title: CEMBA190219_9H_1_CEMBA190219_9H_2_G10_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G10_ad008

status: Public on Oct 08 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: CA

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G10_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G10_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G10_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G10_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G1_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G1_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G1_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G10_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G12_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G1_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G1_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G1_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F9_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F9_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F9_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F9_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F8_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F8_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F9_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F9_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F9_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F8_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F8_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F8_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F7_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F7_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F8_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F7_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_G1_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F7_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F7_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F7_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F6_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F6_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F6_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F5_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F6_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F6_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F5_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F5_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F5_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F5_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F5_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F7_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F4_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F6_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F4_ad012


title: Brain_IV_26w_ART-seq

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

library_source: transcriptomic

data_processing:
Library strategy: ART-seq
Sequence information was extracted in FastQ format using Illumina's bcl2fastq software v1.8.4.
Footprints were mapped to the N. furzeri reference genome using the STAR sequence aligner (version 2.7.1a, (Dobin et al, 2013)).
The relative abundance of footprints per gene was quantified with RSEM (version 1.3.1, (Li & Dewey, 2011))
Genome_build: Nfu_20150522
Supplementary_files_format_and_content: The csv file (FPKM_summary.csv) includes the relative abundance of footprint fragments per gene (FPKM).

molecule: total RNA

organism: Nothobranchius furzeri

source_name: brain

growth_protocol: Animal maintenance was performed as described (Baumgart et al., Aging Cell 2014). To avoid effects of circadian rhythms and feeding, animals were always sacrificed at 10 a.m. in fasted state. For tissue preparation, fish were euthanized with MS-222 and cooled on crushed ice. The protocols of animal maintenance and experimentation were approved by the local authority in the State of Thuringia, Germany.

extract_protocol:
RNA was extracted following manufacturer`s instructions without depletion of ribosomal RNA (ARTseq, Epicentre)
Libraries were prepared following manufacturer's instructions (ARTseq, Epicentre)

tag: tissue

value: brain

value: 26 weeks

tag: rna population

value: ribosome protected fragment (RPFs)


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F6_ad008


title: Brain_II_6w_ART-seq

value: 6 weeks


title: Brain_IV_6w_ART-seq


title: Brain_I_26w_ART-seq


title: Brain_I_6w_ART-seq


title: Brain_III_6w_ART-seq


title: Brain_II_26w_ART-seq


title: Brain_III_26w_ART-seq


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F4_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F3_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F5_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F4_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F3_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F3_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F3_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F3_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F3_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F2_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F3_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F2_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F2_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F2_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F3_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F2_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F4_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F5_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F2_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F2_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F12_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F12_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F12_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F11_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F12_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F11_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F11_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F11_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F11_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F11_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F11_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F10_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F2_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F10_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F10_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F10_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F10_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F1_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F1_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F10_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F1_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F12_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F1_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F12_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F1_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F1_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F12_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E9_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E9_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E9_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E9_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E9_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E8_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F10_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E8_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E7_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E8_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E7_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E7_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E7_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E7_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E7_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F1_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E6_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E6_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E6_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E6_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E6_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E6_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E5_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E5_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E5_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_F4_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E8_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E5_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E8_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E5_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E5_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E8_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E4_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E4_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E4_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E4_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E4_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E3_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E3_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E3_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E4_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E3_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E6_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E3_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E2_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E3_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E3_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E2_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E2_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E2_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E2_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E2_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E12_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E2_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E12_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E12_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E12_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E12_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E4_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E3_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E12_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E11_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E11_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E11_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E12_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E11_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E11_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E11_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E11_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E11_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E10_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E10_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E10_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E10_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E10_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E1_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E1_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D9_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E1_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E1_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D9_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D9_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E1_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D9_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D8_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D9_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D8_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D8_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D9_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D7_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D8_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D8_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D7_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E1_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D8_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D8_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D8_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D7_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E1_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D7_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D7_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D7_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D9_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D6_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D6_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_E10_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D6_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D5_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D5_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D6_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D6_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D5_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_D5_ad010


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title: CEMBA190219_9H_1_CEMBA190219_9H_2_A5_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A5_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A4_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A5_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A4_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A4_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A4_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A4_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A4_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A3_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A3_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A3_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A3_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A2_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A2_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A2_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A2_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A3_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A2_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A6_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A6_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A2_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A5_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A12_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A12_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A12_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A12_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A12_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A2_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A4_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A12_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A12_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A11_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A11_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A11_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A11_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A11_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A11_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A10_ad012


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A10_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A10_ad008


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A10_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A10_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A10_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A10_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A1_ad001


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A12_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A1_ad006


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A10_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A1_ad004


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A1_ad007


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A1_ad010


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A11_ad002


title: CEMBA190219_9H_1_CEMBA190219_9H_2_A1_ad002


title: MU01-3146-GS7

type: RNA

city: Rensselaer

first: Martin

last: Tenniswood

address: 1 Discovery Drive

institute: miR Scientific LLC

hyb_protocol: Following labeling, 21.5uL of biotin-labeled samples were hybridized for 16 hr at 48C on GeneChip miRNA4.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G with AGCC software.

data_processing: CEL files were analyzed for quality using Affymetrix Transcriptome Analysis Console 4.0 software, and the RMA-DBAG was used for summarization

label: biotin

organism: Homo sapiens

source_name: Urine

label_protocol: Standard Affymetrix microRNA labeling protocol

extract_protocol: Standard urine exosome RNA isolation method by Norgen Biotek Corp.

value: Urine

tag: histopathology

value: Gleason Score 7


title: MU01-3160-GS7


title: MU01-3150-GS7


title: MU01-3142Ctrl

value: Control


title: MU01-3158-GS6

value: Gleason Score 6


title: MU01-3155-GS7


title: MU01-3136-GS7


title: MU01-3104-GS7


title: MU01-3161-GS7


title: MU01-3087Ctrl


title: MU01-3110-GS7


title: MU01-3117Ctrl


title: MU01-3049Ctrl


title: MU01-3057-GS9

value: Gleason Score 9


title: MU01-3135Ctrl


title: MU01-3082Ctrl


title: MU01-3123Ctrl


title: MU01-3051Ctrl


title: MU01-3048-GS6


title: MU01-3035-GS6


title: MU01-3037Ctrl


title: MU01-3041-GS7


title: MU01-3083Ctrl


title: MU01-3010-GS7


title: MU01-3026-GS6


title: MU01-3034-GS6


title: MU01-3029Ctrl


title: MU01-3013Ctrl


title: MU01-3009-GS6


title: MU01-3006Ctrl


title: MU01-2965-GS6


title: MU01-2970-GS7


title: MU01-2963Ctrl


title: MU01-2960Ctrl


title: MU01-2973-GS7


title: MU01-2993-GS7


title: MU01-2886-GS7


title: MU01-2955Ctrl


title: MU01-2891-GS6


title: MU01-2894-GS6


title: MU01-2971-GS7


title: MU01-2916-GS7


title: MU01-2912-GS6


title: MU01-2930-GS8

value: Gleason Score 8


title: MU01-2942-GS8


title: MU01-2959-GS7


title: MU01-2934Ctrl


title: MU01-2915-GS6


title: MU01-2953-GS6


title: MU01-2908Ctrl


title: MU01-2872-GS7


title: MU01-2944Ctrl


title: MU01-2871Ctrl


title: MU01-2864-GS6


title: MU01-2856Ctrl


title: MU01-2838-GS6


title: MU01-2852-GS6


title: MU01-2857-GS7


title: MU01-2845Ctrl


title: Gala_nonhost_72hpiVP102_rep2

city: BEAUCOUZE

first: Emilie

last: VERGNE

address: 42 rue Georges MOREL

country: France

institute: INRAE

description: Gala' apple variety, sampled 72 hours post inoculation with nonhost pathogen Venturia pyrina VP102 strain

hyb_protocol: The hybridization performed on a rotative Agilent Hybridization Oven, 17h at 65°C, 10g. Afterwards, the slide were washed, and scanned.

scan_protocol: Scanning was performed on 2µm NimbleGen MS 200 Scanner

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

organism: Malus domestica

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), After purification, labelled samples were combined as 30 pmol for each dye and co-hybridized to the arrays.

growth_protocol: Greenhouse growth conditions is as described in Parisi and Lespinasse (1996): Parisi L, Lespinasse Y 1996. Pathogenicity of Venturia inaequalis strains of race 6 on apple clone (Malus sp.). Plant Disease 80: 1179-1183.

extract_protocol: RNA was extracted with the kit NucleoSpin RNA Plant (Macherey Nagel, Düren, Germany) according to the manufacturer’s instructions but with a modification: 4% of PVP40 (400 mg for 100 ml) were mixed with the initial lysis buffer RAP before use.

treatment_protocol: Mode of inoculum preparation is as described in Parisi and Lespinasse (1996): Parisi L, Lespinasse Y 1996. Pathogenicity of Venturia inaequalis strains of race 6 on apple clone (Malus sp.). Plant Disease 80: 1179-1183. Briefly, the youngest leaf of actively growing shoots was tagged and the plants sprayed with a conidial suspension (2 × 105 conidia ml-1). No treatment correspond to T0 = time zero, so the corresponding plants have literally undergone none treatment.

tag: tissus

value: leaf

tag: genotype

value: Gala' variety

tag: phenotype

value: resistant

tag: treatment


title: Gala_nonhost_T0_with72h_rep2

description: Gala' apple variety, sampled just before inoculation with nonhost pathogen Venturia pyrina VP102 strain

value: healthy, no inoculation

value: no treatment


title: Gala_nonhost_T0_with72h_rep1


title: Gala_nonhost_24hpiVP102_rep2

description: Gala' apple variety, sampled 24 hours post inoculation with nonhost pathogen Venturia pyrina VP102 strain


title: Gala_nonhost_24hpiVP102_rep1

value: inoculation with nonhost pathogen Venturia pyrina


title: GalaRvi6_host_72hpiEUB04_rep1

description: GalaRvi6 transgenic apple line, carrying the Rvi6 resistance gene, sampled 72 hours post inoculation with host pathogen Venturia inaequalis EUB04 strain

value: GalaRvi6 overexpressing transgenic line


title: MU01-2842-GS6


title: Gala_nonhost_T0_with24h_rep1


title: GalaRvi6_host_72hpiEUB04_rep2

value: inoculation with host pathogen Venturia inaequalis EUB04 strain


title: Gala_nonhost_72hpiVP102_rep1


title: MU01-2832Ctrl


title: MU01-2810Ctrl


title: Gala_host_72hpiEUB04_rep2

description: Gala' apple variety, sampled 72 hours post inoculation with host pathogen Venturia inaequalis EUB04 strain

value: susceptible


title: Gala_nonhost_T0_with24h_rep2


title: MU01-2837Ctrl


title: Gala_host_24hpiEUB04_rep2

description: Gala' apple variety, sampled 24 hours post inoculation with host pathogen Venturia inaequalis EUB04 strain


title: MU01-2802-GS6


title: MU01-2801-GS7


title: MU01-2786-GS6


title: MU01-2783-GS7


title: MU01-2778-GS9


title: GalaRvi6_host_8hpiEUB04_rep2

description: GalaRvi6 transgenic apple line, carrying the Rvi6 resistance gene, sampled 8 hours post inoculation with host pathogen Venturia inaequalis EUB04 strain


title: Gala_host_72hpiEUB04_rep1


title: GalaRvi6_host_24hpiEUB04_rep1

description: GalaRvi6 transgenic apple line, carrying the Rvi6 resistance gene, sampled 24 hours post inoculation with host pathogen Venturia inaequalis EUB04 strain


title: GalaRvi6_host_8hpiEUB04_rep1


title: Gala_host_24hpiEUB04_rep1


title: MU01-2749-GS7


title: MU01-2764Ctrl


title: Gala_host_8hpiEUB04_rep2

description: Gala' apple variety, sampled 8 hours post inoculation with host pathogen Venturia inaequalis EUB04 strain


title: GalaRvi6_host_T0_rep1

description: GalaRvi6 transgenic apple line, carrying the Rvi6 resistance gene, sampled just before inoculation with host pathogen Venturia inaequalis EUB04 strain


title: GalaRvi6_host_T0_rep2


title: MU01-2745-GS7


title: MU01-2746-GS6


title: MU01-2719-GS6


title: MU01-2732Ctrl


title: MU01-2741-GS6


title: MU01-2716Ctrl


title: N10

city: Tampa

first: Feng

last: Cheng

state: FL

address: 12901 Bruce B Downs Blvd MDC 30

department: Department of Pharmaceutical Science

institute: University of South Florida

description: Smoking

hyb_protocol: The Molecular Genomics Core at the H. Lee Moffitt Cancer Center & Research Institute performed the Affymetrix arrays.

scan_protocol: Affymetrix Gene Chip Scanner

data_processing: Affymetrix Expression console was used to normalize raw microarray data and to summarize expression of the probe set

label: Biotin

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen, USA) according to the manufacturer's instructions

treatment_protocol: Nuli-1 cells were treated 1 day in normal media, and then two days in media containing 5% CSE, cells were passaged every 3 days. Control Nuli-1 cell culture in normal media and passaged at same time. Both groups are cultured for more than 3 years.

tag: cell line

tag: cell type

value: human bronchial epithelial cell line

tag: group

value: 5% cigarette smoke extract (CSE)

tag: treatment time

value: 3 years


title: Gala_host_T0_rep1

description: Gala' apple variety, sampled just before inoculation with host pathogen Venturia inaequalis EUB04 strain


title: MU01-2701Ctrl

value: Urine


title: N03

description: Control

label_protocol: The Molecular Genomics Core at the H. Lee Moffitt Cancer Center & Research Institute performed the Affymetrix arrays.

value: Control


title: N12

description: Smoking


title: MU01-2668Ctrl


title: MU01-2754-GS6

value: Gleason Score 6


title: N02

description: Control


title: N0

description: Control


title: donor29_rectum_repA

city: Atlanta

first: Kiera

last: Berger

state: GA

address: 950 Atlantic Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

data_processing:
Alignment and Gene Level Raw counts: Reads were aligned with STAR v2.6.1d to GRCh38 using the Gencode v29 primary assembly sequence and annotation. Default parameters were used with --alignSJoverhangMin 8 --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 5 5 5 5 --twopassMode Basic. Parameter --quantMode GeneCounts was also added to obtain raw counts at the gene level.
PSI collapsed exon model: A collapsed model of the Gencode v29 annotation file was created using the DEXSeq prepare annotation python script, keeping only "exonic_part" features.
PSI Inclusion Read (IR) calculation: the GRCh38 fasta index, collapsed exon model, and sample bam file were input in bedtools-2.27.0 coverageBed with parameters -split -s -sorted to obtain overlap of mapped reads with each exonic part.
PSI Exclusion Read (ER) calculation: the splice junction coordinates and counts output by STAR was transformed into intron coordinates and counts in BED format and was input in bedtools-2.27.0 intersectBed along with the GRCh38 fasta index and collapsed exon model with parameters -wao -f 1.0 -s -sorted to obtain a count of the number of reads whose uncovered regions between read splits encompass each exonic part.
PSI Calculation: For each exonic part, normalized IR counts were divided by the sum of normalized IR and ER counts to obtain a score between 0 and 1. IR counts were normalized by both feature length and read length while ER counts were normalized by just read length.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: For each sample, tab-delimited text file includes exonic part IDs, genomic coordinates and strand as well as inclusion and exclusion read counts and calculated percent spliced in (PSI)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: rectum

extract_protocol:
RNA was extracted from tissue biopsies and RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq stranded mRNA library kit
Libraries were prepared for 100bp paired-end sequencing following standard Illumina protocols

value: male

tag: ancestry

value: AA

tag: age at sampling

tag: disease state (diagnosis)

value: Crohn's disease

value: rectum


title: donor32_ileum_repB

source_name: ileum

tag: Sex

value: EA

value: ileum


title: donor16_rectum_repB

value: female

value: ulcerative colitis


title: donor11_ileum_repA


title: GalaRvi6_host_24hpiEUB04_rep2

value: leaf

value: GalaRvi6 overexpressing transgenic line

value: resistant


title: donor11_rectum_repB


title: MU01-2849-GS7

value: Gleason Score 7


title: IP2

city: Shanghai

first: Youqiong

last: Ye

address: 280 Chongqing south road

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
All samples were sequenced by Illumina HiSeq 2500 with single-end 50-bp read length. The deep sequencing data were mapped to human genome version 37 (GRCh37).
After reads were mapped with hisat2, Stringtie was  used to calculate the read counts of each gene which represent their transcriptional expression level. Then we performed DEseq2 to calculate normalized reads counts in each gene and detect enriched transcripts with a double threshold on the log2-fold change (>1) and the correspondent statistical significance (P-value < 0.05).
Genome_build: GRCh37
Supplementary_files_format_and_content: excel file containing log2-fold change between input and IP samples

molecule: polyA RNA

source_name: human cell line

growth_protocol: GSC11 cells were cultured as tumorspheres in DMEM/F12 medium supplemented with B27 supplement (Life Technologies), bFGF and EGF (20 ng/mL each). Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
total RNA was isolated from GSC11 cells using Trizol reagent (Thermo Fisher). Poly (A) mRNA was subsequently purified from total RNA using GenElute™ mRNA Miniprep Kit (Sigma). For IP samples, mRNA was sonicated and subjected to IP using YTHDF2 antibody (Proteintech #24744-1-AP).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Glioblastoma stem cell line

tag: antibody

value: anti-YTHDF2 antibody; Proteintech #24744-1-AP


title: Gala_host_T0_rep2

value: Gala' variety

value: healthy, no inoculation

value: no treatment


title: donor7_rectum_repA


title: MU01-2636-GS6

value: Urine

value: Gleason Score 6


title: MU01-2642-GS7


title: IP1


title: MU01-2634Ctrl

value: Control


title: Input2


title: Input1


title: SuVar_Rep1 [5C]

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

country: India

institute: CSIR Centre for Cellular and Molecular biology

data_processing:
Library strategy: 5C
Illumina bcl2fastq used for basecalling.
A custom reference was created using all possible combinations of sequencing primers used in this study.
Reads were aligned to the custom reference build using bowtie2.
Interaction frequency lists were calculated using a custom Perl script.
Normalized interaction scores were obtained using the my5C web tools.
Genome_build: dm3
Supplementary_files_format_and_content: *.interactions.txt: Normalized pairwise interaction scores.

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown in Schneider’s insect media with 10% heat-inactivated FBS and 1% Penicillion-Streptomycin at 25 degrees centigrade.

extract_protocol:
5C experiment was conducted as described in Dostie and Dekker 2007.
Sequencing library was prepared following manufacturer’s protocol.

treatment_protocol: 1ug of dsRNA against HP1alpha or Su(var)39, prepared using in-vitro transcription, was transfected using Qiagen Effectene. Cells were incubated for 3 days before harvesting.

value: Embryonic cell line

tag: RNAi

tag: replicate


title: SuVar_Rep2 [5C]


title: MU01-2878-GS6

tag: tissue


title: MU01-2597-GS10

tag: histopathology

value: Gleason Score 10


title: HP1_Rep2 [5C]

value: HP1 alpha


title: MU01-2602Ctrl


title: MU01-2654-GS9

value: Gleason Score 9


title: HP1_Rep1 [5C]


title: N13

description: Smoking

value: human bronchial epithelial cell line

value: 5% cigarette smoke extract (CSE)

value: 3 years


title: GFP_Rep2 [5C]

value: GFP (control)


title: MU01-2593Ctrl


title: MU01-2587Ctrl


title: MU01-2583Ctrl


title: MU01-2595-GS8

value: Gleason Score 8


title: GFP_Rep1 [5C]


title: S2_5C_Rep3 [5C]

tag: genotype/variation

value: Wildtype


title: S2_5C_Rep1 [5C]


title: S2_5C_Rep2 [5C]


title: S2_Control [5C]

description: Unprocessed control


title: MU01-2575-GS7

value: Gleason Score 7


title: MU01-2582-GS7


title: MU01-2569Ctrl


title: SuVar_Rep3 [RNA-seq]

data_processing:
Illumina bcl2fastq used for basecalling.
Quality trimming and adapter contaminated reads were removed using CutAdapt.
Reads were aligned to the dm3 build of Drosophila using STAR.
Transcript quantification was done using RSEM.
Differentially expressed genes were identified using EBSeq.
Genome_build: dm3
Supplementary_files_format_and_content: RNAi_geneLevelTPMs.tsv: TPM values.
Supplementary_files_format_and_content: RNAi_transcriptLevelTPMs.tsv: TPM values.
Supplementary_files_format_and_content: HP1_S2.results: DEG analysis.
Supplementary_files_format_and_content: Suvar_S2.results: DEG analysis.

extract_protocol:
RNA was extracted using 1ml TRIzol per million cells.
Library was prepared following manufacturer’s protocols.


title: MU01-2535-GS8


title: SuVar_Rep2 [RNA-seq]


title: HP1_Rep3 [RNA-seq]


title: MU01-2565-GS9


title: MU01-2515Ctrl


title: MU01-2526-GS8


title: MU01-2521Ctrl


title: MU01-2486-GS8


title: MU01-2487-GS7


title: HP1_Rep1 [RNA-seq]


title: HP1_Rep2 [RNA-seq]


title: S2_Rep2 [RNA-seq]


title: SuVar_Rep1 [RNA-seq]


title: S2_Rep3 [RNA-seq]


title: MU01-2443Ctrl


title: MU01-2446-GS7


title: MU01-2456-GS6


title: MU01-2420Ctrl


title: MU01-2439-GS7


title: TOF1_wt_60min_HU_rep2_input

city: Brighton

first: Andrea

last: Keszthelyi

address: University of Sussex, Sussex House, Falmer

department: Genome Damage and Stability Centre

country: United Kingdom

institute: University of Sussex

data_processing:
ChIP-seq: Sequences were aligned to a reference genome (R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database) using Bowtie 2 generating a SAM output file for each sample (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Reads from MySeq were trimmed 25 bp from 3’ and 1 bp from the 5’ end, while reads from NextSeq were not trimmed.
ChIP-seq: SAM files were then converted into sorted BAM files by using SAMtools (http://samtools.sourceforge.net/):
ChIP-seq: Duplicates were then removed using picard (https://broadinstitute.github.io/picard)
ChIP-seq: BAM files were used for Model-based Analysis of ChIP-Seq (MACS2). We used the ‘call peak’ function which also generates genome wide score data. These were used to generate fold enrichment tracks.
ChIP-seq: The data then was sorted into 50 bp bins, normalized to have a mean value of 1, and used for meta data analysis using custom-made R programs
Sync-seq analysis was done by using LocalMapper shell script and Repliscope R package from https://github.com/DNAReplicationLab/ (Dzmitry G Batrakou1, Carolin A Müller1, Rosemary H C Wilson1 and Conrad A Nieduszynski, DNA copy number measurement of genome replication dynamics by high-throughput sequencing – the sort-seq, sync-seq and MFA-seq family – accepted to Nature protocols)
Genome_build: R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database
Supplementary_files_format_and_content: ChIP-seq .wig files were generated by custom R script. Scores represent RPA1 enrichment.
Supplementary_files_format_and_content: Sync-seq .wig files were generated by custom R script. Scores represent ratio between non-replicated and replicated samples.

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

extract_protocol:
Cells were lysed using of 0.5 mm zirconia/silica beads and the FastPrep-24 (MP Biomedicals). . Samples were sonicated using the Focused-Ultrasonicator (Covaris) (Average incident power – 7.5 Watts, Peak Incident Power – 75 Watts, Duty Factor – 10 %, Cycles/Burst – 200, Duration – 20 min for G1 samples and 13.5 for HU and released samples) before ChIP-seq.
Following ChIP with RPA1 antibody (1:10000, Agrisera, AS07214) samples were de-cross-linked by overnight incubation on 65°C with 5 M NaCl and proteinase K (Invitrogen), then RNAse treated. The resulting ssDNA was used to synthetize second strand with random primers (8N, 3 mg/ml stock) by T4  polymerase (NEB). The resulting dsDNA was used to create libraries using the Ultra II library kit (NEB) as per the manufacturer’s instructions with 13 cycles at the amplification step.

treatment_protocol: Cells were grown in YP +2% raffinose to mid-log phase at 25 °C, before being arrested with 10 µg/ml alpha factor peptide. After 1hr 45 min 2% galactose and an additional 5 µg/ml alpha factor was added. After 2hr, when cells were >90% unbudded, 25 µg/ml doxycycline was added. 15 minutes after doxycycline addition temperature was switched to 37°C  and incubated for 1hr. Cells were then released by washing 3 times with pre-heated YP 2% raffinose 2% galactose with 25 µg/ml doxycycline and resuspended in the same media supplemented with 200 mM HU. Time 0 was taken as the time from the first wash. Samples were then incubated for 1 hr at 37°C before being fixed by resuspending in YP + 1% formaldehyde (Sigma) for 45 min at 25 °C. 125 mM glycine was then added followed by a 5 min incubation at 25 °C. Cells were washed with PBS before being pelleted and snap-frozen in liquid nitrogen.

tag: strain

tag: genotype

value: JB1991 + TOF1::tof1-codon-optimised-wildtype (NATNT2)

tag: chip antibody

value: none (input)


title: mrc1_60min_HU_rep2_RPA

value: Mata mrc1::NAT ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3

value: RPA1 antibody (1:10000, Agrisera, AS07214)


title: mrc1_60min_HU_rep2_input


title: mrc1_60min_HU_rep1_RPA


title: Gala_host_8hpiEUB04_rep1

tag: tissus

value: leaf

value: Gala' variety

tag: phenotype

value: susceptible

tag: treatment

value: inoculation with host pathogen Venturia inaequalis EUB04 strain


title: MU01-2405Ctrl

value: Urine

value: Control


title: MU01-2462-GS7


title: MU01-2417-GS9

value: Gleason Score 9


title: S2_Rep1 [RNA-seq]

tag: cell line

tag: cell type

value: Embryonic cell line


title: TOF1_wt_60min_HU_rep2_RPA


title: tof1co830rad9_80minrelease_rep1

description: tof1co830rad9_80minreleaseratio_rep1.wig

data_processing:
Library strategy: Sync-seq
ChIP-seq: Sequences were aligned to a reference genome (R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database) using Bowtie 2 generating a SAM output file for each sample (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Reads from MySeq were trimmed 25 bp from 3’ and 1 bp from the 5’ end, while reads from NextSeq were not trimmed.
ChIP-seq: SAM files were then converted into sorted BAM files by using SAMtools (http://samtools.sourceforge.net/):
ChIP-seq: Duplicates were then removed using picard (https://broadinstitute.github.io/picard)
ChIP-seq: BAM files were used for Model-based Analysis of ChIP-Seq (MACS2). We used the ‘call peak’ function which also generates genome wide score data. These were used to generate fold enrichment tracks.
ChIP-seq: The data then was sorted into 50 bp bins, normalized to have a mean value of 1, and used for meta data analysis using custom-made R programs
Sync-seq analysis was done by using LocalMapper shell script and Repliscope R package from https://github.com/DNAReplicationLab/ (Dzmitry G Batrakou1, Carolin A Müller1, Rosemary H C Wilson1 and Conrad A Nieduszynski, DNA copy number measurement of genome replication dynamics by high-throughput sequencing – the sort-seq, sync-seq and MFA-seq family – accepted to Nature protocols)
Genome_build: R64-1-1, Saccharomyces cerevisiae S288c assembly from Saccharomyces Genome Database
Supplementary_files_format_and_content: ChIP-seq .wig files were generated by custom R script. Scores represent RPA1 enrichment.
Supplementary_files_format_and_content: Sync-seq .wig files were generated by custom R script. Scores represent ratio between non-replicated and replicated samples.

extract_protocol:
Cells were lysed using of 0.5 mm zirconia/silica beads and the FastPrep-24 (MP Biomedicals). . Samples were sonicated using the Focused-Ultrasonicator (Covaris) (Average incident power – 7.5 Watts, Peak Incident Power – 75 Watts, Duty Factor – 10 %, Cycles/Burst – 200, Duration – 20 min for G1 samples and 13.5 for HU and released samples), RNase treated then purified with a Qiagen PCR purification kit.
25-50 ng of genomic DNA was used for library preparation using the Ultra II library kit (NEB) as per the manufacturer’s instructions with 6-7 cycles at the amplification step.

treatment_protocol: Cells were grown in YPD to mid-log phase before either HU being added to 200 mM for 120 minutes (for Rad53 activation experiments in figure 5A) or for experiments started with a G1 arrest, mid-log cells were treated with 10 µg/ml alpha factor peptide. To release cultures into the cell cycle, when cells were >90% unbudded, cultures were washed 3 times in YPD and re-suspended after the third wash in YPD containing 200 mM HU. Time 0 was designated as the time from the first wash. Time points were taken as indicated. For release from HU experiments, HU-containing media was washed off of cells by washing 3 times with YPD before re-suspending in YPD. Time 0 is taken as the time from the first YPD wash. Pellets from 2 ml cultures were collected at the given timepoints.

value: JB1589 + rad9::KanMX


title: tof1co830rad9_HU_rep2


title: MU01-2344Ctrl


title: tof1co830rad9_80minrelease_rep2

description: tof1co830rad9_80minreleaseratio_rep2.wig


title: mrc1_60min_HU_rep1_input


title: tof1co830rad9_G1_rep2

description:
tof1co830rad9_HUratio_rep2.wig
tof1co830rad9_80minreleaseratio_rep2.wig


title: MU01-2380Ctrl


title: MU01-2360Ctrl


title: tof1co830rad9_HU_rep1


title: MU01-2391-GS9


title: MU01-2441-GS8


title: MU01-2392Ctrl


title: tof1co830rad9_G1_rep1

description:
tof1co830rad9_HUratio_rep1.wig
tof1co830rad9_80minreleaseratio_rep1.wig


title: tof1co627rad9_80minrelease_rep2

description: tof1co627rad9_80minreleaseratio_rep2.wig

value: JB1549 + rad9::KanMX


title: MU01-2341-GS9


title: tof1co627rad9_80minrelease_rep1

description: tof1co627rad9_80minreleaseratio_rep1.wig


title: MU01-2319Ctrl


title: MU01-2338Ctrl


title: MU01-2315Ctrl


title: MU01-2308Ctrl


title: MU01-2323-GS9


title: MU01-2313Ctrl


title: tof1co627rad9_HU_rep2


title: tof1co627rad9_HU_rep1


title: tof1rad9_G1_rep2

description:
tof1rad9_HUratio_rep2.wig
tof1rad9_80minreleaseratio_rep2.wig

value: JB1993 + rad9::NATNT2


title: tof1rad9_80minrelease_rep1


title: tof1rad9_80minrelease_rep2


title: tof1rad9_HU_rep1


title: tof1co627rad9_G1_rep1

description:
tof1co627rad9_HUratio_rep1.wig
tof1co627rad9_80minreleaseratio_rep1.wig


title: MU01-2305Ctrl


title: TOF1COrad9_80minrelease_rep2

value: JB1528 + rad9::KanMX


title: tof1co627rad9_G1_rep2

description:
tof1co627rad9_HUratio_rep2.wig
tof1co627rad9_80minreleaseratio_rep2.wig


title: TOF1COrad9_80minrelease_rep1


title: MU01-2848-GS6

value: Gleason Score 6


title: TOF1COrad9_HU_rep2


title: TOF1COrad9_HU_rep1


title: MU01-2304-GS6


title: MU01-2302Ctrl


title: MU01-2289-GS7

value: Gleason Score 7


title: MU01-2291Ctrl


title: MU01-2277-GS8

value: Gleason Score 8


title: MU01-2262Ctrl


title: MU01-2253-GS8


title: MU01-2256-GS7


title: MU01-2238-GS7


title: MU01-2232Ctrl


title: MU01-2275-GS7


title: MU01-2265Ctrl


title: tof1rad9_G1_rep1

description:
tof1rad9_HUratio_rep1.wig
tof1rad9_80minreleaseratio_rep1.wig


title: MU01-2231Ctrl


title: TOF1COrad9_G1_rep2

description:
TOF1COrad9_HUratio_rep2.wig
TOF1COrad9_80minreleaseratio_rep2.wig


title: TOF1COrad9_G1_rep1

description:
TOF1COrad9_HUratio_rep1.wig
TOF1COrad9_80minreleaseratio_rep1.wig


title: TOF1_wt_60min_HU_rep1_RPA

value: JB1991 + TOF1::tof1-codon-optimised-wildtype (NATNT2)


title: TOF1_wt_60min_HU_rep1_input

value: none (input)


title: tof1_830_60min_HU_rep2_input

value: JB1991 + TOF1::tof1-codon-optimised-830-1238_delta (NATNT2)


title: tof1_830_60min_HU_rep2_RPA

value: RPA1 antibody (1:10000, Agrisera, AS07214)


title: MU01-2217-GS8


title: MU01-2203Ctrl


title: MU01-2204Ctrl


title: MU01-2210Ctrl


title: tof1_762_60min_HU_rep2_RPA

value: JB1991 + TOF1::tof1-codon-optimised-762-1238_delta (NATNT2)


title: tof1_830_60min_HU_rep1_input


title: tof1_627_60min_HU_rep2_RPA

value: JB1991 + TOF1::tof1-codon-optimised-627-1238_delta (NATNT2)


title: tof1_627_60min_HU_rep2_input


title: tof1_627_60min_HU_rep1_RPA


title: tof1_60min_HU_rep3_RPA

value: JB1991 + TOF1::hphMX


title: tof1_627_60min_HU_rep1_input


title: MU01-2137Ctrl

value: Urine

value: Control


title: tof1_60min_HU_rep2_RPA


title: MU01-2157Ctrl


title: tof1_830_60min_HU_rep1_RPA


title: wt_60min_HU_rep2_RPA

value: MATa, ade2-1 his3-11 leu2-3 trp1-1 ura3-1 can1-100, UBR1::GAL1-10-Ubiquitin-M-LacI fragment-Myc-UBR1 (HIS3), leu2-3::pCM244 (CMVp-tetR'-SSN6, LEU2) x3


title: MU01-2178Ctrl


title: MU01-2207Ctrl


title: tof1_762_60min_HU_rep2_input


title: MU01-2170-GS7


title: MU01-2108Ctrl


title: MU01-2064Ctrl


title: MU01-2069-GS6


title: MU01-2188Ctrl


title: MU01-2082-GS8


title: MU01-2109-GS7


title: MU01-2179Ctrl


title: wt_60min_HU_rep2_input


title: MU01-2058-GS8


title: MU01-2052Ctrl


title: donor34_rectum_repB

value: female

tag: ancestry

value: AA

tag: age at sampling

value: Crohn's disease

value: rectum


title: tof1_60min_HU_rep3_input


title: MU01-2158Ctrl


title: donor34_ileum_repB

tag: Sex

tag: disease state (diagnosis)

value: ileum


title: donor34_rectum_repA


title: tof1_60min_HU_rep2_input


title: donor34_ileum_repA


title: MU01-2016Ctrl


title: MU01-2033Ctrl


title: donor33_ileum_repB

value: EA


title: donor33_ileum_repA


title: donor32_rectum_repB

value: male


title: donor31_rectum_repB


title: donor33_rectum_repA


title: MU01-1984-GS9

value: Gleason Score 9


title: MU01-2011Ctrl


title: donor32_rectum_repA


title: donor31_ileum_repB


title: donor31_rectum_repA


title: donor32_ileum_repA


title: donor31_ileum_repA


title: donor30_rectum_repB

value: ulcerative colitis


title: donor30_ileum_repB


title: MU01-1898Ctrl


title: MU01-1871-GS7

value: Gleason Score 7


title: MU01-1894Ctrl


title: MU01-1909-GS8

value: Gleason Score 8


title: MU01-1891Ctrl


title: donor30_rectum_repA


title: MU01-1923-GS8


title: MU01-1997-GS8


title: donor29_rectum_repB


title: donor29_ileum_repB


title: MU01-2014Ctrl


title: MU01-1779Ctrl


title: MU01-1828-GS6

value: Gleason Score 6


title: MU01-1749Ctrl


title: donor29_ileum_repA


title: MU01-1760-GS6


title: donor28_rectum_repA


title: donor28_ileum_repA


title: MU01-1835Ctrl


title: MU01-1868-GS7


title: donor27_rectum_repA


title: donor27_rectum_repB


title: donor27_ileum_repB


title: HEK293T non-infecetd Rep3

city: Cambridge

first: Shira

last: Weingarten-Gabbay

state: MA

address: 75 Ames St

institute: The Broad Institute

description:
293_24hr_control_3
Paired-end RNA-seq of transcripts after polyA enrichment

data_processing:
Sequencing reads were mapped to SARS-CoV-2 genome (RefSeq NC_045512.2) and human transcriptome (Gencode v32). Alignment was performed using Bowtie version 1.2.2 (Langmead et al., 2009) with a maximum of two mismatches per read.
The fraction of human and viral reads was determined based on the total number of reads aligned to either SARS-CoV-2 or human transcripts.
Genome_build: SARS-CoV-2 genome (RefSeq NC_045512.2) and human transcriptome (Gencode v32)
Supplementary_files_format_and_content: An xls file containing the number of reads aligned to the human transcriptome and SARS-CoV-2 genome and the percentages of total aligned reads in each cell line at each time point. Three biological replicates were done for HEK293T cells and the number of reads and percentages is indicated for each replicate

source_name: HEK293T non-infecetd

growth_protocol: A549 and HEK293T cells were seeded into 6-well plates at a density of 5 x 10^5 cells per well (one well per condition). After 11-24 hr, the cells were infected with SARS-CoV-2 at an  MOI of 3.

extract_protocol:
At 12, 18 and 24hr post-infection, the cells were lysed in Trizol (Thermo, 15596026) ,and the total RNA was isolated using standard phenol chloroform extraction.
Standard Illumina TruSeq Stranded mRNA (LT) was performed using 500 ng of total RNA (illumina, FC-122-2101). Oligo-dT beads were used to capture polyA-tailed RNA, followed by fragmentation and priming of the captured RNA (8 minutes at 94ºC). Immediately first strand cDNA synthesis was performed. Second strand cDNA synthesis was performed using second strand marking master and DNA polymerase 1 and RNase H. cDNA was adenylated at the 3’ ends followed immediately by RNA end ligation single-index adapters (AR001-AR012). Library amplification was performed for 12-15 cycles under standard illumina library PCR conditions. Library quantitation was performed using Agilent 2200 TapeStation D1000 ScreenTape (Agilent, 5067-5582). RNA sequencing was performed on the NextSeq 550 System using a NextSeq V2.5 High Output 75 cycle kit (illumina, 20024906) or 150 cycles kit (illumina, 20024907) for paired-end sequencing (70nt of each end).
PolyA enrichment followed by Illumina TrueSeq adaptor ligation

value: human embryonic kidny cells

value: control (non-infected)


title: MU01-1748-GS7

value: Urine


title: donor30_ileum_repA


title: MU01-1655-GS8


title: MU01-1624Ctrl

value: Control


title: donor27_ileum_repA


title: MU01-1599Ctrl


title: MU01-1686-GS8


title: MU01-1609Ctrl


title: MU01-1619-GS7


title: HEK293T non-infecetd Rep1

description:
293_24hr_control_1
Paired-end RNA-seq of transcripts after polyA enrichment


title: donor26_ileum_repB


title: donor26_rectum_repA


title: MU01-1596-GS8


title: MU01-1597-GS7


title: HEK293T non-infecetd Rep2

description:
293_24hr_control_2
Paired-end RNA-seq of transcripts after polyA enrichment


title: donor26_ileum_repA


title: MU01-1728-GS7


title: donor25_rectum_repA


title: PS16.22.05

city: Baltimore

first: Christopher

middle: P

last: Morgan

state: MD

address: 670 W Baltimore St

department: Pharmacology

institute: University of Maryland School of Medicine

data_processing:
The small non-coding RNA sequencing (sncRNASeq) analytical pipeline was designed using the snakemake framework and is available via GitHub at https://github.com/acshetty/sncRNA-seq-analysis.
Reference transcriptome sequences in FASTA format were downloaded from public repositories and indexed using the Bowtie short read aligner software. These references included the GRCh38 ncRNA reference from Ensembl, the miRNA reference from miRbase 21, the tRNA reference generated from GRCh37 by GtRNAdb 2.0, and the piRNA reference from piRBase v1.0.
Sequenced reads were trimmed at the 3’ end to remove any trailing adaptor sequence using the Trimmomatic tool. Reads shorter than 15 nucleotides were discarded before downstream analyses.
Trimmed reads for each sample were aligned to each of the different sncRNA class-specific reference transcriptomes using Bowtie. Reads were aligned allowing for 2 mismatches and a seed length of 15 nucleotides. The alignment statistics were summarized for each sample across each of the different references and raw expression values were computed based on the number of reads aligned to each of the sncRNAs specified in their respective reference files.
Expression of sncRNA were adjusted for differences in library sequencing depth to generate counts per million reads (CPM) following TMM normalization using the Bioconductor package ‘edgeR’ (version 3.24.3). sncRNA features were retained for analysis if they were expressed at ≥ 1 CPM in at least 75% of samples.
Genome_build: GRCh38 ncRNA reference from Ensembl, the miRNA reference from miRbase 21, the tRNA reference generated from GRCh37 by GtRNAdb 2.0, and the piRNA reference from piRBase v1.0.
Supplementary_files_format_and_content: Comma separated values file containing normalized log2 counts per million reads for each sample

source_name: Mature sperm

extract_protocol:
Mature sperm were enriched by centrifugation through a 50% PureSperm density gradient (Nidacon). Sperm were lysed and homogenized in TRIzol-LS, supplemented with 0.2 M β-mercaptoethanol. Total RNAwas were isolated using Qiagen’s miRNeasy Mini kit.
small RNA libraries were constructed with 10 ng of small RNA using the TruSeq small RNA Library Prep Kit (Illumina) according to manufacturer's protocol.

tag: subject

tag: collection


title: MU01-1590Ctrl

tag: tissue


title: MU01-1594-GS8

tag: histopathology


title: MU01-1568-GS6


title: MU01-1533-GS7


title: MU01-1480-GS7


title: MU01-1497Ctrl


title: PS16.22.03


title: A549 non-infecetd

description:
A549_24hr_WT
Paired-end RNA-seq of transcripts after polyA enrichment

source_name: A549 non-infecetd

value: lung carcinoma cells


title: PS16.22.04


title: donor24_rectum_repB


title: MU01-1525Ctrl


title: MU01-1582Ctrl


title: MU01-1458Ctrl


title: PS16.22.02


title: PS16.22.06


title: donor24_ileum_repB


title: MU01-1291-GS8


title: MU01-1365R1-GS9


title: MU01-1236Ctrl


title: MU01-1234Ctrl


title: PS16.22.01


title: MU01-1398-GS7


title: MU01-1190-GS7


title: MU01-1479-GS8


title: MU01-1279Ctrl


title: donor25_ileum_repA

value: female


title: donor24_ileum_repA

value: AA


title: PS16.20.05


title: tof1rad9_HU_rep2

value: JB1993 + rad9::NATNT2


title: PS16.20.06


title: donor23_ileum_repB


title: donor23_rectum_repA

value: rectum


title: PS16.20.04


title: PS16.20.03


title: donor24_rectum_repA

value: Crohn's disease


title: donor22_rectum_repB

value: EA


title: MU01-1133-GS7


title: donor23_ileum_repA

value: ileum


title: PS16.20.02


title: MU01-1066-GS10

value: Gleason Score 10


title: donor22_ileum_repB

value: male

value: ulcerative colitis


title: MU01-1153Ctrl


title: PS16.20.01


title: MU01-1009Ctrl


title: MU01-0948Ctrl


title: MU01-0974Ctrl


title: MU01-0914Ctrl


title: donor22_rectum_repA


title: PS16.18.06


title: PS16.18.05


title: donor22_ileum_repA


title: MU01-0843Ctrl


title: MU01-1144Ctrl


title: donor21_rectum_repB


title: PS16.18.04


title: MU01-0533R1-GS6


title: donor21_ileum_repB


title: MU01-0603-GS6


title: MU01-0364-GS8

value: Gleason Score 8


title: MU01-0530-GS8


title: MU01-0733R1-GS6

value: Gleason Score 6


title: donor21_rectum_repA


title: PS16.18.02


title: MU01-0327-GS9

value: Gleason Score 9


title: donor21_ileum_repA


title: PS16.18.01


title: donor20_rectum_repB


title: ISPU-11-000307-GS9


title: ISPU-11-000320-GS7

value: Gleason Score 7


title: ISPU-11-000326-GS9

value: Urine


title: MU01-0053Ctrl

value: Control


title: MU01-1020-GS7


title: PS16.17.05


title: ISPU-11-000258-GS8


title: ISPU-11-000301-GS7


title: ISPU-11-000253-GS7


title: PS16.17.04


title: donor20_ileum_repB


title: PS16.18.03


title: MU01-0081-GS8


title: PS16.17.03


title: donor20_rectum_repA


title: ISPU-11-000209-GS7


title: ISPU-11-000217-GS8


title: ISPU-11-000211-GS8


title: ISPU-11-000203-GS8


title: donor19_rectum_repB


title: ISPU-11-000202-GS7


title: ISPU-11-000206-GS8


title: PS16.17.01


title: PS16.15.06


title: donor20_ileum_repA


title: ISPU-11-000226-GS7


title: donor19_ileum_repA


title: MU03-2427-GS6


title: MU03-2350-GS6


title: donor17_rectum_repB


title: MU01-1817-Ctrl


title: MU01-1739-Ctrl


title: MU01_0015-Ctrl


title: MU01-1808-Ctrl


title: PS16.15.05


title: PS16.15.04


title: donor17_rectum_repA


title: MU03-2335-GS6


title: PS16.15.03


title: PS16.17.02


title: MU01-1724-GS6


title: donor17_ileum_repA


title: MU01-1725-GS6


title: donor16_ileum_repB


title: MU01-1713-GS6


title: PS16.15.01


title: MU01-1705-GS7


title: donor16_rectum_repA


title: MU01-1723-GS6


title: MU01-1703-GS7


title: donor16_ileum_repA


title: PS16.15.02


title: MU01-1694-GS6


title: MU01-1692-GS9


title: donor19_rectum_repA


title: donor15_rectum_repB


title: PS16.14.05


title: MU01-1682-GS7


title: MU01-1691-Ctrl


title: PS16.14.03


title: donor15_ileum_repB


title: donor15_rectum_repA


title: MU01-1657-GS7


title: MU01-1658-GS7


title: PS16.14.04


title: MU01-1660-GS6


title: MU01-1640-Ctrl


title: MU01-1629-Ctrl


title: donor15_ileum_repA


title: PS16.14.06


title: PS16.14.02


title: PS16.14.01


title: ISPU-11-000201-GS7


title: MU01-1622-Ctrl


title: MU01-1617-GS6


title: PS16.13.04


title: MU01-1615-GS7


title: PS16.13.06


title: donor14_ileum_repA


title: PS16.13.05


title: donor14_rectum_repA


title: MU01-1584-GS6


title: MU01-1592-GS5

value: Gleason Score 5


title: MU01-1595-GS9


title: PS16.13.03


title: PS16.13.02


title: MU01-1577-GS7


title: MU01-1558-GS6


title: MU01-1552-GS7


title: donor13_ileum_repB

value: female


title: PS16.13.01


title: MU01-1581-GS7


title: MU01-1551-GS7


title: donor14_ileum_repB


title: donor14_rectum_repB


title: MU01-1532-GS7


title: MU01-1627-Ctrl


title: PS16.12.06


title: MU01-1542-GS6


title: MU01-1536-GS7


title: MU01-1523-GS6


title: donor13_ileum_repA


title: PS16.12.05


title: MU01-1511-GS7


title: donor12_rectum_repB

value: AA


title: donor13_rectum_repB


title: donor13_rectum_repA


title: donor12_ileum_repB


title: PS16.12.04


title: MU01-1522-Ctrl


title: MU01-1645-GS8


title: MU01-1508-GS6


title: PS16.12.03


title: donor12_rectum_repA


title: MU01-1446-Ctrl


title: MU01-1505-GS6


title: PS16.12.02


title: PS16.12.01


title: donor12_ileum_repA


title: donor11_rectum_repA


title: MU01-1434-Ctrl


title: MU01-1402-GS6


title: MU01-1393-GS7


title: PS16.11.05


title: donor10_rectum_repB


title: MU01-1395-GS6


title: MU01-1509-GS6


title: PS16.11.04


title: MU01-1388-GS6


title: MU01-1467-Ctrl


title: PS16.11.03


title: donor10_ileum_repB


title: MU01-1377-GS6


title: donor10_rectum_repA


title: MU01-1319-GS6


title: PS16.11.02


title: MU01-1365-GS9


title: MU01-1370-GS9


title: MU01-1344-GS8


title: PS16.11.01


title: MU01-1304-GS7


title: donor9_rectum_repB


title: PS16.10.06


title: MU01-1295-GS6


title: MU01-1399-GS9


title: donor9_ileum_repB


title: PS16.10.05


title: donor9_rectum_repA


title: MU01-1289-GS7


title: PS16.10.03


title: MU01-1243-GS7


title: donor10_ileum_repA


title: MU01-1242-GS6


title: MU01-1235-GS6


title: MU01-1290-GS7


title: donor8_ileum_repB


title: PS16.10.01


title: PS16.10.02


title: PS16.10.04


title: MU01-1231-GS6


title: MU01-1256-GS6


title: MU01-1224-GS6


title: MU01-1203-GS6


title: MU01-1185-GS6


title: MU01-1186-GS6


title: MU01-1159-GS6


title: donor8_ileum_repA


title: donor8_rectum_repB


title: donor9_ileum_repA


title: MU01-1148-GS9


title: MU01-1154-GS7


title: donor7_rectum_repB


title: MU01-1156-GS6


title: PS16.09.05


title: donor7_ileum_repB


title: PS16.09.04


title: donor8_rectum_repA


title: donor7_ileum_repA


title: PS16.09.02


title: PS16.09.03


title: MU01-1140-GS6


title: MU01-1145-GS8


title: donor6_ileum_repB


title: MU01-1301-GS7


title: donor6_rectum_repA


title: MU01-1078-Ctrl


title: MU01-1091-Ctrl


title: PS16.07.06


title: MU01-1100-Ctrl


title: MU01-1139-GS6


title: MU01-1109-GS6


title: MU01-1059-Ctrl


title: MU01-1063-GS7


title: PS16.07.05x


title: donor6_ileum_repA


title: donor5_rectum_repB


title: PS16.07.04


title: donor5_ileum_repB


title: MU01-1092-GS6


title: MU01-1049-GS7


title: PS16.07.03


title: PS16.07.02x


title: donor5_rectum_repA


title: PS16.09.01


title: MU01-1045-GS6


title: PS16.07.01


title: donor4_rectum_repA


title: MU01-1073-Ctrl


title: PS16.06.06


title: MU01-1042-GS7


title: MU01-1050-GS6


title: donor4_ileum_repA


title: MU01-0995-Ctrl


title: MU01-1004-Ctrl


title: MU01-1033-GS6


title: PS16.09.06


title: PS16.06.05


title: MU01-0993-Ctrl


title: MU01-1021-GS6


title: MU01-1007-GS7


title: MU01-0991-Ctrl


title: PS16.06.04


title: MU01-1048-GS6


title: donor3_ileum_repB


title: PS16.06.03


title: donor3_rectum_repA


title: MU01-1025-GS7


title: MU01-0968-Ctrl


title: donor5_ileum_repA


title: MU01-0978-Ctrl


title: MU01-0966-GS6


title: PS16.06.02


title: MU01-0960-Ctrl


title: donor3_ileum_repA


title: PS16.05.06


title: donor3_rectum_repB


title: donor2_rectum_repB


title: PS16.05.05


title: donor2_ileum_repB


title: MU01-0981-Ctrl


title: MU01-0959-Ctrl


title: MU01-0958-Ctrl


title: MU01-0952-Ctrl


title: MU01-0917-GS6


title: MU01-0921-Ctrl


title: MU01-0924-Ctrl


title: donor2_rectum_repA


title: PS16.05.03


title: donor2_ileum_repA


title: MU01-0906-GS7


title: PS16.05.02


title: MU01-0905-GS8


title: MU01-0886-GS6


title: donor1_rectum_repB


title: PS16.05.01


title: donor1_ileum_repB


title: MU01-0863-GS7


title: PS16.04.06


title: MU01-0862-Ctrl


title: PS16.05.04x


title: PS16.04.05


title: MU01-0859-GS6


title: donor1_rectum_repA


title: MU01-0856-GS7


title: MU01-0925-Ctrl


title: MU01-0850-GS6


title: donor1_ileum_repA


title: PS16.04.04


title: MU01-0813-Ctrl


title: 20183184NO.Input

first: Ding

last: Yu

address: Number 953 Jianchuan Road

institute: Newcore biotechnology

data_processing:
Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of input libraries were aligned to reference genome (UCSC HG19) by STAR software. Then circRNAs were identified by DCC software using the STAR alignment results. After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and choosed by home-made scripts.
Genome_build: hg19
Supplementary_files_format_and_content: bed peak files

source_name: normal oral tissue

extract_protocol: Briefly, fragmented RNA was incubated with anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IP buffer for 2 hours at 4°C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) by following the manufacturer’s instruction. Purified RNA was used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer.

value: normal oral tissue

tag: treatment type

value: Surgery

tag: recurrence

value: No

tag: vital status

value: Alive


title: MU01-0828-GS7


title: MU01-0839-Ctrl


title: PS16.04.03


title: 20183184NO.IP


title: PS16.04.02


title: 20171888NO.Input


title: MU01-0787-GS6


title: MU01-0780-GS6


title: MU01-0765-GS6


title: 20171462NO.Input


title: PS16.02.05


title: PS16.02.04


title: 20171462NO.IP


title: MU01-0754-GS6


title: 20183184AB.Input

source_name: Ameloblastoma tissue

value: Ameloblastoma tissue


title: MU01-0749-GS6


title: MU01-0750-GS7


title: MU01-0738-GS7


title: MU01-0717-Ctrl


title: MU01-0743-Ctrl


title: PS16.02.06


title: PS16.02.01


title: 20171888NO.IP


title: MU01-0737-GS6


title: MU01-0730-GS7


title: 20171888AB.Input


title: MU01-0729-Ctrl


title: MU01-0712-Ctrl


title: MU01-0713-Ctrl


title: PS16.01.06


title: MU01-0701-Ctrl


title: MU01-0706-GS6


title: MU01-0704-Ctrl


title: MU01-0700-Ctrl


title: MU01-0698-Ctrl


title: 20171888AB.IP


title: MU01-0697-Ctrl


title: PS16.02.03x


title: PS16.02.02


title: PS16.01.05


title: MU01-0694-GS6


title: PS16.01.04


title: 20183184AB.IP


title: MU01-1213-GS6


title: 20171462AB.Input


title: PS16.01.02


title: PS16.01.03


title: GM40dmso2

city: Oxford

first: Gabriela

last: Vilema-Enríquez

address: South Parks Road

department: Physiology, Anatomy and Genetics

institute: University of Oxford

data_processing:
Pseudoalignment to Ensembl GRCh38 (version 98) cDNA reference using Kallisto (version 0.46.0) with optional parameter: --bias
Transcript abundance estimates were summarised to gene-level counts using Tximport (version 1.12.3)
Differential gene expression analysis was performed using DESeq2 (version 1.24.0), excluding genes with fewer than 10 counts average across all samples.
For plotting purposes, a variance-stabilizing transformation was applied using DESeq2, setting the 'bind' parameter to 'FALSE'
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalised counts (generated using DESeq2 'counts()' function) for each sample

source_name: Primary fibroblasts

growth_protocol: Fibroblasts lines were obtained from Coriell Institute (USA) and cultured in Minimum Essential Medium (MEM) supplemented with 15% FBS, 1% MEM Non-essential Amino Acid Solution (100X Gibco) and 100 U/ml penicillin/streptomycin.

extract_protocol:
Total RNA from primary fibroblasts was extracted using the RNeasy Mini Kit (Qiagen), including DNAse I treatment to remove genomic DNA contamination.
Material was quantified using RiboGreen (Invitrogen) on the FLUOstar OPTIMA plate reader (BMG Labtech) and the size profile and integrity analysed on the 4200 TapeStation (Agilent, RNA ScreenTape). Input material was normalised to 50 ng prior to library preparation. Polyadenylated transcript enrichment and strand specific library preparation was completed using NEBNext Ultra II mRNA kit (NEB) following manufacturer’s instructions. Libraries were amplified on a Tetrad (Bio-Rad) using in-house unique dual indexing primers (based on DOI: 10.1186/1472-6750-13-104). Individual libraries were normalised using Qubit, and the size profile was analysed on the 2200 or 4200 TapeStation. Individual libraries were normalised and pooled together accordingly. The pooled library was diluted to ~10 nM for storage. The 10 nM library was denatured and further diluted prior to loading on the sequencer. Paired end sequencing was performed using two lanes (669382 and 670822) of a HiSeq4000 75bp platform (Illumina, HiSeq 3000/4000 PE Cluster Kit and 150 cycle SBS Kit).

treatment_protocol: 6 days of compound treatment (A-196/SG2043)

value: Primary fibroblasts

value: DMSO


title: GM40dmso3


title: MU01-0692-Ctrl


title: GM40dmso1


title: PS16.01.01


title: MU01-0688-GS6


title: MU01-0693-Ctrl


title: F_24_3: female root

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

data_processing:
After obtaining clean reads, the clean reads need to be spliced to obtain a reference sequence for subsequent analysis.
We use Trinity to assemble clean reads,then use Tgicl to cluster the transcripts to obtain Unigene.
After the assembly, we performed seven major functional database annotations on the assembled Unigene (NR, NT, GO, KOG, KEGG, SwissPprot,and InterPro).
Supplementary_files_format_and_content: EXCEL files include RPKM values for each sample

organism: Salix linearistipularis

source_name: female root

growth_protocol: Healthy annual shoots of male and female S. linearistipularis trees were collected from Anda Experimental Base of Northeast Forestry University in Anda City of Heilongjiang Province, China (46°27′ N, 125°22′ E). One male individual and one female individual were vegetatively propagated to produce 60 male and 60 female cuttings, respectively.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Hydroponic cuttings of male and female plants were exposed to water or 100 mM NaCl for 6, 12 and 24 h. Root samples were collected (three bioreplicates for each treatment), frozen in liquid nitrogen and ground to a fine powder for RNA extraction.

value: root


title: GM40unt3

value: untreated


title: F_24_2: female root


title: MU01-0691-GS6

value: Gleason Score 6


title: GM40unt2


title: 20171462AB.IP


title: F_24_1: female root


title: MU01-0612-GS6


title: GM40unt1


title: MU01-0624-Ctrl


title: MU01-0651-GS6


title: MU01-0622-GS7


title: MU01-0587-Ctrl


title: MU01-0640-GS6


title: MU01-0600-Ctrl


title: MU01-0584-Ctrl


title: F_12_3: female root


title: GM785A3

value: 5 uM compound A-196


title: F_12_2: female root


title: MU01-0576-Ctrl


title: MU01-0561-Ctrl


title: F_12_1: female root


title: GM785A1


title: F_6_3: female root


title: Conference_nonhost_72hpiVP102_rep2

description: Conference' pear variety, sampled 72 hours post inoculation with nonhost pathogen Venturia inaequalis EUB04 strain

organism: Pyrus communis

growth_protocol: Greenhouse growth conditions were as described in Chevalier et al. (2008): Chevalier M, Tellier M, Lespinasse Y, Caffier V. 2008. How to optimize the Venturia pyrina inoculation on pear leaves in greenhouse conditions? Acta Horticulturae 800: 913-920.

treatment_protocol: Mode of inoculum preparation is as described in Chevalier et al. (2008): Chevalier M, Tellier M, Lespinasse Y, Caffier V. 2008. How to optimize the Venturia pyrina inoculation on pear leaves in greenhouse conditions? Acta Horticulturae 800: 913-920. Briefly, the youngest leaf of actively growing shoots was tagged and the plants inoculated with a conidial suspension (2 × 105 conidia ml-1). No treatment correspond to T0 = time zero, so the corresponding plants have literally undergone none treatment.

value: leaf

tag: genotype

value: Conference' variety

value: resistant


title: GM781A3

value: 1 uM compound A-196


title: F_6_2: female root

value: female


title: MU01-0557-Ctrl

value: Urine

value: Control


title: MU01-0555-Ctrl


title: GM781A1


title: GM781A2


title: Conference_nonhost_72hpiVP102_rep1

tag: tissus

value: inoculation with nonhost pathogen Venturia inaequalis


title: MU01-0542-GS6


title: MU01-0544-GS6


title: MU01-0545-Ctrl


title: F_CK_3: female root


title: Conference_nonhost_T0_with72h_rep2

description: Conference' pear variety, sampled just before inoculation with nonhost pathogen Venturia inaequalis EUB04 strain

tag: phenotype

value: healthy, no inoculation

value: no treatment


title: GM78unt3

tag: treatment


title: F_6_1: female root


title: F_CK_2: female root


title: GM78unt2


title: Conference_nonhost_T0_with72h_rep1


title: Conference_nonhost_24hpiVP102_rep1

description: Conference' pear variety, sampled 24 hours post inoculation with nonhost pathogen Venturia inaequalis EUB04 strain


title: F_CK_1: female root


title: Conference_nonhost_24hpiVP102_rep2


title: GM785A2


title: GM78unt1


title: M_24_3: male root

source_name: male root

value: male


title: GM7810S3

value: Primary fibroblasts

value: 10 uM compound SGC2043


title: M_24_2: male root

value: root


title: MU01-0538-Ctrl


title: GM7810S2


title: MU01-0549-GS7

value: Gleason Score 7


title: MU01-0536-GS7


title: MU01-0508-Ctrl


title: MU01-0498-Ctrl


title: GM7810S1


title: Conference_nonhost_T0_with24h_rep1


title: 60AU_host_72hpiEUB04_rep2

description: 60AU transgenic pear line, carrying the Rvi6 resistance gene, sampled 72 hours post inoculation with host pathogen Venturia pyrina VP102 strain

value: 60AU Rvi6 overexpressing transgenic line


title: MU01-0495-Ctrl


title: Conference_host_72hpiEUB04_rep2

description: Conference' pear variety, sampled 72 hours post inoculation with host pathogen Venturia pyrina VP102 strain

value: susceptible


title: 60AU_host_72hpiEUB04_rep1

value: leaf

value: inoculation with host pathogen Venturia pyrina VP102 strain


title: M_12_3: male root


title: GM7810A3

value: 10 uM compound A-196


title: MU01-0494-GS6

value: Gleason Score 6


title: M_12_2: male root


title: GM7810A2


title: M_12_1: male root


title: 60AU_host_24hpiEUB04_rep2

description: 60AU transgenic pear line, carrying the Rvi6 resistance gene, sampled 24 hours post inoculation with host pathogen Venturia pyrina VP102 strain

value: resistant


title: 60AU_host_24hpiEUB04_rep1


title: M_6_3: male root


title: M_6_2: male root


title: MU01-0491-GS6

value: Urine


title: GM78dmso3

value: DMSO


title: MU01-0493-Ctrl

value: Control


title: MU01-0488-Ctrl


title: MU01-0489-Ctrl


title: Conference_host_72hpiEUB04_rep1

value: Conference' variety


title: GM78dmso2


title: GM7810A1


title: GM78dmso1


title: M_CK_3: male root


title: Conference_nonhost_T0_with24h_rep2

value: healthy, no inoculation

value: no treatment


title: MU01-0480-Ctrl


title: M_24_1: male root

value: male


title: MU01-0460-GS6


title: M_CK_2: male root


title: MU01-0409-GS8

value: Gleason Score 8


title: MU01-0398-GS7


title: Conference_host_24hpiEUB04_rep1

description: Conference' pear variety, sampled 24 hours post inoculation with host pathogen Venturia pyrina VP102 strain


title: 60AU_host_8hpiEUB04_rep1

description: 60AU transgenic pear line, carrying the Rvi6 resistance gene, sampled 8 hours post inoculation with host pathogen Venturia pyrina VP102 strain


title: M_CK_1: male root

value: root


title: Conference_host_24hpiEUB04_rep2


title: 60AU_host_8hpiEUB04_rep2


title: Sample 3 from KC 7 day after partial hepatoctomy

city: Moscow

first: Polina

last: Vishnyakova

address: Oparina 4

country: Russia

institute: National Medical Research Center for Obstetrics, Gynecology and Perinatology

description: NS_Infl_Mm_v2_C2537.rlf was used as Reporter Library File

hyb_protocol: Samples were  hybridized for 18 h at 65C according to the instructions at nCounter® XT Assay User Manual (NanoString tecnology)

scan_protocol: After hybridization samples were placed in the prep station of nCounter FLEX analysis system, there hybridized samples were purified and immobilized in a sample cartridge (cartridge ID 207911400919) according to standard protocol. Then the sample cartridge was scanned on the nCounter FLEX digital analyzer (Scanner ID 1410C0216)

data_processing: The raw data were processed in nSolver Analysis Software 4.0. We used CodeSetContent(Housekeeping) standard normalization

label: NanoString Reporter CodeSet  and Capture ProbeSet

source_name: Kupffer cells

label_protocol: 100 ng of  total RNA was mixed with Reporter CodeSet and Capture ProbeSet from nCounter Mouse Inflammation V2 panel according to the instructions at nCounter® XT Assay User Manual (NanoString tecnology)  User Manual

extract_protocol: Sorted cells from 5 animals were pooled. The total RNA was isolated from cells by using RNeasy Plus Mini Kit (Qiagen) with additional purification and concentration with RNA Clean& Concentrator (Zymo Research).

tag: strain

value: Balb/C

value: Kupffer

tag: days after hepatoctomy


title: Sample 4 from KC 7 day after partial hepatoctomy

tag: cell type


title: 60AU_host_T0_rep2

description: 60AU transgenic pear line, carrying the Rvi6 resistance gene, sampled just before inoculation with host pathogen Venturia pyrina VP102 strain

value: 60AU Rvi6 overexpressing transgenic line


title: Conference_host_8hpiEUB04_rep1

description: Conference' pear variety, sampled 8 hours post inoculation with host pathogen Venturia pyrina VP102 strain

value: leaf

value: susceptible


title: 2--2 [KO2]

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence , then mapped to GRCm38 whole genome using HISAT
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cuffquant and Cuffnorm
Genome_build: GRCm38
Supplementary_files_format_and_content: EXCEL file include FPKM values for each Sample

source_name: HPK1-/-_tumor inflitrating T cell

extract_protocol:
RNA was extracted from Tumor infiltrating cells using the Trizol reagent (Ambion). The NEBNext Ultra RNA Library Prep Kit for Illumina was used to construct the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

tag: time point

value: 21 days after tumor inoculation

value: tumor inflitrating T cell


title: Sample 2 from KC 7 day after partial hepatoctomy


title: M_6_1: male root

tag: Sex


title: 60AU_host_T0_rep1


title: Conference_host_8hpiEUB04_rep2

value: inoculation with host pathogen Venturia pyrina VP102 strain


title: 2--1 [KO1]


title: MU01-0394-GS6

value: Urine

value: Gleason Score 6


title: 1--2 [WT2]

source_name: WT_tumor inflitrating T cell

value: wild type


title: 1--1 [WT1]


title: MU01-0386-GS7

source_name: Urine

value: Gleason Score 7


title: Sample 3 from KC 1 day after partial hepatoctomy


title: Sample 2 from KC 3 day after partial hepatoctomy


title: miRNA_Sample 4 from KC 7 day after partial hepatoctomy

description: NS_M_miR_v1.5.rlf was used as Reporter Library File

hyb_protocol: Samples were  hybridized for 18 h at 65C according to the instructions at nCounter® miRNA Expression Assay User Manual (NanoString tecnology)

scan_protocol: After hybridization samples were placed in the prep station of nCounter FLEX analysis system, there hybridized samples were purified and immobilized in a sample cartridge (cartridge ID 207911410919) according to standard protocol. Then the sample cartridge was scanned on the nCounter FLEX digital analyzer (Scanner ID 1410C0216)

label_protocol: 100 ng of  total RNA was used for the miRNA Sample Preparation Protocol according to the instructions at nCounter® miRNA Expression Assay User Manual. Then prepared samples were labed with  Reporter CodeSet and Capture ProbeSet from Mouse miRNA V 1.5 panel according to the instructions at nCounter® miRNA Expression Assay User Manual(NanoString tecnology)


title: MU01-0340-GS6


title: Conference_host_T0_rep1

description: Conference' pear variety, sampled just before inoculation with host pathogen Venturia pyrina VP102 strain

value: Conference' variety

value: healthy, no inoculation


title: LD

city: Kalyani

first: Partho

middle: Sarothi

last: Ray

state: West Bengal

address: Mohanpur

department: Department of Biological Sciences

institute: Indian Institute of Science Education and Research Kolkata

data_processing:
Paired-end sequence data was geretated from sample using Illumina HiSeq and quality was checked using FastQC software.
Adapter sequences, low quality reads and small fragmented reads(read size below 50 bp) were removed using fastp. Sequence reads were mapped to mouse reference geneome(GRCm38.98) using TopHat2 and sebsequently Cufflink and Cuffmerge package were used for transcript assembly and quantification of gene expression in FPKM. For diffrential gene expression analysis, we used Cuffdiff package.
adapter sequence for read1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
adapter sequence for read2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
Genome_build: mm10
Supplementary_files_format_and_content: excel files include FPKM values for each Sample.

source_name: Abelson murine leukemia virus-induced tumor; ascites

growth_protocol: Mouse macrophage cell line RAW264.7 cells was maintained in RPMI 1640 media supplemented with 10% heat-inactivated fetal bovine serum 100 U/ml penicillin and streptomycin, 4 mM L-Glutamine in a humidified incubator at 37degree celsius and 5% CO2.

extract_protocol:
Total RNA was isolated using RNAiso Plus (Takara Bio Inc., Japan) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Post 24h of seeding, HD cells were stimulated or not stimulated with LPS (500ng/ml) for another 24h. After completion of designated time point LD,HD and HD+LPS cells were harvested for  total RNA extraction.

tag: cell line

value: macrophage cell line

tag: density

value: low dense cells (LD)


title: HD

value: high dense cells (HD)


title: Sample 1 from KC 3 day after partial hepatoctomy

value: Balb/C


title: MU01-0342-GS6

data_processing: CEL files were analyzed for quality using Affymetrix Transcriptome Analysis Console 4.0 software, and the RMA-DBAG was used for summarization

extract_protocol: Standard urine exosome RNA isolation method by Norgen Biotek Corp.

tag: tissue

tag: histopathology


title: Gln repletion (rep3)

city: Daegu

first: Keun-Gyu

last: Park

address: Chilgokjungang-daero 136-gil

country: South Korea

institute: Kyungpook national university

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(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

growth_protocol: H460 cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
RNA was harvested using TRIzol reagent (Thermo Fisher Scientific). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN QuantSeq 3' mRNA-Seq Library Prep Kit (Cat#015.96) with standard protocols.

treatment_protocol: For deprivation of glutamine, cells were maintained for 24 h in glutamine-free RPMI 1640 medium supplemented with 10% dialyzed FBS.

value: lung cancer cell

tag: protocol

value: glutamine-replete


title: Gln repletion (rep2)


title: Sample 2 from KC 1 day after partial hepatoctomy

value: Kupffer


title: Conference_host_T0_rep2

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA.

extract_protocol: RNA was extracted with the kit NucleoSpin RNA Plant (Macherey Nagel, Düren, Germany) according to the manufacturer’s instructions but with a modification: 4% of PVP40 (400 mg for 100 ml) were mixed with the initial lysis buffer RAP before use.

value: leaf

value: no treatment


title: miRNA_Sample 3 from KC 7 day after partial hepatoctomy


title: Gln repletion (rep1)


title: Sample 1 from KC 1 day after partial hepatoctomy


title: miRNA_Sample 2 from KC 7 day after partial hepatoctomy


title: Gln depletion (rep2)

value: glutamine-depleted


title: MU01-0333-GS6


title: Sample 3 from KC before partial hepatoctomy


title: Gln depletion (rep3)


title: Sample 2 from KC before partial hepatoctomy


title: miRNA_Sample 1 from KC 7 day after partial hepatoctomy


title: MU01-0331-GS6


title: Gln depletion (rep1)


title: MU01-0329-GS8

value: Gleason Score 8


title: Sample 1 from KC before partial hepatoctomy


title: MU01-0326-GS7

value: Urine


title: miRNA_Sample 1 from KC 3 day after partial hepatoctomy