title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E6_AD008_indexed


title: lncRNA profile of case696N

status: Public on Aug 31 2020

type: RNA

city: GZ

first: Rui-qi

last: WANG

state: Guangdong

address: 651 DONGFENG EAST ROAD, GUANGZHOU 510060, P. R. CH

department: state key lab

country: China

institute: SUN YAN-SEN UNIVERSITY CANCER CENTER

description: The microarray was used to acquire lncRNA expression profiles of 2412 lncRNAs.

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays,GPR normailization software, log 2 transformation of expression levels was used.

molecule: total RNA

organism: Homo sapiens

source_name: non-small-cell lung cancer

label_protocol: 2.5 μg of total RNA of intrahepatic cholangiocarcinoma/normal intrahepatic bile duct tissue was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: status after 3 years

value: Alive


title: lncRNA profile of case695T

value: Dead


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E6_AD006_indexed

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: SSp

tag: Sex

value: male

tag: age

tag: strain


title: lncRNA profile of case693T


title: genomic DNA from peripheral blood leukocytes 542

type: genomic

city: Ann Arbor

first: Minjung

last: Kho

state: Michigan

address: School of Public Health University of Michigan 1415 Washington Heights

institute: University of Michigan

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium HumanMethylation450 BeadChip or EPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: For each chip, the Minfi R package was used to perform background correction and normalization. The regression on correlated probes (RCP) method was then used to adjust probe-type bias, and ComBat was used to remove confounding effects due to batch or other technical covariates. Data from the two platforms were combined, and ComBat was used to remove the platform effect. Age, gender, and phase effect was preserved when removing platform difference.

label: Cy5 and Cy3

source_name: peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from stored peripheral blood leukocytes using AutoGen FlexStar (AutoGen, Holliston, MA) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA)

tag: tissue

value: peripheral blood leukocytes

tag: gender

value: F

tag: age(yrs)

tag: systolic blood pressure (mmhg)

tag: diastolic blood pressure (mmhg)


title: lncRNA profile of case692N


title: lncRNA profile of case692T


title: lncRNA profile of case698N


title: lncRNA profile of case691T


title: lncRNA profile of case764T


title: lncRNA profile of case690T


title: lncRNA profile of case689N


title: genomic DNA from peripheral blood leukocytes 539

value: M


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E5_AD007_indexed


title: lncRNA profile of case689T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E6_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E4_AD010_indexed


title: lncRNA profile of case688N


title: lncRNA profile of case688T


title: lncRNA profile of case694T


title: genomic DNA from peripheral blood leukocytes 538


title: genomic DNA from peripheral blood leukocytes 537


title: lncRNA profile of case687T


title: lncRNA profile of case687N


title: lncRNA profile of case686T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E6_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 533


title: lncRNA profile of case686N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E5_AD002_indexed


title: lncRNA profile of case685T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E5_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 532


title: lncRNA profile of case684N


title: genomic DNA from peripheral blood leukocytes 531


title: lncRNA profile of case685N


title: lncRNA profile of case684T


title: lncRNA profile of case683T


title: genomic DNA from peripheral blood leukocytes 529


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E5_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E5_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E5_AD012_indexed


title: lncRNA profile of case683N


title: lncRNA profile of case681N


title: lncRNA profile of case681T


title: genomic DNA from peripheral blood leukocytes 528


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E6_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 534


title: genomic DNA from peripheral blood leukocytes 526


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E5_AD006_indexed


title: lncRNA profile of case680N


title: lncRNA profile of case680T


title: genomic DNA from peripheral blood leukocytes 522


title: GL261 cells in vitro 1

city: Hamburg

first: Krystian

middle: Daniel

last: Fita

address: Martinistrasse 52

department: Department of Neurosurgery

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
replicate 1
Cells 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were preprocessed using Genepattern from the Broad Institute and with cubic spline normalization

label: biotin

source_name: cell culture

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: GL261 cells were propagated in DMEM containing 4.5 g/L glucose, 4 mM L-Glutamine, and 1 mM pyruvate (31966-021, Gibco), supplemented with 10% fetal bovine serum, 25 mM HEPES, 100 U/mL, penicillin, and 100 mg/mL streptomycin.

extract_protocol: RNA was extracted from tumor tissue using Nucleospin columns (Macherey Nagel), pooled from 2 or 3 mice and analyzed on Illumina microarray mouse WG-6 v2.0 chips.

treatment_protocol: GL261 cells were injected into WT C57BL/6 or Pfp/Rag2-/- mice and tumors were collected on day 7 (n = 4 per mouse type) or day 14 (n = 4 per type) or when mice became symptomatic (n = 6 per type).

tag: genotype

tag: cell line


title: GL261 cells in vitro 2

description:
replicate 2
Cells 2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E5_AD008_indexed


title: lncRNA profile of case679T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E6_AD004_indexed


title: lncRNA profile of case682T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E4_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 521


title: Healthy mouse brain 2

description:
replicate 2
normal 2

source_name: mouse brain

value: WT


title: genomic DNA from peripheral blood leukocytes 519


title: lncRNA profile of case679N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E3_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 517


title: lncRNA profile of case678T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E4_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 518


title: lncRNA profile of case678N


title: lncRNA profile of case677T


title: genomic DNA from peripheral blood leukocytes 516


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E4_AD008_indexed


title: lncRNA profile of case677N


title: GL261 tumor in Pfp/Rag2 -/- mice, harvested when mice became symptomatic 3

description:
replicate 2
PFP last 3

value: Pfp/Rag2 -/-


title: Healthy mouse brain 1

description:
replicate 1
normal 1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E4_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 515


title: lncRNA profile of case676T


title: genomic DNA from peripheral blood leukocytes 514


title: GL261 tumor in Pfp/Rag2 -/- mice, harvested when mice became symptomatic 2

description:
replicate 3
PFP last 2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E3_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E4_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 512


title: GL261 tumor in Pfp/Rag2 -/- mice, harvested when mice became symptomatic 1

description:
replicate 1
PFP last 1


title: lncRNA profile of case675T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E7_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 511


title: GL261 tumor in WT mice, harvested when mice became symptomatic 2

description:
replicate 2
WT last 2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E3_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 509


title: GL261 tumor in WT mice, harvested when mice became symptomatic 3

description:
replicate 3
WT last 3


title: lncRNA profile of case674T


title: lncRNA profile of case675N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E2_AD012_indexed


title: lncRNA profile of case674N


title: genomic DNA from peripheral blood leukocytes 508


title: genomic DNA from peripheral blood leukocytes 507


title: GL261 tumor in WT mice, harvested when mice became symptomatic 1

description:
replicate 1
WT last 1


title: GL261 tumor in Pfp/Rag2 -/- mice, day 14 post injection 2

description:
replicate 2
PFP D14 2


title: GL261 tumor in WT mice, day 14 post injection 2

description:
replicate 2
WT D14 2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E3_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 506


title: lncRNA profile of case672T


title: GL261 tumor in Pfp/Rag2 -/- mice, day 7 post injection 2

description:
replicate 2
PFP D7 2


title: GL261 tumor in Pfp/Rag2 -/- mice, day 14 post injection 1

description:
replicate 1
PFP D14 1


title: genomic DNA from peripheral blood leukocytes 505


title: GL261 tumor in WT mice, day 14 post injection 1

description:
replicate 1
WT D14 1


title: genomic DNA from peripheral blood leukocytes 504


title: lncRNA profile of case672N


title: genomic DNA from peripheral blood leukocytes 503


title: lncRNA profile of case668N


title: lncRNA profile of case667T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E2_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 502


title: lncRNA profile of case668T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E2_AD010_indexed


title: GL261 tumor in Pfp/Rag2 -/- mice, day 7 post injection 1

description:
replicate 1
PFP D7 1


title: lncRNA profile of case667N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E2_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E2_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 501


title: GL261 tumor in WT mice, day 7 post injection 1

description:
replicate 1
WT D7 1


title: GL261 tumor in WT mice, day 7 post injection 2

description:
replicate 2
WT D7 2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E1_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 499


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E1_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E2_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 498


title: lncRNA profile of case666N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E3_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 496


title: lncRNA profile of case665N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E12_AD008_indexed


title: lncRNA profile of case665T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E1_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 495


title: genomic DNA from peripheral blood leukocytes 494


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E1_AD008_indexed


title: lncRNA profile of case666T


title: genomic DNA from peripheral blood leukocytes 491


title: lncRNA profile of case664N


title: genomic DNA from peripheral blood leukocytes 492


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E1_AD004_indexed


title: lncRNA profile of case662T


title: lncRNA profile of case664T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E2_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E12_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E12_AD010_indexed


title: lncRNA profile of case661T


title: genomic DNA from peripheral blood leukocytes 489


title: lncRNA profile of case660T


title: lncRNA profile of case661N


title: genomic DNA from peripheral blood leukocytes 484


title: lncRNA profile of case660N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E12_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 483


title: genomic DNA from peripheral blood leukocytes 478


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E12_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 477


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E11_AD008_indexed


title: lncRNA profile of case658T


title: lncRNA profile of case659T


title: genomic DNA from peripheral blood leukocytes 476


title: genomic DNA from peripheral blood leukocytes 474


title: genomic DNA from peripheral blood leukocytes 486


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E11_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E12_AD002_indexed


title: lncRNA profile of case656T


title: lncRNA profile of case657T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E1_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E11_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 473


title: genomic DNA from peripheral blood leukocytes 471


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E11_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 468


title: lncRNA profile of case655T


title: lncRNA profile of case652T


title: lncRNA profile of case653T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E10_AD004_indexed


title: lncRNA profile of case654T


title: genomic DNA from peripheral blood leukocytes 466


title: lncRNA profile of case651T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E11_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 460


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E11_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 456


title: lncRNA profile of case650T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E11_AD007_indexed


title: lncRNA profile of case649T


title: lncRNA profile of case648T


title: genomic DNA from peripheral blood leukocytes 450


title: genomic DNA from peripheral blood leukocytes 447


title: genomic DNA from peripheral blood leukocytes 449


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E10_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E10_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D9_AD012_indexed


title: lncRNA profile of case647T


title: genomic DNA from peripheral blood leukocytes 444


title: genomic DNA from peripheral blood leukocytes 445


title: genomic DNA from peripheral blood leukocytes 442


title: lncRNA profile of case646T


title: lncRNA profile of case645T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E10_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 441


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D9_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 436


title: lncRNA profile of case635T


title: lncRNA profile of case641T


title: genomic DNA from peripheral blood leukocytes 437


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D9_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 434


title: lncRNA profile of case644N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D9_AD010_indexed


title: lncRNA profile of case633T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D8_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 431


title: lncRNA profile of case632T


title: genomic DNA from peripheral blood leukocytes 430


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D7_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 429


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D9_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E10_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 428


title: lncRNA profile of case628T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D6_AD012_indexed


title: lncRNA profile of case629T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D8_AD010_indexed


title: lncRNA profile of case642T


title: lncRNA profile of case626T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D7_AD004_indexed


title: lncRNA profile of case644T


title: lncRNA profile of case627T


title: lncRNA profile of case625T


title: genomic DNA from peripheral blood leukocytes 426


title: genomic DNA from peripheral blood leukocytes 422


title: lncRNA profile of case624T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D7_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D7_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 420


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D7_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 419


title: genomic DNA from peripheral blood leukocytes 417


title: genomic DNA from peripheral blood leukocytes 412


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D6_AD008_indexed


title: lncRNA profile of case623T


title: genomic DNA from peripheral blood leukocytes 427


title: lncRNA profile of case622T


title: lncRNA profile of case621T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D7_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 410


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D7_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D6_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D6_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D7_AD010_indexed


title: lncRNA profile of case617T


title: genomic DNA from peripheral blood leukocytes 408


title: lncRNA profile of case613T


title: lncRNA profile of case61N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D6_AD004_indexed


title: lncRNA profile of case612T


title: lncRNA profile of case611T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_E10_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 403


title: lncRNA profile of case611N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D6_AD007_indexed


title: lncRNA profile of case609T


title: lncRNA profile of case609N


title: genomic DNA from peripheral blood leukocytes 411


title: genomic DNA from peripheral blood leukocytes 401


title: genomic DNA from peripheral blood leukocytes 399


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D5_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D5_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D5_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 395


title: lncRNA profile of case607T


title: lncRNA profile of case608N


title: genomic DNA from peripheral blood leukocytes 406


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D4_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D6_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 393


title: genomic DNA from peripheral blood leukocytes 405


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D4_AD008_indexed


title: lncRNA profile of case607N


title: genomic DNA from peripheral blood leukocytes 390


title: lncRNA profile of case605T


title: lncRNA profile of case606T


title: genomic DNA from peripheral blood leukocytes 389


title: genomic DNA from peripheral blood leukocytes 388


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D4_AD002_indexed


title: lncRNA profile of case603T


title: genomic DNA from peripheral blood leukocytes 398


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D3_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 387


title: lncRNA profile of case602T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D3_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 375


title: genomic DNA from peripheral blood leukocytes 392


title: genomic DNA from peripheral blood leukocytes 374


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D5_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D3_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 373


title: lncRNA profile of case601T


title: lncRNA profile of case602N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D3_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D3_AD004_indexed


title: lncRNA profile of case601N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D4_AD007_indexed


title: lncRNA profile of case600N


title: lncRNA profile of case600T


title: genomic DNA from peripheral blood leukocytes 369


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D2_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D2_AD010_indexed


title: lncRNA profile of case599T


title: genomic DNA from peripheral blood leukocytes 368


title: lncRNA profile of case608T


title: lncRNA profile of case603N


title: genomic DNA from peripheral blood leukocytes 367


title: lncRNA profile of case599N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D2_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 365


title: genomic DNA from peripheral blood leukocytes 366


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D2_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 372


title: genomic DNA from peripheral blood leukocytes 361


title: lncRNA profile of case597T


title: genomic DNA from peripheral blood leukocytes 363


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D2_AD004_indexed


title: lncRNA profile of case598N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D2_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 360


title: 2wt-lid

city: HangZhou

first: Ping

last: Song

state: State...

address: 3 East Qingchun Road, Hangzhou, Zhejiang, China

institute: Zhejiang University School of Medicine

library_source: transcriptomic

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: Expression_Transcript.xlsx

source_name: WT Treated with LiCl

extract_protocol:
fresh frozen on dry ice, and RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
The total RNA was processed by NEBNext® Poly(A) mRNA Magnetic Isolation Module (or rRNA removal by RiboZero Magnetic Gold Kit) to enrich mRNA, and the product RNA was used for construction Library, via KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Sequencing libraries, denatured by 0.1 M NaOH to generate single-stranded DNA, as amplified in situ Illumina cBot (TruSeq SR Cluster Kit v3-cBot-HS (# GD-401-3001, Illumina)). The ends of the generated fragments was used to run 150 Cycles by the Illumina HiSeq 4000 Sequencer.

tag: cell type

value: mouse embryonic fibroblasts (MEF)

tag: genotype/variation

tag: treatment

value: LiCl treatment at 20mM for 48 h


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D1_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D2_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 358


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D2_AD008_indexed


title: 2ko-lid

source_name: HSF1-KO treated with LiCl


title: lncRNA profile of case597N


title: 2wt

source_name: WT


title: genomic DNA from peripheral blood leukocytes 356


title: lncRNA profile of case594T


title: lncRNA profile of case598T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D1_AD007_indexed


title: lncRNA profile of case593T


title: 2ko


title: lncRNA profile of case590T


title: genomic DNA from peripheral blood leukocytes 353


title: genomic DNA from peripheral blood leukocytes 355


title: 1wt-lid


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D1_AD004_indexed


title: 1wt


title: lncRNA profile of case590N


title: 1ko-lid


title: lncRNA profile of case58T


title: lncRNA profile of case595T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D12_AD007_indexed


title: lncRNA profile of case589N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D1_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 351


title: 1ko


title: genomic DNA from peripheral blood leukocytes 350


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D1_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D5_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D12_AD010_indexed


title: lncRNA profile of case584T


title: genomic DNA from peripheral blood leukocytes 348


title: wt-lid

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: FPKM

value: wild type

value: LiCl treatment at 20mM for 48 hrs


title: lncRNA profile of case583T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D12_AD001_indexed


title: lncRNA profile of case583N


title: genomic DNA from peripheral blood leukocytes 344


title: ko-lid

value: HSF1 KO


title: lncRNA profile of case582T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D12_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 343


title: wt


title: genomic DNA from peripheral blood leukocytes 352


title: ko


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D12_AD002_indexed


title: lncRNA profile of case582N


title: genomic DNA from peripheral blood leukocytes 340


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D11_AD010_indexed


title: lncRNA profile of case579T


title: TGF-β1 licensed mesenchymal stromal cells [TGF-B-MSC3]

city: Galway

first: Aideen

last: Ryan

address: University Road

country: Ireland

institute: National University of Ireland, Galway

data_processing:
Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8) was used for base-calling
Trimmed reads (trimmed 5’, 3’-adaptor   bases using cutadapt) were aligned to reference genome using Hisat2 software
The transcript abundances   for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were   calculated with R package Ballgown
The differentially expressed genes and transcripts were filtered using   R package Ballgown
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

growth_protocol: After generating single cell suspensions from the bone marrow of Balb/c mice, MSCs were centrifuged at 400 x g for 5 minutes, re-suspended in 25ml culture medium and plated at a density of 9x105 per cm2 in a T175 flask. MSCs were incubated at 37°C, 21% O2, 5% CO2 (Normoxia) or 37°C, 5% O2, 5% CO2 (Hypoxia) and non-adherent cells were removed 24 hours later. Medium was changed every 3-4 days and cells were passaged at 85% confluency.

extract_protocol:
MSCs were collected and lysed using lysis buffer from the Bioline Isolate II RNA mini kits (Qiagen) according to manufacturer’s protocols. RNA was extracted according to manufacturer’s instructions. 1-2µg of total RNA was enriched by oligo(dT) magnetic beads (rRNA removal) and sequencing libraries were prepared.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Balb/c MSCs were seeded at a density of 50,000 cells/ml of MSC medium in a T175 flask. 12 h after seeding, medium was removed and replaced with mouse MSC medium containing recombinant mouse TGF-β1 at a concentration of 50ng/ml (Bio-Techne, Abingdon, UK). Cells were then placed in a humidified tissue culture incubator at 37°C, 5% CO2. 72 h later, medium was removed and cells were washed twice with PBS.

value: Balb/c

tag: site of extraction

value: Bone marrow

value: TGF-beta1 licensed mesenchymal stromal cells

tag: passage


title: TGF-β1 licensed mesenchymal stromal cells [TGF-B-MSC2]


title: genomic DNA from peripheral blood leukocytes 338


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D11_AD008_indexed


title: TGF-β1 licensed mesenchymal stromal cells [TGF-B-MSC1]


title: lncRNA profile of case575T

tag: status after 3 years


title: genomic DNA from peripheral blood leukocytes 337


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D11_AD004_indexed

tag: brain region


title: Mesenchymal stromal cells [MSC3]

source_name: Mesenchymal stromal cells

value: Mesenchymal stromal cells


title: genomic DNA from peripheral blood leukocytes 336


title: lncRNA profile of case574T

value: Alive


title: genomic DNA from peripheral blood leukocytes 330


title: Mesenchymal stromal cells [MSC2]


title: lncRNA profile of case571T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D11_AD012_indexed

value: SSp

tag: Sex


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D11_AD006_indexed

value: male

tag: age


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D10_AD008_indexed

tag: strain


title: genomic DNA from peripheral blood leukocytes 341

tag: tissue

value: peripheral blood leukocytes


title: Mesenchymal stromal cells [MSC1]


title: genomic DNA from peripheral blood leukocytes 329

tag: gender


title: lncRNA profile of case571N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D11_AD002_indexed


title: TdT neg

city: MARSEILLE

first: Sonia

last: Stefanovic

address: 27 BD JEAN MOULIN

country: France

institute: INSERM U1251

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
RNA-Seq reads were aligned using the STAR aligner version 2.5.2
Transcripts abundance was computed using HTSEQ-count 0.9.12 and the background was estimated through read counts from intergenic regions using windows of 5 kb length
Normalisation and differential gene expression analysis between conditions were performed using R (R version 3.3.4) and DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: The final processed data files is the output of the DESEQ2 package. This file contains the gene name, the base mean , the log2foldchange, the test value, the p-value, the adjusted p-value and the normalized count foreach sample.

source_name: Amplified ds cDNA with Ovation V2 Nugen kit

extract_protocol:
Hoxb1GFP progenitor cells and Mef2c-Cre;RosatdT progenitor cells were dissected, pooled and digested for FACS sorting.RNA was harvested using the NucleoSpin® RNA XS kit
Amplified cDNA was prepared from 2 ng of total RNA using the Ovation RNA-seq system V2 (NuGEN Technologies, Inc.) following manufacturer's instructions. Briefly, first-strand cDNA was prepared from total RNA using a combination of random and poly-T DNA/RNA chimeric SPIA primers and reverse transcriptase, resulting in a cDNA/mRNA hybrid molecule. Priming sites created by a heating fragmentation of the mRNA within the cDNA/mRNA complex were used to synthesize the second strand cDNA using a DNA polymerase. The resulting double-stranded cDNA with a unique RNA/DNA heteroduplex at one end was purified using Agencourt RNAClean XP beads (Beckman Coulter Inc.). The purified product was then used as the substrate of a linear amplification process, SPIA (single primer isothermal amplification). During the amplification step, RNase H degrades RNA in DNA/RNA heteroduplex at the 5'end of the first cDNA strand, creating a binding site for the DNA/RNA SPIA chimeric primer, then DNA polymerase starts replication at the 3'end of the primer displacing the existing forward strand. The process including SPIA DNA/RNA primer binding, DNA replication, strand displacement and RNA degradation is repeated and results in rapid generation of microgram quantities of amplified cDNA. Amplified cDNA was purified using AMPure XP beads (Beckman Coulter Inc.) and 500 ng was fragmented by sonication using a Covaris E210 instrument (with duty cycle: 10X, intensity: 5 and cycle/burst: 200 for 180 seconds).    The next steps of RNA-Seq Library preparation were performed using Ovation Ultralow Library System kit (NuGEN Technologies, Inc.) according to manufacturer's instructions. Briefly, in this system 100 ng of amplified cDNA were blunted, phosphorylated and ligated to indexed adapter dimers. The libraries were then enriched by PCR amplification (2 min at 72 degrees Celsius; [30 sec at 94 degrees Celsius, 30 sec at 60 degrees Celsius, 1 min at 72 degrees Celsius] x 6 cycles; 5 min at 72 degrees Celsius) and surplus PCR primers were removed by purification using AMPure XP beads. DNA libraries were checked for quality using 2100 Bioanalyzer (Agilent) and quantified using Kapa Sybr Fast Light Cycler 480 qPCR Kit  (Kapa Biosystems) following manufacturer's instructions.

value: second heart field region

tag: Stage


title: lncRNA profile of case569T

value: Dead


title: lncRNA profile of case569N


title: genomic DNA from peripheral blood leukocytes 328

value: F

tag: age(yrs)

tag: systolic blood pressure (mmhg)


title: GFP neg


title: lncRNA profile of case567T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D11_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 327

tag: diastolic blood pressure (mmhg)


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D10_AD010_indexed


title: TdT_3


title: lncRNA profile of case567N


title: genomic DNA from peripheral blood leukocytes 325


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D11_AD001_indexed


title: TdT_2


title: TdT_1


title: lncRNA profile of case566T


title: lncRNA profile of case565T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D10_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 324

value: M


title: genomic DNA from peripheral blood leukocytes 323


title: genomic DNA from peripheral blood leukocytes 322


title: GFP_2


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D10_AD007_indexed


title: GFP_3


title: lncRNA profile of case562N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C9_AD012_indexed


title: lncRNA profile of case562T


title: genomic DNA from peripheral blood leukocytes 321


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C9_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 320


title: GFP_1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C9_AD007_indexed


title: lncRNA profile of case561T


title: lncRNA profile of case561N


title: genomic DNA from peripheral blood leukocytes 318


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C9_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 317


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C8_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 315


title: genomic DNA from peripheral blood leukocytes 314


title: lncRNA profile of case559N


title: lncRNA profile of case559T


title: lncRNA profile of case558T


title: lncRNA profile of case558N


title: lncRNA profile of case557T


title: genomic DNA from peripheral blood leukocytes 313


title: genomic DNA from peripheral blood leukocytes 312


title: lncRNA profile of case557N


title: genomic DNA from peripheral blood leukocytes 310


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C8_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C8_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C8_AD006_indexed


title: lncRNA profile of case556T


title: lncRNA profile of case556N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C9_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 307


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C8_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 319


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C8_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C8_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C7_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 302


title: lncRNA profile of case555N


title: lncRNA profile of case555T


title: lncRNA profile of case552T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C7_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 301


title: lncRNA profile of case552N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C7_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 299


title: genomic DNA from peripheral blood leukocytes 300


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C7_AD002_indexed


title: lncRNA profile of case550T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C8_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C7_AD001_indexed


title: lncRNA profile of case549T


title: lncRNA profile of case550N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C6_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 298


title: lncRNA profile of case549N


title: genomic DNA from peripheral blood leukocytes 297


title: genomic DNA from peripheral blood leukocytes 306


title: genomic DNA from peripheral blood leukocytes 296


title: genomic DNA from peripheral blood leukocytes 303


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C6_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 295


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C6_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 294


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C6_AD010_indexed


title: lncRNA profile of case548T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C6_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C5_AD012_indexed


title: lncRNA profile of case548N


title: genomic DNA from peripheral blood leukocytes 293


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C6_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 288


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C5_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 287


title: genomic DNA from peripheral blood leukocytes 291


title: lncRNA profile of case542T


title: lncRNA profile of case543N


title: lncRNA profile of case547N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C5_AD008_indexed


title: lncRNA profile of case543T


title: lncRNA profile of case542N


title: phs001866_AP_225

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: RNA-Seq of human breast primary tumor

data_processing:
Quality-control-passed reads were aligned to the human reference CGRh38/hg38 genome using STAR.
The alignment profile was determined by Picard Tools v1.64 (http://broadinstitute.github.io/picard/). Transcript abundance estimates for each sample were performed using Salmon, an expectation-maximization algorithm using the UCSC gene definitions.
Genome_build: CGRh38/hg38 genome
Supplementary_files_format_and_content: Raw read counts for all RNAseq samples were normalized to a fixed upper quartile (166_AP206_UQN.final.tsv). RNAseq normalized gene counts from primary and metastatic tumors were log2 transformed, the zeros were added again after log transformation and the genes were filtered for those expressed in 70% of samples using the cluster 3.0 software and the samples were median centered. (166_AP206_UQN_w0_log2_70p_mdctr.final.tsv)

source_name: breast

extract_protocol:
Tumor tissue was disrupted using roto-stator homogenization. RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to manufacturer protocol. RNA was quantified using a NanoDrop® Spectrophotometer,  and the quality of RNA was  then  analyzed  via  2100 Bioanalyzer Instrumentwhich  using the  RNA 6000 Nano  assay (Agilent)  for determination  of  an  RNA  Integrity  Number  (RIN).
Briefly, 1 μg of total RNA was converted to RNAseq libraries using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced on an Illumina HiSeq 2500 using a 2x50bp configuration with an average of 136 million read pairs per sample.

value: primary tumor


title: lncRNA profile of case541N


title: phs001866_AP_226

description: RNA-Seq of human breast metastatic tumor

value: metastatic tumor


title: lncRNA profile of case541T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C5_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 286


title: genomic DNA from peripheral blood leukocytes 285


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C5_AD004_indexed


title: phs001866_AP_208


title: phs001866_AP_207

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 290


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C5_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C5_AD001_indexed


title: lncRNA profile of case539N


title: lncRNA profile of case539T


title: phs001866_AP_200


title: genomic DNA from peripheral blood leukocytes 281


title: lncRNA profile of case538T


title: phs001866_AP_199

description: RNA-Seq of human breast primary tumor


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C4_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 278


title: lncRNA profile of case535T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C4_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 274


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C4_AD007_indexed


title: Nano9_180323

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

data_processing:
FastQC version 0.11.3 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems. Only the samples which passed QC are included here.
The Tuxedo Suite was used to align reads to the reference transcriptome using TopHat (version 2.0.13) and Bowtie (version 2.2.1). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis. Only the samples which passed QC are included here.
Two different methods were used for expression quantitation, normalization, and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was one method used for expression quantitation and differential expression analysis. This analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
HTSeq (version 0.6.1)   to count non-ambiguously mapped reads only. Data were pre-filtered to remove genes with 0 counts in all samples. DESeq2 (version 1.14.1) for normalization and differential expression
We identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ 1.5.
Genome_build: hg19
Supplementary_files_format_and_content: text file of raw counts

molecule: polyA RNA

source_name: peripheral blood

extract_protocol:
Peripheral blood were collected in PAXgene Blood RNA Tubes (PreAnalytiX) and stored at 4 degree celsius untill RNA extraction. Total RNA were extracted using PAXgene Blood miRNA Kit (PreAnalytiX) according to manufacturer's instrucion within 3 days after collection.
Sample prep was performed with the Illumina TruSeq Stranded library prep kit and poly-A selection, along with Globin-zero Gold rRNA to deplete both globin transcripts and rRNA.

treatment_protocol: Peripheral blood were collected from participants on Week 1 Monday morning (low exposure) and Friday morning (high exposure),followed by Week 2 Monday morning (low exposure) and Friday morning (high exposure)

value: peripheral blood

tag: time point

tag: particle

tag: company

value: B

tag: amplified

value: no

tag: subject


title: Nano9_180329


title: Nano9_180326


title: genomic DNA from peripheral blood leukocytes 272


title: Nano9_180319


title: genomic DNA from peripheral blood leukocytes 271


title: Nano8_180329


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C4_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 268


title: genomic DNA from peripheral blood leukocytes 280


title: lncRNA profile of case530N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C3_AD012_indexed


title: lncRNA profile of case530T


title: lncRNA profile of case537T


title: genomic DNA from peripheral blood leukocytes 270


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C4_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C4_AD010_indexed


title: Nano8_180319


title: Nano8_180326


title: genomic DNA from peripheral blood leukocytes 284


title: lncRNA profile of case52T


title: lncRNA profile of case535N


title: genomic DNA from peripheral blood leukocytes 267


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C3_AD008_indexed


title: lncRNA profile of case52N


title: genomic DNA from peripheral blood leukocytes 266


title: lncRNA profile of case533T


title: lncRNA profile of case526T


title: Nano7_180329

value: control


title: Nano7_180326


title: genomic DNA from peripheral blood leukocytes 265


title: lncRNA profile of case521T


title: lncRNA profile of case523T


title: Nano7_180323


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C3_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 264


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C3_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 263


title: genomic DNA from peripheral blood leukocytes 262


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C3_AD001_indexed


title: Nano7_180319


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C2_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C2_AD010_indexed


title: Nano6_180302

value: A


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C2_AD012_indexed


title: lncRNA profile of case521N


title: Nano6_180226


title: Nano6_180219


title: lncRNA profile of case519T


title: genomic DNA from peripheral blood leukocytes 258


title: lncRNA profile of case520N


title: lncRNA profile of case520T


title: genomic DNA from peripheral blood leukocytes 257


title: Nano5_180226


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C3_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C2_AD006_indexed


title: lncRNA profile of case519N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C2_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 256


title: genomic DNA from peripheral blood leukocytes 260


title: genomic DNA from peripheral blood leukocytes 255


title: Nano5_180223


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C2_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 254


title: lncRNA profile of case518T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C2_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 253


title: Nano5_180302


title: lncRNA profile of case517N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C1_AD012_indexed


title: Nano4_180226


title: lncRNA profile of case516T


title: Nano4_180223


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C1_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 251


title: lncRNA profile of case515T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C1_AD004_indexed


title: lncRNA profile of case515N


title: Nano3_180302


title: lncRNA profile of case518N


title: Nano5_180219


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C1_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 249


title: lncRNA profile of case513T


title: lncRNA profile of case517T


title: Nano3_180223


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C1_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 246


title: Nano4_180302


title: lncRNA profile of case513N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C1_AD010_indexed


title: lncRNA profile of case512T


title: genomic DNA from peripheral blood leukocytes 245


title: Nano3_180219


title: genomic DNA from peripheral blood leukocytes 244


title: genomic DNA from peripheral blood leukocytes 252


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_D10_AD002_indexed


title: Nano11_180427


title: genomic DNA from peripheral blood leukocytes 250


title: lncRNA profile of case511T


title: genomic DNA from peripheral blood leukocytes 242


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C12_AD012_indexed


title: Nano4_180219


title: lncRNA profile of case510T


title: Nano3_180226


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C12_AD007_indexed


title: lncRNA profile of case510N


title: Nano11_180416


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C11_AD012_indexed


title: lncRNA profile of case509T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C11_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 240


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C12_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 239


title: lncRNA profile of case508T


title: genomic DNA from peripheral blood leukocytes 241


title: Nano10_180423

value: yes


title: lncRNA profile of case508N


title: genomic DNA from peripheral blood leukocytes 237


title: Nano10_180427


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C11_AD007_indexed


title: Nano10_180420


title: genomic DNA from peripheral blood leukocytes 236


title: Nano10_180416


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C11_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C10_AD010_indexed


title: Nano11_180420


title: lncRNA profile of case507T


title: genomic DNA from peripheral blood leukocytes 235


title: lncRNA profile of case506T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C10_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 234


title: lncRNA profile of case506N


title: genomic DNA from peripheral blood leukocytes 233


title: lncRNA profile of case505T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C11_AD008_indexed


title: Patient 7 IgD-CD27+ switched memory B cells from the peripheral blood

city: San Francisco

first: Akshaya

last: Ramesh

address: 675 Nelson Rising Lane

institute: UCSF

data_processing:
Quality filtering using the PRICEv1.2
Alignment of filtered reads using STARv2.5.3a
Differential gene expression analysis was conducted using DESeq2 v2.1.14.1
Genome_build: hg38.v91
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all samples

extract_protocol:
Cerebrospinal fluid and corresponding peripheral blood B cells from patients with MS were sorted using FACS and total RNA was extracted using AllPrep DNA/RNA Micro kit (Qiagen, Germantown, MD), automated on the QIAcube robotics platform.
Libraries were generated using Next Ultra II RNA Library Prep kit (New England Biolabs, Ipswich, MA), automated on a Beckman-Coulter Biomek NXP robot.

tag: cell type

value: peripheral blood B cells


title: Patient 7 IgD-CD27++ plasmablasts/plasma cells B cells from the peripheral blood


title: lncRNA profile of case505N

tag: status after 3 years

value: Alive


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C10_AD012_indexed

tag: brain region

value: SSp


title: genomic DNA from peripheral blood leukocytes 232


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C10_AD007_indexed

tag: Sex

value: male


title: genomic DNA from peripheral blood leukocytes 231

value: peripheral blood leukocytes


title: Patient 7 IgD+CD27- naïve B cells from the peripheral blood


title: lncRNA profile of case504T


title: genomic DNA from peripheral blood leukocytes 230


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C10_AD001_indexed

tag: age


title: lncRNA profile of case504N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C11_AD002_indexed

tag: strain


title: genomic DNA from peripheral blood leukocytes 229

tag: tissue


title: Patient 7 IgD+CD27+ unswitched memory B cells from the peripheral blood


title: lncRNA profile of case503T


title: Patient 7 IgD+CD27+ unswitched memory B cells from the CSF

source_name: cerebrospinal fluid

value: cerebrospinal fluid B cells


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C11_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 226

tag: gender


title: genomic DNA from peripheral blood leukocytes 224


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B9_AD012_indexed


title: Patient 7 IgD+CD27- naïve B cells from the CSF


title: lncRNA profile of case502N


title: Patient 7 IgD-CD27++ plasmablasts/plasma cells B cells from the CSF


title: genomic DNA from peripheral blood leukocytes 223


title: lncRNA profile of case501T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B9_AD010_indexed


title: lncRNA profile of case502T


title: Patient 7 IgD-CD27- double negative B cells from the CSF


title: lncRNA profile of case501N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B9_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 222


title: Patient 6 IgD+CD27+ unswitched memory B cells from the peripheral blood


title: genomic DNA from peripheral blood leukocytes 221


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B9_AD007_indexed


title: Patient 7 IgD-CD27- double negative B cells from the peripheral blood


title: lncRNA profile of case500T

value: Dead


title: Patient 6 IgD-CD27+ switched memory B cells from the peripheral blood


title: lncRNA profile of case49T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B9_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B9_AD001_indexed


title: lncRNA profile of case49N


title: Patient 6 IgD-CD27++ plasmablasts/plasma cells B cells from the peripheral blood


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B8_AD001_indexed


title: Patient 7 IgD-CD27+ switched memory B cells from the CSF


title: Patient 6 IgD+CD27- naïve B cells from the peripheral blood


title: genomic DNA from peripheral blood leukocytes 219

value: F


title: genomic DNA from peripheral blood leukocytes 217


title: lncRNA profile of case499T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B8_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 216


title: Patient 6 IgD-CD27- double negative B cells from the peripheral blood


title: Patient 6 IgD+CD27+ unswitched memory B cells from the CSF


title: lncRNA profile of case498T


title: lncRNA profile of case497T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B8_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 215


title: Patient 6 IgD-CD27+ switched memory B cells from the CSF


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B8_AD004_indexed


title: lncRNA profile of case497N


title: genomic DNA from peripheral blood leukocytes 220


title: genomic DNA from peripheral blood leukocytes 213

value: M


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B8_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 214


title: lncRNA profile of case496T


title: Patient 6 IgD-CD27++ plasmablasts/plasma cells B cells from the CSF


title: lncRNA profile of case495T


title: Patient 6 IgD+CD27- naïve B cells from the CSF


title: Patient 6 IgD-CD27- double negative B cells from the CSF


title: genomic DNA from peripheral blood leukocytes 212


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B7_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_C10_AD002_indexed


title: lncRNA profile of case494T


title: genomic DNA from peripheral blood leukocytes 211


title: genomic DNA from peripheral blood leukocytes 209


title: Patient 5 IgD+CD27+ unswitched memory B cells from the peripheral blood


title: Patient 5 IgD-CD27+ switched memory B cells from the peripheral blood


title: genomic DNA from peripheral blood leukocytes 208


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B7_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B7_AD008_indexed


title: lncRNA profile of case493T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B7_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 206


title: Patient 5 IgD-CD27++ plasmablasts/plasma cells B cells from the peripheral blood


title: lncRNA profile of case491T


title: Patient 5 IgD+CD27- naïve B cells from the peripheral blood


title: lncRNA profile of case492T


title: genomic DNA from peripheral blood leukocytes 205


title: Patient 5 IgD-CD27- double negative B cells from the peripheral blood


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B7_AD004_indexed


title: lncRNA profile of case490T


title: genomic DNA from peripheral blood leukocytes 204


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B7_AD002_indexed


title: Patient 5 IgD+CD27+ unswitched memory B cells from the CSF


title: Patient 5 IgD-CD27+ switched memory B cells from the CSF


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B6_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 201


title: Patient 5 IgD-CD27++ plasmablasts/plasma cells B cells from the CSF


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B6_AD012_indexed


title: lncRNA profile of case487T


title: lncRNA profile of case489T


title: genomic DNA from peripheral blood leukocytes 202


title: genomic DNA from peripheral blood leukocytes 200


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B6_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 199


title: lncRNA profile of case487N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B6_AD006_indexed


title: Patient 5 IgD+CD27- naïve B cells from the CSF


title: Patient 5 IgD-CD27- double negative B cells from the CSF


title: genomic DNA from peripheral blood leukocytes 198


title: Patient 4 IgD+CD27+ unswitched memory B cells from the peripheral blood


title: lncRNA profile of case486T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B6_AD004_indexed


title: lncRNA profile of case485T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B5_AD010_indexed


title: lncRNA profile of case488T


title: genomic DNA from peripheral blood leukocytes 197


title: lncRNA profile of case484T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B5_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 196


title: Patient 4 IgD-CD27++ plasmablasts/plasma cells B cells from the peripheral blood


title: lncRNA profile of case484N


title: lncRNA profile of case483T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B5_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B5_AD007_indexed


title: Patient 4 IgD+CD27- naïve B cells from the peripheral blood


title: lncRNA profile of case482T


title: Patient 4 IgD-CD27- double negative B cells from the peripheral blood


title: genomic DNA from peripheral blood leukocytes 192


title: lncRNA profile of case482N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B5_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B5_AD001_indexed


title: Patient 4 IgD+CD27+ unswitched memory B cells from the CSF


title: lncRNA profile of case481T


title: Patient 4 IgD-CD27+ switched memory B cells from the peripheral blood


title: genomic DNA from peripheral blood leukocytes 190


title: genomic DNA from peripheral blood leukocytes 189


title: lncRNA profile of case481N


title: Patient 4 IgD-CD27+ switched memory B cells from the CSF


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B4_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B4_AD008_indexed


title: lncRNA profile of case479T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B4_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 194


title: lncRNA profile of case480N


title: Patient 4 IgD+CD27- naïve B cells from the CSF


title: genomic DNA from peripheral blood leukocytes 187


title: Patient 4 IgD-CD27- double negative B cells from the CSF


title: genomic DNA from peripheral blood leukocytes 193


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B4_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 185


title: lncRNA profile of case478T


title: genomic DNA from peripheral blood leukocytes 183


title: Patient 3 IgD+CD27+ unswitched memory B cells from the peripheral blood


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B4_AD002_indexed


title: Patient 3 IgD-CD27+ switched memory B cells from the peripheral blood


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B3_AD012_indexed


title: lncRNA profile of case477T


title: genomic DNA from peripheral blood leukocytes 182


title: Patient 3 IgD-CD27++ plasmablasts/plasma cells B cells from the peripheral blood


title: lncRNA profile of case475T


title: Patient 4 IgD-CD27++ plasmablasts/plasma cells B cells from the CSF


title: genomic DNA from peripheral blood leukocytes 188


title: lncRNA profile of case476T


title: genomic DNA from peripheral blood leukocytes 179


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B3_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 178


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B3_AD008_indexed


title: Patient 3 IgD+CD27- naïve B cells from the peripheral blood


title: lncRNA profile of case475N


title: Patient 3 IgD-CD27- double negative B cells from the peripheral blood


title: lncRNA profile of case474T


title: genomic DNA from peripheral blood leukocytes 176


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B3_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 177


title: Patient 3 IgD+CD27+ unswitched memory B cells from the CSF


title: Patient 3 IgD-CD27+ switched memory B cells from the CSF


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B3_AD006_indexed


title: lncRNA profile of case474N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B3_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 175


title: lncRNA profile of case473T


title: Patient 3 IgD-CD27++ plasmablasts/plasma cells B cells from the CSF


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B3_AD002_indexed


title: Patient 3 IgD+CD27- naïve B cells from the CSF


title: lncRNA profile of case472T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B3_AD001_indexed


title: lncRNA profile of case472N


title: genomic DNA from peripheral blood leukocytes 170


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B2_AD012_indexed


title: Patient 3 IgD-CD27- double negative B cells from the CSF


title: genomic DNA from peripheral blood leukocytes 169


title: Patient 2 IgD+CD27+ unswitched memory B cells from the peripheral blood


title: Patient 2 IgD-CD27+ switched memory B cells from the peripheral blood


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B2_AD008_indexed


title: lncRNA profile of case471N


title: genomic DNA from peripheral blood leukocytes 168


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B2_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 167


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B2_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B2_AD004_indexed


title: Patient 2 IgD+CD27- naïve B cells from the peripheral blood


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B2_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 174


title: Patient 2 IgD-CD27- double negative B cells from the peripheral blood


title: genomic DNA from peripheral blood leukocytes 164


title: genomic DNA from peripheral blood leukocytes 171


title: lncRNA profile of case469N


title: Patient 2 IgD+CD27+ unswitched memory B cells from the CSF


title: lncRNA profile of case471T


title: genomic DNA from peripheral blood leukocytes 162


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B2_AD001_indexed


title: lncRNA profile of case468T


title: genomic DNA from peripheral blood leukocytes 159


title: lncRNA profile of case469T


title: Patient 2 IgD-CD27+ switched memory B cells from the CSF


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B1_AD012_indexed


title: lncRNA profile of case470T


title: Patient 2 IgD-CD27++ plasmablasts/plasma cells B cells from the CSF


title: lncRNA profile of case468N


title: Patient 2 IgD-CD27++ plasmablasts/plasma cells B cells from the peripheral blood


title: genomic DNA from peripheral blood leukocytes 158


title: lncRNA profile of case470N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B1_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B1_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 155


title: Patient 2 IgD+CD27- naïve B cells from the CSF


title: Patient 2 IgD-CD27- double negative B cells from the CSF


title: lncRNA profile of case467T


title: genomic DNA from peripheral blood leukocytes 165


title: lncRNA profile of case466T


title: genomic DNA from peripheral blood leukocytes 153


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B1_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 150


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B1_AD004_indexed


title: lncRNA profile of case466N


title: genomic DNA from peripheral blood leukocytes 147


title: genomic DNA from peripheral blood leukocytes 146


title: lncRNA profile of case465T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B12_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B1_AD001_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B12_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 145


title: lncRNA profile of case464T


title: lncRNA profile of case465N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B12_AD001_indexed


title: MRD.pos.PROG.pos_Pt.970

city: Aurora

first: Brett

last: Stevens

state: CO

institute: University of Colorado

data_processing:
Raw reads generated from the Illumina HiSeq2500 sequencer were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal are performed using Trimmomatic-0.36 with the following parameters: "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35".
Processed/cleaned reads were then mapped to the Homo sapiens reference sequence (GRCh38, hg38) with STAR-2.6.0c given the following parameters: "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
The subread-1.6.1 package (featureCounts) was used to derive gene counts given the following parameters: “-s 2 -t exon -g gene_name”.
Differential expression analysis and data normalization was performed using DESeq2-1.16.1 with an adjusted p-value threshold of 0.05 within an R-3.4.1 environment. A batch factor was given to the differential expression model in order to control for batch differences.
Genome_build: GRCh38, hg38
Supplementary_files_format_and_content: raw counts produced by deSeq2 analysis provided in txt file

source_name: AML Bone marrow Pt Sample

growth_protocol: Freshly thawed and sorted

extract_protocol:
QIAGEN RNeasy Plus Kit
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols.
Briefly, mRNA was purified from 200ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample on the Illumina HiSeq2500 platform.

value: Primary AML cells

tag: disease state

value: AML

tag: sub-fraction

value: ROSlow enriched LSCs

tag: group

value: progressor


title: MRD.pos.PROG.pos_Pt.976


title: lncRNA profile of case464N


title: genomic DNA from peripheral blood leukocytes 144

tag: age(yrs)

tag: systolic blood pressure (mmhg)

tag: diastolic blood pressure (mmhg)


title: lncRNA profile of case463T


title: MRD.pos.PROG.pos_Pt.RB_0


title: lncRNA profile of case463N


title: genomic DNA from peripheral blood leukocytes 142


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B11_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 141


title: MRD.pos.PROG.neg_Pt.966

value: non progressor


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B1_AD002_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B11_AD010_indexed


title: lncRNA profile of case462N


title: MRD.pos.PROG.neg_Pt.FJ_0


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B11_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 148


title: genomic DNA from peripheral blood leukocytes 140


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B11_AD007_indexed


title: MRD.pos.PROG.neg_Pt.1020_0


title: lncRNA profile of case461T


title: genomic DNA from peripheral blood leukocytes 135


title: genomic DNA from peripheral blood leukocytes 134


title: MRD.neg.PROG.neg_Pt.691


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B11_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B11_AD004_indexed


title: lncRNA profile of case459T


title: lncRNA profile of case462T


title: genomic DNA from peripheral blood leukocytes 132


title: genomic DNA from peripheral blood leukocytes 131


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B10_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B10_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 136


title: lncRNA profile of case457N


title: lncRNA profile of case456T


title: genomic DNA from peripheral blood leukocytes 130


title: lncRNA profile of case458N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B10_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 129


title: lncRNA profile of case455T


title: MRD.neg.PROG.neg_Pt.719


title: lncRNA profile of case455N


title: lncRNA profile of case461N


title: lncRNA profile of case460N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A9_AD010_indexed


title: lncRNA profile of case454T


title: genomic DNA from peripheral blood leukocytes 128


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A9_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B11_AD002_indexed


title: MRD.neg.PROG.neg_Pt.478


title: genomic DNA from peripheral blood leukocytes 126


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_B10_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 125


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A9_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 133


title: lncRNA profile of case454N


title: genomic DNA from peripheral blood leukocytes 123


title: lncRNA profile of case453T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A9_AD001_indexed


title: lncRNA profile of case453N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A8_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 120


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A8_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A8_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A8_AD006_indexed


title: lncRNA profile of case452T


title: lncRNA profile of case451N


title: lncRNA profile of case451T


title: lncRNA profile of case450T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A8_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A8_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 116


title: genomic DNA from peripheral blood leukocytes 114


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A7_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 113


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A7_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 111


title: lncRNA profile of case449T


title: lncRNA profile of case450N


title: lncRNA profile of case449N


title: genomic DNA from peripheral blood leukocytes 109


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A7_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 112


title: genomic DNA from peripheral blood leukocytes 122


title: lncRNA profile of case447T


title: lncRNA profile of case448T


title: genomic DNA from peripheral blood leukocytes 118


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A7_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 108


title: genomic DNA from peripheral blood leukocytes 107


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A7_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 105


title: genomic DNA from peripheral blood leukocytes 104


title: genomic DNA from peripheral blood leukocytes 103


title: genomic DNA from peripheral blood leukocytes 101


title: lncRNA profile of case446T


title: lncRNA profile of case445T


title: genomic DNA from peripheral blood leukocytes 102


title: lncRNA profile of case446N


title: lncRNA profile of case443N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A7_AD007_indexed


title: siPAX9 3

city: New Haven

first: Susan

middle: J

last: Baserga

state: CT

address: 333 Cedar St., SHM C114

institute: Yale University

data_processing:
Data analysis was performed using Partek® Flow® software 657 (version 7.0 Copyright; 2018,Partek, Inc., St. Louis, MO, USA).
Reads were aligned to the genome (UCSC hg19) using Bowtie 2.
Reads were quantified to the transcriptome using Cufflinks.
mRNAs were considered differentially expressed if the fold change was ≥ 2 or ≤ -2 and the q value ≤ 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files including fold change information and statistics for every gene

source_name: MCF10A cells

growth_protocol: MCF10A cells (ATCC CRL-10317) were grown in Dulbecco’s modified Eagle’s medium/Nutrient mixture F-12 (DMEM-F12, Gibco 1130-032) supplemented with 5% horse serum (Gibco 16050), 20 ng/mL epidermal growth factor (Sigma E4127), 0.5 μg/mL hydrocortisone (Sigma H0135), 100 ng/mL Cholera toxin (Sigma C8052), and 10 μg/mL insulin (Sigma I1882) at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
RNA was harvested using TRIzol according to the manufacturer’s instructions.
The Yale Center for Genomic Analysis synthesized the PolyA+ mRNA library following Illumina mRNA sample preparation guidelines and also performed the single-end RNA sequencing using the  Illumina HiSeq 2500 sequencing system.

treatment_protocol: siRNA knockdown was performed in 6-well plates with 1x105 cells per well. After 24 hours, siRNAs (30 nM final) were reverse transfected for 72 hours using Lipofectamine® RNAimax as per the manufacturer’s instructions.

value: breast epithelial cells

tag: treatment

value: siRNAs targeting PAX9 for 72 hours

tag: cell line


title: genomic DNA from peripheral blood leukocytes 99


title: lncRNA profile of case443T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A6_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A6_AD007_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A6_AD010_indexed


title: lncRNA profile of case441N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A6_AD002_indexed


title: lncRNA profile of case442T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A6_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 97


title: lncRNA profile of case440T


title: siPAX9 1


title: siPAX9 2


title: genomic DNA from peripheral blood leukocytes 95


title: lncRNA profile of case439T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A7_AD001_indexed


title: siNT 3

value: non-targeting siRNAs for 72 hours


title: lncRNA profile of case438T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A5_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 93


title: genomic DNA from peripheral blood leukocytes 91


title: siNT 2


title: siNT 1


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A5_AD010_indexed


title: lncRNA profile of case437T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A5_AD006_indexed


title: genomic DNA from peripheral blood leukocytes 92


title: genomic DNA from peripheral blood leukocytes 90


title: lncRNA profile of case435T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A5_AD004_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A6_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 89


title: lncRNA profile of case433T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A5_AD001_indexed


title: lncRNA profile of case434T


title: RA2d_d2_2

city: Stockholm

first: Johan

last: Ericson

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Instituet

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite
Gene level abundances were estimated as FPKMs using StringTie
The read summarization to each gene (i.e. counts) was calculated using featureCounts
Multiple ENSEMBL gene IDs were summed up per known HUGO gene symbol
Genome_build: Reads were mapped to the human genome assembly, build GRCh37 using STAR (v 2.6.1a)
Supplementary_files_format_and_content: FPKM in txt format

source_name: Neural progenitor cells

growth_protocol: hESCs were differentiated in N2B27 medium in different conditions.

extract_protocol:
total RNA, Quick-RNA Mini Prep Plus kit (Zymo Research)
Illumina TruSeq Stranded mRNA
poly-A selection

treatment_protocol: RA was added (or not added in the control) to culture for 1, 2, or 4 days of the differentiation. The cells were treated also with inhibitors of TGFb and BMP signaling and the activator of SHH signaling SAG1.3

tag: line

tag: Stage

value: 2 days

value: RA 2 days


title: HESC980_2

source_name: Embryonic stem cells

value: undifferentiated cells

value: No


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A4_AD010_indexed

value: SSp

value: male


title: genomic DNA from peripheral blood leukocytes 88

value: peripheral blood leukocytes


title: RA2d_d2_1


title: lncRNA profile of case433N

source_name: non-small-cell lung cancer

tag: status after 3 years

value: Alive


title: HESC980_1


title: genomic DNA from peripheral blood leukocytes 87

value: F


title: lncRNA profile of case432T

value: Dead


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A4_AD007_indexed

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region


title: lncRNA profile of case432N


title: phs001866_AP_99

description: RNA-Seq of human breast primary tumor

value: primary tumor


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A4_AD006_indexed

tag: Sex


title: phs001866_AP_98

value: metastatic tumor


title: genomic DNA from peripheral blood leukocytes 84

source_name: peripheral blood leukocytes


title: phs001866_AP_97

description: RNA-Seq of human breast primary tumor


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A4_AD001_indexed

tag: age


title: lncRNA profile of case431T


title: lncRNA profile of case431N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A3_AD012_indexed

tag: strain


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A4_AD004_indexed


title: phs001866_AP_96


title: genomic DNA from peripheral blood leukocytes 82

tag: tissue


title: genomic DNA from peripheral blood leukocytes 85

tag: gender


title: phs001866_AP_95

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 81

value: M


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A3_AD008_indexed


title: phs001866_AP_94


title: lncRNA profile of case430T


title: lncRNA profile of case430N


title: genomic DNA from peripheral blood leukocytes 83


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A3_AD007_indexed


title: genomic DNA from peripheral blood leukocytes 80


title: lncRNA profile of case427T


title: phs001866_AP_93

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case429T


title: phs001866_AP_92


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A3_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A3_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 78


title: lncRNA profile of case426T


title: lncRNA profile of case425T


title: phs001866_AP_91

description: RNA-Seq of human breast primary tumor


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A3_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 74


title: phs001866_AP_88


title: genomic DNA from peripheral blood leukocytes 76


title: lncRNA profile of case423T


title: phs001866_AP_87

description: RNA-Seq of human breast primary tumor


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A3_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 72


title: phs001866_AP_86


title: phs001866_AP_85

description: RNA-Seq of human breast primary tumor


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A2_AD010_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A2_AD008_indexed


title: genomic DNA from peripheral blood leukocytes 69


title: genomic DNA from peripheral blood leukocytes 66


title: phs001866_AP_83

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_84


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A2_AD012_indexed


title: genomic DNA from peripheral blood leukocytes 65


title: lncRNA profile of case422N


title: genomic DNA from peripheral blood leukocytes 77


title: lncRNA profile of case422T


title: genomic DNA from peripheral blood leukocytes 64


title: lncRNA profile of case423N


title: lncRNA profile of case421N


title: phs001866_AP_80


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A2_AD004_indexed


title: lncRNA profile of case421T


title: genomic DNA from peripheral blood leukocytes 63


title: genomic DNA from peripheral blood leukocytes 60


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A2_AD002_indexed


title: lncRNA profile of case420N


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A1_AD012_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A2_AD007_indexed


title: lncRNA profile of case41T


title: genomic DNA from peripheral blood leukocytes 58


title: phs001866_AP_78


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A2_AD006_indexed


title: phs001866_AP_77

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case419T


title: phs001866_AP_76


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A1_AD008_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A1_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 55


title: phs001866_AP_75

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 57


title: lncRNA profile of case420T


title: lncRNA profile of case417T


title: genomic DNA from peripheral blood leukocytes 54


title: phs001866_AP_72


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A11_AD006_indexed


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A11_AD002_indexed


title: phs001866_AP_79

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 52


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A1_AD007_indexed


title: lncRNA profile of case416T


title: lncRNA profile of case417N


title: phs001866_AP_71

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 50


title: lncRNA profile of case415T


title: genomic DNA from peripheral blood leukocytes 49


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A11_AD001_indexed


title: phs001866_AP_70


title: phs001866_AP_69

description: RNA-Seq of human breast primary tumor


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A11_AD012_indexed


title: lncRNA profile of case415N


title: lncRNA profile of case418T


title: genomic DNA from peripheral blood leukocytes 47


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A10_AD012_indexed


title: phs001866_AP_67

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_68


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A1_AD002_indexed


title: phs001866_AP_66


title: lncRNA profile of case412T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A12_AD001_indexed


title: genomic DNA from peripheral blood leukocytes 48


title: lncRNA profile of case467N


title: lncRNA profile of case411T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A10_AD010_indexed


title: phs001866_AP_65

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 43


title: lncRNA profile of case414T


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A11_AD010_indexed


title: genomic DNA from peripheral blood leukocytes 41


title: phs001866_AP_64


title: lncRNA profile of case411N


title: lncRNA profile of case413T


title: genomic DNA from peripheral blood leukocytes 40


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A10_AD008_indexed


title: phs001866_AP_60


title: genomic DNA from peripheral blood leukocytes 46


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A12_AD010_indexed


title: phs001866_AP_59

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 36


title: genomic DNA from peripheral blood leukocytes 44


title: phs001866_AP_58


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A10_AD004_indexed


title: genomic DNA from peripheral blood leukocytes 33


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A10_AD002_indexed


title: phs001866_AP_57

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 32


title: lncRNA profile of case403N


title: lncRNA profile of case403T


title: genomic DNA from peripheral blood leukocytes 30


title: phs001866_AP_63

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_56


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A11_AD007_indexed


title: lncRNA profile of case402N


title: phs001866_AP_55

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 29


title: lncRNA profile of case410N


title: genomic DNA from peripheral blood leukocytes 37


title: lncRNA profile of case410T


title: genomic DNA from peripheral blood leukocytes 28


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A10_AD001_indexed


title: phs001866_AP_54


title: lncRNA profile of case402T


title: lncRNA profile of case400T


title: lncRNA profile of case401T


title: lncRNA profile of case399T


title: genomic DNA from peripheral blood leukocytes 25


title: phs001866_AP_52


title: phs001866_AP_53

description: RNA-Seq of human breast primary tumor


title: 180626_CEMBA_mm_P56_P63_5B_CEMBA180529_5B_1_CEMBA180529_5B_2_A12_AD002_indexed


title: genomic DNA from peripheral blood leukocytes 23


title: phs001866_AP_51

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 22


title: 180612_CEMBA_mm_P56_P63_3D_CEMBA180416_3D_5_CEMBA180416_3D_6_H5_AD012_indexed

value: AI


title: phs001866_AP_50


title: genomic DNA from peripheral blood leukocytes 19


title: phs001866_AP_49

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_48


title: genomic DNA from peripheral blood leukocytes 18


title: phs001866_AP_47

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case395T


title: genomic DNA from peripheral blood leukocytes 17


title: genomic DNA from peripheral blood leukocytes 16


title: phs001866_AP_246


title: lncRNA profile of case395N


title: lncRNA profile of case394T


title: phs001866_AP_245

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case398T


title: genomic DNA from peripheral blood leukocytes 12


title: phs001866_AP_244


title: genomic DNA from peripheral blood leukocytes 13


title: phs001866_AP_243

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 9


title: lncRNA profile of case394N


title: lncRNA profile of case396T


title: lncRNA profile of case392T


title: genomic DNA from peripheral blood leukocytes 21


title: genomic DNA from peripheral blood leukocytes 8


title: phs001866_AP_242


title: lncRNA profile of case392N


title: lncRNA profile of case393N


title: lncRNA profile of case393T


title: genomic DNA from peripheral blood leukocytes 7


title: lncRNA profile of case391T


title: phs001866_AP_238


title: genomic DNA from peripheral blood leukocytes 5


title: lncRNA profile of case391N


title: phs001866_AP_237

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 3


title: lncRNA profile of case390T


title: lncRNA profile of case397T


title: phs001866_AP_235

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case390N