012


title: PIT_P3-PIT_P4-A9-AD010


title: PIT_P3-PIT_P4-C5-AD007


title: PIT_P1-PIT_P2-B7-AD002


title: PIT_P1-PIT_P2-A2-AD008


title: PIT_P5-PIT_P6-G3-AD006


title: PIT_P7-PIT_P8-F4-AD008


title: PIT_P1-PIT_P2-D3-AD012


title: PIT_P5-PIT_P6-A4-AD001


title: PIT_P7-PIT_P8-G6-AD004


title: PIT_P5-PIT_P6-C4-AD010


title: PIT_P1-PIT_P2-D10-AD002


title: PIT_P7-PIT_P8-C11-AD002


title: PIT_P7-PIT_P8-A12-AD008


title: PIT_P1-PIT_P2-C7-AD006


title: PIT_P1-PIT_P2-D5-AD008


title: PIT_P5-PIT_P6-F9-AD001


title: PIT_P7-PIT_P8-F7-AD012


title: PIT_P7-PIT_P8-F5-AD006


title: PIT_P5-PIT_P6-A4-AD012


title: PIT_P7-PIT_P8-E11-AD004


title: PIT_P3-PIT_P4-B11-AD007


title: PIT_P5-PIT_P6-E10-AD001


title: PIT_P7-PIT_P8-B2-AD010


title: PIT_P3-PIT_P4-C6-AD008


title: PIT_P7-PIT_P8-H2-AD002


title: PIT_P5-PIT_P6-C9-AD012


title: PIT_P3-PIT_P4-D9-AD006


title: PIT_P1-PIT_P2-F1-AD004


title: PIT_P3-PIT_P4-F11-AD004


title: PIT_P7-PIT_P8-D8-AD004


title: PIT_P3-PIT_P4-C6-AD006


title: PIT_P5-PIT_P6-C1-AD004


title: PIT_P5-PIT_P6-B6-AD004


title: PIT_P5-PIT_P6-C12-AD008


title: PIT_P5-PIT_P6-H8-AD012


title: PIT_P1-PIT_P2-E3-AD004


title: PIT_P5-PIT_P6-H3-AD012


title: PIT_P3-PIT_P4-C2-AD004


title: PIT_P3-PIT_P4-F2-AD006


title: PIT_P3-PIT_P4-A5-AD006


title: PIT_P3-PIT_P4-E8-AD010


title: PIT_P7-PIT_P8-G5-AD007


title: PIT_P5-PIT_P6-G12-AD002


title: PIT_P5-PIT_P6-F9-AD006


title: PIT_P1-PIT_P2-C8-AD001


title: PIT_P3-PIT_P4-G3-AD001


title: PIT_P3-PIT_P4-H12-AD006


title: PIT_P1-PIT_P2-D1-AD007


title: PIT_P1-PIT_P2-E7-AD004


title: PIT_P5-PIT_P6-G1-AD002


title: PIT_P3-PIT_P4-A4-AD012


title: PIT_P5-PIT_P6-E9-AD010


title: PIT_P3-PIT_P4-F8-AD010


title: PIT_P1-PIT_P2-F3-AD012


title: PIT_P5-PIT_P6-E11-AD002


title: PIT_P3-PIT_P4-B7-AD006


title: PIT_P7-PIT_P8-D3-AD006


title: PIT_P1-PIT_P2-E1-AD010


title: PIT_P7-PIT_P8-B4-AD012


title: PIT_P3-PIT_P4-F11-AD007


title: PIT_P5-PIT_P6-A8-AD004


title: PIT_P7-PIT_P8-F8-AD006


title: PIT_P5-PIT_P6-D12-AD010


title: PIT_P5-PIT_P6-A6-AD007


title: PIT_P1-PIT_P2-C3-AD002


title: PIT_P3-PIT_P4-E11-AD008


title: PIT_P5-PIT_P6-F10-AD002


title: PIT_P1-PIT_P2-D1-AD006


title: PIT_P5-PIT_P6-E10-AD006


title: PIT_P5-PIT_P6-F9-AD010


title: PIT_P1-PIT_P2-G11-AD010


title: PIT_P3-PIT_P4-D1-AD001


title: PIT_P1-PIT_P2-A2-AD006


title: PIT_P7-PIT_P8-F3-AD007


title: PIT_P7-PIT_P8-E11-AD006


title: PIT_P3-PIT_P4-B8-AD010


title: PIT_P5-PIT_P6-E1-AD012


title: PIT_P3-PIT_P4-A4-AD008


title: PIT_P3-PIT_P4-B6-AD006


title: PIT_P7-PIT_P8-E12-AD010


title: PIT_P1-PIT_P2-G8-AD008


title: PIT_P1-PIT_P2-C3-AD001


title: PIT_P5-PIT_P6-A2-AD007


title: PIT_P5-PIT_P6-D2-AD010


title: PIT_P5-PIT_P6-G12-AD010


title: PIT_P3-PIT_P4-F6-AD002


title: PIT_P7-PIT_P8-G9-AD012


title: PIT_P3-PIT_P4-B3-AD008


title: PIT_P7-PIT_P8-E6-AD012


title: PIT_P3-PIT_P4-E1-AD007


title: PIT_P5-PIT_P6-G1-AD012


title: PIT_P7-PIT_P8-D11-AD002


title: PIT_P5-PIT_P6-C12-AD002


title: PIT_P3-PIT_P4-F7-AD004


title: PIT_P7-PIT_P8-E2-AD002


title: PIT_P7-PIT_P8-E1-AD006


title: PIT_P1-PIT_P2-H6-AD001


title: PIT_P5-PIT_P6-D11-AD008


title: PIT_P1-PIT_P2-G9-AD002


title: PIT_P7-PIT_P8-G6-AD006


title: PIT_P5-PIT_P6-D4-AD002


title: PIT_P5-PIT_P6-C11-AD006


title: PIT_P1-PIT_P2-D5-AD002


title: PIT_P1-PIT_P2-D7-AD008


title: PIT_P1-PIT_P2-A8-AD004


title: PIT_P7-PIT_P8-F12-AD001


title: PIT_P5-PIT_P6-B9-AD002


title: PIT_P3-PIT_P4-F5-AD002


title: PIT_P5-PIT_P6-G7-AD004


title: PIT_P7-PIT_P8-A6-AD012


title: PIT_P3-PIT_P4-F8-AD002


title: PIT_P1-PIT_P2-F3-AD001


title: PIT_P7-PIT_P8-F12-AD008


title: PIT_P5-PIT_P6-F3-AD002


title: PIT_P5-PIT_P6-A6-AD004


title: PIT_P7-PIT_P8-H8-AD007


title: PIT_P1-PIT_P2-A5-AD010


title: PIT_P1-PIT_P2-A11-AD008


title: PIT_P1-PIT_P2-C11-AD008


title: PIT_P5-PIT_P6-D4-AD012


title: PIT_P3-PIT_P4-A6-AD007


title: PIT_P5-PIT_P6-E12-AD012


title: PIT_P1-PIT_P2-B11-AD001


title: PIT_P3-PIT_P4-F11-AD001


title: PIT_P1-PIT_P2-G8-AD007


title: PIT_P7-PIT_P8-D11-AD007


title: PIT_P3-PIT_P4-A4-AD002


title: PIT_P5-PIT_P6-G10-AD002


title: PIT_P5-PIT_P6-E2-AD007


title: PIT_P7-PIT_P8-F1-AD010


title: PIT_P5-PIT_P6-D1-AD002


title: PIT_P5-PIT_P6-F12-AD012


title: PIT_P1-PIT_P2-H4-AD002


title: PIT_P3-PIT_P4-G1-AD012


title: PIT_P1-PIT_P2-F4-AD001


title: PIT_P5-PIT_P6-B3-AD006


title: PIT_P7-PIT_P8-B1-AD006


title: PIT_P1-PIT_P2-G2-AD010


title: PIT_P1-PIT_P2-C7-AD002


title: PIT_P5-PIT_P6-G8-AD002


title: PIT_P3-PIT_P4-A10-AD004


title: PIT_P7-PIT_P8-B10-AD010


title: PIT_P7-PIT_P8-A4-AD012


title: PIT_P7-PIT_P8-H2-AD010


title: PIT_P1-PIT_P2-E8-AD007


title: PIT_P5-PIT_P6-E5-AD007


title: PIT_P1-PIT_P2-C12-AD007


title: PIT_P3-PIT_P4-B6-AD012


title: PIT_P7-PIT_P8-F11-AD002


title: PIT_P3-PIT_P4-C7-AD010


title: PIT_P7-PIT_P8-E2-AD012


title: PIT_P3-PIT_P4-B3-AD006


title: PIT_P3-PIT_P4-H12-AD002


title: PIT_P7-PIT_P8-H4-AD008


title: PIT_P7-PIT_P8-B7-AD007


title: PIT_P1-PIT_P2-A1-AD006


title: PIT_P1-PIT_P2-C5-AD010


title: PIT_P7-PIT_P8-B12-AD004


title: PIT_P1-PIT_P2-E1-AD002


title: PIT_P5-PIT_P6-D4-AD008


title: PIT_P7-PIT_P8-E9-AD004


title: PIT_P7-PIT_P8-D1-AD008


title: PIT_P3-PIT_P4-E5-AD002


title: PIT_P7-PIT_P8-E10-AD001


title: PIT_P5-PIT_P6-A7-AD001


title: PIT_P3-PIT_P4-F3-AD008


title: PIT_P5-PIT_P6-H4-AD007


title: PIT_P3-PIT_P4-A11-AD008


title: PIT_P5-PIT_P6-G5-AD012


title: PIT_P3-PIT_P4-G6-AD008


title: PIT_P5-PIT_P6-D9-AD010


title: PIT_P3-PIT_P4-D9-AD007


title: PIT_P5-PIT_P6-C5-AD010


title: PIT_P7-PIT_P8-B2-AD012


title: PIT_P7-PIT_P8-E12-AD002


title: PIT_P5-PIT_P6-C12-AD010


title: PIT_P3-PIT_P4-G3-AD004


title: PIT_P7-PIT_P8-D3-AD010


title: PIT_P3-PIT_P4-B10-AD001


title: PIT_P3-PIT_P4-G4-AD007


title: PIT_P1-PIT_P2-D10-AD007


title: PIT_P1-PIT_P2-D11-AD007


title: PIT_P1-PIT_P2-D11-AD004


title: PIT_P3-PIT_P4-C9-AD010


title: PIT_P7-PIT_P8-E12-AD007


title: PIT_P5-PIT_P6-G12-AD012


title: PIT_P3-PIT_P4-A12-AD012


title: PIT_P5-PIT_P6-D2-AD006


title: PIT_P1-PIT_P2-G9-AD007


title: PIT_P7-PIT_P8-A9-AD010


title: PIT_P5-PIT_P6-D12-AD012


title: PIT_P7-PIT_P8-F2-AD007


title: PIT_P7-PIT_P8-B9-AD002


title: PIT_P3-PIT_P4-E12-AD007


title: PIT_P5-PIT_P6-D5-AD010


title: PIT_P7-PIT_P8-H10-AD007


title: PIT_P1-PIT_P2-C9-AD004


title: PIT_P7-PIT_P8-D8-AD012


title: PIT_P5-PIT_P6-F3-AD007


title: PIT_P3-PIT_P4-C5-AD006


title: PIT_P1-PIT_P2-A4-AD007


title: PIT_P7-PIT_P8-B1-AD008


title: PIT_P7-PIT_P8-C2-AD012


title: PIT_P7-PIT_P8-F10-AD002


title: PIT_P3-PIT_P4-A5-AD007


title: PIT_P1-PIT_P2-G6-AD004


title: PIT_P1-PIT_P2-A4-AD008


title: PIT_P5-PIT_P6-G5-AD010


title: PIT_P3-PIT_P4-H9-AD007


title: PIT_P7-PIT_P8-H8-AD006


title: PIT_P5-PIT_P6-E5-AD012


title: PIT_P5-PIT_P6-C5-AD006


title: PIT_P1-PIT_P2-C2-AD010


title: PIT_P1-PIT_P2-H10-AD007


title: PIT_P3-PIT_P4-F5-AD010


title: PIT_P1-PIT_P2-D5-AD012


title: PIT_P7-PIT_P8-E1-AD008


title: PIT_P3-PIT_P4-D7-AD007


title: PIT_P3-PIT_P4-H5-AD002


title: PIT_P3-PIT_P4-B12-AD012


title: PIT_P5-PIT_P6-A5-AD012


title: PIT_P1-PIT_P2-C10-AD002


title: PIT_P3-PIT_P4-E9-AD007


title: PIT_P3-PIT_P4-E2-AD007


title: PIT_P3-PIT_P4-B8-AD006


title: PIT_P5-PIT_P6-E3-AD007


title: PIT_P5-PIT_P6-D5-AD001


title: PIT_P5-PIT_P6-H10-AD008


title: PIT_P1-PIT_P2-F11-AD006


title: PIT_P7-PIT_P8-F4-AD001


title: PIT_P5-PIT_P6-B8-AD008


title: PIT_P3-PIT_P4-C2-AD012


title: PIT_P5-PIT_P6-G6-AD008


title: PIT_P7-PIT_P8-G12-AD007


title: PIT_P7-PIT_P8-C2-AD002


title: PIT_P1-PIT_P2-F12-AD004


title: PIT_P1-PIT_P2-H10-AD002


title: PIT_P7-PIT_P8-H8-AD010


title: PIT_P7-PIT_P8-G7-AD001


title: PIT_P7-PIT_P8-C3-AD002


title: PIT_P3-PIT_P4-H6-AD010


title: PIT_P5-PIT_P6-G6-AD012


title: PIT_P7-PIT_P8-B6-AD012


title: PIT_P7-PIT_P8-E10-AD006


title: PIT_P1-PIT_P2-C11-AD012


title: PIT_P3-PIT_P4-C11-AD006


title: PIT_P1-PIT_P2-G1-AD010


title: PIT_P3-PIT_P4-A9-AD012


title: PIT_P7-PIT_P8-E3-AD008


title: PIT_P7-PIT_P8-B5-AD001


title: PIT_P3-PIT_P4-G6-AD004


title: PIT_P5-PIT_P6-H3-AD007


title: PIT_P1-PIT_P2-C11-AD010


title: PIT_P7-PIT_P8-D6-AD010


title: PIT_P3-PIT_P4-B12-AD010


title: PIT_P5-PIT_P6-A2-AD012


title: PIT_P1-PIT_P2-G6-AD006


title: PIT_P7-PIT_P8-B9-AD006


title: PIT_P5-PIT_P6-C8-AD007


title: PIT_P5-PIT_P6-H4-AD012


title: PIT_P1-PIT_P2-H6-AD006


title: PIT_P3-PIT_P4-E6-AD002


title: PIT_P1-PIT_P2-E7-AD006


title: PIT_P5-PIT_P6-C7-AD006


title: PIT_P5-PIT_P6-B8-AD006


title: PIT_P3-PIT_P4-G2-AD010


title: PIT_P7-PIT_P8-F6-AD012


title: PIT_P5-PIT_P6-E3-AD001


title: PIT_P1-PIT_P2-C4-AD010


title: PIT_P7-PIT_P8-H3-AD001


title: PIT_P5-PIT_P6-C6-AD001


title: PIT_P1-PIT_P2-F10-AD001


title: PIT_P1-PIT_P2-G8-AD012


title: PIT_P1-PIT_P2-G7-AD001


title: PIT_P5-PIT_P6-A4-AD007


title: PIT_P3-PIT_P4-G7-AD010


title: PIT_P3-PIT_P4-C1-AD012


title: PIT_P3-PIT_P4-D9-AD004


title: PIT_P5-PIT_P6-H2-AD002


title: PIT_P3-PIT_P4-F12-AD010


title: PIT_P1-PIT_P2-F2-AD012


title: PIT_P1-PIT_P2-B5-AD007


title: PIT_P3-PIT_P4-E1-AD012


title: PIT_P3-PIT_P4-G10-AD001


title: PIT_P3-PIT_P4-C10-AD001


title: PIT_P5-PIT_P6-F12-AD008


title: PIT_P5-PIT_P6-F4-AD010


title: PIT_P7-PIT_P8-A5-AD006


title: PIT_P3-PIT_P4-D9-AD008


title: PIT_P7-PIT_P8-E3-AD012


title: PIT_P7-PIT_P8-H5-AD008


title: PIT_P3-PIT_P4-D11-AD012


title: PIT_P7-PIT_P8-C2-AD010


title: PIT_P7-PIT_P8-C8-AD002


title: PIT_P7-PIT_P8-E3-AD004


title: PIT_P5-PIT_P6-B3-AD004


title: PIT_P1-PIT_P2-E6-AD006


title: PIT_P1-PIT_P2-A11-AD001


title: PIT_P3-PIT_P4-A1-AD004


title: PIT_P7-PIT_P8-C10-AD004


title: PIT_P7-PIT_P8-E5-AD002


title: PIT_P5-PIT_P6-D6-AD012


title: PIT_P3-PIT_P4-B10-AD006


title: PIT_P3-PIT_P4-C1-AD001


title: PIT_P1-PIT_P2-H12-AD006


title: PIT_P7-PIT_P8-G8-AD002


title: HUDEP-2_Replicate-2

city: Boston

first: Divya

last: Vinjamur

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
Basecalls performed using CASAVA version 1.4
ATAC-seq reads were aligned to the hg19 genome assembly using bowtie2 with default parameters
Duplicate reads were removed using samtools using default parameters
peaks were called using MACS2 with q value 0.05
bigWig files were generated using deeptools with bamCoverage options with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files containing genome wide peak positions

organism: Homo sapiens

source_name: HUDEP-2 cells

growth_protocol: HUDEP-2 cells were grown in expansion phase culture conditions.

extract_protocol:
DNA was extracted using Qiagen minielute kit
Libraries were prepared using Nextera library preparation kit.

tag: cell line

tag: culture conditions

value: Expansion phase culture


title: PIT_P3-PIT_P4-B10-AD002


title: HUDEP-2_Replicate-1


title: HUDEP-2_Replicate-3


title: PIT_P7-PIT_P8-E8-AD007


title: PIT_P7-PIT_P8-F11-AD001


title: PIT_P3-PIT_P4-B12-AD007


title: 215-3-A [Genesips_24]

city: Stanford

first: Joshua

last: Knowles

state: California

address: 300 Pasteur Dr.

institute: Stanford University

library_source: transcriptomic

data_processing:
STAR v2.5.1b  was used to align RNA-seq reads to the human genome built GRCh37. Using featureCounts v1.5.2 , we counted the uniquely mapping reads overlapping genes as annotated by GRCh37.
We filtered out lowly expressed genes (at least 1 counts-per-million (CPM) in 30% or more of samples). We used the R packages edgeR and limma to normalize the RNA-seq expression data.
The edgeR function calcNormFactors() is used to compute TMM [63] weights which are applied using the limma function voom(). The final normalized expression values that are output by voom() are on the log2 counts-per-million (CPM) scale.
statistical analyses and data processing steps were done using R v3.0.3
Code for the various analyses described in the paper has been published on GitHub (https://github.com/gitMarcH/iPSCsInsulinResistance).
Genome_build: human genome built GRCh37
Supplementary_files_format_and_content: GENESIPS_IRIS_validation_rawCounts.tab

molecule: total RNA

source_name: Insulin sensitive_iPSC_treated

growth_protocol: The cells were maintained in feeder-free conditions using mTesr1 (Stem Cell technologies, Inc) supplemented with 1 mM L-Glutamine, 1mM Penicillin-Streptomycin, 0.1 μg/ml Fungizone. ) on 5% matrigel coated 6-well TC plates. For passaging, cells were washed once with PBS and treated with pre-warmed 1 mM EDTA (Sigma), incubated at 37 degrees for 1-5 minutes, and resuspended in fresh mTesr1 medium 2 μM Thiazovivin (Millipore). After 12 hours incubation in Thiazovivin, medium was changed daily with fresh mTesr1

extract_protocol:
Cells were washed once in PBS and harvested for RNA extraction using PureLInk RNA mini kit (Thermo Fisher Scientific)
RNA libraries were prepared at Novogene (TruSeq RNA Sample Prep Kit v2 protocol) and the RNA was sequenced using the Illumina HiSeq 2500 system

treatment_protocol: Cells were grown to ~90-100% confluency, washed once with PBS and were treated with either DMSO (D) or 1 uM Atorvastatin (A) (Selleckhem) for 12h

tag: cell type

value: iPSC

tag: treatment

value: yes

tag: disease state

value: Insulin sensitive

value: Female

tag: race

value: White

tag: sspg

tag: bmi

tag: sequencing batch

value: Erythroblasts


title: 215-3-D [Genesips_23]

source_name: Insulin sensitive_iPSC_no treament

value: no


title: PIT_P3-PIT_P4-A12-AD007


title: 780-2-D [Genesips_21]


title: PIT_P1-PIT_P2-E3-AD008


title: 475-1-A [Genesips_20]

value: Male


title: PIT_P5-PIT_P6-A6-AD002


title: PIT_P1-PIT_P2-A11-AD012


title: 475-1-D [Genesips_19]


title: 541-2-A [Genesips_18]


title: PIT_P7-PIT_P8-G3-AD012


title: PIT_P3-PIT_P4-F1-AD012


title: 541-2-D [Genesips_17]


title: 239-3-D [Genesips_15]

source_name: Insulin resistant_iPSC_no treament

value: Insulin resistant


title: PIT_P7-PIT_P8-B4-AD001


title: 239-3-A [Genesips_16]

source_name: Insulin resistant_iPSC_treated


title: 336-3-A [Genesips_14]


title: PIT_P5-PIT_P6-A8-AD007


title: PIT_P7-PIT_P8-B12-AD008


title: PIT_P1-PIT_P2-F5-AD004


title: 336-3-D [Genesips_13]


title: 420-1-A [Genesips_12]


title: PIT_P1-PIT_P2-A7-AD002


title: 780-2-A [Genesips_22]


title: PIT_P3-PIT_P4-E12-AD012


title: PIT_P7-PIT_P8-C12-AD008


title: 193-4-A [Genesips_10]


title: PIT_P7-PIT_P8-C3-AD010


title: 108-2-A [Genesips_8]

value: unknown


title: 193-4-D [Genesips_9]


title: PIT_P3-PIT_P4-B2-AD001


title: PIT_P1-PIT_P2-H1-AD008


title: 108-2-D [Genesips_7]


title: 688-1-A [Genesips_6]


title: PIT_P1-PIT_P2-H3-AD001


title: PIT_P3-PIT_P4-G6-AD010


title: PIT_P3-PIT_P4-F6-AD008


title: PIT_P1-PIT_P2-C11-AD006


title: 688-1-D [Genesips_5]


title: PIT_P3-PIT_P4-B12-AD004


title: 243-1-D [Genesips_3]


title: PIT_P5-PIT_P6-H6-AD008


title: 255-1-A [Genesips_2]

value: Activated T-Cells


title: PIT_P7-PIT_P8-B3-AD010


title: 255-1-D [Genesips_1]


title: PIT_P7-PIT_P8-F10-AD006


title: PIT_P1-PIT_P2-E3-AD007


title: NG-Capture C siFra1 rep3

city: Montpellier

first: Isabelle

last: Jariel-Encontre

state: Montpellier Cedex5

address: 208 Avenue des Apothicaires

country: France

institute: IRCM-U1194- INSERM

description: chimeric genomic DNA - 3C libraries

data_processing:
Library strategy: NG-Capture C
Data were analyzed using scripts available at https://github.com/telenius/captureC/releases
R was used to normalize data.
Differential analysis between the siCTL and the siFra-1 condition was performed using DESeq2
Peak calling was performed using the PeakC R package (Geeven et al., 2018) using the following parameters: alphaFDR=0.1, wSize=5 and qWr=1.
Adjacent restriction fragments called by PeakC were then merged into a single region using BEDTools
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files

source_name: MDA-MB-231 cell line

growth_protocol: MDA-MB-231 cells (ATCC, Rockville, MD, USA) were cultured cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum and penicillin/streptomycin (100µg/ml each) in a humidified 5% CO2 atmosphere at 37°C. Cells freshly amplified and frozen after obtention from the ATCC were used every 3months and were routinely tested for the absence of mycoplasma contamination

extract_protocol:
The experiments were performed as previously described in (Davies et al., 2016b). Briefly, 3C libraries were generated using 900 U of the Dpn II restriction enzyme (NEB: R0543M) for 11 million cells and 720 U of the T4 DNA HC ligase (Life Technologies: EL0013). 3C libraries were sonicated (Bioruptor® Pico sonication device; 5 cycles; 30s ON/OFF). Samples were indexed to allow multiplexing using Illumina paired-end sequencing adaptors (NEB: E6040, E7335) and the Herculase II polymerase (Agilent: 600677). Oligonucleotide capture was then performed using 70-mer biotinylated DNA oligonucleotides designed at each of the studied target gene promoters (http://apps.molbiol.ox.ac.uk/CaptureC/cgi-bin/CapSequm.cgi). The hybridization reaction was performed using Nimblegen SeqCap EZ kits (Roche: 05634261001, 07145594001, 06777287001). After a 72h hybridization step, streptavidin bead pulldown (Invitrogen: 65305) was performed, followed by multiple washes (according to SeqCap EZ SR user’s guide) followed by PCR amplification of the captured material. A second capture step was performed as above.
Samples were indexed to allow multiplexing using Illumina paired-end sequencing adaptors (NEB: E6040, E7335) and the Herculase II polymerase (Agilent: 600677).

treatment_protocol: Cells were transfected with either a control siRNA (siCTL) or a mix of siRNAs directed against Fra-1 (siFra-1) (4.5nM of siRNAs for 72 hours) using INTERFERin, according to the manufacturer's instructions. Experiments were carried out in 3 independent replicates.

value: breast cancer cell line

tag: tumor type

value: triple negative - basal b

tag: knockdown

value: si Fra-1


title: PIT_P1-PIT_P2-F6-AD001

value: Pituitary


title: NG-Capture C siFra1 rep1

description: chimeric genomic DNA - 3C libraries


title: 420-1-D [Genesips_11]


title: NG-Capture C siFra1 rep2

description: chimeric genomic DNA - 3C libraries


title: PIT_P1-PIT_P2-D10-AD006

value: male


title: NG-Capture C siCTL rep3

description: chimeric genomic DNA - 3C libraries

value: si control


title: NG-Capture C siCTL rep2

description: chimeric genomic DNA - 3C libraries


title: PIT_P1-PIT_P2-H2-AD002


title: NG-Capture C siCTL rep1

description: chimeric genomic DNA - 3C libraries


title: PIT_P7-PIT_P8-F10-AD007


title: PIT_P3-PIT_P4-B2-AD006


title: CTCF_2

description: CTCFB

data_processing:
Reads were aligned to hg19 genome using Bowtie2 allowing no more than 2 mismatches and no multiple alignment sites.
Aligned reads were processed with R package PASHA (Fenouil et al., 2013; doi: 10.1093/bioinformatics/btw206) to eliminate PCR artefacts, extend reads to an estimated fragment length and generate WIG files.
R Package PASHA was used to normalize the WIG files to calculate the scores per million reads sequenced and Input DNA signal was subtracted from normalized WIG files.
Wig files from biological replicates were merged.
Peaks were called using Thresholding function of Integrated Genome Browser (https://bioviz.org/) with the following settings : H3K4me1  threshold=30, Max gap=1000, Min run=250; H3K4me3 threshold=30, Max gap=500, Min run=150; H3K27ac threshold=50, Max gap=500, Min run=150; p300/CBP  threshold=60, Max gap=50, Min run=50 ; PolII  threshold=50, Max gap=800, Min run=100; CTCF threshold=50, Max gap=50, Min run=50
Genome_build: Hg19
Supplementary_files_format_and_content: wig files

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the appropriate antibodies.
ChIP-seq libraries were prepared  using the TruSeq ChIP sample reparation kit from Illumina by the MGX sequencing Platform (Montpellier, France)

treatment_protocol: experiments were carried out in 2 independent replicates except for p300/CBP

tag: chip antibody

value: CTCF C15410210 from Diagenode


title: CTCF_1

description: CTCFA


title: PIT_P1-PIT_P2-B1-AD004


title: 243-1-A [Genesips_4]

value: iPSC

value: yes


title: PIT_P1-PIT_P2-D4-AD004


title: Pol II_1

value: pol II sc-55492 from Santa Cruz Biotechnology


title: p300/CBP

value: p300/CBP Ab14984  from Abcam


title: PIT_P5-PIT_P6-A12-AD004


title: Pol II_2


title: PIT_P7-PIT_P8-A10-AD012


title: H3K27ac_2

value: H3K27ac Ab4729 from Abcam


title: PIT_P7-PIT_P8-E8-AD001


title: H3K27ac_1


title: PIT_P1-PIT_P2-F11-AD008


title: H3K4me3_1

value: H3K4me3 Ab8580 from Abcam


title: H3K4me1_2

value: H3K4me1 Ab8895 from Abcam


title: H3K4me1_1


title: PIT_P1-PIT_P2-E5-AD007


title: PIT_P1-PIT_P2-E8-AD001


title: PIT_P3-PIT_P4-H8-AD008


title: PIT_P7-PIT_P8-G6-AD012


title: MDA-MB-231 sphere siEZH2 rep2

city: London

first: Sladana

last: Zagorac

address: Du Cane Road

country: United Kingdom

institute: Imperial College London

data_processing:
Basecalls performed using CASAVA version 1.4
Sequence reads were mapped to the hg19 genome assembly using TopHat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genomic Suite (Partek Incorporated)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 adherent cells were cultured in DMEM supplemented with 10%FCS and 1%Pen-Sprep-Glutamine.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions (TRI Reagent, Sigma).
Libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer's instructions.

treatment_protocol: MDA-MB-231 spheres were cultured in DMEM/F12 supplemented with 1-in-50 B27, 20ng/ml EGF, 20ng/ml FGF in suspension in non-adherent plates for described incubation times. For siRNA experiemnts, cells were reverse transfected with siRNAs and incubated in sphere media for 48h.

value: MDA-MB-231 mammospheres

tag: duration of treatment


title: Input_2

value: none (input)


title: PIT_P1-PIT_P2-A6-AD010

tag: tissue


title: MDA-MB-231 sphere siNC rep2

value: siNC


title: MDA-MB-231 sphere siEZH2 rep1


title: PIT_P5-PIT_P6-B12-AD006

tag: age


title: PIT_P7-PIT_P8-H3-AD008

tag: strain


title: MDA-MB-231 sphere siNC rep1


title: MDA-MB-231 sphere siSCIRT#2 rep 3


title: PIT_P5-PIT_P6-F6-AD002

tag: Sex


title: MDA-MB-231 sphere siSCIRT#2 rep 2

tag: cell line


title: PIT_P1-PIT_P2-G12-AD006


title: PIT_P3-PIT_P4-C10-AD002


title: MDA-MB-231 sphere siSCIRT#2 rep 1


title: PIT_P1-PIT_P2-D2-AD008


title: PIT_P5-PIT_P6-G11-AD002


title: MDA-MB-231 sphere siSCIRT#1 rep 3


title: MDA-MB-231 sphere siSCIRT#1 rep 2


title: PIT_P1-PIT_P2-C8-AD008


title: MDA-MB-231 sphere siSCIRT#1 rep 1


title: PIT_P5-PIT_P6-H7-AD006


title: H3K4me3_2

value: breast cancer cell line


title: PIT_P1-PIT_P2-D8-AD006


title: Input_1

value: triple negative - basal b


title: MDA-MB-231 sphere siNC rep 3


title: PIT_P5-PIT_P6-G12-AD007


title: MDA-MB-231 5d sphere rep 1

value: 5d MDA-MB-231 mammospheres

value: 5 day


title: PIT_P1-PIT_P2-E8-AD002

value: Pituitary

value: male


title: MDA-MB-231 5d sphere rep 2


title: MDA-MB-231 sphere siNC rep 2


title: PIT_P1-PIT_P2-F2-AD001


title: MDA-MB-231 sphere siNC rep 1


title: PIT_P3-PIT_P4-B3-AD004


title: MDA-MB-231 16h sphere rep 2

value: 16h MDA-MB-231 mammospheres

value: 16 hour


title: PIT_P7-PIT_P8-D5-AD001


title: PIT_P3-PIT_P4-G3-AD002


title: MDA-MB-231 adherent cells rep 2

value: adherent

value: 0 hour


title: MDA-MB-231 adherent cells rep 1


title: PIT_P5-PIT_P6-H1-AD004


title: MDA-MB-231 mammospheres, SOX2_ChIPSeq 2

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 300 bp to create summary windows. Alignments were done using Bowtie2
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

growth_protocol: MDA-MB-231 spheres were cultured in DMEM/F12 supplemented with 1-in-50 B27, 20ng/ml EGF, 20ng/ml FGF in suspension in non-adherent plates for described incubation times.

extract_protocol:
Following ChIP protocol, DNA was recovered using phenol-chloroform extraction protocol.
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® following the manufacturer's instructions.

value: SOX2 (Cell signalling, Catalog# 5024S)


title: PIT_P3-PIT_P4-H9-AD004


title: PIT_P7-PIT_P8-D6-AD002


title: PIT_P7-PIT_P8-H11-AD012


title: PIT_P5-PIT_P6-E5-AD010


title: MDA-MB-231 mammospheres, EZH2_ChIPSeq 2

value: EZH2 (Active Motif, Catalog# 39875)


title: PIT_P3-PIT_P4-B3-AD001


title: PIT_P3-PIT_P4-H11-AD007


title: MDA-MB-231 mammospheres, Input DNA (control for EZH2 and SOX2)

description: Input


title: PIT_P7-PIT_P8-H4-AD012


title: MDA-MB-231 mammospheres, EZH2_ChIPSeq 1


title: PIT_P5-PIT_P6-C5-AD004


title: PIT_P5-PIT_P6-C12-AD004


title: PIT_P5-PIT_P6-F1-AD002


title: MDA-MB-231 sphere-derived cells, SCIRT_ChartSeq 1

data_processing:
Library strategy: Chart-Seq
Alignment: Sequence reads were obtained and mapped to the human (Feburary, 2009) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 300 bp to create summary windows. Alignments were done using Bowtie 1.0.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm using default settings.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig

extract_protocol:
Following CHART protocol, RNase H elution step was used to recover genomic DNA associated with endogenous SCIRT transcripts and genomic DNA associated with an RNA control corresponding to E.coli LacZ sequence.
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® following the manufacturer's instructions.

value: 16h MDA-MB-231 sphere-derived cells

tag: oligonucleotide

value: SCIRT


title: PIT_P7-PIT_P8-A6-AD008


title: PIT_P5-PIT_P6-G10-AD008


title: MDA-MB-231 sphere-derived cells, Input DNA

tag: cell type

value: input DNA


title: PIT_P1-PIT_P2-B8-AD012


title: PIT_P3-PIT_P4-G6-AD012


title: MDA-MB-231 16h sphere rep 1


title: PIT_P3-PIT_P4-C5-AD010


title: PIT_P5-PIT_P6-H10-AD006


title: PIT_P5-PIT_P6-A10-AD007


title: PIT_P7-PIT_P8-B1-AD010


title: MDA-MB-231 sphere-derived cells, LacZ_ChartSeq 1

value: LacZ


title: MDA-MB-231 mammospheres, SOX2_ChIPSeq 1


title: CLL_no1

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

country: Germany

institute: Max Planck Institute for Molecular Genetics

description:
bisulfite treated genomic DNA
RRBS

data_processing:
Bulk RRBS processing: Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.05 -s 16 -w 100 -S 1 -R -u -m 0. Methylation rates were called using custom scripts and subsequently filtered for coverage (min 5).
Single cell processing: Adapter clipping and quality trimming using cutadapt. Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.1 -s 12 -q 20 -w 100 -S 1 -R -u -m 0. Methylation rates were called using mcall  and subsequently filtered for coverage (min 10, max 250).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file from coverage filtered Bed file (<chr> <start> <end> <methylation rate>)

source_name: blood

extract_protocol:
Genomic DNA for RRBS library generation was isolated and quantified using previously described methods (Boyle et al., 2012)
RRBS library generation was performed as previously described (Boyle et al., 2012). Genomic DNA was enzymatically sheered using MspI endonuclease (New England Biolabs, catalogue number R0106L), which exposes a CpG site at the 3’-end. Barcoded Illumina sequencing adapters were added to each end of the DNA strand. The DNA was then subjected to two rounds of sodium bisulfite conversions using the Epitect Bisulfite Conversion Kit (Qiagen, catalogue number 59104). A final, large-scale PCR was conducted on the converted DNA (which uracil is replaced by thymine) and the product was submitted for sequencing.

value: CLL

tag: patient id

tag: diagnosis

tag: ighv

tag: treatment status


title: CLL_no2

description:
bisulfite treated genomic DNA
RRBS


title: CLL_no3

description:
bisulfite treated genomic DNA
RRBS


title: MBL_no1

description:
bisulfite treated genomic DNA
RRBS

value: MBL


title: MBL_no3

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-C3-AD007


title: MDA-MB-231 sphere-derived cells, SCIRT_ChartSeq 2


title: CLL_no5

description:
bisulfite treated genomic DNA
RRBS


title: MBL_no2

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-F3-AD002


title: MDA-MB-231 sphere-derived cells, LacZ_ChartSeq 2


title: CLL_no4

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-A8-AD006


title: MBL_no5

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-B7-AD007


title: PIT_P3-PIT_P4-A9-AD006


title: MBL_no4

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-C11-AD004


title: MBL20

description:
bisulfite treated genomic DNA
RRBS

value: Mutated


title: MBL19

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-B12-AD012


title: MBL18

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-A7-AD010


title: MBL17

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-B3-AD006


title: PIT_P7-PIT_P8-D1-AD007


title: MBL16

description:
bisulfite treated genomic DNA
RRBS

value: Unmutated


title: MBL15

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-C12-AD001


title: PIT_P1-PIT_P2-A8-AD006


title: MBL12

description:
bisulfite treated genomic DNA
RRBS


title: MBL14

description:
bisulfite treated genomic DNA
RRBS


title: MBL11

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-C6-AD004


title: PIT_P7-PIT_P8-G8-AD001


title: PIT_P1-PIT_P2-A8-AD001


title: PIT_P1-PIT_P2-F6-AD004


title: MBL10

description:
bisulfite treated genomic DNA
RRBS


title: MBL7

description:
bisulfite treated genomic DNA
RRBS


title: MBL8

description:
bisulfite treated genomic DNA
RRBS


title: MBL9

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-F9-AD008


title: PIT_P1-PIT_P2-G7-AD010


title: PIT_P3-PIT_P4-D8-AD010


title: PIT_P7-PIT_P8-H10-AD004


title: PIT_P1-PIT_P2-H9-AD010


title: MBL13

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-H7-AD006


title: MBL3

description:
bisulfite treated genomic DNA
RRBS


title: MBL4

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-F1-AD008


title: MBL2

description:
bisulfite treated genomic DNA
RRBS


title: MBL1

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-C12-AD004


title: PIT_P7-PIT_P8-B6-AD002


title: PIT_P7-PIT_P8-B6-AD004


title: 21A

description:
bisulfite treated genomic DNA
RRBS

value: pre-treatment


title: PIT_P5-PIT_P6-H8-AD001

value: Pituitary


title: 21B

description:
bisulfite treated genomic DNA
RRBS


title: 20C

description:
bisulfite treated genomic DNA
RRBS

value: post-treatment


title: PIT_P5-PIT_P6-F7-AD006

value: male


title: 20B

description:
bisulfite treated genomic DNA
RRBS


title: 20A

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-B10-AD002


title: PIT_P3-PIT_P4-C9-AD006


title: PIT_P7-PIT_P8-E6-AD004


title: MBL5

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-F10-AD004


title: 19F

description:
bisulfite treated genomic DNA
RRBS


title: 19E

description:
bisulfite treated genomic DNA
RRBS


title: MBL6

description:
bisulfite treated genomic DNA
RRBS


title: 19D

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-C9-AD006


title: 19C

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-A4-AD006


title: 19B

description:
bisulfite treated genomic DNA
RRBS


title: 19A

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-F11-AD004


title: 18D

description:
bisulfite treated genomic DNA
RRBS


title: 18E

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-A1-AD001


title: PIT_P5-PIT_P6-D1-AD007


title: PIT_P7-PIT_P8-G3-AD001


title: 18C

description:
bisulfite treated genomic DNA
RRBS


title: 18B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-H12-AD004


title: 17E

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-G8-AD004


title: PIT_P7-PIT_P8-E3-AD006


title: 17C

description:
bisulfite treated genomic DNA
RRBS


title: 17B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-E6-AD010


title: PIT_P1-PIT_P2-G11-AD006


title: 17D

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-B4-AD006


title: 16E

description:
bisulfite treated genomic DNA
RRBS


title: 17A

description:
bisulfite treated genomic DNA
RRBS


title: 16D

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-C9-AD001


title: PIT_P7-PIT_P8-B3-AD008


title: PIT_P1-PIT_P2-A7-AD007


title: 16C

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-E9-AD001


title: PIT_P3-PIT_P4-E10-AD002


title: 16B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-H1-AD007


title: PIT_P5-PIT_P6-A12-AD007


title: 16A

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-C5-AD007


title: PIT_P3-PIT_P4-F7-AD012


title: PIT_P7-PIT_P8-G8-AD006


title: 15B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-H5-AD007


title: Donor 6-CD8+CD161+ alt splice

type: RNA

city: Houston

first: vanaja

last: konduri

state: Texas

address: One Baylor Plaza

department: Pathology&Immunology

institute: Baylor College of Medicine

description:
Donor 6-CD8+CD161+
RMA expression value derived from Transcriptome Analysis Console v3.0

hyb_protocol: Samples were hybridized with GeneChip Human WT Pico-Clariom D Exon Arrays (Affymetrix) and scanned at the Sequencing and Microarray Facility at the University of Texas MDAnderson Cancer Center.

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

data_processing: Raw data were processed with Transcriptome Analysis Console v3.0 (Affymetrix).  Data analysis and statistical evaluations were performed with R version 3.4.3. Class comparison paired T test was used with an FDR of 0.05% to 0.1%.

label: biotin

source_name: Peripheral blood PBMC

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).

extract_protocol: RNA was isolated from the cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA.

treatment_protocol: CD8+CD161+ and CD8+CD161- T cells were magnetically sorted from healthy donor peripheral blood.

tag: cells

value: CD8+CD161+ T cells

tag: treatment

value: PDAC antigen-loaded autologous DC


title: PIT_P1-PIT_P2-B5-AD012


title: 15A

description:
bisulfite treated genomic DNA
RRBS


title: 14C

description:
bisulfite treated genomic DNA
RRBS


title: Donor 5-CD8+CD161+ alt splice

description:
Donor 5-CD8+CD161+
RMA expression value derived from Transcriptome Analysis Console v3.0


title: Donor 6-CD8+CD161- alt splice

description:
Donor 6-CD8+CD161-
RMA expression value derived from Transcriptome Analysis Console v3.0

value: CD8+CD161- T cells


title: PIT_P5-PIT_P6-C2-AD006


title: 15C

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-G1-AD006


title: 18A

description:
bisulfite treated genomic DNA
RRBS


title: Donor 5-CD8+CD161- alt splice

description:
Donor 5-CD8+CD161-
RMA expression value derived from Transcriptome Analysis Console v3.0


title: PIT_P1-PIT_P2-B9-AD001


title: PIT_P1-PIT_P2-H2-AD012


title: 14B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-G1-AD004


title: PIT_P1-PIT_P2-A5-AD008


title: 14A

description:
bisulfite treated genomic DNA
RRBS


title: Donor 4-CD8+CD161+ alt splice

description:
Donor 4-CD8+CD161+
RMA expression value derived from Transcriptome Analysis Console v3.0


title: 15D

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-B5-AD008


title: PIT_P3-PIT_P4-E7-AD002


title: 13D

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-D9-AD002


title: PIT_P5-PIT_P6-F1-AD006


title: PIT_P3-PIT_P4-E6-AD004


title: Donor 3-CD8+CD161+ alt splice

description:
Donor 3-CD8+CD161+
RMA expression value derived from Transcriptome Analysis Console v3.0


title: 13C

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-G7-AD001


title: PIT_P3-PIT_P4-E6-AD006


title: Donor 3-CD8+CD161- alt splice

description:
Donor 3-CD8+CD161-
RMA expression value derived from Transcriptome Analysis Console v3.0


title: PIT_P7-PIT_P8-F8-AD001


title: PIT_P3-PIT_P4-H7-AD002


title: 13A

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-H3-AD010


title: Donor 2-CD8+CD161+ alt splice

description:
Donor 2-CD8+CD161+
RMA expression value derived from Transcriptome Analysis Console v3.0


title: PIT_P7-PIT_P8-D1-AD006


title: 12B

description:
bisulfite treated genomic DNA
RRBS


title: 12A

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-H11-AD007


title: PIT_P5-PIT_P6-E9-AD008


title: Donor 1-CD8+CD161+ alt splice

description:
Donor 1-CD8+CD161+
RMA expression value derived from Transcriptome Analysis Console v3.0


title: Donor 2-CD8+CD161- alt splice

description:
Donor 2-CD8+CD161-
RMA expression value derived from Transcriptome Analysis Console v3.0


title: PIT_P7-PIT_P8-F6-AD006


title: 11E

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-C10-AD001


title: Donor 1-CD8+CD161- alt splice

description:
Donor 1-CD8+CD161-
RMA expression value derived from Transcriptome Analysis Console v3.0


title: Donor 4-CD8+CD161- alt splice

description:
Donor 4-CD8+CD161-
RMA expression value derived from Transcriptome Analysis Console v3.0


title: 11D

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-E12-AD002


title: PIT_P3-PIT_P4-B10-AD004


title: 13B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-E7-AD006


title: 11C

description:
bisulfite treated genomic DNA
RRBS
Sample excluded from analysis for quality control reasons. Processed data not available.


title: PIT_P7-PIT_P8-B7-AD006


title: PIT_P3-PIT_P4-F8-AD012


title: PIT_P7-PIT_P8-F9-AD012


title: PIT_P1-PIT_P2-B11-AD012


title: 11A

description:
bisulfite treated genomic DNA
RRBS


title: 10E

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-G12-AD012


title: 10D

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-D10-AD008


title: PIT_P7-PIT_P8-H4-AD002


title: 10C

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-E5-AD010


title: PIT_P3-PIT_P4-D10-AD001


title: PIT_P3-PIT_P4-A3-AD007


title: PIT_P7-PIT_P8-C7-AD010


title: 10B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-B1-AD012


title: 11B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-D8-AD002


title: 10A

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P3-PIT_P4-E3-AD007


title: PIT_P5-PIT_P6-F3-AD004


title: P291

city: Düsseldorf

first: Goran

last: Pavic

state: NRW

address: Moorenstrasse 5

department: Neurologische Klinik

institute: Universitätsklinikum Düsseldorf

hyb_protocol: After fragmentation labeled cDNA was hybridized to Applied Biosystems™ Clariom™ S Mouse Gene Expression Microarrays for 16 hr at 45°C and stained by streptavidin/phycoerythrin conjugate, according to the manufacturer's protocol. Fluidics Station 450 was used.

scan_protocol: Using the Affymetrix Calvin Scan Acquisition on the Affymetrix GeneChip Scanner 3000 7G with the Affymetrix GeneChip Command Console Scan Control Version 4.0.0.1567.

data_processing:
Data analyses on Affymetrix CEL files were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probes within each probe set were summarized by GeneSprings’ ExonSSTRMAWithoutStabilization algorithm after quantile normalization of probe-level signal intensities across all samples to reduce interarray variability (Bolstad et al., 2003). Input data preprocessing was concluded by baseline transformation to the median of all samples. After grouping of samples (five biological replicates each) according to their respective experimental condition, a given probe set had to be expressed above background (i.e., fluorescence signal of that probe set was detected within the 20th and 100th percentiles of the raw signal distribution of a given array) in all five replicates in at least one of three conditions to be further analyzed in pairwise comparisons.
Clariom_S_Mouse.r1.pgf
Clariom_S_Mouse.r1.mps

source_name: spinal cord

label_protocol: According to the manufacturer's protocol: 10 ng of total RNA were converted to cDNA, amplified to complementary RNA (cRNA) followed by in vitro transcription and biotin labeling of cDNA.

growth_protocol: We used male wild-type (WT) C57BL/6J mice (Janvier, Le Genest Saint Isle, France). At the beginning of experiments mice weighted 20 to 25 g, were 6 to 12 weeks of age.

extract_protocol: For RNA analysis tissue samples were collected directly after the euthanasia and snap frozen. Total RNA was extracted using the TRIzolTM reagent (Thermofisher Scientific, Waltham, MA, USA).

treatment_protocol: Two models were compared, cerebral (cPT) vs spinal cord photothrombosis (scPT).

tag: condition

value: 7d scPT


title: P287


title: P290


title: P285


title: G2169

source_name: cerebrum

value: 7d cPT


title: G2171


title: 9C

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-C3-AD006


title: PIT_P3-PIT_P4-H5-AD001


title: G2166


title: PIT_P1-PIT_P2-H5-AD004


title: G2128

value: 3d scPT


title: 9B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-A1-AD012


title: PIT_P7-PIT_P8-D9-AD001


title: 9A

description:
bisulfite treated genomic DNA
RRBS


title: 8D

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-D1-AD010


title: PIT_P3-PIT_P4-E2-AD010


title: 8B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-B10-AD010


title: G2200

value: 3d cPT


title: PIT_P5-PIT_P6-H12-AD010


title: PIT_P5-PIT_P6-H5-AD002


title: PIT_P3-PIT_P4-H4-AD004


title: 7C

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-A6-AD004


title: PIT_P5-PIT_P6-A10-AD006


title: G2123


title: 8C

description:
bisulfite treated genomic DNA
RRBS


title: G2126


title: G2127


title: 7B

description:
bisulfite treated genomic DNA
RRBS


title: G2168


title: G2198


title: PIT_P1-PIT_P2-C9-AD001


title: PIT_P5-PIT_P6-E1-AD002


title: PIT_P5-PIT_P6-A5-AD007


title: 7A

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-B8-AD006


title: G2196


title: PIT_P1-PIT_P2-G4-AD012


title: G2195


title: PIT_P5-PIT_P6-G3-AD001


title: 6C

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-E1-AD012


title: 6A

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-C1-AD002


title: PIT_P1-PIT_P2-D11-AD010


title: PIT_P7-PIT_P8-B6-AD010


title: PIT_P3-PIT_P4-H10-AD004


title: 5E

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-A10-AD007


title: G2132

value: 1d scPT


title: G2133


title: PIT_P1-PIT_P2-F4-AD004


title: 5D

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-H9-AD008


title: PIT_P5-PIT_P6-H7-AD001


title: PIT_P1-PIT_P2-G4-AD010


title: 5C

description:
bisulfite treated genomic DNA
RRBS


title: 5B

description:
bisulfite treated genomic DNA
RRBS


title: G2129


title: G2130


title: PIT_P7-PIT_P8-A8-AD008


title: 5A

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-B4-AD002


title: G2193

value: 1d cPT


title: PIT_P7-PIT_P8-F5-AD012


title: 6B

description:
bisulfite treated genomic DNA
RRBS

value: CLL


title: G2190


title: G2189


title: PIT_P1-PIT_P2-D4-AD002


title: 4D

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-A12-AD002


title: PIT_P5-PIT_P6-G4-AD010


title: 4A

description:
bisulfite treated genomic DNA
RRBS


title: 4B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-G6-AD001


title: PIT_P3-PIT_P4-B6-AD010


title: PIT_P7-PIT_P8-F6-AD002


title: PIT_P7-PIT_P8-D3-AD004


title: PIT_P3-PIT_P4-C4-AD004


title: PIT_P5-PIT_P6-G2-AD007


title: 4C

description:
bisulfite treated genomic DNA
RRBS


title: G2192


title: 3C

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-A1-AD010


title: 3B

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P7-PIT_P8-C11-AD006


title: PIT_P5-PIT_P6-A9-AD002


title: PIT_P3-PIT_P4-C3-AD008


title: 3A

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P1-PIT_P2-F4-AD002


title: PIT_P1-PIT_P2-G4-AD008


title: PIT_P3-PIT_P4-D2-AD006


title: G1935

value: Kontrolle scPT


title: 2C

description:
bisulfite treated genomic DNA
RRBS

value: Mutated


title: G1932

value: Kontrolle cPT


title: G1938


title: G1933


title: G1934


title: 2B

description:
bisulfite treated genomic DNA
RRBS

value: pre-treatment


title: PIT_P1-PIT_P2-F8-AD007

value: Pituitary


title: G1930


title: ENDOC-βH1 cells non treated rep 1 -long RNA seq [MON3619]

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

description:
MON3619
processed data file: nanopore_filtered.tsv

data_processing:
All Illumina reads were processed first with cutadapt (version 2.8) to remove the adapter sequences (CTGTAGGCACCATCAAT). Then STAR version 2.7.3a was used to align the reads to transcriptome reference of ENSEMBL build GRCh38.99. The R-package riboWaltz (v1.1.0) was used to calculate the P-site offsets to identify the position of the ribosome P-site.
The nanopore PASSED fastq files were processed using our inhouse BioWDL pipeline TALON-WDL (https://github.com/biowdl/TALON-WDL). This pipeline uses minimap2 version 2.17 (https://github.com/lh3/minimap2) for the alignment with the reference genome GRCh38. Minimap2 settings for noisy nanopore direct RNA-seq were used as recommended by the developer. The alignments are further polished using TranscriptClean version 2.0.2 (https://github.com/mortazavilab/TranscriptClean). Splice junctions were corrected according to known splice junctions that were extracted from the GENCODE gene annotation version 33. Known variants were preserved based on https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/00-common_all.vcf.gz. The final identification of known and novel transcripts was done with the platform agnostic tool TALON version 4.4.2 (https://github.com/mortazavilab/TALON).
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV and Text

source_name: Human fetal pancreatic bulbs

growth_protocol: EndoC-βH1 cells were maintained in low glucose DMEM supplemented with 5.5 μg/ml human transferrin, 10 mM Nicotinamide, 6.7 ng/ml Selenit, 50 μM β-mercaptoethanol, 2% human albumin, 100 units/ml Penicillin and 100 μg/ml streptomycin. Cells were seeded in ECM, fibronectin pre-coated culture plates.

extract_protocol:
Lysates for ribosome profiling libraries were prepared following Ingolia et.al protocol. For long-RNA sequencing, RNA isolation was performed using Trizol extraction.
For generating ribosome profiling libraries Ingolia et.al protocol was followed. Libraries for the direct RNA sequencing were generated using the recommended protocol for the SQK-RNA001 kit (Oxford Nanopore Technologies).
For ribosome profiling Illumina next generation sequencing was performed. For long-RNA sequencing, libraried were loaded on MinION R9.4 flow cells (Oxford Nanopore Technologies) for 48 hours.

treatment_protocol: Inflammatory stress was induced by a mixture of 1000 U/ml IFNγ and 2 ng/ml IL1β for 24 h. For freezing initiation ribosomes cells were treated with 2ug/ml harringtonine for 30 minutes at 37⁰C. Cycloheximide (100ug/ml) was added for 30 seconds. Ten million cells were used per condition.

tag: treatment 1

value: untreated

tag: library

value: Long-RNA sequencing

tag: molecule subtype

value: poly-A mRNA


title: G1931


title: ENDOC-βH1 cells non treated rep 3 -long RNA seq [KOE4644]

description:
KOE4644
processed data file: nanopore_filtered.tsv


title: 2A

description:
bisulfite treated genomic DNA
RRBS

tag: tissue


title: PIT_P7-PIT_P8-A4-AD004

tag: age

value: male


title: ENDOC-βH1 cells treated with cytokines rep 1 -long RNA seq [MON3618]

description:
MON3618
processed data file: nanopore_filtered.tsv

value: IFNγ +IL1β


title: PIT_P5-PIT_P6-G4-AD008

tag: strain


title: PIT_P7-PIT_P8-D8-AD010

tag: Sex


title: PIT_P3-PIT_P4-C12-AD001


title: ENDOC-βH1 cells non treated rep 2 -long RNA seq [KOE4643]

description:
KOE4643
processed data file: nanopore_filtered.tsv


title: PIT_P5-PIT_P6-H9-AD002


title: 1D

description:
bisulfite treated genomic DNA
RRBS

value: Unmutated


title: ENDOC-βH1 cells treated with cytokines rep 3 -long RNA seq [KOE4642]

description:
KOE4642
processed data file: nanopore_filtered.tsv


title: PIT_P5-PIT_P6-D1-AD001


title: 1C

description:
bisulfite treated genomic DNA
RRBS


title: PIT_P5-PIT_P6-F5-AD004


title: PIT_P7-PIT_P8-A2-AD004


title: PIT_P3-PIT_P4-H4-AD010


title: PIT_P7-PIT_P8-C11-AD008


title: G1929


title: PIT_P7-PIT_P8-E11-AD012


title: ENDOC-βH1 cells non treated rep 3 -ribosome profiling [NT2]

description:
NT2_AHVKNCBGXC_S2
processed data file: data_control_rpf_forgeo
named as “co3” in the processed file

tag: treatment 2

value: Harringtonine+Cyclohexamide

value: Ribosome profiling

value: Footprint mRNA


title: ENDOC-βH1 cells treated with cytokines rep 2 -long RNA seq [KOE4641]

description:
KOE4641
processed data file: nanopore_filtered.tsv


title: ENDOC-βH1 cells non treated rep 2 -ribosome profiling [NT1]

description:
NT1_AHVKNCBGXC_S1
processed data file: data_control_rpf_forgeo
named as “co2” in the processed file


title: PIT_P5-PIT_P6-B4-AD001


title: ENDOC-βH1 cells non treated rep 1 -ribosome profiling [EndoNT]

description:
EndoNT_AH3T5CBGX9_S2
processed data file: data_control_rpf_forgeo
named as “co1” in the processed file


title: PIT_P1-PIT_P2-B12-AD008


title: PIT_P5-PIT_P6-A2-AD008


title: seq&Nicd OE-rep3

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

country: China

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome using STAR v2.6.1a_08-27 with default parameters
DESeq2  was used for relative quantitation of genes expression and differential expression analysis.
Genome_build: Ensemble Drosophila melanogaster BDGP6
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

organism: Drosophila melanogaster

source_name: intestinal progenitor cells

extract_protocol:
Drosophila midgut were removed and digested using Elastase (Sigma, cat. no. E0258). About 10000 ISCs labeled with green fluorescent protein (GFP) were sorted using FACSAria II cell sorter (Becton Dickinson) and RNA was harvested using the  Arcturus PicoPure RNA isolation kit (Applied Biosystems). The RNA was then amplified using Arcturus RiboAmp HS PLUS RNA ampliﬁcation kit (Applied Biosystems).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: midgut

value: intestinal progenitor cells

value: adult stage day 7

tag: genotype

value: seq&Nicd overexpressed


title: ENDOC-βH1 cells treated with cytokines rep 3 -ribosome profiling [EndoCyto]

description:
EndoCyto_AH3T5CBGX9_S3
processed data file: data_cyto_rpf_forgeo
named as “cyto3” in the processed file

tag: cell type


title: seq&Nicd OE-rep2


title: PIT_P3-PIT_P4-A3-AD002


title: seq&Nicd OE-rep1


title: PIT_P3-PIT_P4-E4-AD006


title: ENDOC-βH1 cells treated with cytokines rep 2 -ribosome profiling [CYT2]

description:
CYT2_AHVKNCBGXC_S4
processed data file: data_cyto_rpf_forgeo
named as “cyto2” in the processed file


title: PIT_P3-PIT_P4-G6-AD006


title: PIT_P7-PIT_P8-G2-AD007


title: ENDOC-βH1 cells treated with cytokines rep 1 -ribosome profiling [CYT1]

description:
CYT1_AHVKNCBGXC_S3
processed data file: data_cyto_rpf_forgeo
named as “cyto1” in the processed file


title: PIT_P5-PIT_P6-C12-AD001


title: Nicd OE-rep2

value: Nicd overexpressed


title: PIT_P5-PIT_P6-H3-AD006


title: 1B

description:
bisulfite treated genomic DNA
RRBS

value: CLL

tag: patient id


title: 1A

description:
bisulfite treated genomic DNA
RRBS

tag: diagnosis

value: pre-treatment


title: PIT_P5-PIT_P6-E7-AD006

value: Pituitary


title: rJIAPBTregp

city: Utrecht

first: Lisanne

last: Lutter

address: Lundlaan 6

institute: University Medical Center Utrecht

data_processing:
Illumina Nextseq500 reads were trimmed and clipped for quality control in Trimmomatic.
Read quality was checked for each sample using FastQC v0.11.3.
Sequencing reads were mapped against the reference human genome (hg19, NCBI37) using BWA (v0.7.5a, mem –t 7 –c 100 –M -R).
RPKM counts were calculated and log2-transformed.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes RPKMs (log2-transformed) for each sample.

source_name: PB Treg

growth_protocol: Synovial fluid mononuclear cells (SFMCs) and peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll Isopaque and subsequently FACS-sorted based on CD3+CD4+CD25+CD127low (regulatory T cells) and CD3+CD4+CD25-CD127+ (effector T cells).

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex). Libraries were sequenced using the Nextseq500 platform (Illumina), producing single end reads of 75bp.

value: peripheral blood

value: CD4 regulatory T cell

tag: patient

tag: group

value: child


title: PIT_P3-PIT_P4-G1-AD010

value: male


title: PIT_P3-PIT_P4-B7-AD001


title: Nicd OE-rep1


title: PIT_P3-PIT_P4-H4-AD008


title: PIT_P1-PIT_P2-E9-AD004


title: PIT_P1-PIT_P2-B8-AD002


title: PIT_P3-PIT_P4-H2-AD001


title: rJIAPBTreg2


title: PIT_P3-PIT_P4-F11-AD010


title: PIT_P5-PIT_P6-G1-AD001


title: dpn OE-rep2

value: dpn overexpressed


title: rJIAPBTreg3


title: PIT_P1-PIT_P2-F10-AD002


title: Nicd OE-rep3


title: JIASFTreg4

source_name: SF Treg

value: synovial fluid


title: ttk-RNAi-rep3

value: ttk-RNAi


title: rJIAPBTreg1


title: PIT_P3-PIT_P4-E8-AD001


title: PIT_P7-PIT_P8-B1-AD002


title: PIT_P5-PIT_P6-C8-AD002


title: PIT_P7-PIT_P8-G6-AD010


title: JIASFTreg2


title: PIT_P1-PIT_P2-E5-AD002


title: ttk-RNAi-rep2


title: ttk-RNAi-rep1


title: JIASFTreg1


title: PIT_P5-PIT_P6-G11-AD006


title: dpn OE-rep3


title: PIT_P7-PIT_P8-F12-AD006


title: Ctrl-rep3

value: Wild type


title: PIT_P5-PIT_P6-A9-AD008


title: JIASFTeff4

source_name: SF Teff

value: CD4 effector T cell


title: PIT_P3-PIT_P4-B7-AD008

source_name: C57BL/6J Male P56 Mouse Brain


title: dpn OE-rep1

value: midgut


title: Ctrl-rep2

value: intestinal progenitor cells


title: JIASFTeff3


title: PIT_P3-PIT_P4-E1-AD006


title: PIT_P5-PIT_P6-G11-AD001


title: PIT_P5-PIT_P6-F6-AD004


title: JIASFTeff2


title: ttk-RNAi-Su(H)-TA-Dam-rep3

data_processing:
Library strategy: DamID-seq
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 genome using Bowtie v1.1.2 with -v 3 -m 1 parameters.
Peaks were called using MACS version 1.4.2 with default parameters.
Genome_build: Ensemble Drosophila melanogaster BDGP6.
Supplementary_files_format_and_content: bigwig files were generated using Homer package.

source_name: midgut

extract_protocol:
Drosophila DamID was carried out according to iDamIDseq based on a method from Gutierrez-Triana JA et al.2016
Libraries were prepared for sequencing using standard Illumina protocols

value: adult stage day 2

value: ttk-RNAi and Su(H) overexpression


title: JIASFTreg3


title: JIASFTeff1


title: PIT_P5-PIT_P6-B9-AD001


title: PIT_P1-PIT_P2-C10-AD010


title: ttk-RNAi-Su(H)-TA-Dam-rep2


title: PIT_P3-PIT_P4-G11-AD012


title: childPBTregp


title: PIT_P1-PIT_P2-G5-AD007


title: ttk-RNAi-Su(H)-TA-Dam-rep1


title: childPBTreg2


title: PIT_P5-PIT_P6-F11-AD004


title: seq OE-Su(H)-TA-Dam-rep2

value: Seq overexpression and Su(H) overexpression


title: PIT_P5-PIT_P6-D7-AD007


title: PIT_P7-PIT_P8-F12-AD010


title: childPBTreg1


title: PIT_P7-PIT_P8-E8-AD004


title: PIT_P1-PIT_P2-H2-AD008


title: PIT_P1-PIT_P2-B9-AD008


title: seq OE-Su(H)-TA-Dam-rep1


title: PIT_P7-PIT_P8-E12-AD008


title: PIT_P1-PIT_P2-E11-AD002


title: aJIAPBTregp


title: Ctrl-rep1

value: adult stage day 7


title: PIT_P5-PIT_P6-E6-AD007


title: Ctrl-Su(H)-TA-Dam

value: Su(H) overexpression


title: Ttk_oDam-rep3

value: Ttk overexpression


title: PIT_P1-PIT_P2-D8-AD010

value: Pituitary


title: aJIAPBTreg2

value: peripheral blood

value: CD4 regulatory T cell


title: aJIAPBTreg1

value: child


title: PIT_P7-PIT_P8-F5-AD004

value: male


title: PIT_P1-PIT_P2-G9-AD006


title: PIT_P5-PIT_P6-A11-AD004


title: Ttk_oDam-rep2


title: adultPBTreg4

value: adult


title: PIT_P3-PIT_P4-A7-AD012


title: Ttk_oDam-rep1


title: adultPBTreg3


title: PIT_P1-PIT_P2-E6-AD001


title: PIT_P1-PIT_P2-D1-AD008


title: PIT_P5-PIT_P6-D7-AD001


title: Ctrl_oDam-rep3


title: adultPBTreg2


title: PIT_P7-PIT_P8-E10-AD010


title: Ctrl_oDam-rep2


title: adultPBTreg1


title: PIT_P5-PIT_P6-B9-AD008


title: PIT_P1-PIT_P2-D12-AD006


title: PIT_P5-PIT_P6-F11-AD002


title: adultPBTeff4

source_name: PB Teff


title: PIT_P1-PIT_P2-H10-AD012


title: adultPBTeff3


title: PIT_P3-PIT_P4-H11-AD012


title: PIT_P3-PIT_P4-B5-AD012


title: PIT_P7-PIT_P8-G11-AD004


title: PIT_P5-PIT_P6-D5-AD004


title: adultPBTeff2


title: CD5memBC_H11

description: single cell RRBS

data_processing:
Bulk RRBS processing: Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.05 -s 16 -w 100 -S 1 -R -u -m 0. Methylation rates were called using custom scripts and subsequently filtered for coverage (min 10).
Single cell processing: Adapter clipping and quality trimming using cutadapt. Bisulfite-converted reads were aligned to the hg19 reference genome with bsmap using the following parameter: -v 0.1 -s 12 -q 20 -w 100 -S 1 -R -u -m 0. Methylation rates were called using mcall.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file from coverage filtered Bed file (<chr> <start> <end> <methylation rate>)

value: HD

value: CD5+ memory B cell

tag: ighv

tag: treatmentstatus


title: CD5memBC_H12

description: single cell RRBS


title: CD5memBC_H10

description: single cell RRBS


title: PIT_P5-PIT_P6-C11-AD007


title: adultPBTeff1

value: CD4 effector T cell


title: PIT_P3-PIT_P4-B9-AD008


title: CD5memBC_H09

description: single cell RRBS


title: PIT_P1-PIT_P2-F5-AD007


title: CD5memBC_H08

description: single cell RRBS


title: PIT_P1-PIT_P2-A7-AD008


title: PIT_P5-PIT_P6-D10-AD008


title: H3K27ac_SFTregH3

data_processing:
Reads were mapped to the reference genome hg19 with Bowtie 2.1.0 for H3K27ac ChIP-seq using default settings .
Peaks were called using MACS-2.1.0. Enriched regions were identified compared to the input control using MACS2 callpeak--nomodel --exttsize 300 --gsize=hs -p 1e-9.
Differential binding analysis was performed using DiffBind v1.8.5; TMM was used for read normalization. Enhancer gene associations were determined as the nearest TSS to the center of the enhancer and super-enhancer locus. Super-enhancers were identified by employing the ROSE algorithm using a stitching distance of the MACS2 called peaks of 12.5kb, peaks were excluded that were fully contained in the region spanning 1000bp upstream and downstream of an annotated TSS (-t 1000).
Genome_build: hg19
Supplementary_files_format_and_content: Cod file, containing peak coordinates

growth_protocol: Synovial fluid mononuclear cells (SFMCs) and peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll Isopaque density gradient centrifugation, frozen in 10% DMSO and Treg were sorted after thawing.

extract_protocol:
For each sample, cells were crosslinked with 2% formaldehyde and crosslinking was stopped by adding 0.2 M glycine. Nuclei were isolated in 50 mM Tris (pH 7.5), 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, and 1% Triton X-100 and lysed in 20 mM Tris (pH 7.5), 150mMNaCl, 2mMEDTA, 1% NP-40, 0.3% SDS. Lysates were sheared using Covaris microTUBE (duty cycle 20%, intensity 3, 200 cycles per burst, 60-s cycle time, eight cycles) and diluted in 20 mM Tris (pH 8.0), 150 mM NaCl, 2 mM EDTA, 1% X-100. Sheared DNA was incubated overnight with anti-histone H3 acetyl K27 antibody (ab4729; Abcam) pre-coupled to protein A/G magnetic beads. Cells were washed and crosslinking was reversed by adding 1% SDS, 100mM NaHCO3, 200mM NaCl, and 300 µg/ml proteinase K.
DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research), end-repair, a-tailing, and ligation of sequence adaptors was done using Truseq nano DNA sample preparation kit (Illumina). Samples were PCR amplified, checked for the proper size range and absence of adaptor dimers, and barcoded libraries were sequenced 75 bp single-end on an Illumina NextSeq500 sequencer.

value: Juvenile Idiopathic Arthritis

value: synovial fluid

value: regulatory T cells

tag: chip antibody


title: CD5memBC_H07

description: single cell RRBS


title: H3K27ac_SFTregH2

value: anti-histone H3 acetyl K27 antibody (ab4729; Abcam)


title: Ctrl_oDam-rep1

value: midgut

value: adult stage day 2

value: Wild type


title: PIT_P1-PIT_P2-D4-AD008

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


title: PIT_P3-PIT_P4-G9-AD001


title: PIT_P1-PIT_P2-B10-AD008


title: PIT_P5-PIT_P6-G10-AD006


title: PIT_P1-PIT_P2-E5-AD008


title: CD5memBC_G12

description: single cell RRBS


title: H3K27ac_PBTregH3

value: healthy


title: H3K27ac_SFTregH1


title: CD5memBC_G11

description: single cell RRBS


title: PIT_P5-PIT_P6-E10-AD002

value: Pituitary


title: CD5memBC_G10

description: single cell RRBS


title: PIT_P3-PIT_P4-B1-AD002


title: PIT_P7-PIT_P8-A8-AD002


title: CD5memBC_G09

description: single cell RRBS


title: H3K4me1_SFTregD3

data_processing:
Reads were mapped to the reference genome hg38 with BWA for H3K4me1 ChIP-seq using default settings .
Peaks were called using MACS-2.1.0. Enriched regions were identified compared to the input control using MACS2 callpeak--nomodel --exttsize 300 --gsize=hs -p 1e-9.
Differential binding analysis was performed using DiffBind v1.8.5; TMM was used for read normalization. Enhancer gene associations were determined as the nearest TSS to the center of the enhancer and super-enhancer locus. Super-enhancers were identified by employing the ROSE algorithm using a stitching distance of the MACS2 called peaks of 12.5kb, peaks were excluded that were fully contained in the region spanning 1000bp upstream and downstream of an annotated TSS (-t 1000).
Genome_build: hg38
Supplementary_files_format_and_content: Cod file, containing peak coordinates

extract_protocol:
For each sample, cells were crosslinked with 2% formaldehyde and crosslinking was stopped by adding 0.2 M glycine. Nuclei were isolated in 50 mM Tris (pH 7.5), 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, and 1% Triton X-100 and lysed in 20 mM Tris (pH 7.5), 150mMNaCl, 2mMEDTA, 1% NP-40, 0.3% SDS. Lysates were sheared using Covaris microTUBE (duty cycle 20%, intensity 3, 200 cycles per burst, 60-s cycle time, eight cycles) and diluted in 20 mM Tris (pH 8.0), 150 mM NaCl, 2 mM EDTA, 1% X-100. Sheared DNA was incubated overnight with anti-histone H3 (mono methyl K4) antibody (ab8895; Abcam) pre-coupled to protein A/G magnetic beads. Cells were washed and crosslinking was reversed by adding 1% SDS, 100mM NaHCO3, 200mM NaCl, and 300 µg/ml proteinase K.
DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research), end-repair, a-tailing, and ligation of sequence adaptors was done using Truseq nano DNA sample preparation kit (Illumina). Samples were PCR amplified, checked for the proper size range and absence of adaptor dimers, and barcoded libraries were sequenced 75 bp single-end on an Illumina NextSeq500 sequencer.


title: PIT_P1-PIT_P2-E2-AD001

extract_protocol:
The snmC-seq2 protocol was applied to individual nuclei isolated from pituitary pooled from 30 adult male C57BL/6 mice
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.


title: H3K27ac_PBTregH1

value: peripheral blood


title: PIT_P1-PIT_P2-H11-AD002


title: CD5memBC_G08

description: single cell RRBS


title: CD5memBC_G07

description: single cell RRBS


title: PIT_P7-PIT_P8-E3-AD002


title: PIT_P5-PIT_P6-D8-AD010


title: PIT_P1-PIT_P2-G3-AD004


title: CD5memBC_F12

description: single cell RRBS


title: PIT_P1-PIT_P2-E10-AD004


title: H3K4me1_SFTregD2

value: anti-histone H3 (mono methyl K4) antibody (ab8895; Abcam)


title: PIT_P1-PIT_P2-C1-AD001


title: CD5memBC_F11

description: single cell RRBS


title: H3K4me1_SFTregD1


title: PIT_P7-PIT_P8-G7-AD002


title: PIT_P1-PIT_P2-B3-AD004


title: PIT_P1-PIT_P2-E8-AD010


title: H3K27ac_PBTregH2


title: PIT_P3-PIT_P4-G8-AD012


title: H3K4me1_PBTregD3


title: H3K4me1_PBTregD2


title: H3K4me1_PBTregD1


title: PIT_P3-PIT_P4-E1-AD004


title: CD5memBC_F09

description: single cell RRBS


title: PIT_P3-PIT_P4-E3-AD008


title: PIT_P5-PIT_P6-D3-AD012


title: CD5memBC_F08

description: single cell RRBS


title: D32

city: Leicester

first: Izabella

middle: Zofia Anna

last: Pawluczyk

address: University Road

department: Cardiovascular Sciences

institute: University of Leicester

data_processing:
7.5 million reads per sample  -   annotation reference miRbase 20
reads were converted to tags per million (tpm) (no. of reads for particular microRNA divided by total number of mapped reads multiplied by 1 million)
Fold changes of group means between cohorts were calculated.
EdgeR statistical software (Bioconductor) used to evaluate differential expression between cohorts. For normalisation used trimmed mean of M values method based on log fold and absolute gene wise changes in expression between samples.
Supplementary_files_format_and_content: Excel

source_name: Renal Biopsy

extract_protocol:
100ng total RNA converted to microRNA NGS libraries using NEBNEXT library generation kit (New England Biolabs Inc).
Libraries fractionated on a LabChip XT
Samples sequenced on the Illumina NextSeq 500

treatment_protocol: RNA was extracted from biposies using Qagen miRNeasy kit

value: Renal Biopsy

tag: disease state

value: Thin membrane nephropathy


title: D33


title: PIT_P5-PIT_P6-C3-AD004

value: male


title: CD5memBC_F07

description: single cell RRBS

value: HD


title: D21


title: PIT_P5-PIT_P6-H9-AD001


title: D16


title: PIT_P7-PIT_P8-A9-AD012


title: PIT_P1-PIT_P2-H4-AD010


title: CD5memBC_F10

description: single cell RRBS

value: CD5+ memory B cell


title: PIT_P3-PIT_P4-B2-AD002


title: CD5memBC_E12

description: single cell RRBS


title: CD5memBC_E11

description: single cell RRBS


title: PIT_P5-PIT_P6-A6-AD006


title: CD5memBC_E10

description: single cell RRBS


title: D14


title: PIT_P7-PIT_P8-E6-AD006


title: D10


title: PIT_P1-PIT_P2-G6-AD002


title: PIT_P7-PIT_P8-B10-AD012


title: PIT_P3-PIT_P4-G12-AD001


title: PIT_P5-PIT_P6-A9-AD007


title: PIT_P5-PIT_P6-G3-AD004


title: PIT_P7-PIT_P8-C6-AD012


title: C27

value: Membranous nephropathy


title: C12


title: PIT_P5-PIT_P6-D1-AD006


title: PIT_P3-PIT_P4-G4-AD001


title: CD5memBC_E07

description: single cell RRBS


title: PIT_P1-PIT_P2-A5-AD012


title: CD5memBC_D12

description: single cell RRBS


title: PIT_P1-PIT_P2-F1-AD001


title: PIT_P1-PIT_P2-A9-AD012


title: C11


title: C10


title: CD5memBC_D11

description: single cell RRBS


title: PIT_P3-PIT_P4-A4-AD001


title: C8


title: PIT_P5-PIT_P6-E9-AD007


title: CD5memBC_D10

description: single cell RRBS


title: CD5memBC_E09

description: single cell RRBS


title: PIT_P3-PIT_P4-B8-AD002


title: C7


title: CD5memBC_D09

description: single cell RRBS


title: PIT_P3-PIT_P4-B2-AD008


title: PIT_P5-PIT_P6-E3-AD006


title: PIT_P3-PIT_P4-F5-AD008


title: PIT_P1-PIT_P2-E12-AD007


title: CD5memBC_D08

description: single cell RRBS


title: B27

value: IgAN progressor


title: CD5memBC_E08

description: single cell RRBS


title: CD5memBC_D07

description: single cell RRBS


title: PIT_P7-PIT_P8-G4-AD012


title: B25


title: PIT_P3-PIT_P4-C3-AD002


title: PIT_P3-PIT_P4-E3-AD006


title: CD5memBC_C12

description: single cell RRBS


title: B24


title: PIT_P1-PIT_P2-E8-AD012


title: B16


title: PIT_P5-PIT_P6-A12-AD008


title: B13


title: PIT_P1-PIT_P2-B4-AD010


title: PIT_P5-PIT_P6-G4-AD002


title: PIT_P5-PIT_P6-F10-AD001


title: CD5memBC_C11

description: single cell RRBS


title: CD5memBC_C10

description: single cell RRBS


title: PIT_P3-PIT_P4-F1-AD004


title: PIT_P3-PIT_P4-E10-AD006


title: PIT_P5-PIT_P6-C9-AD006


title: A32

value: IgAN non progressor


title: B2


title: CD5memBC_C09

description: single cell RRBS


title: A29


title: PIT_P7-PIT_P8-E11-AD002


title: PIT_P7-PIT_P8-H1-AD006


title: CD5memBC_C07

description: single cell RRBS


title: PIT_P7-PIT_P8-F9-AD006


title: PIT_P5-PIT_P6-B6-AD010


title: PIT_P5-PIT_P6-H4-AD001


title: A15


title: CD5memBC_B12

description: single cell RRBS


title: PIT_P3-PIT_P4-C4-AD006


title: A14


title: PIT_P1-PIT_P2-G12-AD007


title: A13


title: PIT_P5-PIT_P6-A9-AD012


title: PIT_P3-PIT_P4-D11-AD001


title: A8


title: PIT_P5-PIT_P6-D11-AD001


title: Adjacent normal tissue 4

city: Shanghai

first: En-Wei

last: Tao

address: 145 Middle Shandong Road, Shanghai, 200001, China.

institute: Ren-Ji Hospital, Shanghai Jiao-Tong University School of Medicine

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequencing quality was examined by FastQC software and trimmed reads (pass Illumina quality filter, trimmed 3’-adaptor bases by cutadapt) were aligned to mature-tRNA and pre-tRNA sequence getting from GtRNAdb using NovoAlign software (v2.07.11).
The remaining reads are aligned to transcriptome sequences (mRNA/ rRNA /snRNA /snoRNA /piRNA /miRNA).
The expression profiling and differentially expressed tRFs & tiRNAs were then calculated (based on the normalized TPM values).
Genome_build: GtRNAdb and miRBase 21
Supplementary_files_format_and_content: text files include TPM values for each Sample

source_name: frozen mucosal tissue

extract_protocol:
Total RNA was extracted from tissues using Trizol reagent (Life Technologies, USA). The integrity and quantity of RNA were checked before the sequencing experiment. Due to the decoration of tRNA-derived small RNAs which interferes with small RNA-seq library construction, RNA Pretreatment Kit (#: AS-FS-005, Arraystar, USA) included removing 3’- aminoacyl, 3’-cP, phosphorylates 5’-OH, and demethylates m1A, m1G, and m3C were used in order to get efficient cDNA reverse transcription.
After sequentially ligated to 3’ and 5’ small RNA adapters (#: AS-FS-003, Arraystar, USA), cDNA was synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~135-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. Finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer (Agilent, USA). The libraries were denatured and diluted to a loading volume of 1.3ml and loading a concentration of 1.8pM. Diluted libraries were loaded onto reagent cartridge and forwarded to sequencing run on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (#FC-404-2005, Illumina), according to the manufacturer’s instructions.

value: Adjacent normal tissue


title: PIT_P1-PIT_P2-H4-AD008


title: CD5memBC_B09

description: single cell RRBS


title: CD5memBC_B08

description: single cell RRBS


title: PIT_P5-PIT_P6-A10-AD001


title: Adjacent normal tissue 3


title: CD5memBC_C08

description: single cell RRBS


title: PIT_P7-PIT_P8-C5-AD004


title: CD5memBC_B07

description: single cell RRBS


title: CD5memBC_B11

description: single cell RRBS


title: PIT_P7-PIT_P8-E12-AD006


title: CD5memBC_A12

description: single cell RRBS


title: CD5memBC_A11

description: single cell RRBS


title: PIT_P5-PIT_P6-A3-AD012


title: Adjacent normal tissue 2


title: PIT_P7-PIT_P8-A9-AD004


title: Adjacent normal tissue 1


title: PIT_P1-PIT_P2-F1-AD010


title: PIT_P1-PIT_P2-E10-AD006


title: Colorectal cancer tissue 4

value: Colorectal cancer tissue


title: CD5memBC_A10

description: single cell RRBS


title: CD5memBC_B10

description: single cell RRBS


title: Colorectal cancer tissue 3


title: PIT_P7-PIT_P8-C6-AD008


title: PIT_P3-PIT_P4-E2-AD004


title: PIT_P3-PIT_P4-B2-AD010


title: CD5memBC_A09

description: single cell RRBS


title: PIT_P5-PIT_P6-D12-AD008


title: Colorectal cancer tissue 2


title: PIT_P3-PIT_P4-A1-AD002


title: CD5memBC_A07

description: single cell RRBS


title: Colorectal cancer tissue 1


title: CD5memBC_A08

description: single cell RRBS


title: PIT_P5-PIT_P6-A11-AD012


title: PIT_P5-PIT_P6-C7-AD001


title: PIT_P7-PIT_P8-A7-AD004


title: H3K27ac CHIP of endoderm cells [YFH14]

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

data_processing:
Illumina’s bcl2fastq was used to convert bcl files to FASTQ files and de-multiplex the samples.
For each sample, raw reads from re-sequencing were pooled together. Pooled raw reads were filtered based on a mean base quality score > 20, and adapters were trimmed by “trim_galore” (version 0.4). Trimmed reads were mapped to hg19 using Bowtie1 with the parameters “-m1, -v2 --best --strata -X 1500”. For each condition/treatment, aligned read files from replicate samples were merged together using function merge from samtools (Version 1.3.1). For all merged files, duplicates were removed using Picard (Version 1.115).
We used program called findPeaks from Homer (Version 4.8.3) to call all reported ChIP-seq peaks. The basic idea is to identify regions in the genome where we find more sequencing reads than we would expect to see by chance. Peak calling for all samples used pooled input sample as noise control. findPeaks was run default parameters, with “-F 2 -L 0 -C 1.5 -fdr 0.001”.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bedgraph files using bedGraphToBigWig.

source_name: ES derived endoderm cells

growth_protocol: Human embryonic stem cells were cultured with TesR-E8 medium in Matrigel -coated plates. Endoderm cells were induced by endoderm differentiation kit (StemCell Technologies) for 3 days.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: induced endoderm cells

value: anti-H3K27ac (abcam, ab177178)


title: PIT_P1-PIT_P2-H8-AD004


title: PIT_P1-PIT_P2-F6-AD010


title: PIT_P5-PIT_P6-D6-AD007


title: CD5naiBC_H06

description: single cell RRBS

value: CD5+ naive B cell


title: PIT_P7-PIT_P8-C9-AD010


title: CD5naiBC_H05

description: single cell RRBS


title: PIT_P3-PIT_P4-H2-AD002


title: CD5naiBC_H04

description: single cell RRBS


title: CD5naiBC_H03

description: single cell RRBS


title: PIT_P1-PIT_P2-E6-AD004


title: PIT_P7-PIT_P8-F5-AD001


title: H3K27ac CHIP of ES cells [YFH11]

source_name: ES cells


title: H3K27ac CHIP of endoderm cells [YFH12]


title: PIT_P1-PIT_P2-E11-AD004


title: H3K27ac CHIP of endoderm cells [YFH13]


title: H3K27ac CHIP of ES cells [YFH10]


title: PIT_P3-PIT_P4-E10-AD004


title: CD5naiBC_H02

description: single cell RRBS


title: PIT_P5-PIT_P6-H2-AD007


title: PIT_P1-PIT_P2-B7-AD007


title: Kcr CHIP of endoderm cells [YFH8]

value: Pan anti-crotonyllysine rabbit antibody (PTM biolabs., PTM 501)


title: CD5naiBC_G05

description: single cell RRBS


title: PIT_P7-PIT_P8-E10-AD002

value: Pituitary


title: PIT_P5-PIT_P6-G8-AD010


title: PIT_P3-PIT_P4-D1-AD010