title: CEMBA180917_4G_7_CEMBA180917_4G_8_C4_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C4_ad007

status: Public on Sep 10 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: LSX

tag: Sex

value: male

tag: age

tag: strain


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C3_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C3_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C3_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C3_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C4_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C2_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C2_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C3_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C3_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C2_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C2_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C2_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C12_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C12_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C11_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C11_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C11_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C12_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C2_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C11_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C11_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C11_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C11_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C10_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C3_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C10_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C10_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C10_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C10_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C1_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C1_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C1_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C1_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C12_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B9_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B9_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B9_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B9_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B9_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B8_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B8_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B8_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B8_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B8_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B7_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B7_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B8_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B7_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B7_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B7_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C1_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B7_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C10_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_C1_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B6_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B7_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B6_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B6_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B6_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B6_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B6_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B6_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B5_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B5_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B5_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B5_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B4_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B4_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B3_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B4_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B4_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B4_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B3_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B3_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B3_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B3_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B3_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B2_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B2_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B12_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B2_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B2_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_D2_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B2_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B12_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B2_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B5_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B12_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B12_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B4_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B12_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B5_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B11_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B11_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B12_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B11_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B11_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B11_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B11_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B10_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B10_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B10_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B2_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B1_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B10_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B1_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B1_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B1_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B10_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B12_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A9_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A9_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B1_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A9_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A9_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B1_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B11_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A9_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A8_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A8_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A8_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A7_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A8_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A7_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_B10_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A7_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A6_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A6_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A6_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A6_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A5_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A5_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A6_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A6_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A5_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A5_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A5_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A5_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A4_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A4_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A4_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A4_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A3_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A7_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A4_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A5_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A3_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A3_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A3_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A3_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A2_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A3_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A2_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A6_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A2_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A2_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A2_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A2_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A2_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A4_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A12_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A12_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A12_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A12_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A12_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A11_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A11_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A11_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A11_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A11_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A10_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A10_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A1_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A1_ad006


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A10_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A11_ad010


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A10_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A1_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A1_ad007


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A1_ad004


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A1_ad002


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A1_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H9_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H9_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H9_ad012


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A12_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A11_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H8_ad008


title: CEMBA180917_4G_7_CEMBA180917_4G_8_A10_ad012


title: PFC SEV 1

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

country: China

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GCF_000772875.2
Supplementary_files_format_and_content: TXT file contain counts for each sample

molecule: total RNA

organism: Macaca mulatta

source_name: prefrontal cortex

growth_protocol: The animal studies were performed according to the guidelines and regulations of the Institute of Laboratory Animal Science, Peking Union Medical College and Chinese Academy of Medical Science (Peking, China).

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rhesus macaque of both sexes were exposed to about 2.5%-3% sevoflurane inhalation anesthesia on approximately postnatal day 7 and then again 14 and 28 days, for four hour each time.

tag: tissue

value: prefrontal cortex

value: post natal day 28


title: PFC CON 1


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H7_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H8_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H7_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H9_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H6_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H7_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H7_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H3_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H3_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H5_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H4_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H6_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H6_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H5_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H6_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H4_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H3_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H3_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H8_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H4_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H4_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H11_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H2_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H2_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H11_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H10_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H10_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H11_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H1_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H1_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H1_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H1_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H2_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G9_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H10_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G7_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G8_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G8_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G7_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G8_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G9_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G6_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G6_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G6_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G5_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G5_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G5_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G2_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G5_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G3_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G3_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G3_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G3_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G4_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G2_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G2_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G4_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_H1_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G9_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G2_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G2_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G12_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G6_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G4_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G11_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G11_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G12_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G10_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G10_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G11_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G1_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G10_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G10_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G1_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G1_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G1_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G1_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F8_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F7_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F8_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F7_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F9_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F6_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F9_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F7_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F5_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F6_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F9_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F5_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F5_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F6_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G1_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F4_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F4_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F4_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F3_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F3_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F3_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F3_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F4_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F4_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F2_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F2_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F2_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F2_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F2_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F2_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F12_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F2_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F12_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F12_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F11_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F11_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F5_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F12_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F11_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F10_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F11_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F4_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F3_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F10_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F10_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_G1_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F7_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F1_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F1_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F1_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F1_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F1_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F1_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E9_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F1_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F1_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E8_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E9_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_F10_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E9_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E7_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E7_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E6_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E8_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E6_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E5_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E7_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E7_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E6_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E5_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E7_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E5_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E5_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E5_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E4_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E4_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E3_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E3_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E4_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E4_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E3_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E4_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E3_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E3_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E2_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E2_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E12_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E2_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E2_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E2_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E2_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E1_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E11_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E11_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E5_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E12_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E1_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E12_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E10_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E11_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E1_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E1_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E10_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D9_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E1_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D8_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D9_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D9_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E3_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E2_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D8_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D8_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D7_ad012


title: Bone marrow of NP23-NHD13 double transgenic mouse M57-7487-NN

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

description:
M57-7487-NN-BM
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14.
Alignment performed using BWA v0.7.17.
Local realignment performed using GATK v3.8-1-0-gf15c1c3ef.
Somatic variant calling performed using MuTect2 v3.8-1-0-gf15c1c3ef.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv: Tab-separated text file includes somatic variant calling.

source_name: C57Bl6-NIH mouse

extract_protocol: Libraries were prepared according to the Nextera DNA Library Preparation protocol for the SureSelectXT Mouse All Exon Kit (Cat. No. 5190-4641, G7550C).

tag: strain/background

tag: genotype/variation

value: NP23-NHD13 double transgenic

tag: disease

value: Thymic AML

value: Bone marrow


title: Thymus of NP23-NHD13 double transgenic mouse M56-7453-NN

description:
M56-7453-NN-Thy
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv

value: Thymus


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D7_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D7_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D6_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D6_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D9_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D6_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_E1_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D7_ad007


title: Thymus of NP23-NHD13 double transgenic mouse M55-7451-NN

description:
M55-7451-NN-Thy
processed data file: GEO_seq_Study202_np23nhd13WES_mutect2_filtered.tsv


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D5_ad012


title: HeLa LATS1/2 KO 2

city: Shanghai

first: Wentao

last: Yu

address: 320 Yue Yang Road

department: Center for Excellence in Molecular Cell Science,Shanghai Institute of Biochemistry and Cell Biology

institute: Chinese Academy of Sciences

description: LATSKO_FC1.5_FDR0.05_4196_merge_counts_genename.xlsx

data_processing:
Reads with Phred quality scores below 30 were trimmed with trimmomatic.
Trimmed reads were then mapped with the Hisat2 algorithm (version 2.1.0) to genome GRCh38.84.
Gene expression levels were quantified by the software package HTSeq (v0.6.1p1).
The differentially expressed genes were generated by DESeq2 with FC>1.5 and adjust p-value<0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: 70% cell density

extract_protocol:
HeLa cells were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cervix

tag: cell type

value: Cancer cells

tag: cell line

value: HeLa cells

tag: genotype


title: HeLa YAP-5SA 2

description: YAP5SA_FC1.5_FDR0.05_3276_merge_counts_genename.xlsx


title: HeLa Control (for LATS1/2 KO and YAP-5SA) 1

value: wild type


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D6_ad012


title: HeLa YAP-5SA 1


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D7_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D8_ad008


title: HeLa LATS1/2 KO 1


title: HeLa LATS1/2 KO 3


title: HeLa YAP-5SA 3


title: HeLa Control (for LATS1/2 KO and YAP-5SA) 2


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D5_ad010


title: HeLa YAP KO 3

description: YAPKO_FC1.5_FDR0.05_1444_merge_counts_genename.xlsx

value: Yap -/-


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D4_ad001


title: HeLa YAP KO 2


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D4_ad012


title: HeLa YAP KO 1


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D4_ad008


title: HeLa Control (for YAP KO) 3


title: HeLa Control (for LATS1/2 KO and YAP-5SA) 3


title: HeLa Control (for YAP KO) 2


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D4_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D5_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D4_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D4_ad006


title: hESC-sev

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCh_38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: human embryonic stem cell

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: human embryonic stem cell


title: HeLa Control (for YAP KO) 1


title: hESC-ctrl


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D3_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D3_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D3_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D3_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D2_ad001


title: No84-supernatant

city: Zhejiang

first: Chong

last: Liu

address: NO.866 of Yuhang Tong Road

institute: Medical College of Zhejiang University

data_processing:
Illumina SNPcalling software used for basecalling
Sequenced reads were  masked for low-complexity or low-quality sequence, Cutadapt (Version 1.2.1) (Martin M, 2011 ) is used to  remove the 3' joint end, at least 10bp overlap (AGATCGGAAG), allowing 20% base error rate
Sequenced reads mapped to hg8 whole genome using Bowtie2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by HTSeq 0.6.1p2 ;differential expression genes were screen using DESeq (version 1.18.0)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

source_name: PDGFRA negative glioma cells

growth_protocol: Primary cells were maintained in human glioma cells complete medium for 18 hours before panning with pdgfra antibody, including Neurobasal (1×,Gibco #21103049) media supplemented with Penicillin/Streptomycin(100×,invitrogen,#15140-122), L-Glutamine(2mM,Gibco,#21051-024), Sodium Pyruvate(100×,invitrogen,#11360-070),d-Biotin（10ng/ml, Sigma,#B4639), Gentamycin(50µg/ml, Sigma,#46305), Trace Element B(1000×,Cellgro ,# 99-175-CI), B27 minus VA(50×,Gibco,#12587010), SATO【10µl/mL,Neurobasal (Gibco,#21103-049)；Transferrin (100 µg/mL,Sigma#T-1147) ; BSA (100 µg/mL,Sigma #A-4161); Putrescine (16 µg/mL,Sigma #P-5780); Progesterone (60 ng/mL,Sigma #P8783); Sodium selenite (40 ng/mL,Sigma #S5261)】, Insulin(5µl/mL,Sigma,# I-6634)

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols.Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesize dusing random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on a Hiseq platform (Illumina)

treatment_protocol: 0.5 square centimeter of human GBM was cut off and flash frozen in liquid nitrogen. Primary glioma cells were maintained in human glioma cells complete medium for 18 hours before panning with Mouse Anti-Human CD140a(BD Biosciences 556001) and AffiniPure Goat Anti-Mouse IgG (H+L)(Jackson ImmunoResearch),the panned cells and the supernatant cells were used for RNA-seq.

value: PDGFRA negative glioma cells

tag: passage

tag: primary antibody

tag: secondary antibody


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D3_ad008


title: No81-panned

source_name: PDGFRA positive glioma cells

value: PDGFRA positive glioma cells

value: Mouse Anti-Human CD140a(BD Biosciences 556001)

value: AffiniPure Goat Anti-Mouse IgG (H+L)(Jackson ImmunoResearch)


title: No63-supernatant


title: No84-panned


title: No81-supernatant


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D2_ad010

value: LSX

value: male


title: No80-panned


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D4_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D2_ad008


title: H84

source_name: Glioblastoma tissue

value: brain tumor


title: No63-panned


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D2_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D2_ad007


title: H80


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D3_ad001


title: H81


title: No80-supernatant


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D2_ad006


title: H74


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D2_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D12_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D2_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D12_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D12_ad010


title: H31


title: H5


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D11_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D12_ad007


title: H1944-SMARCA4-NoDOX_SMARCA4_R2

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP version ‘2013-10-10’, allowing a maximum of two mismatches per 50 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’).
Peaks relative to the input controls were identified using Macs2 (v.2.1.0) callpeak function (parameters '-t treatmentfile -c controlfile -f BAM -g 2.7e9 -n name --outdir outdir')
Genome_build: GRCh38
Supplementary_files_format_and_content: One bigWig file for each sample containing the normalized coverage in log counts per million, one peak file for each treatment sample

source_name: NCI-H1944 cells

growth_protocol: RPMI 1640 supplemented with 10% FBS, 2 mM L-Glutamine and 100 U/mL penicillin-streptomycin

extract_protocol:
NCI-H1944 cells (20 million) stably transduced with doxycycline-inducible shSMARCA2 and either LACZ or SMARCA4 WT were treated with vehicle or 0.5 ug/mL doxycycline for 4 d to obtain significant SMARCA2 knockdown. Cells were fixed with 1% formaldehyde for 10 min, quenched with 0.125 M glycine for 10 min, washed with cold PBS three times and snap frozen. ChIP for SMARCA2 and SMARCA4 was performed by Active Motif Epigenetic Services. Chromatin was isolated with the addition of lysis buffer followed by disruption with a Dounce homogenizer. Lysates were sonicated, and DNA was sheared to an average length of 300-500 bp. ChIPs were performed with 30 ug of precleared chromatin and 5uL of anti-SMARCA2 (Abcam, ab15597) or 10uL anti-SMARCA4 antibody (Abcam, ab110641). Complexes were washed, eluted from the beads with SDS buffer and subjected to RNase and Proteinase K treatment. Crosslinks were reversed overnight at 65ºC, and DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina-compatible libraries were generated using an automated system (Apollo 342, Wafergen Biosytems/Takara) and sequenced on the Illumina NextSeq 500 (single-end 75 bp reads).

tag: construct

value: Cells transduced with pLenti6.3-SMARCA4-WT, selected with 8ug/mL blasticidin for 5 days.

tag: antibody

value: Vehicle


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D11_ad010


title: H1944-SMARCA4-NoDOX_Input

value: INPUT


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D11_ad008


title: H1944-SMARCA4-NoDOX_SMARCA4_R1


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D11_ad007


title: H1944-SMARCA4-DOX_SMARCA4_R2

value: 0.5ug/mL doxycycline


title: H1944-SMARCA4-DOX_SMARCA4_R1


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D10_ad012


title: H1944-SMARCA4-DOX_Input


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D10_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D10_ad007


title: H1944-LACZ-NoDOX_SMARCA4_R2

value: Cells transduced with pLenti6.3-LACZ, selected with 8ug/mL blasticidin for 5 days.


title: H63


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D1_ad010


title: H1944-LACZ-NoDOX_SMARCA2_R1


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D1_ad008


title: H1944-LACZ-NoDOX_SMARCA2_R2


title: H1944-LACZ-NoDOX_SMARCA4_R1


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D1_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D1_ad001


title: H1944-LACZ-NoDOX_Input


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D1_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D1_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C9_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_D10_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C9_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C9_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C9_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C8_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C7_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C7_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C7_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C7_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C7_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C7_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C6_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C6_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C8_ad008


title: OvCa-870

type: RNA

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

hyb_protocol: Standard Illumina hybridization protocol for cRNA target (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All probe and gene values are provided, with no additional filtering.

label: biotin

source_name: Ovarian carcinoma

label_protocol: Ambion TotalPrep cRNA target synthesis for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from homogenized ovarian carcinoma tissues using Qiagen RNeasy reagents on a QIACube instrument.

tag: subject age

tag: bmi

value: ovarian carcinoma

tag: tumor stage

tag: tumor grade (0=low;1=high)

tag: norepinephrine content (0=below median value of 1.05 pg/ml;1=above median)


title: OvCa-854

tag: tissue


title: OvCa-871


title: OvCa-856


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C8_ad001

tag: brain region

tag: Sex

tag: age

tag: strain


title: OvCa-845


title: OvCa-844


title: OvCa-843


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C8_ad007


title: OvCa-861


title: OvCa-838


title: OvCa-841


title: OvCa-860


title: OvCa-836


title: OvCa-840


title: OvCa-817


title: OvCa-826


title: OvCa-812


title: OvCa-857


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C6_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C6_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C6_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C5_ad002


title: OvCa-808


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C5_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C5_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C5_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C4_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C4_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C4_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C4_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C4_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C3_ad007


title: OvCa-805


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C3_ad001


title: OvCa-806


title: OvCa-804


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C3_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C3_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C3_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C4_ad001


title: OvCa-653


title: OvCa-803


title: OvCa-596


title: OvCa-800


title: OvCa-802


title: OvCa-594


title: OvCa-644


title: OvCa-597


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C2_ad008


title: OvCa-645


title: OvCa-586


title: OvCa-820


title: OvCa-576


title: OvCa-582


title: OvCa-658


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C2_ad007


title: OvCa-574


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C3_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C2_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C2_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C12_ad012


title: OvCa-572


title: OvCa-571


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C2_ad001


title: OvCa-564


title: OvCa-560


title: OvCa-563


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C12_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C12_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C11_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C2_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C11_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C11_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C11_ad010


title: OvCa-558


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C10_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C10_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C10_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C10_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C10_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C12_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C1_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C1_ad012


title: OvCa-567


title: OvCa-549


title: OvCa-529


title: OvCa-521


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C1_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C1_ad010


title: OvCa-533


title: OvCa-545


title: OvCa-510


title: OvCa-514


title: OvCa-512


title: OvCa-507


title: OvCa-520


title: OvCa-526


title: OvCa-505


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C1_ad007


title: OvCa-500


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C1_ad004


title: OvCa-502


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B9_ad001


title: OvCa-498


title: OvCa-484


title: OvCa-483


title: CEMBA180917_4G_5_CEMBA180917_4G_6_C1_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B9_ad004


title: OvCa-478


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B9_ad008


title: OvCa-474


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B9_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B9_ad007


title: OvCa-472


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B8_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B9_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B8_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B9_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B8_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B8_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B8_ad007


title: OvCa-471


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B8_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B8_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B7_ad001


title: OvCa-468


title: OvCa-470


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B9_ad006


title: OvCa-455


title: OvCa-473


title: OvCa-460


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B7_ad010


title: OvCa-458


title: OvCa-464


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B7_ad007


title: OvCa-449


title: OvCa-450


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B7_ad006


title: OvCa-444


title: OvCa-446


title: OvCa-447


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B7_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B7_ad002


title: OvCa-456


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B7_ad012


title: OvCa-440


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B6_ad001


title: OvCa-420


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B6_ad010


title: OvCa-436


title: OvCa-411


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B6_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B6_ad007


title: OvCa-410


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B6_ad006


title: OvCa-425


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B6_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B6_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B5_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B5_ad007


title: OvCa-399


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B6_ad008


title: OvCa-393


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B5_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B5_ad004


title: OvCa-388


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B5_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B4_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B4_ad012


title: OvCa-373


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B4_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B4_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B4_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B4_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B3_ad001


title: OvCa-363


title: OvCa-370


title: OvCa-361


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B5_ad008


title: OvCa-337


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B3_ad010


title: OvCa-329


title: OvCa-309


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B5_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B3_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B3_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B3_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B3_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B3_ad004


title: OvCa-403


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B2_ad010


title: OvCa-330


title: OvCa-371


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B2_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B2_ad004


title: PBMC17006-Tcm

city: Seoul

first: Sun-Hee

last: Heo

address: Seoul

country: South Korea

institute: Asan Medical Center

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Homo sapiens using Hisat2-2.0.5, which is capable of reporting split-read alignments across splice junctions and determined using Stringtie-1.3.3b software in default options.
The reference genome sequence of Homo sapiens (hg19) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Genome_build: hg19
Supplementary_files_format_and_content: xlsx files include FPKM values for each Sample

source_name: PBMC

extract_protocol:
Total RNA was extracted from sorted cells using the TRIzol Reagent (Invitrogen) following the manufacturer’s instructions. mRNA-focused sequencing libraries from total RNA were generated using TruSeq RNA Library Prep Kit v2 (Illumine) according to TruSeq RNA Sample Preparation v2 Guide.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In order to T cell activation, 12-well plates were coated using 0.5 ug/ml CD3 antibodies (Catalog No. 130-093-387; Miltenyi Biotec) overnight at 4℃. CD3 positive cells were seeded at 2.5x10^5 cells per well in a CD3 antibody coated 12-well plate. Cells were incubated in RPMI1640 media with 1 ug/ml anti-human CD28 Antibody. For discovery of T memory regulatory factors, cells were incubated with 10 ng/ml interleukin-7 and 10 ng/ml interleukin-15 for 3 days.

value: Blood

tag: treatment


title: PBMC17006-Tem

tag: genotype

value: wild type


title: OvCa-327


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B2_ad006


title: SUDHL1-siHLX

city: Braunschweig

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

country: Germany

institute: Leibniz Institute DSMZ

hyb_protocol: Samples were prepared for and measured on Affymetrix HG-U133-plus2 Chip (Santa Clara/CA).

scan_protocol: GeneChips were scanned using the scanner GCS3000 and GCOS1.2 Software Suite (Affymetrix).

data_processing: After RMA-background correction, quantile normalisation of spot intensities, data were logarithmically transformed. Data processing was done via R/Bioconductor using limma and affy packages.

source_name: ALCL cell line SU-DHL-1

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from total RNA.

extract_protocol: Total RNA was extracted using Trizol reagent.

value: siHLX

tag: cell line


title: SUDHL1-siCTR

value: siCTR


title: 22mo_Day5Loaded_mouse29

city: St. Louis

first: Christopher

middle: John

last: Chermside-Scabbo

state: Missouri

address: 425 S Euclid Ave

department: Orthopaedic Surgery

institute: WASHINGTON UNIVERSITY in St. Louis

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCm38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Tibia

extract_protocol:
Left and right tibias were stripped of muscle, cut at the distal tibiofibular junction and 2mm distal to the tibial plateau, centrifuged to remove the bone marrow, and snap frozen in liquid nitrogen. Samples were stored at -80°C until RNA extraction. Samples were pulverized using a mikro-dismembrator (Braun Biotech International), and total RNA was extracted using TRIzol (Ambion) with the Total RNA Purification Kit (Norgen #17200). RNA concentrations were measured with the Nanodrop ONE (Thermo Scientific), and RNA quality was evaluated with the Bioanalyzer 2100 (Agilent Technologies). The median RNA integrity number (RIN) was 7.5 with a range of 6.6-8.7.
Ribo-Zero Gold

value: Tibia

tag: loading status

value: Non-Loaded

tag: days of loading


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B12_ad008


title: 22mo_Day5NonLoaded_mouse30

value: Loaded


title: 22mo_Day5Loaded_mouse30


title: PBMC17006-Tscm


title: 22mo_Day5NonLoaded_mouse29


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B2_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B2_ad012


title: PBMC17006-CD8


title: Wild-type#3

city: Taipei

first: Chen-Yun

last: Chen

address: 128 Sec. 2, Academia Rd.

department: Institute of Biomedical Science

country: Taiwan

institute: Acdemia Sinica

description: Gene expression data from P1 ventricle

hyb_protocol: 11 ug labeled samples were hybridized to GeneChip at 45℃ for 16.5 hours.

scan_protocol: The GeneChips were scanned with Affymetrix GeneChip Scanner 7G according to the manufacturer's instructions.

data_processing: Data were analized by GeneSpring software

source_name: neonatal ventricles

label_protocol: cDNA were biotin labeled by in vitro transcription followed by fragmentation following the manufactory’s suggestion (GeneChip Expression Analysis Technical Manual rev5, Affymetrix)

growth_protocol: Cardiac specific miR-125b-1 knockout mice were generated by crossing mice carrying loxP-flanked miR-125b-1 with mice carrying cardiac specific promoter driven Cre

extract_protocol: Total RNA was extracted using Trizol method according to the manufacturer's instructions.

treatment_protocol: Ventricles were removed from P1 neonates

value: ventricles

tag: developmental stage


title: Cardiac specific miR-125b-1 KO#1

description: Gene expression data from P1 ventricle

value: aMHC-Cre; 125b1f/f


title: Cardiac specific miR-125b-1 KO#3

description: Gene expression data from P1 ventricle


title: Wild-type#2

description: Gene expression data from P1 ventricle


title: Wild-type#1

description: Gene expression data from P1 ventricle


title: SUDHL1-HHEX

value: HHEX


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B2_ad007

value: LSX

value: male


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B12_ad007


title: Cardiac specific miR-125b-1 KO#2

description: Gene expression data from P1 ventricle


title: SUDHL1-pCMV

value: pCMV


title: PBMC17003-Tem


title: PBMC17003-Tcm


title: 22mo_Day5NonLoaded_mouse28


title: PBMC17003-Tscm


title: 22mo_Day5Loaded_mouse27


title: 22mo_Day5NonLoaded_mouse27


title: PBMC17003-CD8


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B12_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B12_ad006


title: 22mo_Day5Loaded_mouse26


title: 22mo_Day5NonLoaded_mouse26


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B11_ad007


title: 22mo_Day3Loaded_mouse25


title: 22mo_Day3NonLoaded_mouse25


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B11_ad004


title: 22mo_Day5Loaded_mouse28


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B11_ad010


title: Healthy Control 2

city: Shijiazhuang

last: Fu

state: Hebei

address: No. 139 ziqiang road

department: Hepatology

institute: The Third Hospital of Hebei Medical University

description:
HC2
Blood

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Read alignment software, software HISAT, version 2.0, parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Perform expression level for mRNAs by calculating RPKM. Estimate the expression levels of all transcripts. Software StringTie, version 1.3.0, parameters -b dta -q phred33-quals.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include RPKM values for each Sample.

source_name: plasma

extract_protocol:
Total RNA of plasma was extracted using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
mRNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final DNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp).

value: Plasma

tag: diagnosis

value: Healthy


title: HCV-related hepatic fibrosis patient 1

description:
HCV1
Blood

value: HCV with severe hepatic fibrosis (F3-4)


title: HCV-related hepatic fibrosis patient 2

description:
HCV2
Blood


title: HCV-related hepatic fibrosis patient 3

description:
HCV3
Blood


title: 22mo_Day3Loaded_mouse24


title: 22mo_Day3NonLoaded_mouse24


title: Healthy Control 1

description:
HC1
Blood


title: NCI-H1944_K785R_shSMARCA2_SAM24357813 (RNA-seq)

data_processing: Reads were aligned to the GRCh38 and GRCm38 genomes using GSNAP. Multimappers to both organisms were removed. Concordant and unique reads with <= 3 mismatches to the human genome and >3 mismatches to the mouse genome were called human-specific. Genes were quantified using human-specific reads via the HTSeqGenie Bioconductor package. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

extract_protocol: Total RNA was isolated from cell pellets using RNeasy Plus Mini Kit (Qiagen). RNA was treated with RNase-free DNase. 3 replicate samples were collected for each treatment condition. The concentration of RNA was determined using NanoDrop 8000 (Thermo Scientific). Approximately 500 ng of total RNA was used as an input for library preparation using Illumina TruSeq RNA Sample Preparation Kit v2. The libraries were multiplexed and sequenced on Illumina HiSeq4000.

tag: name

tag: cellline

value: Lung

tag: growth protocol

value: RPMI 1640 supplemented with 10% FBS, 2 mM L-Glutamine and 100 U/mL penicillin-streptomycin

tag: construct

tag: hairpin

value: After blasticidin selection, cells were infected with pLKO-shSMARCA2. Cells were selected for 72 h with 3ug/mL puromycin.


title: 22mo_Day3Loaded_mouse23

tag: tissue


title: 22mo_Day3NonLoaded_mouse23


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B12_ad010

tag: brain region


title: NCI-H1944_K785R_shSMARCA2_SAM24357812 (RNA-seq)

extract_protocol: Total RNA was is!Sample_raw_file_1olated from cell pellets using RNeasy Plus Mini Kit (Qiagen). RNA was treated with RNase-free DNase. 3 replicate samples were collected for each treatment condition. The concentration of RNA was determined using NanoDrop 8000 (Thermo Scientific). Approximately 500 ng of total RNA was used as an input for library preparation using Illumina TruSeq RNA Sample Preparation Kit v2. The libraries were multiplexed and sequenced on Illumina HiSeq4000.


title: NCI-H1944_K785R_shSMARCA2_SAM24357811 (RNA-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B11_ad008

tag: Sex


title: Sample1_6-19_S17_001_2    WT

city: Boston

first: Yongjie

last: Yang

state: MA

address: 136 Harrison Ave

institute: Tufts University School of Medicine

description: ribosome-bound RNA

data_processing:
RNA-seq reads were aligned with the mm10 genome assembly using STAR (V. 2.5.3a)
Reads quantification was performed with RSEM (V. 1.3.0)
Data was filtered to only keep genes with cpm (counts per million reads) greater than 1 for at least 3 samples
Gene count analysis and sample comparisons were performed using edgeR with the test model glmFit, a negative binomial generalized log-linear model to the read counts for each gene
Genome_build: mm10
Supplementary_files_format_and_content: raw counts for each gene
Supplementary_files_format_and_content: edgeR output

source_name: TRAP isolated RNA from WT cortex

extract_protocol:
Ribosome-bound RNAs were isolated as described previously (47). Briefly, somatosensory cortical sections (1 mm) from Fmr1+/yAldh1l1-TRAP and Fmr1−/yAldh1l1-TRAP mice were prepared on a mouse brain matrix. The anti-eGFP antibody (mouse clone HtzGFP-19C8, Memorial Sloan Kettering Cancer Center) was coupled to magnetic beads (Dynabeads, Invitrogen) as described in the kit instructions. Tissue homogenates were prepared and mixed with eGFP antibody-coupled beads for immunoprecipitation. Following immunoprecipitation, RNA was isolated using the TRIzol reagent and precipitated with isopropanol.
Libraries were prepared according to Illumina's instructions with TrUSeq Stranded Total RNA with RiboZero Gold kit
Pair-end (100bp) RNA-seq

value: WT

tag: mouse strain

tag: age


title: 22mo_Day3Loaded_mouse22

tag: strain


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B10_ad007


title: Sample1_6-19_S17_001    WT

description: ribosome-bound RNA

tag: genotype


title: 22mo_Day3NonLoaded_mouse22


title: NCI-H1944_K785R_shNTC_SAM24357810 (RNA-seq)

value: After blasticidin selection, cells were infected with pLKO-shNTC. Cells were selected for 72 h with 3ug/mL puromycin.


title: Sample1_6-12_S15_001_2    WT

description: ribosome-bound RNA


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B10_ad004


title: 22mo_Day3Loaded_mouse21

value: Tibia


title: Healthy Control 3

description:
HC3
Blood


title: Sample1_6-12_S15_001    WT

description: ribosome-bound RNA


title: NCI-H1944_K785R_shNTC_SAM24357808 (RNA-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B12_ad002


title: NCI-H1944_K785R_shNTC_SAM24357809 (RNA-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B10_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B10_ad002


title: Sample1_5-22_S13_001_2    WT

description: ribosome-bound RNA


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B10_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B10_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B12_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B10_ad012


title: NCI-H1944_WT_shSMARCA2_SAM24357807 (RNA-seq)


title: 22mo_Day1Loaded_mouse20


title: Sample1_5-22_S13_001    WT

description: ribosome-bound RNA


title: 22mo_Day1NonLoaded_mouse20

value: Non-Loaded


title: NCI-H1944_WT_shSMARCA2_SAM24357806 (RNA-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B1_ad008


title: Sample1_6-14_S18_001_2    KO

description: ribosome-bound RNA

source_name: TRAP isolated RNA from Fmr1 KO cortex

value: Fmr1 KO


title: 22mo_Day1Loaded_mouse19

value: Loaded


title: NCI-H1944_WT_shSMARCA2_SAM24357805 (RNA-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B1_ad006

source_name: C57BL/6J Male P56 Mouse Brain


title: 22mo_Day1NonLoaded_mouse19


title: NCI-H1944_WT_shNTC_SAM24357804 (RNA-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B1_ad004


title: 22mo_Day3NonLoaded_mouse21


title: Sample1_6-14_S18_001    KO

description: ribosome-bound RNA


title: 22mo_Day1Loaded_mouse18


title: Fmr1-KO_5-29_S16_001    KO

description: ribosome-bound RNA


title: 22mo_Day1NonLoaded_mouse18


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B5_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B1_ad002


title: NCI-H1944_WT_shNTC_SAM24357802 (RNA-seq)


title: NCI-H1944_LACZ_shSMARCA2_SAM24357801 (RNA-seq)

value: LACZ


title: Sample1_5-24_S14_001_2    KO

description: ribosome-bound RNA


title: Sample1_5-24_S14_001    KO

description: ribosome-bound RNA


title: 22mo_Day1Loaded_mouse17


title: NCI-H1944_WT_shNTC_SAM24357803 (RNA-seq)


title: NCI-H1944_LACZ_shSMARCA2_SAM24357800 (RNA-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A9_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A9_ad010


title: NCI-H1944_LACZ_shSMARCA2_SAM24357799 (RNA-seq)


title: 22mo_Day1NonLoaded_mouse17


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A9_ad008


title: NCI-H1944_LACZ_shNTC_SAM24357798 (RNA-seq)


title: Fmr1-KO_5-29_S16_001_2    KO

description: ribosome-bound RNA


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B1_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A9_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_B1_ad012


title: SLX12477_WT_mouse2_scRNA-seq

city: Cambridge

first: Sam

last: Watcham

address: Jeffery Cheah Biomedical Centre

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
Reads aligned to mm10 and processed using Cell Ranger v1.3.
Counts extracted using Scanpy in python
Each sample was filtered for potential doublets by simulating synthetic doublets from pairs of scRNAseq profiles and assigning scores based on a k nearest-neighbour classifier on principle component analysis (PCA) transformed data. The top 4.5% of cells with the highest doublet scores from each sample were removed from further analysis. Cells with >10% of unique molecular identifier (UMI) counts mapping to mitochondrial genes, expressing fewer than 500 genes, or with the total number of UMI counts further than 3 standard deviations from the mean for all cells were excluded. The remaining cells were used for all analyses in the manuscript.
Genome_build: mm10
Supplementary_files_format_and_content: Counts: Normalised UMI counts per gene, per cell

source_name: LK blood progenitors from WT mouse 2

extract_protocol:
Bones were crushed in PBS with 2% fetal bovine serum (2% FBS) and the cells filtered through a 40µm strainer, depleted of red blood cells and stained with relevant antibodies.
Cells were washed in PBS with 0.04% BSA and re-suspended before loading 10,000 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3ʹ Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA tape-station (Agilent. 5067-5584). Quantification of library construction was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA tape-station (Agilent. 5067-5584).

tag: cell type

value: Blood (Lin-c-Kit+)

tag: treatment

value: uninfected


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A9_ad006

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.

value: LSX

value: male


title: NCI-H1944_LACZ_shNTC_SAM24357797 (RNA-seq)


title: SLX12477_WT_mouse1_scRNA-seq

source_name: LK blood progenitors from WT mouse 1


title: 5mo_Day5NonLoaded_mouse15

tag: loading status

tag: days of loading


title: NCI-H1944_LACZ_shNTC_SAM24357796 (RNA-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A9_ad004


title: 5mo_Day5NonLoaded_mouse14


title: 5mo_Day5Loaded_mouse14


title: 22mo_Day1Loaded_mouse16


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A9_ad012


title: SLX12477_INF_mouse2_scRNA-seq

source_name: LK blood progenitors from Infected mouse 1

value: Plasmodium infected


title: SLX12477_INF_mouse1_scRNA-seq


title: 22mo_Day1NonLoaded_mouse16


title: 5mo_Day5Loaded_mouse13


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A8_ad002


title: 5mo_Day5Loaded_mouse15


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A8_ad001


title: 5mo_Day5Loaded_mouse12


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A7_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A9_ad002


title: C48_2

city: Macau

first: wenwen

last: Zhang

address: University of Macau,  Avenida de Universidade, Taipa

country: Macau

institute: Zhang Wenwen

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  the V. parahaemolyticus RIMD2210633 genome  ( ASM19609v1) or C. elegans genome (WBcel235)using Tophat2 with the default parameterization, respectively
Reads aligned to annotated genes were quantified with the htseq-count program using gene annotations from Ensembl release 92
Determined uniquely mapped read counts were served as input to DESeq2 (version 1.14.1) for pairwise detection and quantification of differential gene expression with default parameterization (pmid 25516281)
Genome_build: V. parahaemolyticus RIMD2210633 genome  ( ASM19609v1) or C. elegans genome (WBcel235)
Supplementary_files_format_and_content: tab-delimited text files include read count for each Sample

organism: Caenorhabditis elegans

source_name: Host

extract_protocol:
Total RNA was then isolated from C. elegans containing bacteria using the mirVana kit (Ambion) following the user manual. The isolated total RNA was treated with DNase I (Fermentas) (0.25 U/1 μg of RNA) for 30 mins, followed by purification with ethanol. The Ribo-Zero Magnetic Gold Kit (Epidemiology) from Epicentre/Illumina was used to removed rRNA in the samples following the manufacturer’s instructions.
cDNA libraries for Illumina sequencing were constructed with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420) following the manufacture instruction. For organism dual RNA-Seq, ~ 100 ng rRNA-depleted RNA were used for cDNA library preparation

value: Whole organism


title: 5mo_Day5NonLoaded_mouse12


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A7_ad007

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: C48_1


title: 5mo_Day5Loaded_mouse11


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A7_ad012


title: SK-Hep-1 +NC+GW

city: fuzhou

first: xiongfei

last: huang

state: fujian

address: 1 Xue Yuan Road,University Town

institute: :Fujian mecical university

description: SK-Hep-1 cell

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 2 out of 4 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.

source_name: SK-Hep-1 +NC+GW

label_protocol: Briefly, total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: HepG2 cells and SK-hep-1 cells were grown in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HepG2 cels and SK-Hep-1 cells were transfected with lentiviral mediated FXR overexpressive vector or the negative control.After the cells were treated with FXR agonist GW4064 2uM for 24 h, total RNA were isolated for detection of gene expression .

tag: cell line

value: SK-Hep-1 cell

value: control

value: FXR agonist GW4064 2uM for 24 h


title: SK-Hep-1 +FXR+GW

description: SK-Hep-1 cell

source_name: SK-Hep-1 +FXR+GW

value: FXR overexpression


title: HepG2+ FXR+GW

description: HepG2 cell

source_name: HepG2+ FXR+GW

value: HepG2 cell


title: HepG2+ NC +GW

description: HepG2 cell

source_name: HepG2+ NC +GW


title: AdV/DC_Patient 5

city: Pittsburgh

first: Deena

middle: Marie

last: Maurer

address: 200 Lothrop Street

department: Immunology

institute: University of Pittsburgh

description: Gene expression data from previously matured DC transduced with the AdV DC Vaccine (AdVTMM2), melanoma

hyb_protocol: the arrays were washed and stained on a GeneChip Fluidics Station 450

scan_protocol: Scanning was carried out with the GeneChip Scanner 3000 and image analysis with the Affymetrix GeneChip Command Console Scan Control(all from Affymetrix, Santa Clara, CA).

data_processing: R/Bioconductor was used for the primary analysis. (Oligo & Limma Packages)

source_name: Dendritic Cell, Melanoma

label_protocol: cDNAs were fragmented, biotinylated, and hybridized to the GeneChip Human Gene 2.0 ST Arrays (Affymetrix WT Terminal Labeling Kit).

growth_protocol: Patient immature dendritic cells were generated from elutriated monocytes using GM-CSF and IL-4 for 5 days. On day 6, immature DC were matured using IFNG and LPS for 24hrs. 24hrs. Post-maturation, mDC were transduced with the adenovirus vaccine for 3hrs.

extract_protocol: Total RNA was extracted by using RNeasy kit (Qiagen, Germantown, , MD, USA). The RNA concentration was measured using Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). 300ng of total RNA per sample was amplified according to manufacturer's instructions (Ambion WT Expression Kit).

treatment_protocol: Matured DC (mDC) were transduced with the recombinant Adenovirus vaccine (encoding three full length antigens: Tyrosinase, MART-1, MAGE-A6) for 3hrs at 37°C.

tag: subject id

value: Patient 5

tag: patient diagnosis

value: melanoma

value: Dendritic Cell

tag: dc subtype

tag: clinical outcome

value: PD

tag: overall survival (months)


title: AdV/DC_Patient 8

value: Patient 8

value: SD


title: AdV/DC_Patient 7

value: Patient 7


title: C36_3

value: WT

tag: tissue


title: AdV/DC_Patient 9

value: Patient 9


title: 5mo_Day5NonLoaded_mouse11

value: Tibia

value: Loaded


title: AdV/DC_Patient 4

value: Patient 4


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A7_ad002

city: La Jolla

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

tag: brain region

value: LSX

value: male


title: 5mo_Day3Loaded_mouse10

value: Non-Loaded


title: 5mo_Day5NonLoaded_mouse13


title: C36_2

value: Whole organism


title: 5mo_Day3NonLoaded_mouse10


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A7_ad006

tag: Sex


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A7_ad004


title: C48_3


title: 5mo_Day3Loaded_mouse9


title: AdV/DC_Patient 35

value: Patient 35


title: AdV/DC_Patient 34

value: Patient 34


title: AdV/DC_Patient 6

value: Patient 6

value: melanoma


title: C24_3


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A7_ad008


title: C24_2


title: AdV/DC_Patient 33

value: Patient 33

value: Dendritic Cell

value: PD


title: C36_1


title: AdV/DC_Patient 31

value: Patient 31


title: 5mo_Day3NonLoaded_mouse9


title: C24_1

value: WT


title: C12_3


title: 5mo_Day3NonLoaded_mouse8


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A6_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A6_ad008


title: 5mo_Day3Loaded_mouse7


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A6_ad001


title: C12_2


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A6_ad012


title: AdV/DC_Patient 32

value: Patient 32


title: 5mo_Day3NonLoaded_mouse7

value: Tibia


title: C12_1


title: 5mo_Day3Loaded_mouse6

value: Loaded


title: AdV/DC_Patient 30

value: Patient 30


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A6_ad004

value: LSX


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A6_ad006

value: male


title: 5mo_Day3NonLoaded_mouse6

value: Non-Loaded


title: 5mo_Day1Loaded_mouse5


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A6_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A5_ad001


title: 5mo_Day3Loaded_mouse8


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A5_ad008


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A5_ad002


title: AdV/DC_Patient 29

value: Patient 29


title: 5mo_Day1NonLoaded_mouse5


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A5_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A5_ad004


title: AdV/DC_Patient 3

value: Patient 3


title: AdV/DC_Patient 28

value: Patient 28


title: 5mo_Day1NonLoaded_mouse3


title: AdV/DC_Patient 27

value: Patient 27


title: 5mo_Day1Loaded_mouse4


title: 5mo_Day1Loaded_mouse3


title: AdV/DC_Patient 26

value: Patient 26

value: melanoma


title: AdV/DC_Patient 25

value: Patient 25

value: Dendritic Cell


title: AdV/DC_Patient 24

value: Patient 24

value: PD


title: 5mo_Day1Loaded_mouse2


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A4_ad001


title: 5mo_Day1NonLoaded_mouse4


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A5_ad012


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A4_ad010


title: 5mo_Day1NonLoaded_mouse2


title: 5mo_Day1Loaded_mouse1


title: AdV/DC_Patient 22

value: Patient 22


title: AdV/DC_Patient 21

value: Patient 21


title: AdV/DC_Patient 20

value: Patient 20

value: PR


title: AdV/DC_Patient 2

value: Patient 2


title: AdV/DC_Patient 23

value: Patient 23


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A4_ad012

value: LSX

value: male


title: 5mo_Day1NonLoaded_mouse1

value: Tibia

value: Non-Loaded


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A4_ad006


title: 2BC6: Animal 6 treated PFC

city: Blacksburg

first: Ramu

last: Anandakrishnan

state: VA

address: 1410 Prices Fork Rd., Lab 101

department: Biomedical Sciences

institute: Edward Via College of Osteopathic Medici

data_processing:
The STAR v2.7.3a software package was used to map the fastq format sequencing data. STAR was run with runThreadN=8, outSAMtype=BAM SortedByCoordinate, quantMode=GeneCounts, outSAMstrandField=intronMotif, and outFilterIntronMotifs=RemoveNoncanonicalreads.
The Cufflinks software suite was used to assemble transcriptomes and quantify RNA expression level for each sample.
Genome_build: Rattus_norvegicus.Rnor_6.0
Supplementary_files_format_and_content: Tab delimited file containing gene id and FPKM values calculated by cufflinks.

organism: Rattus norvegicus

source_name: Prefrontal cortex tissue

growth_protocol: All rats were provided with normal food and water ad libitum and housed with 12-hour light-dark cycle. All methods were performed in accordance with the relevant guidelines and regulations. All animal experimental procedures and animal housing were approved by the Institutional Animal Care and Use Committee of Virginia Tech (protocol No. 15-099) and University of Virginia (protocol No.3539).

extract_protocol:
Rats were euthanized by cervical dislocation after seven days.  Using a rat brain matrix, a 1mm coronal section from the dorsal end of prefrontal cortex was sampled from the euthanized rats. RNA was extracted using the PureLink™ RNA Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: COM was performed by an experienced Doctor of Osteopathy. Three of six rats underwent seven days of COM treatement after being anesthesized with 1.5-3% isoflurane. Untreated rats were anesthsized as well.

value: 18-month old

value: COM


title: 2BC5: Animal 5 treated PFC


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A4_ad002

first: Joseph


title: 2BC4: Animal 4 treated PFC


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A3_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A3_ad010


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A4_ad007


title: 2BC3: Animal 3 untreated PFC


title: 2BC1: Animal 1 untreated PFC


title: AdV/DC_Patient 19

value: Patient 19

value: melanoma

value: SD


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A3_ad008


title: AdV/DC_Patient 17

value: Patient 17

value: Dendritic Cell


title: AdV/DC_Patient 18

value: Patient 18


title: AdV/DC_Patient 16

value: Patient 16


title: AdV/DC_Patient 15

value: Patient 15


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A3_ad007


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A4_ad004


title: AdV/DC_Patient 11

value: Patient 11

value: PD


title: V48_3

organism: Vibrio parahaemolyticus

source_name: Bacteria

value: WT

value: Whole organism


title: V48_2


title: AdV/DC_Patient 12

value: Patient 12


title: 2BC2: Animal 2 untreated PFC

value: male


title: AdV/DC_Patient 14

value: Patient 14


title: AdV/DC_Patient 13

value: Patient 13


title: AdV/DC_Patient 10

value: Patient 10

value: PR


title: V36_3


title: V48_1


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A3_ad002

value: LSX


title: V36_1


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A2_ad001


title: V36_2


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A3_ad004


title: V24_3


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A2_ad008


title: Day 6 Mature DC_Patient 8

description: Gene expression data from mDC, melanoma

value: Patient 8

value: melanoma

value: day 6 mDC

value: SD


title: Day 6 Mature DC_Patient 9

description: Gene expression data from mDC, melanoma

value: Patient 9

value: Dendritic Cell


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A2_ad010


title: Day 6 Mature DC_Patient 7

description: Gene expression data from mDC, melanoma

value: Patient 7


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A3_ad006


title: H1944_G1232S_shSMARCA2_R2 (ATAC-seq)

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP version ‘2013-10-10’, allowing a maximum of two mismatches per 50 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap’).
Genome_build: GRCh38
Supplementary_files_format_and_content: One bigWig file for each sample containing the normalized coverage in log counts per million

source_name: NCI-H1944 cells

extract_protocol:
NCI-H1944 cells (100,000) transduced with LACZ, SMARCA4 WT or mutant were pelleted and resuspended in 50 mL cold ATAC-resuspension buffer (ATAC-RSB) (10 mM Tris HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% Igepal CA-630, 0.1% Tween-20 and 0.01% digitonin. Cells were incubated on ice for 3 min and lysis buffer was washed out using 1 mL cold ATAC-RSB containing 0.1% Tween-20. Cells were inverted several times and nuclei was pelleted at 500xg for 10 min at 4 °C. Supernatant was discarded and nuclei were resuspended in 50 μl transposition mixture (2.5 uL Tn5 transposase, 25uL 2x TD buffer, 16.5 uL PBS, 0.5 uL1% digitonin, 0.5 uL 10% Tween-20, 5 uL H2O). The transposase reaction was performed for 30 min at 37 °C in a thermomixer with 1000 rpm.
DNA was purified using the Qiagen MinElute purification kit. DNA libraries were PCR amplified using previously published protocols (PMID: 25559105; PMID: 28846090). The libraries were multiplexed and sequenced on Illumina HiSeq4000.

value: lung cancer cell line NCI-H1944

tag: construct

value: Cells transduced with pLenti6.3-SMARCA4-G1232S, selected with 8ug/mL blasticidin for 5 days.

tag: hairpin

value: After blasticidin selection, cells were infected with pLKO-shSMARCA2. Cells were selected for 72 h with 3ug/mL puromycin.


title: Day 6 Mature DC_Patient 35

description: Gene expression data from mDC, melanoma

value: Patient 35


title: V24_2

tag: strain

value: WT

value: Whole organism


title: V24_1

tag: genotype


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A2_ad007

value: male

tag: age


title: V12_3


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A2_ad012


title: Day 6 Mature DC_Patient 34

description: Gene expression data from mDC, melanoma

value: Patient 34

tag: cell type


title: V12_2


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A2_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A2_ad004


title: H1944_R1192C_shSMARCA2_R2 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-R1192C, selected with 8ug/mL blasticidin for 5 days.


title: H1944_G1232S_shNTC_R2 (ATAC-seq)

value: After blasticidin selection, cells were infected with pLKO-shNTC. Cells were selected for 72 h with 3ug/mL puromycin.


title: H1944_A1186T_shSMARCA2_R2 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-A1186T, selected with 8ug/mL blasticidin for 5 days.


title: H1944_A1186T_shNTC_R2 (ATAC-seq)


title: V12_1


title: H1944_R1192C_shNTC_R2 (ATAC-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A2_ad002

value: LSX


title: Day 6 Mature DC_Patient 5

description: Gene expression data from mDC, melanoma

value: Patient 5

value: melanoma

value: day 6 mDC

value: PD


title: Day 6 Mature DC_Patient 32

description: Gene expression data from mDC, melanoma

value: Patient 32

value: Dendritic Cell


title: H1944_G1162C_shSMARCA2_R2 (ATAC-seq)

value: lung cancer cell line NCI-H1944

value: Cells transduced with pLenti6.3-SMARCA4-G1162C, selected with 8ug/mL blasticidin for 5 days.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A12_ad007


title: Day 6 Mature DC_Patient 33

description: Gene expression data from mDC, melanoma

value: Patient 33


title: Day 6 Mature DC_Patient 4

description: Gene expression data from mDC, melanoma

value: Patient 4


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A12_ad012


title: Day 6 Mature DC_Patient 31

description: Gene expression data from mDC, melanoma

value: Patient 31


title: H1944_G1162C_shNTC_R2 (ATAC-seq)


title: Day 6 Mature DC_Patient 6

description: Gene expression data from mDC, melanoma

value: Patient 6

value: SD


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A12_ad010

value: male


title: Day 6 Mature DC_Patient 30

description: Gene expression data from mDC, melanoma

value: Patient 30


title: Day 6 Mature DC_Patient 3

description: Gene expression data from mDC, melanoma

value: Patient 3


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A12_ad008

value: LSX


title: H1944_R1135W_shSMARCA2_R2 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-R1135W, selected with 8ug/mL blasticidin for 5 days.

value: After blasticidin selection, cells were infected with pLKO-shSMARCA2. Cells were selected for 72 h with 3ug/mL puromycin.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A12_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A12_ad004


title: H1944_G1159V_shSMARCA2_R2 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-G1159V, selected with 8ug/mL blasticidin for 5 days.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A11_ad007


title: FR.T4_replicate 1

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

country: Italy

institute: University of Verona

description: Corvina berries undergoing forced postharvest dehdration collected 65 days after harvest. It is the first of three biological replicates used in the study.

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a ScanArray 4000XL (Perkin-Elmer) at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: Corvina berries

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: Grape bunches from Vitis vinifera L. cv. Corvina harvested during the 2011 vintage were grown in the Valpolicella region (Verona, north-east Italy) and collected at full commercial maturity. Approximately 200 kg of grape bunches were placed on wooden racks and stored for dehydration in Gargagnago di Sant’Ambrogio di Valpolicella, Italy (45◦31′20′′ N,10◦50′05′′ E). In the fruttaio, collected grapes were split into two dehydrating rooms where specific environmental conditions were set up to reproduce a natural (NT) and a forced (FR) dehydration process. Natural dehydration conditions were obtained as described in Zenoni et al. (2016). Forced dehydration conditions were obtained by using a fan close to the batch of grapes to promote a faster drying; in this way, FR grapes were exposed to an average airflow of about 1 m/s that in turn contributed to remove part of the humid air stacking around the clusters, almost without affecting temperature. Both drying processes were stopped when grapes reached ∼30% of the weight loss (i.e., after 120 and 65 days for NT and FR conditions, respectively).

extract_protocol: Total RNA extraction was performed from ~200 mg of berry tissue (pericarp without seeds) using the Spectrum Plant Total RNA kit (Sigma-Aldrich) as previously described (Fasoli et al., 2012).

tag: cultivar

value: Corvina

tag: year

tag: time point

value: 65 days after harvest

tag: treatment

value: forced postharvest dehdration


title: H1944_R973L_shSMARCA2_R2 (ATAC-seq)

tag: cell line

value: lung cancer cell line NCI-H1944

value: Cells transduced with pLenti6.3-SMARCA4-R973L, selected with 8ug/mL blasticidin for 5 days.


title: H1944_R1135W_shNTC_R2 (ATAC-seq)

value: After blasticidin selection, cells were infected with pLKO-shNTC. Cells were selected for 72 h with 3ug/mL puromycin.


title: FR.T4_replicate 2

description: Corvina berries undergoing forced postharvest dehdration collected 65 days after harvest. It is the second of three biological replicates used in the study.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A11_ad010


title: Day 6 Mature DC_Patient 28

description: Gene expression data from mDC, melanoma

tag: subject id

value: Patient 28

tag: patient diagnosis

value: melanoma

value: Dendritic Cell

tag: dc subtype

value: day 6 mDC

value: PD


title: H1944_G1159V_shNTC_R2 (ATAC-seq)


title: FR.T4_replicate 3

description: Corvina berries undergoing forced postharvest dehdration collected 65 days after harvest. It is the third of three biological replicates used in the study.


title: H1944_R973L_shNTC_R2 (ATAC-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A11_ad012

value: male


title: Day 6 Mature DC_Patient 29

description: Gene expression data from mDC, melanoma

value: Patient 29

tag: clinical outcome

tag: overall survival (months)


title: FR.T2_replicate 2

description: Corvina berries undergoing forced postharvest dehdration collected 33 days after harvest. It is the second of three biological replicates used in the study.

value: 33 days after harvest


title: Day 6 Mature DC_Patient 26

description: Gene expression data from mDC, melanoma

value: Patient 26


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A11_ad002

tag: brain region

value: LSX

tag: Sex


title: FR.T2_replicate 3

description: Corvina berries undergoing forced postharvest dehdration collected 33 days after harvest. It is the third of three biological replicates used in the study.


title: Day 6 Mature DC_Patient 25

description: Gene expression data from mDC, melanoma

value: Patient 25


title: FR.T1_replicate 2

description: Corvina berries undergoing forced postharvest dehdration collected 22 days after harvest. It is the second of three biological replicates used in the study.

value: Corvina

value: 22 days after harvest


title: Day 6 Mature DC_Patient 23

description: Gene expression data from mDC, melanoma

value: Patient 23


title: H1944_E882K_shSMARCA2_R2 (ATAC-seq)

value: lung cancer cell line NCI-H1944

tag: construct

value: Cells transduced with pLenti6.3-SMARCA4-E882K, selected with 8ug/mL blasticidin for 5 days.

tag: hairpin

value: After blasticidin selection, cells were infected with pLKO-shSMARCA2. Cells were selected for 72 h with 3ug/mL puromycin.


title: H1944_E882K_shNTC_R2 (ATAC-seq)

value: After blasticidin selection, cells were infected with pLKO-shNTC. Cells were selected for 72 h with 3ug/mL puromycin.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A11_ad008

tag: strain


title: Day 6 Mature DC_Patient 24

description: Gene expression data from mDC, melanoma

value: Patient 24

value: melanoma


title: FR.T1_replicate 3

description: Corvina berries undergoing forced postharvest dehdration collected 22 days after harvest. It is the third of three biological replicates used in the study.

value: forced postharvest dehdration


title: FR.T2_replicate 1

description: Corvina berries undergoing forced postharvest dehdration collected 33 days after harvest. It is the first of three biological replicates used in the study.


title: FR.T1_replicate 1

description: Corvina berries undergoing forced postharvest dehdration collected 22 days after harvest. It is the first of three biological replicates used in the study.


title: NT.T5_replicate 2

description: Corvina berries undergoing natural postharvest dehdration collected 120 days after harvest. It is the second of three biological replicates used in the study.

value: 120 days after harvest

value: natural postharvest dehdration


title: Day 6 Mature DC_Patient 22

description: Gene expression data from mDC, melanoma

value: Patient 22

value: Dendritic Cell

value: day 6 mDC

value: PD


title: H1944_K785R_shSMARCA2_R2 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-K785R, selected with 8ug/mL blasticidin for 5 days.


title: NT.T5_replicate 1

description: Corvina berries undergoing natural postharvest dehdration collected 120 days after harvest. It is the first of three biological replicates used in the study.

value: Corvina


title: Day 6 Mature DC_Patient 20

description: Gene expression data from mDC, melanoma

value: Patient 20

value: PR


title: H1944_T910M_shSMARCA2_R2 (ATAC-seq)

value: lung cancer cell line NCI-H1944

value: Cells transduced with pLenti6.3-SMARCA4-T910M, selected with 8ug/mL blasticidin for 5 days.


title: H1944_K785R_shNTC_R2 (ATAC-seq)


title: Day 6 Mature DC_Patient 27

description: Gene expression data from mDC, melanoma

value: Patient 27


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A10_ad004

value: LSX

value: male

tag: age


title: Day 6 Mature DC_Patient 2

description: Gene expression data from mDC, melanoma

value: Patient 2

value: melanoma

tag: cell type


title: NT.T4_replicate 3

description: Corvina berries undergoing natural postharvest dehdration collected 65 days after harvest. It is the third of three biological replicates used in the study.

tag: cultivar

value: 65 days after harvest


title: H1944_WT_shSMARCA2_R2 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-WT, selected with 8ug/mL blasticidin for 5 days.

value: After blasticidin selection, cells were infected with pLKO-shSMARCA2. Cells were selected for 72 h with 3ug/mL puromycin.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A11_ad001


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A11_ad004


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A10_ad012


title: Day 6 Mature DC_Patient 19

description: Gene expression data from mDC, melanoma

value: Patient 19

value: Dendritic Cell

value: SD


title: Day 6 Mature DC_Patient 21

description: Gene expression data from mDC, melanoma

value: Patient 21

value: day 6 mDC


title: NT.T5_replicate 3

description: Corvina berries undergoing natural postharvest dehdration collected 120 days after harvest. It is the third of three biological replicates used in the study.

value: Corvina

tag: year

value: 120 days after harvest

value: natural postharvest dehdration


title: NT.T4_replicate 2

description: Corvina berries undergoing natural postharvest dehdration collected 65 days after harvest. It is the second of three biological replicates used in the study.

tag: time point


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A10_ad010


title: Day 6 Mature DC_Patient 18

description: Gene expression data from mDC, melanoma

value: Patient 18


title: H1944_LACZ_shSMARCA2_R2 (ATAC-seq)

value: lung cancer cell line NCI-H1944

value: Cells transduced with pLenti6.3-LACZ, selected with 8ug/mL blasticidin for 5 days.


title: H1944_WT_shNTC_R2 (ATAC-seq)

value: After blasticidin selection, cells were infected with pLKO-shNTC. Cells were selected for 72 h with 3ug/mL puromycin.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A10_ad007

value: LSX

value: male


title: H1944_LACZ_shNTC_R2 (ATAC-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A10_ad008


title: NT.T4_replicate 1

description: Corvina berries undergoing natural postharvest dehdration collected 65 days after harvest. It is the first of three biological replicates used in the study.

value: 65 days after harvest

tag: treatment


title: NT.T3_replicate 3

description: Corvina berries undergoing natural postharvest dehdration collected 52 days after harvest. It is the third of three biological replicates used in the study.

value: 52 days after harvest


title: Day 6 Mature DC_Patient 17

description: Gene expression data from mDC, melanoma

value: Patient 17

value: melanoma

value: PD


title: NT.T3_replicate 2

description: Corvina berries undergoing natural postharvest dehdration collected 52 days after harvest. It is the second of three biological replicates used in the study.


title: H1944_G1232S_shSMARCA2_R1 (ATAC-seq)

tag: cell line

value: Cells transduced with pLenti6.3-SMARCA4-G1232S, selected with 8ug/mL blasticidin for 5 days.

value: After blasticidin selection, cells were infected with pLKO-shSMARCA2. Cells were selected for 72 h with 3ug/mL puromycin.


title: Day 6 Mature DC_Patient 15

description: Gene expression data from mDC, melanoma

tag: subject id

value: Patient 15

value: Dendritic Cell

value: day 6 mDC


title: H1944_G1232S_shNTC_R1 (ATAC-seq)


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A10_ad002


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A10_ad006


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A10_ad001


title: H1944_R1192C_shNTC_R1 (ATAC-seq)

value: Cells transduced with pLenti6.3-SMARCA4-R1192C, selected with 8ug/mL blasticidin for 5 days.


title: CEMBA180917_4G_5_CEMBA180917_4G_6_A1_ad001


title: Day 6 Mature DC_Patient 13

description: Gene expression data from mDC, melanoma

value: Patient 13

tag: patient diagnosis


title: Day 6 Mature DC_Patient 14

description: Gene expression data from mDC, melanoma

value: Patient 14

tag: dc subtype


title: Day 6 Mature DC_Patient 16

description: Gene expression data from mDC, melanoma

value: Patient 16

tag: clinical outcome


title: H1944_A1186T_shSMARCA2_R1 (ATAC-seq)

value: lung cancer cell line NCI-H1944

value: Cells transduced with pLenti6.3-SMARCA4-A1186T, selected with 8ug/mL blasticidin for 5 days.


title: NT.T3_replicate 1

description: Corvina berries undergoing natural postharvest dehdration collected 52 days after harvest. It is the first of three biological replicates used in the study.

value: Corvina

value: natural postharvest dehdration


title: NT.T2_replicate 1

description: Corvina berries undergoing natural postharvest dehdration collected 33 days after harvest. It is the first of three biological replicates used in the study.

value: 33 days after harvest


title: NT.T1_replicate 3

description: Corvina berries undergoing natural postharvest dehdration collected 22 days after harvest. It is the third of three biological replicates used in the study.

value: 22 days after harvest