title: Nucleus from Hippocampus brain region A3-DG_S872_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S872_L001_R1_001


title: Nucleus from Hippocampus brain region A3-DG_S869_L001_R1

status: Public on Aug 16 2016

type: SRA

city: Cambridge

first: Naomi

last: Habib

state: MA

address: 75 Ames st

department: Zhang

country: USA

institute: Broad Institute

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S869_L001_R1_001

library_source: transcriptomic

data_processing:
sNUc-Seq libraries were aligned using Bowtie2 to the mouse transcriptome (RefSeq mm10 and Ensemble GRCm38 merged using Cufflink). RSEM v1.27 was used to estimate gene expression, in transcript per million (TPM) values, and TPM estimates were transformed to log-space by taking log(TPM+1).  A library was filtered out if it had less than 2,000 detected genes or more than 8,000 detected genes. All libraries were normalized using a normalization procedure based on Bland-Altman (MA) plot and density estimation. For a pair of cells, we normalize one cell with respect to another so that genes are not differentially expressed on average, but using only a small set of highly expressed and lowly variable genes, which provides robustness against typical noise in single cells RNA-seq data.
Genome_build: RefSeq mm10 and Ensembl GRCm38
Supplementary_files_format_and_content: tab delimited matrix with RSEM computed log(TPM+1) values after normalization

molecule: nuclear RNA

organism: Mus musculus

source_name: Mouse Hippocampus region

extract_protocol:
nuclei isolation by gradient centrifugation and FACS sorting
SMART-Seq2 protocol, with MAXIMA -h RT enzyme, applied on single nuclei sorted by FACS

tag: age

value: 12 weeks

tag: strain


title: Nucleus from Hippocampus brain region A3-DG_S868_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S868_L001_R1_001


title: Nucleus from Hippocampus brain region A3-DG_S867_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S867_L001_R1_001


title: Nucleus from Hippocampus brain region A3-DG_S866_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S866_L001_R1_001


title: Nucleus from Hippocampus brain region A3-DG_S870_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S870_L001_R1_001


title: Nucleus from Hippocampus brain region A3-DG_S892_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S892_L001_R1_001


title: Nucleus from Hippocampus brain region A3-DG_S865_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S865_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S839_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S839_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S836_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S836_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S838_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S838_L001_R1_001


title: Nucleus from Hippocampus brain region A3-DG_S871_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S871_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S831_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S831_L001_R1_001


title: Nucleus from Hippocampus brain region A3-DG_S885_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S885_L001_R1_001


title: Nucleus from Hippocampus brain region A3-DG_S881_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S881_L001_R1_001


title: Nucleus from Hippocampus brain region A3-DG_S888_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A3-DG_S888_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S829_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S829_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S827_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S827_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S828_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S828_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S826_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S826_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S822_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S822_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S830_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S830_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S817_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S817_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S800_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S800_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S803_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S803_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S801_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S801_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S804_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S804_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S805_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S805_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S798_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S798_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S795_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S795_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S797_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S797_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S794_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S794_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S793_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S793_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S799_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S799_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S791_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S791_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S840_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S840_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S789_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S789_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S788_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S788_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S790_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S790_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S787_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S787_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S786_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S786_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S784_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S784_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S785_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S785_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S783_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S783_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S776_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S776_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S782_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S782_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S772_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S772_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S777_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S777_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S773_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S773_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S779_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S779_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S769_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S769_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S569_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S569_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S557_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S557_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S568_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S568_L001_R1_001


title: Nucleus from Hippocampus brain region A2-P1-DG_S792_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A2-P1-DG_S792_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S558_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S558_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S552_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S552_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S553_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S553_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S567_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S567_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S556_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S556_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S545_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S545_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S550_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S550_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S549_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S549_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S551_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S551_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S548_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S548_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S541_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S541_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S542_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S542_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S543_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S543_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S540_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S540_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S539_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S539_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S547_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S547_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S537_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S537_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S536_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S536_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S532_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S532_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S535_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S535_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S530_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S530_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S534_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S534_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S565_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S565_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S529_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S529_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S528_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S528_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S526_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S526_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S520_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S520_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S524_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S524_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S519_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S519_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S518_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S518_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S512_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S512_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S517_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S517_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S516_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S516_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S515_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S515_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S511_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S511_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S509_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S509_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S510_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S510_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S506_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S506_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S555_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S555_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S507_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S507_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S505_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S505_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S531_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S531_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S493_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S493_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S494_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S494_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S490_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S490_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S527_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S527_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S482_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S482_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S485_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S485_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S483_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S483_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S484_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S484_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S521_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S521_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S283_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S283_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S508_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S508_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S282_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S282_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S281_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S281_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S279_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S279_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P3-CA23_S481_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P3-CA23_S481_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S277_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S277_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S270_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S270_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S272_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S272_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S269_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S269_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S268_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S268_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S271_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S271_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S266_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S266_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S274_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S274_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S264_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S264_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S263_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S263_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S262_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S262_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S267_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S267_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S265_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S265_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S260_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S260_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S261_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S261_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S259_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S259_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S250_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S250_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S256_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S256_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S254_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S254_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S253_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S253_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S249_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S249_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S251_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S251_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S248_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S248_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S280_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S280_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S243_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S243_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S245_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S245_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S246_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S246_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S242_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S242_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S273_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S273_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S239_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S239_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S275_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S275_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S240_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S240_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S238_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S238_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S234_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S234_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S228_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S228_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S231_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S231_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S226_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S226_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S237_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S237_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S258_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S258_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S224_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S224_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S221_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S221_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S217_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S217_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S220_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S220_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S214_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S214_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S218_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S218_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S215_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S215_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S213_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S213_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S210_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S210_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S209_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S209_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S208_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S208_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S206_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S206_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S211_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S211_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S232_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S232_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S203_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S203_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S230_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S230_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S201_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S201_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S199_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S199_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S207_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S207_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S198_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S198_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S227_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S227_L001_R1_001


title: H2013430_S12

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

country: China

institute: Kunming Institute of Zoology

description: pooling bisulfate PCR products from bis treated DNA that extracted from prefrontal cortex tissue

library_source: genomic

data_processing:
Quality and adaptor trimming was performed using TrimGalore! with default parameters
Reads were mapped to the respective reference genomes (hg19, pantro4,rheMac3,macFas5 and nomLeu3) and methylation calling was done using Bismark with default parameters
Duplicates were removed using Bismark deduplication script with default parameters
Non-human species coordinates were converted to hg19 using UCSC liftover tool
Genome_build: hg19
Supplementary_files_format_and_content: Miseq_Methylated_Read_Count.txt file contains the number of methylated reads per CpG site and individual. Columns 1-3 show chromosome, start and end coordinates of each CpG, respectively. Columns 4-41 show number of methylated reads per sample
Supplementary_files_format_and_content: Miseq_Coverage_Read_Count.txt file contains the number reads per CpG site and individual. Columns 1-3 show chromosome, start and end coordinates of each CpG, respectively. Columns 4-41 show number of total reads per sample

molecule: genomic DNA

organism: Homo sapiens

source_name: Prefrontal Cortex

extract_protocol:
Genomic DNA was extracted according to the DNeasy Blood&Tissue Kit (QIAGEN) protocol.
DNA libraries were prepared for sequencing using Nextera XT DNA Sample Preparation protocol

treatment_protocol: We used the EpiTect Bisulfite Kits (Qiagen, Valencia, CA) to conduct bisulfite conversions of genomic DNA following the manufacturer's instructions. Sodium bisulfite converts unmethylated cytosine to uracil, which is then PCR amplified as thymidine and methylated cytosine remain cytosine.

tag: tissue

value: Prefrontal Cortex


title: Nucleus from Hippocampus brain region A1-P2-DG_S195_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S195_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S194_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S194_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S222_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S222_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S466_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S466_L001_R1_001


title: H2013422_S16


title: Nucleus from Hippocampus brain region A1-P2-DG_S223_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S223_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-DG_S219_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S219_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S468_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S468_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S461_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S461_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S460_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S460_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S463_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S463_L001_R1_001


title: H2013379_S13


title: Nucleus from Hippocampus brain region A1-P2-CA1_S455_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S455_L001_R1_001


title: H2013352_S17


title: Nucleus from Hippocampus brain region A1-P2-CA1_S440_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S440_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S445_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S445_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S439_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S439_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S458_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S458_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S438_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S438_L001_R1_001


title: H2013336_S14

description: pooling bisulfate PCR products from bis treated DNA that extracted from prefrontal cortex tissue


title: Nucleus from Hippocampus brain region A1-P2-DG_S196_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-DG_S196_L001_R1_001


title: H2013314_S4


title: Nucleus from Hippocampus brain region A1-P2-CA1_S435_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S435_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S437_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S437_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S436_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S436_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S434_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S434_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S433_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S433_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S432_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S432_L001_R1_001


title: H2012386_S9


title: H2012300_S7


title: Nucleus from Hippocampus brain region A1-P2-CA1_S431_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S431_L001_R1_001


title: H2012338_S2


title: H2013381_S18


title: Nucleus from Hippocampus brain region A1-P2-CA1_S430_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S430_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S429_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S429_L001_R1_001


title: H2012274_S10


title: Nucleus from Hippocampus brain region A1-P2-CA1_S428_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S428_L001_R1_001


title: H2012202_S8


title: Nucleus from Hippocampus brain region A1-P2-CA1_S427_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S427_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S425_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S425_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S459_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S459_L001_R1_001


title: H2012194_S15


title: Nucleus from Hippocampus brain region A1-P2-CA1_S424_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S424_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S419_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S419_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S423_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S423_L001_R1_001


title: H200965_S19

description: pooling bisulfate PCR products from bis treated DNA that extracted from prefrontal cortex tissue


title: Nucleus from Hippocampus brain region A1-P2-CA1_S420_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S420_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S422_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S422_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S416_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S416_L001_R1_001


title: H200955_S1


title: Nucleus from Hippocampus brain region A1-P2-CA1_S415_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S415_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S414_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S414_L001_R1_001


title: H200936_S3


title: Nucleus from Hippocampus brain region A1-P2-CA1_S413_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S413_L001_R1_001


title: H2009149_S6


title: Nucleus from Hippocampus brain region A1-P2-CA1_S412_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S412_L001_R1_001


title: H004_S23


title: Nucleus from Hippocampus brain region A1-P2-CA1_S410_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S410_L001_R1_001


title: H2013390_S11


title: H003_S22


title: Nucleus from Hippocampus brain region A1-P2-CA1_S407_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S407_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S408_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S408_L001_R1_001


title: H002_S21


title: Nucleus from Hippocampus brain region A1-P2-CA1_S406_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S406_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S404_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S404_L001_R1_001


title: H001_S20


title: Nucleus from Hippocampus brain region A1-P2-CA1_S403_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S403_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S402_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S402_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S417_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S417_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S399_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S399_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S400_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S400_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S398_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S398_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S401_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S401_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S396_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S396_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S393_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S393_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S411_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S411_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S391_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S391_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S390_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S390_L001_R1_001


title: H200951_S5

description: pooling bisulfate PCR products from bis treated DNA that extracted from prefrontal cortex tissue


title: Nucleus from Hippocampus brain region A1-P2-CA1_S386_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S386_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S387_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S387_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S389_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S389_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S99_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S99_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S98_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S98_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S165_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S165_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S164_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S164_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S421_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S421_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S163_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S163_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S162_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S162_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S397_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S397_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S97_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S97_L001_R1_001


title: ma26871_S28

organism: Macaca mulatta


title: ma26306_S30


title: Nucleus from Hippocampus brain region A1-P1-DG_S160_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S160_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P2-CA1_S409_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S409_L001_R1_001


title: ma26304_S29


title: Nucleus from Hippocampus brain region A1-P2-CA1_S392_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S392_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S161_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S161_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S159_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S159_L001_R1_001


title: ma26300_S31

description: pooling bisulfate PCR products from bis treated DNA that extracted from prefrontal cortex tissue


title: Nucleus from Hippocampus brain region A1-P1-DG_S157_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S157_L001_R1_001


title: ma26187_S43


title: Nucleus from Hippocampus brain region A1-P1-DG_S156_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S156_L001_R1_001


title: ma26183-2_S41


title: Gibbon_S24

organism: Hoolock leuconedys


title: Nucleus from Hippocampus brain region A1-P1-DG_S167_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S167_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S152_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S152_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S151_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S151_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S150_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S150_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S155_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S155_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S147_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S147_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S146_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S146_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S149_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S149_L001_R1_001


title: WT, 240min 100% nitrogen gas, 1st replicate

city: Glassboro

first: Mark

last: Hickman

state: NJ

address: 201 Mullica Hill Road

department: Biological Sciences

institute: Rowan University

data_processing:
Each raw file is a de-multiplexed fastq file
FASTQ Quality Trimmer, 5' and 3' ends, window size=1,step size=1,min score=10
Reads aligned to yeast genome using TopHat2
Number of reads per feature was calculating using HTSeq,mode=union
Genome_build: saccharomyces_cerevisiae_R64-1-1_20110208.fasta
Supplementary_files_format_and_content: tab-delimited text files, first column= feature, second column=number of reads that overlap feature

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: strain yMH914 (S288C background with repaired HAP1)

growth_protocol: A saturated culture was diluted and then placed in 100% nitrogen for the indicated time, with the gas flowing through flasks. Cells were collected in mid-log (1-2x10^cels/ml), filtered and frozen in liquid nitrogen.

extract_protocol:
The Qiagen RNeasy kit, using mechanical lysis with beads, to isolate total RNA. PolyA selection was done through oligo-dT capture
TruSeq RNA Sample Preparation Kit (Illumina)
Multiplex eight samples and then sequence in one sequencing lane

tag: time in 100% n2

value: 240 minutes

tag: genotype

value: MATa ura3D0 his3D200 leu2D0 lys2-128d HAP1


title: Nucleus from Hippocampus brain region A1-P1-DG_S158_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S158_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S145_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S145_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S142_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S142_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S143_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S143_L001_R1_001


title: WT, 60min 100% nitrogen gas, 1st replicate

value: 60 minutes


title: WT, 180min 100% nitrogen gas, 1st replicate

value: 180 minutes


title: WT, 120min 100% nitrogen gas, 1st replicate

value: 120 minutes


title: Nucleus from Hippocampus brain region A1-P1-DG_S154_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S154_L001_R1_001


title: ma26299_S27


title: ce080366_S45

organism: Macaca fascicularis


title: WT, 5min 100% nitrogen gas, 1st replicate

value: 5 minutes


title: WT, 30min 100% nitrogen gas, 1st replicate

value: 30 minutes


title: ce071572_S46


title: Nucleus from Hippocampus brain region A1-P1-DG_S144_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S144_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S140_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S140_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S138_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S138_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S141_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S141_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S137_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S137_L001_R1_001


title: WT, 0min 100% nitrogen gas, 1st replicate

value: 0 minutes


title: WT, 10min 100% nitrogen gas, 1st replicate

value: 10 minutes


title: Nucleus from Hippocampus brain region A1-P1-DG_S166_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S166_L001_R1_001


title: ce071454_S48

description: pooling bisulfate PCR products from bis treated DNA that extracted from prefrontal cortex tissue


title: ce071426_S44


title: Nucleus from Hippocampus brain region A1-P1-DG_S134_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S134_L001_R1_001


title: ce071410_S47


title: Nucleus from Hippocampus brain region A1-P1-DG_S132_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S132_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S135_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S135_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S131_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S131_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S133_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S133_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S130_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S130_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S126_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S126_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S127_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S127_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S128_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S128_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S139_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S139_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S122_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S122_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S123_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S123_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S120_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S120_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S124_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S124_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S117_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S117_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S119_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S119_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S121_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S121_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S113_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S113_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S116_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S116_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S118_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S118_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S112_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S112_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S115_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S115_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S125_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S125_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S110_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S110_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S106_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S106_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S114_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S114_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S136_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S136_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S111_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S111_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S103_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S103_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S102_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S102_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S100_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S100_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S104_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S104_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S101_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S101_L001_R1_001


title: Nucleus from Hippocampus brain region A1-P1-DG_S105_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P1-DG_S105_L001_R1_001


title: sample_B2

city: Buffalo

first: Jayasha

last: Shandilya

state: New York

address: 619 Cooke Hall

institute: SUNY at University at Buffalo

data_processing:
Raw sequencing reads were mapped to Mus musculus (GRCm38/mm10 build) genome using TopHat (v2.0.7)
Isoform level abundance was quantified as Fragments per Kilobase of transcript per million mapped reads(FPKM) using Cufflinks (v2.1.1).
Differentially expressed genes were calculated using cuffdiff and plots were generated by cummeRbund (v.2.0)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-limited text containing FPKM values for each sample with corresponding p-values.

molecule: total RNA

source_name: Circumvallate/Foliate taste papillae

extract_protocol:
Total RNA was extracted using the Nucleospin RNA XS kit (Clontech, Mountain View, CA).
The TruSeq RNA sample preparation kit (Illumina, San Diego, CA) was used to prepare cDNA libraries from RNA samples. Samples were polyA selected to isolate mRNA, the mRNA was cleaved, reverse transcribed, end-repaired and enriched as per the manufacturer's protocol.

treatment_protocol: The tongue was removed and injected with enzymatic solution before being incubated in oxygenated Tyrode's solution for 20 min. Taste receptor cells were harvested from CV/Foliate papillae for RNA extraction.

tag: cell type

value: isolated taste cells

value: 6 months


title: sample_B


title: sample_s3

value: 2 months


title: WIBR3

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Illumina pipeline Casava 1.82
Reads were mapped to the human genome (hg19) using TopHat (v2.0.11) in sensitive mode (tophat --library-type fr-firststrand -g 1 --no-novel-juncs --no-novel-indels –b2-sensitive)
Gene counts were generated using HTSeq-count (0.6.1)
Repeats counts were generated using the multiCov tool from the bedtools (2.25) software
Genome_build: hg19
Supplementary_files_format_and_content: read counts on genes: htseq-cout output (pileup); read counts on repeats: bedtools multiBamCov output (txt)

growth_protocol: NHSM (Gafni et al. 2013) or hESM

extract_protocol: Illumina Truseq Stranded RNA

value: embryonic stem cells

tag: es state

value: Primed

tag: medium

value: hESM


title: sample_B1


title: WIBR2


title: LISp38_NHSM

source_name: LIS p38 from Hanna lab  in Gafni et al. Medium (NHSM)

value: Naive

value: NHSM (Gafni et al.)


title: WIBR3_AAVS1-GFP

source_name: WIBR3 AAVS1-GFP


title: sample_s2


title: C1AAVs1GFP_NHSM

source_name: C1 AAVS1-GFP from Hanna lab  in Gafni et al. Medium (NHSM)


title: WIBR2_NHSM

source_name: WIBR2 in Gafni et al. Medium (NHSM)


title: sample_s


title: (delta) mbaI strain grown to stationary phase with 1 uM 3-OH-C10-HSL signal added, bio rep1

city: Salt Lake City

first: Aaron

middle: W

last: Puri

state: UT

address: 1390 Presidents Circle

institute: University of Utah

description: rRNA-depleted total RNA

data_processing:
The raw reads from the sequencing facility were aligned to the Methylobacter tundripaludum strain 21/22 genome as downloaded from JGI's IMG on Jan. 13 2016.
Alignment was performed using BWA version 0.7.12-r1044 using the BWA-MEM algorithm and default parameters (Li and Durbin, 2010).
The alignments were post-processed into sorted BAM files with SAMTools version 1.2-232-g87cdc4a (Li et al., 2009).
Reads were attributed to open reading frames (ORFs) as well as the mbaI' pseudogene T451DRAFT_0802 using the htseq-count tool from the 'HTSeq' framework version 0.6.1p1 in the 'intersection-nonempty' mode (Anders et al., 2015).
Differential abundance analysis was performed with DESeq2 1.2.10 (Anders and Huber, 2010; Anders et al., 2013) using R 3.3.0.
Genome_build: Downloaded from JGI's IMG on Jan. 13 2016.
Supplementary_files_format_and_content: Raw counts. Tab delimited text file. Locus tag annotations can be found at: https://img.jgi.doe.gov/). The genome ID is: 2563366535

organism: Methylobacter tundripaludum 21/22

source_name: Pure bacterial liquid culture

growth_protocol: M. tundripaludum 21/22 was cultured in an atmosphere of 25% methane in air. Plates were incubated at room temperature in sealed jars (Oxoid Limited, Hampshire, United Kingdom), while liquid cultures were grown at 18C in 250-ml glass serum bottles (Kimble Chase, Vineland, NJ, USA) or 18- by 150-mm tubes (Bellco Glass, Vineland, NJ, USA) sealed with rubber stoppers and aluminum seals (Wheaton, Millville, NJ, USA). Cultures were grown in nitrate mineral salts (NMS) medium containing 0.2 g/L MgSO4·7H2O, 0.2 g/L CaCl2·6H2O, 1 g/L KNO3, and 30 uM LaCl as well as 1X trace elements. 500X trace elements contains 1.0 g/L Na2-EDTA, 2.0 g/L FeSO4·7H2O, 0.8 g/L ZnSO4·7H2O, 0.03 g/L MnCl2·4H2O, 0.03 g/L H3BO3, 0.2 g/L CoCl2·6H2O, 0.6 g/L CuCl2·2H2O, 0.02 g/L NiCl2·6H2O, and 0.05 g/L Na2MoO·2H2O. A final concentration of 5.8 mM phosphate buffer, pH 6.8 was added immediately before use.

extract_protocol:
A 1:10 volume of stop solution (5% buffer-saturated phenol in ethanol) was added to cells prior to harvesting the cells by centrifugation. Cells were resuspended in RNA extraction buffer (1:3 ratio of 5% cetrimonium bromide in 2.5 M NaCl to 0.1 M phosphate buffer [pH 5.8]) and lysed by bead beating with 0.1-mm zirconia-silica beads (Biospec Products) in 50% phenol–chloroform–isoamyl alcohol (at a 25:24:1 ratio),0.5% sodium dodecyl sulfate, and 0.5% N-lauroylsarcosine sodium salt. After centrifugation, the aqueous layer was harvested and mixed with an equal volume of chloroform-isoamyl alcohol (24:1 ratio). The aqueous layer was harvested again, and RNA was precipitated with 150 mM sodium acetate, 1.5 mM MgCl2, and 50% isopropanol (all final concentrations) overnight at 80°C. The precipitated RNA was harvested by centrifugation and treated with DNase I (Life Technologies) before purification with the RNeasy minikit and RNase-free DNase (Qiagen). We ensured that the harvested RNA was DNA free by using iScript reverse transcription supermix (Bio- Rad) with and without reverse transcriptase.
Illumina HiSeq2500 1x50 (single ended) library construction prepared by GENEWIZ (South Plainfield, NJ, USA)

treatment_protocol: The strain was grown the absence or presence of 1 uM 3-OH-C10-HSL.

tag: mutation

value: (delta) mbaI (T451DRAFT_0796)

tag: treatment

value: 1 uM 3-OH-C10-HSL added at beginning of growth


title: (delta) mbaI strain grown to stationary phase with 1 uM 3-OH-C10-HSL signal added, bio rep2

description: rRNA-depleted total RNA


title: (delta) mbaI strain grown to log phase without signal added, bio rep2

description: rRNA-depleted total RNA


title: (delta) mbaI strain grown to log phase with 1 uM 3-OH-C10-HSL signal added, bio rep1

description: rRNA-depleted total RNA


title: (delta) mbaI strain grown to stationary phase without signal added, bio rep1

description: rRNA-depleted total RNA


title: (delta) mbaI strain grown to log phase without signal added, bio rep1

description: rRNA-depleted total RNA


title: BC181 [ChIP-Seq]

status: Public on Aug 15 2016

city: Cincinnati

first: Kohta

last: Ikegami

state: OH

address: 240 Albert Sabin Way, Cincinnati, OH 45229

department: Division of Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
seq-Wako_H3K4me3_305-34819_RiEV_KI2009_N2_MXEMB
Barcode: TCAGGAC

data_processing:
Unique sequencing reads were aligned to the C. elegans reference genome (ce6, WS190) using bowtie, allowing up to two mismatches
ChIP-seq reads were extended to the original DNA fragment size estimated computationally as the distance between positive- and negative-strand reads with the highest cross-correlation.
The number of overlapping reads per base was computed using 'basealigncount' function in Zinba (Rashid et al., Genome Biology 2011)
Processed data files are in wig format representing overlappaing read counts at each base in the genome.
Genome_build: ce6, WS190

organism: Caenorhabditis elegans

source_name: Mixed-stage embryos

growth_protocol: The C. elegans N2 strain animals in the liquid S-medium were fed with bacteria HB101 until becoming gravid adults. Mixed-stage embryos were harvested from the adults by hypochlorite treatment.

extract_protocol:
The C. elegans N2 strain mixed-stage embryos were cross-linked in 2% formaldehyde for 30 min at 25ºC. Chromatin extract was prepared by sonication in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl). Five to ten micrograms of antibodies were immobilized on sepharose beads and incubated with the chromatin extract for >12 hours at 4ºC. After washing the immunoprecipitants followed by RNase treatment and reverse-crosslinking, DNA were extracted and purified.
DNA was blunt-ended and A-overhanged with Exo(-) Klenow fragment in the presence of dATP. DNA fragments were ligated with adaptors. DNA was amplified by PCR with single-end primers. Amplicon was loaded on an agarose gel, and DNA at 200-500 bp was recovered from the gel.

treatment_protocol: For RNAi, the N2 strain worms were first arrested at the L1 larva stage in the liquid S medium for synchronization. Synchronized L1 worms were fed with a bacteria strain HB101, which do not contain induction vectors, at 20ºC for 36 hours (L4 stage) in the liquid S medium. L4 worms were harvested, washed and transferred to a new S medium supplemented with a bacteria strain HT115 expressing interfering double-strand RNA from L4440 vector under IPTG (RNAi bacteria). Worms were grown with the RNAi bacteria at 20ºC until the gravid stage. Embryos were harvested from the gravid adults by hypochlorite treatment and used in experiments. In parallel, worms were fed with HT115 bacteria bearing L4440 vector without target DNA insertion (empty vector RNAi).

value: Empty vector RNAi

tag: chip antibody


title: (delta) mbaI strain grown to stationary phase without signal added, bio rep2

description: rRNA-depleted total RNA


title: MORC3_ChIPseq_input_replicate 2

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

data_processing:
Raw sequencing reads were mapped to mm9 genome with Bowtie (Langmead et al., 2009) by allowing up to two mismatches and only keeping uniquely mapped reads. PCR duplicated reads were removed with SAMtools (Li et al., 2009). Heatmap were generated in R with package ngs.plot (Shen et al., 2014). For H3K4me1 (GSM769008), H3K9me3 (GSM1000147), H3K27me3 (GSM1000089), and RNA Polymerase II (GSM723019) ChIPseq, raw sequencing data were downloaded from ENCODE project and processed the same way as described above.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig of ChIPseq reads

source_name: V6.5 embryonic stem cells

growth_protocol: V6.5 embryonic stem cells were passaged on MEFs in serum/LIF

extract_protocol:
Cells were fixed by treatment with 1% Formaldehyde and 1xPBS for ten minutes at room temperature, then quenched by addition of glycine to a final concentration of 0.14 M and incubated a further ten minutes. Cells were washed with 1xPBS, then aliquoted and flash frozen.  Ten million cells per replicate were thawed on ice and resuspended in 1 mL 10 mM Tris pH 8.0, 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, and 1 mM PMSF and incubated with rotation for fifteen minutes at room temperature. Nuclei were pelleted by centrifugation at 1500g for five minutes at 4 °C. The nuclei were resuspended in 10 mM Tris pH 8.0, 200 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, and 1 mM PMSF, and incubated for ten minutes at room temperature with rotation, and again centrifuged. Nuclei were then resuspended in 10 mM Tris pH 8.0, 10 mM EDTA, 0.5 mM EGTA, 0.1% SDS, and 1 mM PMSF, and disrupted by sonication at high intensity using a Bioruptor (Diagenode).  Sonicated lysate was cleared by centrifugation at 16,000xg for ten minutes, and the supernatant was used for ChIP. Samples were diluted with an equal volume 16.7 mM Tris pH 8.0, 0.01% SDS, 1.1 % Triton, 1.2 mM EDTA, and 167 mM NaCl. The samples were then pre- cleared with 30 μL Protein A magnetic Dynabeads (Thermo Fisher Scientific) (which had been washed with 16.7 mM Tris pH 8.0, 0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, and 167 mM NaCl prior to use) and incubated for two hours at 4 °C. The beads were then collected on a magnet and the supernatant retained. Ten percent of the sample was saved for input. The sample was then split into two halves; one half was treated with 1 μL rabbit IgG while the other half was incubated with 1 μL anti-MORC3 antibody (100-401-N96S, Rockland). Samples were incubated overnight at 4 °C with rotation.  60 μL of Protein A beads (which had been washed with 16.7 mM Tris pH 8.0, 0.01 % SDS, 1.1 % Triton, 1.2 mM EDTA, and 167 mM NaCl prior to use) were added to each sample and incubated for a further two hours. The beads were washed twice, four minutes each with rotation with 50 mM HEPES pH 7.9, 1% Triton X-100, 0.1% deoxycholate, 1 mM EDTA, and 140 mM NaCl, and then washed twice, four minutes each with rotation with 50 mM HEPES pH 7.9, 0.1 % SDS, 1 % Triton X-199, 0.1% deoxycholate, 1 mM EDTA, and 500 mM NaCl, and then washed twice, four minutes each with rotation with 500 μL 10 mM Tris pH 8.0 and 1 mM EDTA. The purified DNA was eluted by incubation with elution buffer (100 μL 50 mM Tris pH 8.0, 1 mM EDTA, and 1% SDS) at 65 °C for ten minutes. Eluent was collected on a magnetic rack, and then the beads were resuspended with 150 μL elution buffer and incubated at 65 °C for ten minutes. The two eluents were pooled and de-crosslinked by incubation at 65 °C overnight.  The samples were brought to room temperature and then warmed to 37 °C and then incubated with 10 μg RNase A. Samples were then treated with 15 μg Proteinase K and incubated for two hours at 56 °C. Finally, the samples were purified with Qiagen MinElute columns.
Purified DNA was quantified with Qubit High Sensitivity reagent (Thermo Fisher Scientific) and libraries were generated with the Ovation Ultralow Library System kit (Nugen) using 10 ng input DNA.

value: embryonic stem cell

tag: passage

value: Passage 28

tag: antibody


title: MORC3_ChIPseq_input_replicate 3


title: BC175 [ChIP-Seq]

description:
seq-SDQ2357_AMA1_RiEV_KI1967_N2_MXEMB
Barcode: AGATGGT

value: SDQ2357_AMA1 [Novus Biologicals, catalog# 38520002, lot# G3048-029, Animal SDQ2357]


title: BC176 [ChIP-Seq]

description:
seq-SDQ2357_AMA1_RiNPP13_KI1967_N2_MXEMB
Barcode: CGAGAAG

value: NPP-13 RNAi


title: BC216 [ChIP-Seq]

description:
seq-SDQ2358_AMA1_RiNPP13_KI2009_N2_MXEMB
Barcode: GTTAATC

value: SDQ2358_AMA1 [Novus Biologicals, catalog# 38520002, lot# G3048-029, Animal SDQ2358]


title: RGC from H9 ES cells (Whole RNA-seq) 2

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Whole RNA-seq RGC

data_processing:
Paired-end RNA-seq reads were aligned to human genome hg19 using Bowtie-2. We used reads with maximum 2 mismatches; fragments that matched to N locations in the genome (N<=10) were assigned weights = 1/N; fragments that matched to >10 locations were ignored. Finally we estimated FPKM based on gene length and total number of reads in each sample. For gene expression profiling we used only 5’-end sequences. Data obtained with 3’ ends yielded expression profiles that closely matched to profiles identified with 5’ ends. One sample (H9, replication #3) failed quality control for 5’-end sequences; thus we used 3’-end sequences. Statistical analysis was done with ExAtlas (https://lgsun.irp.nia.nih.gov/exatlas) based on FPM (fragments matched to a transcript per 1M fragments mapped to the genome). Data were normalized using quantile method.
Genome_build: hg19
Supplementary_files_format_and_content: text, fpkm, fpm

source_name: RGC from H9 ES cells

growth_protocol: H9 hESCs were cultured on MEFs in DMEM-F12 with GlutaMAX, 20% KSR, 10 ng/ml bFGF, 0.1 mM NEAA and 100 μ M β -mercaptoethanol and 0.5 × penicillin/streptomycin.

extract_protocol:
Total RNA were extracted using the RNeasy kit and treated with DNase.
Whole transcriptome libraries generation and rRNA depletion were performed by the Australian Genomic Research Facility, sequenced by Illumina HiSeq 2000 using pair-end method (100bp).
stranded RNA-seq library

treatment_protocol: Embryoid bodies (day 0) were derived from H9 hESCs in a 6-well ultra-low attachment plate (Corning) and cultured in RGC differentiation medium 1 (DMEM F12 with GlutaMAX, 10% KSR, 1X B27, 1 ng/ml noggin, 1 ng/ml DKK1 and 5 ng/ml IGF1). On day 4, embryoid bodies were plated into a 6-well plate pre-coated with poly-L-lysine (100 μ g/well) and Matrigel (40 μ l/well) and cultured in RGC differentiation medium 2 (DMEM F12 with GlutaMAX, 10% KSR, 1X B27, 1X N2, 10 ng/ml noggin, 10 ng/ml DKK1, 10 ng/ml IGF1 and 5 ng/ml bFGF). On day 30 cells were dissociated and enriched for THY1.1 positive RGCs using a MACS manual separator or the MultiMACS Separator. THY1.1-enriched cells were then grown in RGC differentiation medium 2 for another 15 days.

value: Differentiated ES cells


title: H9 ES cells (Whole RNA-seq) 2

description: Whole RNA-seq H9

source_name: H9 ES cells

value: H9 ES cells


title: MORC3_ChIPseq_replicate 3

value: 1 μL anti-MORC3 antibody (100-401-N96S, Rockland)


title: H9 ES cells (Whole RNA-seq) 1

description: Whole RNA-seq H9


title: fp_harr_8hr_s2

city: Rehovot

first: Idit

middle: Anna

last: Gelbart

address: Weizmann Institute of Science

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: linker: CTGTAGGCACCATCAAT

data_processing:
Library strategy: ribosome profiling
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v1.1.2 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded. Next, remaining reads were aligned to the human and IAV genomes.
All remaining reads were aligned to the human transcriptome (canonical known genes).
Wig files were then generated by summing the numbers of reads obtained from each position in the human genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: hg19 + EF4678
Supplementary_files_format_and_content: Wiggle files, generated as described in the above data processing steps.

source_name: human lung adenocarcinoma epithelial cells

extract_protocol:
Cells were lysed with 0.5% Triton, and the lysate was cleared by centrifugation, treated with RNase I for 45min and then loaded on a sucrose cushion. RNA was then isolated from cells using the acid:phenol extraction method.
Small RNA fragments were size selected via gel purification, dephosphorylated, ligated, and reverse transcribed. The resulting cDNA was circularized and PCR amplified.

tag: cell line

tag: pathogen

value: Influenza A

tag: virus strain

value: A/Puerto Rico/8/1934 H1N1 (PR8)


title: H9 ES cells (Whole RNA-seq) 3

description: Whole RNA-seq H9


title: MORC3_ChiPseq_replicate 2


title: MORC3_ChIPseq_input_replicate 1


title: MORC3_ChIPseq_replicate 1


title: BC215 [ChIP-Seq]

description:
seq-SDQ2358_AMA1_RiEV_KI2009_N2_MXEMB
Barcode: GATCTTG


title: RGC from H9 ES cells (Whole RNA-seq) 1

description: Whole RNA-seq RGC


title: BC182 [ChIP-Seq]

description:
seq-Wako_H3K4me3_305-34819_RiNPP13_KI2009_N2_MXEMB
Barcode: ATAGACA


title: 17 Day Differentiated EMP-iPrECs rep. 2

city: Tuscon

first: Cindy

middle: K

last: Miranti

state: AZ

address: 1515 N Campbell

department: Department of Cellular and Molecular Medicine University of Arizona Cancer Center

institute: University of Arizona

description:
EMP_17day_b
processed data file: EMP-gene-count-matrix.tsv

data_processing:
Sequenced reads were mapped to the hg19 whole genome using the Subread aligner (v1.4.3).
Reads were assigned to genes using featureCounts.
Raw read counts were voom transformed and differential expression performed using limma.
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated files include raw read counts for each sample

source_name: 17 Day Differentiated EMP-iPrECs

growth_protocol: All iPrECs were cultured in Keratinocyte Serum-Free Media (KSFM) supplemented with bovine pituitary extract (BPE) and epidermal growth factor (EGF Human recombinant)

extract_protocol:
Total RNA was isoated using Life Technologies Rneasy kits. RNA was purified using Life Technologies Purelink RNA mini kits.
TruSeq mRNA libraries were prepared for sequencing using standard Illumina protocols from PolyA-enriched RNA.
Illumina RNAseq - single read, 50bp, approximately 30M reads per sample

treatment_protocol:
Differentiation: Cells were grown to confluence and differentiation was induced by supplementing complete KSFM media with 5nM R1881 (synthetic androgen) and 2ng/mL KGF (keratinocyte growth factor)
Luminal cell isolation: 14 and 17 day iPrEC differentiated cultured were treated with calcium-magnesium free PBS supplemented with 1mM EDTA and dissociation buffer for 40-45 minutes. Gentle pipeting over the luminal cells dissociates them from the basal cells. Luminal cells were isolated and pelleted prior to RNA extraction.

tag: source cell type

value: immortalized basal prostate epithelial cells

tag: days of differentiation

tag: transformations of iprecs

value: Erg and Myc over expression; loss of Pten via shRNA

tag: cell passage number

tag: cell immortalization

value: HPV E6/E7 and hTert


title: 14 Day Differentiated EMP-iPrECs rep. 3

description:
EMP_14day_c
processed data file: EMP-gene-count-matrix.tsv

source_name: 14 Day Differentiated EMP-iPrECs


title: 14 Day Differentiated EMP-iPrECs rep. 1

description:
EMP_14day_a
processed data file: EMP-gene-count-matrix.tsv


title: 11 Day Differentiated EMP-iPrECs rep. 1

description:
EMP_11day_a
processed data file: EMP-gene-count-matrix.tsv

source_name: 11 Day Differentiated EMP-iPrECs


title: 14 Day Differentiated EMP-iPrECs rep. 2

description:
EMP_14day_b
processed data file: EMP-gene-count-matrix.tsv


title: RGC from H9 ES cells (Whole RNA-seq) 3

description: Whole RNA-seq RGC


title: 8 Day Differentiated EMP-iPrECs rep. 3

description:
EMP_8day_c
processed data file: EMP-gene-count-matrix.tsv

source_name: 8 Day Differentiated EMP-iPrECs


title: 17 Day Differentiated EMP-iPrECs rep. 1

description:
EMP_17day_a
processed data file: EMP-gene-count-matrix.tsv


title: (delta) mbaI strain grown to log phase with 1 uM 3-OH-C10-HSL signal added, bio rep2

description: rRNA-depleted total RNA


title: KRB - Rep 3

city: Toronto

first: Qun

last: Pan

address: 160 College St.

country: Canada

institute: University of Toronto

description: RNA-Seq performed on polyadenylated RNA

data_processing: We considered every internal exon in each annotated transcript a potential “cassette” exon. Each “cassette” AS event is defined by three exons: C1, A and C2, where A is the alternative exon, C1 is the 5´ constitutive exon and C2 is the 3´ constitutive exon. For each event we define two constitutive junctions, C1A (connecting exons C1 and A) and AC2 (connecting exons A and C2), and one alternative (or “skipped”) junction, C1C2 (connecting exons C1 and C2). For each sample, the mRNA-Seq data were aligned against the human genome using Bowtie (Langmead et al., Genome Biol. 2009 10), allowing for a maximum of two mismatches. Reads that did not map to the genome were then aligned to the full non-redundant set of junction sequences and, for each junction, the number of reads with one unique alignment mapping to it were counted. The percent inclusion, or “percent spliced-in” (PSI) value, for each internal exon was defined as: PSI = 100 × average(#C1A,#AC2) / (#C1C2 + average(#C1A,#AC2)) , where #C1A, #AC2 and #C1C2 are the read counts for the associated junctions.

source_name: Intestinal organoids

growth_protocol: The crypt-containing organoids were cultured by plating onto the center of a 24-well plate and grown in 500 ul crypt culture medium supplemented with growth factors (R-spondin 1, Noggin, EGF). Organoids were allowed to grow 7 days, followed by passaging onto 6-well plates for stimulation (roughly 10-15 isolated organoids).

extract_protocol:
Total RNA was extracted from the organoid samples using the GeneJET™ RNA Purification Kit  according to the manufacturer’s protocol and treated with DNAse I at 37oC to remove genomic DNA.
Standard Illumina sequencing protocol

treatment_protocol: Organoid samples were treated for 4 hours with either 5 uM thapsigargin for ER stress or Kreb's Ringer Krebs Ringer Bicarbonate (KRB) buffer for nutrient starvation conditions

tag: strain

value: Intestinal stem cells

tag: passages


title: 17 Day Differentiated EMP-iPrECs rep. 3

description:
EMP_17day_c
processed data file: EMP-gene-count-matrix.tsv


title: KRB - Rep 2

description: RNA-Seq performed on polyadenylated RNA

tag: cell type

value: Kreb's Ringer Krebs Ringer Bicarbonate (KRB) buffer


title: 8 Day Differentiated EMP-iPrECs rep. 2

description:
EMP_8day_b
processed data file: EMP-gene-count-matrix.tsv


title: 8 Day Differentiated EMP-iPrECs rep. 1

description:
EMP_8day_a
processed data file: EMP-gene-count-matrix.tsv


title: KRB - Rep 1

description: RNA-Seq performed on polyadenylated RNA


title: 4 Day Differentiated EMP-iPrECs rep. 2

description:
EMP_4day_b
processed data file: EMP-gene-count-matrix.tsv

source_name: 4 Day Differentiated EMP-iPrECs


title: CTL #2 - Rep 3

description: RNA-Seq performed on polyadenylated RNA


title: CTL #2 - Rep 2

description: RNA-Seq performed on polyadenylated RNA


title: Basal EMP-iPrECs rep. 3

description:
EMP_basal_c
processed data file: EMP-gene-count-matrix.tsv

source_name: Basal EMP-iPrECs


title: CTL #2 - Rep 1

description: RNA-Seq performed on polyadenylated RNA


title: 4 Day Differentiated EMP-iPrECs rep. 1

description:
EMP_4day_a
processed data file: EMP-gene-count-matrix.tsv


title: Thapsigargin - Rep 3

description: RNA-Seq performed on polyadenylated RNA

value: 5 uM thapsigargin


title: Thapsigargin - Rep 2

description: RNA-Seq performed on polyadenylated RNA


title: 17 Day Differentiated iPrECs (Luminal cells only) rep. 3

description:
iPrEC_17Tday_c
processed data file: iPrEC-gene-count-matrix.tsv


title: Basal EMP-iPrECs rep. 1

description:
EMP_basal_a
processed data file: EMP-gene-count-matrix.tsv


title: 11 Day Differentiated EMP-iPrECs rep. 2

description:
EMP_11day_b
processed data file: EMP-gene-count-matrix.tsv


title: Thapsigargin - Rep 1

description: RNA-Seq performed on polyadenylated RNA


title: 17 Day Differentiated iPrECs (Luminal cells only) rep. 2

description:
iPrEC_17Tday_b
processed data file: iPrEC-gene-count-matrix.tsv


title: 17 Day Differentiated iPrECs (Luminal cells only) rep. 1

description:
iPrEC_17Tday_a
processed data file: iPrEC-gene-count-matrix.tsv


title: CTL #1 - Rep 1

description: RNA-Seq performed on polyadenylated RNA


title: CTL #1 - Rep 2

description: RNA-Seq performed on polyadenylated RNA


title: CTL #1 - Rep 3

description: RNA-Seq performed on polyadenylated RNA


title: 14 Day Differentiated iPrECs (Luminal cells only) rep. 3

description:
iPrEC_14Tday_c
processed data file: iPrEC-gene-count-matrix.tsv


title: 14 Day Differentiated iPrECs (Luminal cells only) rep. 2

description:
iPrEC_14Tday_b
processed data file: iPrEC-gene-count-matrix.tsv


title: 4 Day Differentiated EMP-iPrECs rep. 3

description:
EMP_4day_c
processed data file: EMP-gene-count-matrix.tsv


title: Sample 17

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

data_processing:
The sequencing run here had a mean read length of 168 bp and consisted of 79.3 million reads total for the two samples (34.5 million for sample 9 and 44.8 million for sample 10).
These were aligned to the mouse mm9 trancsriptome  using RNA-STAR 2.5.2
Reads counts were gather and normalized using trimmed mean of M-values (TMM) method
Differential genes were identified using 2 fold change and p <= 0.05 for student'sttest
Adjusted p values were calculated using Benjamini and Hochberg method. Only genes with an adjusted p value <= 0.05 were considered differentially expressed.
Genome_build: mouse mm9 transcriptome

source_name: High fat Diet+B-LGND2

extract_protocol:
Total RNA was extracted from adipose tissue using the qiagen RNA isolation kit and its quality was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies).
1µg of total RNA was enriched for Poly A RNA using the Dynabeads® mRNA DIRECT™ Micro Purification Kit according to manufacturer’s standard protocol. The resulting enriched RNA samples were then used to prepare barcoded libraries for sequencing using the Ion Total RNAseq V2 kit and the Ion Xpress 1-48 Barcode kit. Libraries were amplified 16 cycles and the quality of the libraries was confirmed on an Agilent Bioanalyzer using a DNA High Sensitivity chip. The libraries were pooled based on concentrations from the High Sensitivity chip, purified on a Pippin Prep gel, quantified by the Agilent Bioanalyzer and sequenced on an Ion Torrent Proton sequencer.

tag: gender

value: male

tag: tissue

value: white adipose

tag: diet

value: high fat


title: 14 Day Differentiated iPrECs (Luminal cells only) rep. 1

description:
iPrEC_14Tday_a
processed data file: iPrEC-gene-count-matrix.tsv


title: Sample 16

tag: treatment


title: 11 Day Differentiated iPrECs rep. 2

description:
iPrEC_11day_b
processed data file: iPrEC-gene-count-matrix.tsv

source_name: 11 Day Differentiated iPrECs


title: Sample 18


title: 11 Day Differentiated iPrECs rep. 3

description:
iPrEC_11day_c
processed data file: iPrEC-gene-count-matrix.tsv


title: Sample 15

source_name: High fat Diet+Vehicle

value: vehicle


title: Basal EMP-iPrECs rep. 2

description:
EMP_basal_b
processed data file: EMP-gene-count-matrix.tsv


title: 8 Day Differentiated iPrECs rep. 2

description:
iPrEC_8day_b
processed data file: iPrEC-gene-count-matrix.tsv

source_name: 8 Day Differentiated iPrECs


title: 8 Day Differentiated iPrECs rep. 3

description:
iPrEC_8day_c
processed data file: iPrEC-gene-count-matrix.tsv


title: Sample 11

source_name: Normal Diet+Vehicle

value: normal


title: 8 Day Differentiated iPrECs rep. 1

description:
iPrEC_8day_a
processed data file: iPrEC-gene-count-matrix.tsv


title: Sample 13


title: Nucleus from Hippocampus brain region A1-P2-CA1_S388_L001_R1

description:
Single nucleus RNA-seq (sNuc-Seq) cDNE library
A1-P2-CA1_S388_L001_R1_001

source_name: Mouse Hippocampus region

tag: age

value: 12 weeks


title: Sample 10


title: 4 Day Differentiated iPrECs rep. 2

description:
iPrEC_4day_b
processed data file: iPrEC-gene-count-matrix.tsv

source_name: 4 Day Differentiated iPrECs


title: Sample 12


title: 11 Day Differentiated EMP-iPrECs rep. 3

description:
EMP_11day_c
processed data file: EMP-gene-count-matrix.tsv


title: 4 Day Differentiated iPrECs rep. 3

description:
iPrEC_4day_c
processed data file: iPrEC-gene-count-matrix.tsv


title: mrna_2hr_s4

description: linker: CTGTAGGCACCATCAAT

data_processing:
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v1.1.2 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded. Next, remaining reads were aligned to the human and IAV genomes.
All remaining reads were aligned to the human transcriptome (canonical known genes).
Wig files were then generated by summing the numbers of reads obtained from each position in the human genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: hg19 + EF467821.1
Supplementary_files_format_and_content: Wiggle files, generated as described in the above data processing steps.

organism:
Homo sapiens
Influenza A virus

value: human lung adenocarcinoma epithelial cells


title: mrna_uninf_s4

description: linker: CTGTAGGCACCATCAAT


title: mrna_4hr_s4

description: linker: CTGTAGGCACCATCAAT


title: Basal iPrECs rep. 1

description:
iPrEC_basal_a
processed data file: iPrEC-gene-count-matrix.tsv

source_name: Basal iPrECs


title: mrna_8hr_s4

description: linker: CTGTAGGCACCATCAAT


title: Basal iPrECs rep. 2

description:
iPrEC_basal_b
processed data file: iPrEC-gene-count-matrix.tsv


title: Sample 14


title: 11 Day Differentiated iPrECs rep. 1

description:
iPrEC_11day_a
processed data file: iPrEC-gene-count-matrix.tsv


title: mrna_8hr_s3

description: linker: CTGTAGGCACCATCAAT


title: mrna_4hr_s3

description: linker: CTGTAGGCACCATCAAT


title: LAPC9 miR-141 rep2

city: Smithville

first: Liu

last: Can

state: Texas

address: 1808 Park Road 1C

department: Department of Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (hg19) by TopHat (version 2.0.6).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on March 9, 2012) was enumerated using htseq-count from HTSeq package (version 0.5.3p9).
genome build: hg19
Supplementary_files_format_and_content: Number of fragments (raw counts) in each gene

source_name: prostate cancer cell line_miR-141

growth_protocol: LAPC9 were freshly purified from xenograft maintained in NOD/SCID mice subcutaneously.

extract_protocol:
total RNA were extracted by Rneasy mini Kit (Qiagen). NuGen Ovation RNA-Seq System v2 Kit (Cat# 7102-32) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: miR-141 and NC oligos were transfected at 30nM final concentration using Lipofectamine RNAiMax.

value: prostate


title: LAPC9 NC

source_name: prostate cancer cell line_negative_control


title: Du145 miR-141 rep2

growth_protocol: Du145 cells were routinely cultured in RPMI+7%FBS.


title: LAPC9 miR-141 rep1


title: mrna_2hr_s3

description: linker: CTGTAGGCACCATCAAT


title: fp_chx_8hr_s4

description: linker: CTGTAGGCACCATCAAT

data_processing:
Library strategy: ribosome profiling
Prior to alignment, linker and polyA sequences were removed from the 3' ends of reads.
Bowtie v1.1.2 (allowing up to 2 mismatches) was used to perform the alignments. First, reads that aligned to human rRNA sequences were discarded. Next, remaining reads were aligned to the human and IAV genomes.
All remaining reads were aligned to the human transcriptome (canonical known genes).
Wig files were then generated by summing the numbers of reads obtained from each position in the human genome. For this, each read was counted once. For the ribosome footprints samples, the calculated position of the ribosome P-site was used; for the mRNA samples, the 5' end of each read was used.
Genome_build: hg19 + EF467821.1
Supplementary_files_format_and_content: Wiggle files, generated as described in the above data processing steps.

source_name: ribosome profiling_8h


title: fp_chx_4hr_s4

description: linker: CTGTAGGCACCATCAAT

source_name: ribosome profiling_4h


title: fp_chx_2hr_s4

description: linker: CTGTAGGCACCATCAAT

source_name: ribosome profiling_2h


title: fp_chx_uninf_s4

description: linker: CTGTAGGCACCATCAAT

source_name: ribosome profiling_uninfected


title: fp_chx_8hr_s3

description: linker: CTGTAGGCACCATCAAT


title: 4 Day Differentiated iPrECs rep. 1

description:
iPrEC_4day_a
processed data file: iPrEC-gene-count-matrix.tsv


title: fp_chx_4hr_s3

description: linker: CTGTAGGCACCATCAAT


title: Du145 NC rep1


title: Delta-CPS1 48 hour spherule 2

city: Tucson

first: Adam

middle: Scott

last: Buntzman

state: Arizona

address: Keating Bio5 Room 319

department: Medicine

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence,
Reads were paired, concatenated, cleaned, and processed through the Tuxedo 2.0 pipeline (Tophat, Cufflinks, Cuffmerge, CuffDiff) on the University of Arizona iPlant Cyberinfrastructure.
Genome_build: GenBank Bioproject PRJNA46299, Coccidioides immitis RS (rs_3)

organism: Coccidioides posadasii

source_name: in vitro spherule culture

growth_protocol: Converse medium (100 ml) was inoculated with 300,000,000 wild type or Δcps1 spores and grown at 38 degrees celcius for 48 hours while shaking at 180 rpm.

extract_protocol: RNA Libraries were prepared using standard Illumina protocols in the University of Arizona Genetics Sequencing Core Facility.

value: Silveira

tag: genotype

value: CPS1 deletion


title: Delta-CPS1 48 hour spherule 1


title: Du145 NC rep2

tag: cell line


title: Silveira 48 hour spherule 2

value: wild type


title: Basal iPrECs rep. 3

description:
iPrEC_basal_c
processed data file: iPrEC-gene-count-matrix.tsv

value: immortalized basal prostate epithelial cells


title: fp_chx_uninf_s3

description: linker: CTGTAGGCACCATCAAT

tag: pathogen


title: fp_chx_2hr_s3

description: linker: CTGTAGGCACCATCAAT

value: Influenza A

tag: virus strain

value: A/Puerto Rico/8/1934 H1N1 (PR8)


title: 3'READS+_5,000 ng input, batch 2

status: Public on Aug 14 2016

city: Newark

first: Bin

last: Tian

email: btian@wistar.org, dinghaiz@gmail.com

address: 205 South Orange Ave., F-Bay 7

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers University, New Jersey Medical School

data_processing:
Illumina's bcl2fastq (v2.16.0.10) was used for basecalling with parameter “--barcode-mismatches 0”.
The sequence corresponding to 5’ adapter was first removed from raw 3’READS+ reads using cutadapt (v 1.4.2), with the parameters “ -a cutadapt=TGGAATTCTCGGGTGCCAAGG -n 1 -O 5 -m 25  -f fastq -q 10 ”
The 5’ random nucleotides and 5’Ts in the reads were trimmed, and the random nucleotides and 5'T length were attached to the read name, using a custom python script.
The reads were then mapped to the human (hg19) genome using bowtie2 (v 2.2.3) with the parameters “--very-sensitive”
Only reads with a mapping quality score (MAPQ) ≥10 were used for further analysis. The trimmed 5’Ts of each read were then compared to the genomic region downstream of the last aligned position of the read to identify aligned 5’Ts. The reads with ≥2 non-genomic 5’Ts after this process were called polyA site supporting (PASS) reads. Cleavage sites within 24 nt of each other were clustered into pAs as previously described (Hoque et al., 2013). UPM of a transcript with a given pA was calculated with unique PASS reads, based on 5’ random nucleotides, number of 5’Ts, and cleavage site location. These are all done with custom python scripts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include unique read counts for each pA cluster.

extract_protocol:
Total RNA from Hela cells were extracted using TRIzol.
Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 12 µl of oligo(dT)25 magnetic beads (NEB) in 200 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III (NEB) in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 oC  for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN, Sigma) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn (Life Technologies), and 0.25 µl of T4 RNA ligase 1 (NEB) in a 5 µl reaction at 22 oC  for 1 hr. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1 (Life Technologies). After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H (Epicentre) at 37 oC  for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 oC, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version, NEB) at 22 oC for 1 hr in a 5 µl reaction containing 15% PEG 8000 (NEB) and 0.2 µl of SuperaseIn (Life Technologies). The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase (Promega), followed by PCR amplification using Phusion high-fidelity DNA polymerase (NEB) and bar-coded PCR primers for 12-18 cycles (12 cycles for 15 µg input RNA, 13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg). Both RT primer (5’-GTTCAGAGTTCTACAGTCCGACGATC) and PCR primers with indexes were described previously in (Hoque et al., 2013). PCR products were size-selected twice with AMPure XP beads (Beckman Coulter), using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer (Agilent).

value: Hela

tag: input amount

tag: library protocol


title: 3'READS+_5,000 ng input, batch 1


title: mrna_uninf_s3

description: linker: CTGTAGGCACCATCAAT


title: Silveira 48 hour spherule 1


title: 3'READS+_15,000 ng input, batch 2


title: 3'READS+_200 ng input, batch 2


title: 3'READS+_400 ng input, batch 2


title: 3'READS+_1,000 ng input, batch 1


title: Du145 miR-141 rep1


title: 3'READS+_200 ng input, batch 1


title: 3'READS+_1,000 ng input, batch 2


title: 3'READS+_100 ng input, batch 2


title: 184

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH-Science for Life Laboratory

data_processing:
Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
The paired-end reads were trimmed with respect to quality and remaining adapter sequences using Trim Galore and aligned to the human genome reference hg19 with TopHat version 2.0.4
The aligned reads were assembled into transcripts using Cufflinks version 2.0.2
Genome_build: hg19, ENSEMBL v71
Supplementary_files_format_and_content: tab-delimited text files include output from Cufflinks for each Sample 1-33

source_name: skeletal muscle

extract_protocol:
Trizol® method
RNA libraries were prepared for sequencing using standard Illumina protocols for paired end sequencing and clustered on cBot

value: skeletal muscle

value: female

tag: biopsy location

value: left leg

tag: exercise ststus

value: untrained

tag: time point

value: pre-training period 2

tag: original sample id


title: 192

value: right leg

value: trained

value: post-training period 2


title: 176


title: 188

value: male

value: post-training period 1


title: 150


title: 166


title: 158


title: 142


title: 134


title: 173


title: 189


title: 102


title: 181


title: 164


title: 156


title: 105


title: 179


title: 222


title: 163


title: 187


title: 128


title: 144


title: 120


title: 112


title: 136


title: 216


title: 171


title: 107


title: 139


title: 115


title: 178


title: 110


title: 146


title: 215


title: 170


title: 124


title: 149


title: 195


title: 154