title: stripped root 40ºC rep2


title: root hair 40ºC rep2

status: Public on Aug 01 2017

type: SRA

city: Columbia

first: Md Shakhawat

last: Hossain

state: Missouri

address: 201 Life Science Center 1201 Rollins Road

department: Plant Sciences

country: USA

institute: University of Missouri

library_source: genomic

data_processing:
Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature
Genome_build: Glycine max reference genome version 1.0
Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions

molecule: genomic DNA

organism: Glycine max

source_name: root hair

growth_protocol: Seeds from soybean cultivar Williams 82 were surface sterilized with 30% bleach, rinsed several times with sterilized double-distilled H2O (dd H2O), once with 0.01 M HCl for 10 min, and then thoroughly rinsed several times with sterilized ddH2O. Sterilized seeds were placed on nitrogen-free B&D agar medium (Broughton & Dilworth, 1971) in large, glass petri dishes and allowed to germinate in a growth chamber in the dark at 25°C and 80% humidity.

extract_protocol:
Root hairs and stripped roots were isolated after 3 hours of incubation as described by Wan et al. (2005). Genomic DNA was extracted using the DNeasy® Plant Mini Kit (Qiagen) following the manufacturer’s instructions.
One µg of gDNA was spiked with 5ng of unmethylated Lambda DNA (Promega), and randomly sheared to an average of 300 bp using the Covaris S220 instrument. Sheared DNA was end-repaired, A-tailed and ligated using TruSeq DNA sample preparation kit (Illumina, San Diego, CA). Bisulfite treatment was performed twice using the EpiTect Bisulfite kit (Qiagen) following the manufacturer's protocol for DNA isolated from formalin-fixed paraffin-embedded tissue (FFPE) tissue samples. The bisulfite-converted library was amplified (9 cycles) by PCR with KAFA HiFi Uracil+ DNA polymerase (Kapa Biosystems) according to the manufacturer’s conditions.

treatment_protocol: After three days of germination, half of the seedlings (approximately 1000) were transferred to another chamber for heat (40°C) treatment and remaining half were kept in a chamber at 25°C, considered the mock control. To avoid drying, we maintained high humidity (80%) in the growth chamber.

tag: cell type

value: root hair

tag: cultivar

value: Williams 82 (wild type)

tag: tissue

value: root


title: root hair 40ºC rep1


title: C57injur-80

city: Santa Barbara

first: Kenneth

middle: S.

last: Kosik

state: California

address: UC Santa Barbara

department: NRI

institute: UCSB

library_source: transcriptomic

data_processing:
Reads were mapped to the mm10 mouse genome using Bowtie2.
Duplicate reads removed using samtools.
Reads were summarized on a gene annotation using RsubReads.
Genome_build: mm10
Supplementary_files_format_and_content: matrix of counts for each cell (as column) and each gene (as row)

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
After dissection, the naïve or IVA DRG neurons were filtered through a 35um mesh and resuspended in 2ml of complete media before being layered on a Percoll solution (density of 1.040) as described in (Delree et al., 1989) to remove myelin debris. The lower 5ml fraction was washed in PBS and the pellet was resuspended in C1 cell wash buffer. Cells were counted and resuspended at a concentration of 310 cells per ul, stained for viability on ice for 30 minutes and then captured by the C1 from Fluidigm using the large chip. Cells were imaged at 4X magnification. Cell lysis, reverse transcription and pre-amplification were performed on the C1 as described by the manufacturer.
cDNA was diluted and library prepared for Illumina sequencing using the Nextera kit and according to the Fluidigm protocol. Libraries were sequenced on a NextSeq 500 using a high-output 150 cycles chip. Up to 192 cells were sequenced at once and cells from all conditions were combined on each sequencing run.

treatment_protocol: After dissociation cells were plated on bare plastic at high density (5000 to 10000 cells per cm2) and allowed to grow for 48 h with the addition of ara-c 24 h after plating. After 48 hr cells were lifted using trypsin and lightly triturated to ensure dissociation of all processes.

tag: strain

value: dorsal root ganglia

tag: treatment

value: injured


title: C57injur-78


title: C57injur-88


title: C57injur-75


title: root hair 25ºC rep2


title: C57injur-86


title: stripped root 25ºC rep1

source_name: stripped root

value: root without root hair


title: C57injur-73


title: root hair 25ºC rep1


title: C57injur-71


title: C57injur-69


title: C57injur-72


title: C57injur-70


title: C57injur-66


title: C57injur-64


title: C57injur-67


title: C57naive-151

value: none (naive)


title: C57naive-150


title: C57injur-68


title: C57naive-148


title: C57naive-146


title: C57injur-65


title: C57naive-147


title: C57naive-144


title: C57injur-74


title: C57naive-145


title: C57naive-143


title: C57naive-149


title: HGSC_JH993

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

data_processing:
RNA sequences were aligned to the NCBI human genome build 37 using STAR aligner (v2.3.1z).
Quantification of genes annotated in Gencode (version 18) was performed using featureCounts (v1.4.3).
DESeq2 (doi:10.1101/002832) was used to normalize feature counts.
Picard and RSeQC 50 was used to collect QC metrics (http://broadinstitute.github.io/picard/)
Genome_build: NCBI human genome build 37
Supplementary_files_format_and_content: Tab delimited text file containing Gene ID, Chr, Start, End, Strand, Length and counts

molecule: total RNA

organism: Homo sapiens

source_name: primary ovarian tumor tissue

extract_protocol:
DNA and RNA were co-isolated from frozen tissue tumor blocks, and RNA was isolated from normal tissues utilizing Ambion’s ToTALLY RNA™ RNA Isolation Kit (Part Number AM1910, ©Ambion, Inc.).  DNA concentration was confirmed using a PicoGreen protocol. RNA quality was confirmed by utilizing an Agilent Bioanalyzer and assigning an RNA Integrity Number (RIN) to each sample.
RNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Sample Preparation Kit.  Briefly, 500ng of total RNA was purified by Ribo-Zero to remove rRNA and fragmented by divalent cations under elevated temperature. The fragmented RNA underwent first strand synthesis using reverse transcriptase and random primers.  Second strand synthesis created the cDNA fragments using DNA polymerase I and RNaseH.   The cDNA fragments then went through end repair, adenylation of the 3’ ends, and ligation of adapters.  The cDNA library was enriched using 10 cycles of PCR and purified.

tag: stic

value: No

tag: age

value: IIIA

value: Optimal

value: Ovarian Ca

tag: platinumstatus

value: Sensitive

tag: recurrence

value: N

tag: vitalstatus

value: Alive

tag: race

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_RG953

value: IIIC


title: C57naive-142


title: HGSC_JH1085

value: IA


title: HGSC_JH1075

value: Yes

value: IV

value: Suboptimal

value: Y


title: C57naive-140

value: dorsal root ganglia


title: Medial entorhinal cortex (small RNA)

city: Trondheim

first: Lene

middle: Christin

last: Olsen

address: Erling Skjalgsons gt. 1

department: Medical Faculty

country: Norway

institute: Norwegian University of Science and Technology - NTNU

data_processing:
Base calling using Illumina's CASAVA 1.8.3
Removed adapters, reads below 15 nts and low quality ends using Cutadapt v.1.0 with settings -m 15 -q 20
Removed low quality reads using fastq_quality_filter from the FASTX Toolkit v.0.0.13 with settings -v -q 20 -p 50 -Q 33
Aligned to the rat genome (rn4) using Bowtie v. 0.12.7 and settings -f -k 5 --best --strata
Annotation and read count against mature miRNA gff file from miRBase v. 20 was done using HTSeqCount v.0.5.4p3 with settings -i Name -t miRNA --stranded=no
Genome_build: rn4

organism: Rattus norvegicus

source_name: Medial entorhinal cortex

extract_protocol:
The Norgene Total RNA purification kit from Norgene Biotek was used according to the manufacturer's recommendations. The RNA quantity was determined by NanoDrop, and the quantity on the Bioanalyzer Nano Chip.
The library was prepared with the Illumina’s small RNA TruSeq kit according to the manufacturer's recommendations, except size selection was up to 35 bp, before sequencing on one lane on the Illumina HiSeq2000 using standard Illumina protocol

treatment_protocol: Long Evans rats were deeply anesthetized and sacrificed by guillotine. The brain was rapidly extracted, and the medial entorhinal cortex dissected under the microscope and placed in RNAlater

value: Long Evans


title: HGSC_JH1069

value: No

value: IIC

value: OTHER


title: C57naive-139

value: none (naive)


title: C57naive-138


title: HGSC_JH1066

value: Optimal

value: Ovarian Ca

value: Sensitive


title: C57injur-63

value: injured


title: C57naive-137


title: C57naive-136


title: C57naive-152


title: HGSC_JB5982

value: Fallopian Tube Ca

value: N

value: Alive

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JB5962

value: Yes

value: IIIC

value: Resistant


title: HGSC_JH1035

value: Unknown

value: Endometrial cancer


title: C57naive-135

value: dorsal root ganglia


title: C57naive-134


title: HGSC_JB5861

value: IV


title: HGSC_JB5893

value: Fallopian tube Ca


title: C57naive-132

value: none (naive)


title: C57naive-131


title: HGSC_JB5841

value: Optimal

value: Y


title: HGSC_JH1072

value: Ovarian Ca

value: Sensitive

value: ASIAN


title: C57naive-129


title: HGSC_JB5615

value: No

value: Fallopian Tube Ca

value: Alive


title: C57naive-133


title: C57naive-128


title: HGSC_JB5860

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: C57naive-130


title: HGSC_JB5617

value: Yes

value: IIIC


title: HGSC_JB5585

value: Resistant

value: Dead


title: C57naive-127

value: dorsal root ganglia


title: C57naive-125


title: HGSC_JB5565

value: Suboptimal


title: HGSC_JB5567


title: HGSC_JB5548


title: C57naive-124

value: none (naive)


title: HGSC_JB5537

value: N


title: C57naive-123


title: C57naive-121


title: HGSC_JB5516

value: Optimal


title: C57naive-122


title: HGSC_JB5506

value: Ovarian Ca

value: Y


title: C57naive-120


title: HGSC_JB5471

value: IV

value: Sensitive


title: C57naive-119


title: C57naive-118


title: HGSC_JB5464

value: Fallopian Tube Ca


title: HGSC_JB5439

value: Alive

value: BLACK


title: C57injur-62

value: injured


title: HGSC_JB5318

value: No

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JB5427


title: C57naive-126


title: C57injur-58


title: C57injur-61


title: HGSC_JB5293

value: Yes

value: IIIC


title: HGSC_JB5268

value: Not available


title: HGSC_JB5287


title: HGSC_JB5276


title: C57injur-57

value: dorsal root ganglia


title: HGSC_JB5234

value: Resistant


title: C57injur-56


title: C57injur-55


title: HGSC_JB5223

value: Optimal


title: HGSC_JB5523

value: Dead


title: HGSC_JB5214

value: Ovarian Ca

value: Y


title: HGSC_JB5087

value: IV

value: Sensitive


title: C57injur-53


title: HGSC_JB5051

value: Fallopian Tube Ca

value: Alive


title: HGSC_JB5019

value: N


title: Casinjur-52

value: CAST/Ei

value: injured


title: Casinjur-51


title: Casinjur-50


title: HGSC_JB4976

value: No

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: C57injur-60


title: HGSC_JB4998

value: IIIC


title: C57injur-59

value: dorsal root ganglia


title: C57naive-117

value: none (naive)


title: Casinjur-48


title: HGSC_JB4960

value: Yes

value: Optimal


title: HGSC_JB4952

value: Peritoneum Ca NOS


title: HGSC_JB4912

value: Ovarian Ca

value: ASIAN


title: Casinjur-47


title: HGSC_JB4900

value: Sensitive

value: Y


title: Casinjur-43


title: Casinjur-45


title: HGSC_JB4886

value: Suboptimal

value: Fallopian Tube Ca

value: Alive


title: C57injur-54

value: injured


title: HGSC_JB4904

value: IV

value: Dead


title: Casinjur-44

value: CAST/Ei


title: Casinjur-46


title: Casinjur-42


title: Casinjur-41


title: HGSC_JB4887

value: No

value: IIIC

value: N

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: Casinjur-40

value: dorsal root ganglia


title: HGSC_JB4878

value: Optimal

value: Ovarian Ca


title: Casinjur-49


title: HGSC_JB4841

value: Yes

value: IIIB

value: Sensitive


title: Casinjur-39


title: Casinjur-38


title: HGSC_JB4833

value: Y


title: HGSC_JB4838

value: Fallopian Tube Ca

value: Alive


title: Casinjur-37

value: injured


title: HGSC_JB4962

value: IV

value: ASIAN


title: HGSC_JB4757

value: No

value: Dead


title: Casinjur-35

value: CAST/Ei


title: Casinjur-34


title: HGSC_JB4752

value: IIIC

value: WHITE


title: HGSC_JB4744

value: Suboptimal

value: N

value: OTHER

value: primary tumor tissue from high grade serous ovarian tumors


title: Casinjur-33

value: dorsal root ganglia


title: HGSC_JB4733

value: Yes

value: Optimal

value: Resistant


title: HGSC_JB4675

value: Ovarian Ca

value: Fallopian Tube Ca

value: Y


title: HGSC_JB4860

value: Sensitive

value: Alive


title: HGSC_JB4684

value: IV


title: Casinjur-31

value: CAST/Ei

value: injured


title: HGSC_JB4442

value: Dead

value: WHITE


title: Casinjur-26


title: HGSC_JB4548


title: Casinjur-30


title: HGSC_JB4674

value: No

value: Peritoneum Ca NOS


title: Casinjur-27


title: Casinjur-32


title: Casinjur-36


title: Casinjur-28


title: Casinjur-25


title: HGSC_JB 5727

value: IIIC

value: N

value: HISPANIC

value: primary tumor tissue from high grade serous ovarian tumors


title: Casinjur-23

value: dorsal root ganglia


title: HGSC_JB4234

value: Yes

value: Optimal

value: Ovarian Ca

value: ASIAN


title: HGSC_GL5113

value: Fallopian Tube Ca

value: Sensitive

value: Y

value: Alive


title: HGSC_JB 5705


title: Casinjur-20

value: CAST/Ei

value: injured


title: HGSC_GL4226

value: No

value: WHITE


title: Casinjur-21


title: HGSC_JB4853

value: IIC


title: Casinjur-29


title: Casinjur-19


title: Casinjur-22


title: HGSC_40211

value: III

value: Suboptimal

value: Not available

value: Dead


title: HGSC_914T

value: IIIC

value: N

value: primary tumor tissue from high grade serous ovarian tumors


title: Casinjur-18

value: dorsal root ganglia


title: Casinjur-17


title: HGSC_40208

value: Yes


title: HGSC_JB 5768

value: IV

value: Optimal

value: Ovarian Ca

value: Fallopian Tube Ca

value: Sensitive


title: HGSC_40204

value: No

value: Y


title: HGSC_40203


title: HGSC_40209

value: Alive


title: Casinjur-16

value: CAST/Ei

value: injured


title: HGSC_40202

value: III

value: Suboptimal

value: Not available


title: HGSC_40201

value: IIIC


title: Casinjur-11


title: Casinjur-12


title: HGSC_40200

value: primary tumor tissue from high grade serous ovarian tumors


title: Casinjur-9

value: dorsal root ganglia


title: Casinjur-8


title: HGSC_40199

value: Dead


title: HGSC_40197

value: Yes


title: Casinjur-10


title: HGSC_40193

value: II

value: Unknown


title: HGSC_40191

value: Optimal


title: HGSC_323T

value: Ovarian Ca

value: Sensitive

value: WHITE


title: HGSC_40190

value: Y


title: Casinjur-14

value: CAST/Ei


title: Casinjur-5

value: injured


title: Casinjur-6


title: 779e/E47 WT3

city: La Jolla

first: Roman

last: Sasik

state: CA

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

data_processing:
RNA-seq fastq files with approximately 40 x 10^6 reads per sample were processed into transcript-level summaries using kallisto. Reference transcriptome was current human GENCODE Release 23 (GRCh38.p3.)
Transcript-level summaries were combined into gene-level summaries by adding all transcript counts from the same gene. Gene counts were normalized across samples using DESeq normalization.
The gene list was filtered based on mean abundance (across samples). Differential expression was assessed with an R package limma applied to log2-transformed counts.
Statistical significance of each test was expressed in terms of local false discovery rate (lfdr) using the limma function eBayes.
Genome_build: hg19

source_name: PDX (patient-derived) cell line from a primary pancreas tumor transduced with a retrovirus that expressed human E47

growth_protocol: As previously described (Kim et al, Pancreas 2015), ATCC (Rockville, MD) human pancreatic adenocarcinoma cell lines PANC-1 (CRL-1469), BxPC-3 (CRL-1687), and MiaPaCa2 (CRL-1420) were cultured in RPMI 1640 or DMEM supplemented with 10% FBS. Patient-derived cell lines, 1334 and 779e, were grown in high glucose DMEM, initially supplemented with 30% FBS, 2mM Glutamine, 1mM sodium pyruvate, 1X non-essential amino acids, 200IU/ml Pen, 200ug/ml Strep, and 1X Fungizone. All cells were grown in 5% CO2 at 37°C.

extract_protocol:
Total RNA from three biological replicates of untreated control cells and cells treated with tamoxifen was isolated using Qiagen RNeasy Kits. Total RNA was assessed for quality using an Agilent Tapestation, and samples with RNA Integrity Numbers (RIN) greater than 8 were used to make RNA libraries
Libraries were generated using Illumina’s TruSeq Stranded mRNA Sample Prep Kit following manufacturer’s instructions, modifying the shear time to 5 minutes.
RNA libraries were multiplexed and sequenced with 100 basepair (bp) paired end reads (PE100) to a depth of approximately 40 million reads per sample on an Illumina HiSeq2500/HiSeq4000.

treatment_protocol: Cell lines were treated -/+ 4micomolar tamoxifen for 48-72 hours to induce nuclear translocation of E47.

value: polyclonal cell line

tag: treatment (-/+ tamoxifen to induce nuclear localization of e47)

value: (+) tamoxifen

tag: genotype

value: KRAS-G12V, p53-R209K and frameshift->S215stop, p16-silenced, SMAD4-WT

tag: original source of cells

value: primary pancreas tumor


title: Casinjur-7


title: 779e/E47 WT2


title: 779e/E47 WT1


title: Casinjur-4


title: Casinjur-13


title: Casnaive-134

value: none (naive)


title: Casinjur-2

value: dorsal root ganglia


title: 779e/E47 NT2

value: (-) tamoxifen


title: 779e/E47 NT3


title: Casnaive-133


title: 779e/E47 NT1


title: Casinjur-15


title: 1334/E47 WT3

source_name: PDX (patient-derived) cell line from a liver metastasis from a primary pancreas tumor transduced with a retrovirus that expressed human E47

value: KRAS-G12V, p53-R175H, p16-WT, SMAD4-WT

value: liver metastasis


title: Casnaive-132


title: Casnaive-131


title: 1334/E47 WT2

source_name: PDX (patient-derived) cell line from a liver metastasis from a primary pancreas tumor  transduced with a retrovirus that expressed human E47


title: Casinjur-24


title: 1334/E47 WT1


title: 1334/E47 NT3


title: Casnaive-128


title: 1334/E47 NT2


title: Casinjur-3


title: Casnaive-130


title: Casnaive-123


title: PANC-1/E47 WT1

source_name: an established cell line from a primary pancreas tumor transduced with a retrovirus that expressed human E47

value: established pancreatic adenocarcinoma cell line

value: KRAS-G12D, p53-R273H/C, p16-HD, SMAD4-WT

value: tumor in the head of the pancreas of a 56 year-old male


title: Casnaive-124


title: Casnaive-125


title: Casnaive-127


title: Casnaive-126


title: Casnaive-122


title: PANC-1/E47 WT3


title: 1334/E47 NT1


title: Casnaive-121


title: PANC-1/E47 WT2


title: Casnaive-119


title: Casnaive-120


title: PANC-1/E47 NT1


title: Casnaive-118


title: PANC-1/E47 NT2


title: MIA PaCa-2/E47 WT2

description: MIA PaCa-2_5

value: KRAS-G12C, p53-R248W, p16-HD, SMAD4-WT

value: tumor in the body and tail of the pancreas of a 65 year-old male


title: Casnaive-129


title: Casnaive-117


title: MIA PaCa-2/E47 WT3

description: MIA PaCa-2_6


title: MIA PaCa-2/E47 WT1

description: MIA PaCa-2_4


title: MIA PaCa-2/E47 NT3

description: MIA PaCa-2_3


title: MIA PaCa-2/E47 NT2

description: MIA PaCa-2_2


title: MIA PaCa-2/E47 NT1

description: MIA PaCa-2_1


title: PANC-1/E47 NT3


title: Casnaive-116


title: Casnaive-114


title: BxPC-3/E47 WT3

value: KRAS-WT, p53-Y220C, p16-HD, SMAD4-HD (HD=homozygous deletion)

value: tumor in the body of the pancreas of a 61 year-old female


title: Casnaive-113

value: CAST/Ei


title: Casnaive-112


title: Casnaive-115


title: Casnaive-111


title: BxPC-3/E47 NT3


title: BxPC-3/E47 WT1


title: Casnaive-109


title: BxPC-3/E47 NT2


title: BxPC-3/E47 NT1


title: Casnaive-108


title: SW1573ZERO_3

city: Charlestown

first: Aaron

last: Hata

state: MA

address: 149 13th Street

department: Cancer Center

institute: Massachusetts General Hospital

data_processing:
RNA-Seq data processing was performed using Sanofi’s NGS data analysis framework called Synapse
RNA-Seq reads were initially mapped and aligned to GRCh38 using STAR aligner (v.2.4.0h1)
Mapped reads were assembled into possible transcripts by using Cufflinks (v2.2.1) with the reference gene annotation GENCODE v21
A read summarization tool, featureCounts was used to count the number of reads mapped to each of genes annotated in GENCODE v21
Genome_build: GRCh38
Supplementary_files_format_and_content: gene expression FPKM data file in tab delimited txt format

source_name: SW1573 NSCLC cell line

growth_protocol: cells were grown in RPMI or DMEM/F12 supplemented with 5% FBS at 37 degrees C and 5% CO2

extract_protocol:
Total cellular RNA using Qiagen RNEasy kit
Strand-specific RNA-seq library preparation using the Ovation Universal RNA-Seq System 1-96

treatment_protocol: Cells were treated with vehicle or the indicated concentrations of pimasertib, SAR405838 or combination for 24 hours

tag: cell line

value: Non-Small Cell Lung Cancer (NSCLC)

tag: drug

value: untreated

tag: concentration


title: SW1573ZERO_1

tag: cell type


title: Casnaive-104


title: SW1573VEH_2

value: DMSO vehicle


title: Casnaive-106


title: Casnaive-105


title: SW1573VEH_3


title: Casnaive-110


title: Casnaive-103


title: Casnaive-102


title: SW1573ZERO_2


title: SW1573VEH_1


title: Casnaive-101


title: BxPC-3/E47 WT2

value: (+) tamoxifen


title: SW1573SAR1000_3


title: SW1573SAR100_3


title: Casnaive-99

value: none (naive)


title: Casnaive-100

value: dorsal root ganglia


title: SW1573SAR1000_1


title: SW1573SAR1000_2


title: SW1573SAR100_2


title: SW1573SAR100_1


title: C57injur-51

value: injured


title: C57injur-52


title: Casnaive-98


title: SW1573SAR10_2

value: 10 nM


title: SW1573SAR10_1


title: Casnaive-107


title: SW1573SAR10_3


title: SW1573PIM1000_2

value: pimasertib


title: C57injur-50


title: C57injur-47


title: C57injur-46


title: SW1573PIM1000_3


title: SW1573PIM100_3


title: SW1573PIM100_2


title: C57injur-44


title: C57injur-45


title: C57injur-48


title: SW1573PIM10_3


title: C57injur-43


title: Casnaive-97


title: C57injur-42


title: SW1573PIM10_2


title: C57injur-41


title: C57injur-40


title: SW1573PIM_SAR1000_3

value: pimasertib + SAR405846


title: SW1573PIM_SAR1000_2

value: pimasertib + SAR405845


title: C57injur-39


title: C57injur-49


title: C57injur-38


title: C57injur-37


title: SW1573PIM100_1


title: SW1573PIM1000_1


title: C57injur-36


title: SW1573PIM10_1


title: SW1573PIM_SAR100_1

value: pimasertib + SAR405841


title: C57injur-35


title: SW1573PIM_SAR1000_1

value: pimasertib + SAR405844


title: SW1573PIM_SAR10_3

value: pimasertib + SAR405840


title: SW1573PIM_SAR100_2

value: pimasertib + SAR405842


title: SW1573PIM_SAR10_2

value: pimasertib + SAR405839


title: C57injur-32


title: SW1573PIM_SAR10_1

value: pimasertib + SAR405838


title: LU99AZERO_3

source_name: LU-99A NSCLC cell line

value: Non-Small Cell Lung Cancer (NSCLC)


title: C57injur-29


title: LU99AZERO_2

value: untreated


title: LU99AZERO_1


title: C57injur-28


title: C57injur-27


title: LU99AVEH_3

value: DMSO vehicle


title: C57injur-30


title: LU99AVEH_2


title: C57injur-26


title: SW1573PIM_SAR100_3

value: pimasertib + SAR405843


title: C57injur-24


title: LU99ASAR1000_2


title: C57injur-25


title: C57injur-34


title: LU99ASAR1000_1


title: C57injur-22


title: LU99AVEH_1


title: LU99ASAR100_3


title: C57injur-23


title: C57injur-20


title: LU99ASAR100_2


title: C57injur-19


title: C57injur-18


title: C57injur-31


title: C57injur-17


title: LU99ASAR10_2


title: C57injur-16


title: LU99ASAR100_1


title: LU99ASAR10_1


title: C57injur-15


title: C57injur-33


title: LU99ASAR1000_3


title: LU99APIM1000_3


title: LU99APIM1000_1


title: C57injur-13


title: C57injur-12


title: LU99APIM100_3


title: LU99APIM100_2


title: C57injur-21


title: C57injur-10


title: LU99APIM100_1


title: LU99APIM10_2


title: LU99ASAR10_3


title: C57injur-8


title: LU99APIM10_1


title: C57injur-9


title: LU99APIM10_3


title: C57injur-7


title: LU99APIM_SAR1000_3


title: C57injur-6


title: LU99APIM_SAR1000_2


title: LU99APIM_SAR1000_1


title: C57injur-5


title: LU99APIM1000_2


title: C57injur-14


title: LU99APIM_SAR100_3


title: LU99APIM_SAR100_1


title: C57injur-4


title: LU99APIM_SAR10_3


title: C57injur-1


title: C57injur-2


title: LU99APIM_SAR100_2


title: C57naive-116

value: none (naive)


title: LU99APIM_SAR10_1


title: C57naive-111

value: dorsal root ganglia


title: C57naive-112


title: C57naive-113


title: H358ZERO_3

source_name: NCI-H358 NSCLC cell line


title: C57naive-110


title: H358ZERO_2


title: LU99APIM_SAR10_2


title: C57naive-109


title: H358VEH_3


title: C57naive-107


title: H358ZERO_1


title: H358VEH_2


title: C57naive-106


title: C57naive-105


title: C57injur-3

value: injured


title: C57naive-103


title: C57naive-102


title: H358SAR1000_1


title: H358SAR100_3


title: H358SAR1000_2


title: H358SAR100_2


title: C57naive-101


title: C57naive-100


title: C57naive-99


title: C57naive-98


title: H358SAR100_1


title: C57naive-97


title: H358SAR10_1

value: 10 nM


title: H358SAR10_2


title: C57naive-93


title: C57naive-95


title: H358PIM1000_2

value: pimasertib


title: C57naive-96


title: H358PIM1000_1


title: C57naive-94


title: C57naive-92


title: H358PIM100_3


title: H358SAR1000_3


title: C57naive-104


title: C57naive-108


title: H358PIM100_2


title: H358PIM100_1


title: H358VEH_1


title: C57naive-91


title: H358PIM10_3


title: H358SAR10_3


title: C57naive-90


title: C57naive-89


title: H358PIM10_2


title: C57naive-87


title: H358PIM1000_3


title: C57naive-88


title: C57naive-86


title: H358PIM_SAR1000_1


title: C57naive-85


title: H358PIM_SAR100_2


title: H358PIM_SAR1000_2


title: C57naive-84


title: H358PIM_SAR100_3


title: H358PIM_SAR100_1


title: C57naive-82


title: H358PIM_SAR1000_3

value: pimasertib + SAR405846


title: C57naive-81


title: C57naive-80


title: H358PIM_SAR10_2


title: C57naive-77


title: H1944ZERO_3

source_name: NCI-H1944 NSCLC cell line


title: H358PIM_SAR10_1


title: H1944ZERO_2


title: C57naive-76


title: C57naive-79


title: H358PIM10_1


title: H1944ZERO_1


title: H1944VEH_3


title: C57naive-74


title: C57naive-73


title: H1944VEH_2


title: C57naive-72


title: H1944VEH_1


title: C57naive-71


title: C57naive-83


title: H1944SAR1000_3


title: H358PIM_SAR10_3


title: C57naive-70


title: H1944SAR1000_2


title: H1944SAR1000_1


title: C57naive-67


title: C57naive-68


title: H1944SAR100_2


title: C57naive-66


title: H1944SAR100_1


title: C57naive-69


title: C57naive-75


title: H1944SAR10_3


title: H1944SAR10_2


title: C57naive-64


title: C57naive-63


title: H1944SAR10_1


title: H1944PIM1000_3


title: C57naive-65


title: H1944PIM1000_2


title: C57naive-61


title: C57naive-60


title: C57naive-62


title: C57naive-59


title: H1944PIM100_3


title: H1944PIM1000_1


title: C57naive-57


title: H1944SAR100_3


title: H1944PIM100_1


title: C57naive-56


title: C57naive-58


title: H1944PIM100_2


title: H1944PIM10_2


title: C57naive-51


title: C57naive-52


title: C57naive-50


title: H1944PIM_SAR1000_3


title: H1944PIM_SAR1000_2

value: pimasertib + SAR405845


title: C57naive-54


title: C57naive-49


title: C57naive-48


title: C57naive-47


title: H1944PIM_SAR1000_1


title: H1944PIM_SAR100_3


title: C57naive-46


title: H1944PIM_SAR100_2


title: C57naive-45


title: H1944PIM_SAR100_1

value: pimasertib + SAR405841


title: H1944PIM_SAR10_3


title: H1944PIM_SAR10_2


title: C57naive-43


title: C57naive-42


title: H1944PIM_SAR10_1


title: DV90ZERO_3

source_name: DV-90 NSCLC cell line


title: C57naive-39


title: DV90ZERO_2


title: H1944PIM10_1


title: C57naive-36


title: DV90ZERO_1


title: C57naive-37


title: C57naive-44


title: DV90VEH_2


title: DV90VEH_1


title: C57naive-31


title: H1944PIM10_3


title: C57naive-30


title: DV90VEH_3


title: C57naive-28


title: C57naive-27


title: DV90SAR1000_2


title: DV90SAR1000_1


title: C57naive-24


title: DV90SAR100_3


title: RNA of Rapeseed Beebread

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

country: China

institute: Nanjing University

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to pre-miRNA sequence in miRBase_v21
Sequenced reads with no mismatches and no more than 2 shifts were identified as one miRNA and formed the final miRNA expression profiles.
Genome_build: miRBase_v21
Supplementary_files_format_and_content: tab-delimited text files include microRNA names, sequences and counts in each sample

organism: Apis mellifera

source_name: Rapeseed Beebread

extract_protocol:
Total RNA was extracted from 10g of Royal Jelly/Honey/Bee Bread/Pollen using the Trizol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: product/source

value: Beebread


title: DV90SAR100_1


title: RNA of Rapeseed Honey

source_name: Rapeseed Honey

value: Honey


title: C57naive-22

tag: tissue


title: RNA of Rapeseed Pollen

source_name: Rapeseed Pollen

value: Pollen


title: C57naive-23

tag: strain


title: DV90SAR10_3


title: C57naive-35

tag: treatment


title: C57naive-19


title: C57naive-21


title: DV90SAR100_2


title: RNA of Rapeseed Royal Jelly

source_name: Rapeseed Royal Jelly

value: Royal Jelly


title: DV90SAR10_2


title: C57naive-17


title: DV90SAR10_1


title: C57naive-14


title: DV90PIM1000_3


title: DV90PIM1000_2


title: C57naive-15


title: C57naive-13


title: DV90SAR1000_3


title: DV90PIM1000_1


title: C57naive-12


title: C57naive-11


title: DV90PIM100_2


title: DV90PIM100_3


title: DV90PIM100_1


title: C57naive-10


title: WAT_shLNC10_1

city: Singapore

first: Xiaoran

last: Chai

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Illumina Casava1.9 software used for basecalling for sample sh-control and sh-lncBATE10, Illumina Casava1.5 software used for basecalling for sample overexpression-control and overexpression-lncBATE10.
Sequenced reads were trimmed for adaptor sequence, additional trmming of last 5 base pair is performed to sample overexpression-control and overexpression-lncBATE10, then mapped to mm10 whole genome using tophat-2.0.9 with parameters --bowtie-n
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks-2.1.1 with parameters -b -u --max-bundle-frags 100000000
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Primary brown and white adipocytes and SVF cells were fractionated and cultured according to published methods with a few modifications34,35. Briefly, 2-week-old C57BL/6 mice were killed. Interscapular BATs were collected and digested with collagenase (0.2%). SVF cells were collected by centrifugation, red blood cells were lysed with NH4Cl and then the SVF was filtered through a 40 µm membrane. Primary white SVF cells and adipocytes from subcutaneous fat were isolated and fractionated according to published methods36. Primary SVF cells were cultured to confluence in DMEM with 10% new-born calf serum (Invitrogen) and induced to differentiate for 2 days with DMEM containing 10% fetal bovine serum (FBS, Invitrogen), 850nMinsulin (Sigma), 0.5 µMdexamethasone (Sigma), 250 µM 3-isobutyl-1-methylxanthine, phosphodiesterase inhibitor (IBMX, Sigma), 1 µM Rosiglitazone (Cayman Chemical), 1nM T3 (Sigma) and 125nM indomethacin (Sigma). The induction medium was replaced withDMEMcontaining 10%FBS and 160nM insulin for 2 days. Then cells were incubated inDMEMwith 10% FBS.

extract_protocol:
cells were differentiated for 5 days; RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: Empty vector or expression plasmid (8 µg) was co-transfected with retrovirus packaging vector pCL-Eco (4 µg) into 80% confluent 293T cells (100mmplate) usingFuGene6 according to the manufacturer’s protocol (Roche). Virus supernatant was collected 2 days after transfection. Primary white and brown fat SVF cells and C2C12 myoblasts were cultured to 30–50% confluence and infected with retrovirus in the presence of 4 µg ml−1 polybrene (Sigma). The infection efficiency was generally higher than 80%, as judged by GFP expression when viewed under the microscope or by FACS analysis

value: post natal day 21

value: white fat

value: primary white adipocytes cultures

tag: post-treatment

value: cells were differentiated for 5 days


title: DV90PIM10_3

value: Non-Small Cell Lung Cancer (NSCLC)


title: C57naive-8

value: none (naive)


title: C57naive-9

value: dorsal root ganglia


title: WAT_shCNT_1

tag: age

value: shCNT


title: KD rep2

city: Bunkyo-ku

first: Yutaro

last: Hori

state: Tokyo

department: Department of Scinece

country: Japan

institute: The University of Tokyo

data_processing:
Sequeced reads were mapped to mm10 genome with Tophat with Bowtie2 as the aligner.
The abundance of each transcript model and statistical results were computed using Cuffdiff based on UCSC genome annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file including fpkm values reported by Cuffdiff

source_name: Heart ventricle

extract_protocol:
Total RNA was extracted with Seasol-RNA I Super G (Nacalai).
Libraries were prepared from 10ng of total RNA exactly according to Smart-Seq2 protocol (Picelli et al 2013) with 12cycles of preamiplification PCR and 9 cycles of enrichment PCR after tagmentation with Nextera XT kit.

tag: developmental stage

value: Tbx5ua -/-

value: heart ventricle


title: KD rep3


title: WT rep3

value: wild type


title: C57naive-6


title: DV90PIM_SAR1000_2

value: pimasertib + SAR405845


title: DV90PIM10_1

value: pimasertib

value: 10 nM


title: KD rep1


title: C57naive-5


title: C57naive-4


title: C57naive-2


title: Adult

data_processing:
Sequeced reads were mapped to mm10 genome with Tophat with Bowtie as the aligner.
The mapped reads were assembled using Cufflinks. The obtained transcript annotation files were merged using Cuffmerge with UCSC transcript annotation as the reference.
The abundance of each transcript model was computed using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file including fpkm values for each sample and transcript anntotation file generated by cuffmerge.

extract_protocol:
Total RNA was extracted with Seasol-RNA I Super G (Nacalai).
Libraries were prepared from 1ug of total RNA exactly according to Illumina's instructions accompanying the TruSeq Stranded Total RNA kit (RS-122-2201).

value: 8 week

value: Heart ventricle


title: DV90PIM_SAR1000_1

value: pimasertib + SAR405844


title: DV90PIM_SAR100_3

value: pimasertib + SAR405843


title: C57naive-1


title: Normoxia Blimp1 KD ATAC-seq rep2

city: Stanford

first: Shin-Heng

last: Chiou

address: 450 Serra Mall

department: Genetics

institute: Stanford University

description:
shBl_nor2
S8-CAGAGAGG
technical replicate of sample "S7-CTCTCTAC"

data_processing:
Reads were trimmed using cutadapt and aligned to the mouse genome (mm9) using Bowtie2. Subsequently, peaks were called using MACS2 after being filtered using a custom blacklist, as previously described in Buenrostro et al. 2013. Nat Methods 12:1213-8.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include peaks and insert count for each Sample

source_name: Normoxia Blimp1 KD

extract_protocol:
ATACSeq libraries were prepared for sequencing using standard protocols described in Buenrostro et al. 2013. Nat Methods 12:1213-8.
ATACSeq libraries were prepared for sequencing using standard protocols described in Buenrostro et al. 2013. Nat Methods 12:1213-8.

tag: strain background

value: B6/129 mixed

tag: genotype/variation

tag: mouse id

value: PDAC liver metastasis cell line

tag: cell line genotype

value: Blimp1 KD

tag: cultured under


title: DV90PIM_SAR100_2

value: Non-Small Cell Lung Cancer (NSCLC)

value: pimasertib + SAR405842


title: E13.5


title: Normoxia Blimp1 KD ATAC-seq rep1

description:
shBl_nor1
S7-CTCTCTAC
technical replicate of sample "S8-CAGAGAGG"


title: DV90PIM_SAR100_1

value: pimasertib + SAR405841


title: E10.5


title: DV90PIM_SAR1000_3

value: pimasertib + SAR405846


title: DV90PIM_SAR10_3

value: pimasertib + SAR405840


title: DV90PIM10_2


title: purified Tomato-positive PDAC cancer cells from mouse 2854 LN metastasis

description:
2854-LNM-T+lin-
processed data column: 2854-LNM

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 mouse genome using STAR aligner (2.4.2a) with the following parameters: --runThreadN 2 --outFileNamePrefix 011116_shBlimp1_nor_1_ --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Read counts were calculated using HTSeq script htseq-count with the following specifications: --order=pos --stranded=no --type=exon --idattr=gene_name --mode=intersection-nonempty. Subsequently, transcripts per million (TPM) were derived by using htseq-count-derived read counts normalized against the length of coding regions of each gene and subsequently convert the sum of this product of all genes to one million for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count for each Sample ...

source_name: LN met (PDAC)

extract_protocol:
RNA samples were extracted with Qiagen micro DNA/RNA extraction kit according to manufacturer's recommended procedure.  RNA quality was measured with bioanalyzer and all samples submitted for RNASeq had an RIN score at least > 8
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LN met (PDAC)

value: freshly sorted pancreatic cancer cells

tag: cell subtype/sorted-fraction

tag: gfp-negative and gfp-positive paired sample

value: no


title: DV90PIM_SAR10_2

tag: cell line

tag: drug

value: pimasertib + SAR405839


title: Normoxia control KD ATAC-seq rep1

description:
shGFP_nor1
S5-AGGCAGAA
technical replicate of sample "S6-TCCTGAGC"

source_name: Normoxia control KD

tag: cell type

value: control


title: purified Tomato-positive PDAC cancer cells from mouse 2854 primary tumor

description:
2854-T-T+lin-
processed data column: 2854-T

source_name: primary PDAC

value: primary PDAC


title: purified Tomato-positive PDAC cancer cells from mouse 2854 Lung metastasis

description:
2854-LM-T+lin-
processed data column: 2854-LM

source_name: Lung met (PDAC)

value: Lung met (PDAC)


title: Hypoxia Blimp1 KD ATAC-seq rep2

description:
shBl_hyp2
S4-ACCACTGT
technical replicate of sample "S3-GTCGTGAT"

source_name: Hypoxia Blimp1 KD


title: A427ZERO_3

source_name: A427 NSCLC cell line

value: untreated

tag: concentration


title: DV90PIM_SAR10_1

value: pimasertib + SAR405838

value: 10 nM


title: WT rep2

tag: genotype

value: wild type

tag: tissue

value: heart ventricle


title: A427ZERO_2

value: Non-Small Cell Lung Cancer (NSCLC)


title: purified Tomato-positive PDAC cancer cells from mouse 2752 thoracic metastasis

description:
2752-TM-T+lin-
processed data column: 2752-TM

source_name: Thoracic met (PDAC)

value: B6/129 mixed

value: Thoracic met (PDAC)


title: purified Tomato-positive PDAC cancer cells from mouse 2752 primary tumor

description:
2752-T-T+lin-
processed data column: 2752-T


title: Hypoxia Blimp1 KD ATAC-seq rep1

description:
shBl_hyp1
S3-GTCGTGAT
technical replicate of sample "S4-ACCACTGT"

value: PDAC liver metastasis cell line

value: Blimp1 KD


title: WT rep1

tag: strain


title: Hypoxia control KD ATAC-seq rep1

description:
shGFP_hyp1
S1-GCTACGCT
technical replicate of sample "S2-CGAGGCTG"

source_name: Hypoxia control KD


title: purified Tomato-positive PDAC cancer cells from mouse 2752 Liver metastasis

description:
2752-LM-T+lin-
processed data column: 2752-LM

source_name: Liver met (PDAC)

value: Liver met (PDAC)


title: A427VEH_3

value: DMSO vehicle


title: purified Tomato-positive PDAC cancer cells from mouse 2691 primary tumor

description:
2691-T1-T+lin-
processed data column: 2691-T1

value: freshly sorted pancreatic cancer cells

value: no


title: A427ZERO_1


title: A427VEH_2


title: IL-17C+KO involved 2465

city: Ann Arbor

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

institute: University of Michigan

description: RNA extracted from full-thickness biopsy or lesional or uninvolved mouse skin

data_processing:
Illumina adaptor sequences were removed using CutAdapt (version 1.6) with a maximum error rate setting (-e) of 5% and a minimum post-processing read length (-m) of 20 base pairs
Reads were trimmed to remove bases with low PHRED quality scores (CutAdapt and Fast-X toolkit)
Filtered reads were mapped to the UCSC mouse genome (mm10) using Tophat2 (version 2.0.12)
Overlap between mapped reads and known human genes was tabulated using the htseq-count function from the HTSeq python library (version 0.5.4p3)
Cufflinks (version 2.2.1) was used to calculate fragments per kilobase of exon per million fragments mapped (FPKM) for each gene feature.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data includes raw read counts and FPKM values for all human genes (UCSC, mm10) and each sample (.txt files).

source_name: skin

growth_protocol: IL-17C+ and IL-17+KO mice were bred and housed in full barrier facility with vented racks and provided with food and water ad libitum. Mice were euthanized at 10 or 14 weeks of age and involved and uninvolved areas of dorsal skin were collected for use in the analyses.

extract_protocol:
RNA was isolated from skin adjacent to that used for histology and immunostaining as previously described (Wolfram et al. 2009, Am J Pathol 174:1443-1458).
Sequencing of fragmented complementary cDNA was performed using the Illumina Genome Analyzer Iix

treatment_protocol: Mice were euthanized with an overdose of ketamine/xylazine followed by cervical dislocation. Two biopsies were then taken from each mouse; one biopsy was obtained from lesional skin and the other from uninvolved skin.

tag: skin type

value: involved

tag: individual


title: purified GFP/Hmga2-positive Tomato-positive PDAC cancer cells from mouse 2691

description:
2691-T-G+T+
processed data column: 2691-SM

value: primary PDAC

value: yes


title: Normoxia control KD ATAC-seq rep2

description:
shGFP_nor2
S6-TCCTGAGC
technical replicate of sample "S5-AGGCAGAA"

value: control


title: A427SAR1000_2


title: IL-17C+KO uninvolved 2392

value: uninvolved


title: A427SAR1000_3


title: IL-17C+KO uninvolved 2465


title: IL-17C+ involved 2296


title: purified Tomato-positive PDAC cancer cells from mouse 2691 Liver metastasis

description:
2691-LM-T+lin-
processed data column: 2691-G-T+


title: A427VEH_1


title: Hypoxia control KD ATAC-seq rep2

description:
shGFP_hyp2
S2-CGAGGCTG
technical replicate of sample "S1-GCTACGCT"


title: purified Tomato-positive PDAC cancer cells from mouse 2691 splenic metastasis

description:
2691-SM-T+lin-
processed data column: 2691-LM

source_name: Splenic met (PDAC)

value: Splenic met (PDAC)


title: IL-17C+ involved 2275


title: A427SAR100_3


title: purified EpCAM-negative GFP/Hmga2-positive Tomato-positive PDAC cancer cells from mouse 2689

description:
2689-T-T+G+E-
processed data column: 2689-G+T+


title: A427SAR1000_1


title: IL-17C+ uninvolved 2237


title: purified GFP/Hmga2-negative Tomato-positive PDAC cancer cells from mouse 2691

description:
2691-T-G-T+
processed data column: 2691-LNM


title: A427SAR100_2


title: purified Tomato-positive PDAC cancer cells from mouse 2691 LN metastasis

description:
2691-LNM-T+lin-
processed data column: 2691-G+T+

value: LN met (PDAC)


title: IL-17C+ involved 2237


title: IL-17C+ uninvolved 2296


title: purified EpCAM-negative GFP/Hmga2-negative Tomato-positive PDAC cancer cells from mouse 2689

description:
2689-T-T+G-E-
processed data column: 2689-G-T+


title: IL-17C+ uninvolved 2275


title: A427SAR10_3

value: 10 nM


title: A427SAR10_2

value: Non-Small Cell Lung Cancer (NSCLC)


title: purified Tomato-positive PDAC cancer cells from mouse 2542 primary tumor

description:
2542-T2-T+lin-
processed data column: 2542-T2

value: B6/129 mixed


title: purified GFP/Hmga2-positive Tomato-positive PDAC cancer cells from mouse 2542

description:
2542-T1-G+T+
processed data column: 2542-LNM


title: purified GFP/Hmga2-negative Tomato-positive PDAC cancer cells from mouse 2542

description:
2542-T1-G-T+
processed data column: 2542-LM


title: IL-17C+KO involved 2392


title: HEV71D23A_replicate

city: Wuhan

first: xi

last: zhou

state: Hubei

address: Luojia Hill

department: State Key Laboratory of Virology, College of Life Sciences

institute: Wuhan University

description: small RNA

data_processing:
The sequencing reads were mapped to the human genome (release hg19) byusing Bowite 2.2.5 and the cellular miRNA expression level was determined on the
basis of the number of reads that was identical to the annotated miRNA sequences in miRBase version 18, only allowing −2 or +2 nt to be templated by
the corresponding genomic sequence at the 3′ end. Viral small RNA (vsRNA) reads which cannot bemapped to human genome were then mapped to HEV71 genome
with 100% identity.The subsequent analysis of length and location of these vsRNAs were calculated using in-house Perl scripts. Pairs of complementary
22-nt vsRNAs in each library in different distance categories were computed using principles as previously described(Li et al., 2016; Li et al., 2013).
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: HEK 293T cells

extract_protocol: TruSeq Small RNA Library Preparation Kits (Illumina)

value: WT

tag: treatment

value: D23A HEV71 virus


title: A427SAR10_1


title: A427SAR100_1


title: HEV71D23A

description: small RNA


title: A427PIM1000_3

value: pimasertib


title: A427PIM1000_1


title: A427PIM1000_2


title: A427PIM100_3


title: purified GFP/Hmga2-positive Tomato-positive PDAC cancer cells from mouse 2518

description:
2518-T-G+T+
processed data column: 2518-G+T+

tag: strain background


title: A427PIM100_2


title: purified Tomato-positive PDAC cancer cells from mouse 2518 primary tumor

description:
2518-T-T+lin-
processed data column: 2518-T

tag: genotype/variation


title: purified Tomato-positive PDAC cancer cells from mouse 2492 primary tumor

description:
2492-T1-T+lin-
processed data column: 2492-T1

tag: mouse id


title: purified Tomato-positive PDAC cancer cells from mouse 2542 Liver metastasis

description:
2542-LM-T+lin-
processed data column: 2542-G-T+

value: Liver met (PDAC)


title: purified Tomato-positive PDAC cancer cells from mouse 2492 LN metastasis

description:
2492-LNM-T+lin-
processed data column: 2492-LNM


title: A427PIM100_1


title: HEV71D23A in NoDice cells

description: small RNA

value: NoDice


title: purified GFP/Hmga2-negative Tomato-positive PDAC cancer cells from mouse 2518

description:
2518-T-G-T+
processed data column: 2518-G-T+

value: freshly sorted pancreatic cancer cells


title: A427PIM10_3


title: A427PIM10_2


title: Shef6EOS#2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: PBAT

data_processing:
Raw sequence reads from PBAT libraries were trimmed to remove poor quality reads and adapter contamination using Trim Galore (v0.4.1), trimming off the first 6 bp of each read (options --clip_r1 6 --clip_r2 6). The remaining sequences were mapped using Bismark (v0.14.4) (Krueger and Andrews, 2011) with the following set of parameters to the human reference genome GRCh37 in paired-end mode: --pbat to be able to count overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode for Read 1: --pbat; or single-end mode for Read 2: defaults. Reads were then deduplicated and CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor (v0.14.4) with default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

extract_protocol: Post-bisulfite adaptor tagging (PBAT) libraries for whole-genome DNA methylation analysis were prepared directly from cell lysates following recently described protocols (Miura et al., 2012; Smallwood et al., 2014). PBAT libraries were prepared by bisulfite converting Proteinase K digested cell lysates using the EZ DNA Methylation-Direct Kit (Zymo). After cleanup, 1st strand synthesis was performed using Klenow Exo- DNA Polymerase (NEB) and 6N-forward oligos at 37°C for 90 minutes. Subsequently, samples were treated with Exonuclease I (NEB) for 1 hour at 37°C, and DNA was purified using AMPure XP beads (Beckman Coulter). Samples were eluted in 2nd strand synthesis mix with Klenow Exo- and 6N-reverse oligos and incubated at 37°C for 90 minutes. DNA was purified and amplified with KAPA HiFi HotStart DNA Polymerase (Roche). All amplified libraries were purified and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer. High-throughput sequencing was carried out with a 125 bp paired-end protocol on a HiSeq 2000 instrument (Illumina).

value: ESC

value: conventional


title: Shef6EOS#3

description: PBAT


title: cR-S6VPCY_P33#2

description: PBAT

value: reset


title: Shef6EOS#1

description: PBAT


title: purified Tomato-positive PDAC cancer cells from mouse 2542 LN metastasis

description:
2542-LNM-T+lin-
processed data column: 2542-G+T+

value: no


title: purified GFP/Hmga2-negative Tomato-positive PDAC cancer cells from mouse 2317

description:
2317-T1-G-T+
processed data column: 2317-G-T+

value: primary PDAC

value: yes


title: cR-S6VPCY_P33#1

description: PBAT


title: cR-S6-2_P9#2

description: PBAT


title: A427PIM10_1


title: HEV71WT

description: small RNA

value: WT HEV71 virus


title: purified Tomato-positive PDAC cancer cells from mouse 2255 LN metastasis

description:
2255-LNM-T+lin-
processed data column: 2255-LNM

value: LN met (PDAC)


title: A427PIM_SAR1000_3

value: pimasertib + SAR405846


title: cR-S6-2_P9#1

description: PBAT


title: cR-S6EOS-2_P5#3

description: PBAT


title: A427PIM_SAR1000_2

value: Non-Small Cell Lung Cancer (NSCLC)

value: pimasertib + SAR405845


title: purified Tomato-positive PDAC cancer cells from mouse 2254 primary tumor

description:
2254-T1-T+lin-
processed data column: 2254-T1

value: B6/129 mixed


title: cR-S6EOS-2_P5#2

description: PBAT


title: A427PIM_SAR1000_1

value: pimasertib + SAR405844


title: purified GFP/Hmga2-positive Tomato-positive PDAC cancer cells from mouse 0784

description:
0784-T2-G+T+
processed data column: 0784-P


title: purified Tomato-positive PDAC cancer cells from mouse 2254 Liver metastasis

description:
2254-LM-T+lin-
processed data column: 2254-LM


title: purified GFP/Hmga2-positive Tomato-positive PDAC cancer cells from mouse 2317

description:
2317-T1-G+T+
processed data column: 2317-G+T+


title: cR-S6-2_P9#3

description: PBAT


title: purified GFP/Hmga2-negative Tomato-positive PDAC cancer cells from mouse 0784

description:
0784-T2-G-T+
processed data column: 0784-G+T+


title: Overexpression GFP-KSRP small RNA

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg19 whole genome or miRBase database.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for mature microRNA and pri-RNA in each Sample

source_name: THP-1 cells

growth_protocol: THP-1 cells were cultured in RPMI1640 supplemented with 10% FBS.

extract_protocol:
RNA were harvested using Trizol reagent,Illumina TruSeq RNA Sample Prep kit were used with 1μg of total RNA for the construction of sequencing libraries
RNA libraries and miRNA libaries were prepared for sequencing using standard Illumina protocols
ployA riched RNA-Seq and small RNA-Seq

treatment_protocol: THP-1 cells were transient transfected pEGFP and pEGFP-KSRP plasmids, after 48hours, FACS sorting GFP positive cells to do ployA riched RNA seq and small RNA seq.

tag: sample type

value: small RNA seq


title: Control Sample-GFP small RNA


title: cR-S6EOS-2_P5#1

description: PBAT


title: A427PIM_SAR100_2

value: pimasertib + SAR405842


title: A427PIM_SAR100_1

value: pimasertib + SAR405841


title: purified Tomato-positive disseminated PDAC cancer cells from mouse 0784 peritoneal cavity

description:
0784-P-T+lin-
processed data column: 0784-G-T+

source_name: DTC

value: DTC

value: freshly sorted pancreatic cancer cells


title: purified Tomato-positive PDAC cancer cells from mouse 0758 primary tumor - technical replicate2

description:
0758-T1-T+lin-_46_2
read count merged with file "0758-T1-T+lin-_46_1"
processed data column: 0758-T1


title: Control Sample-GFP polyA RNA

value: ploy-A (riched) RNA


title: purified Tomato-positive PDAC cancer cells from mouse 2255 primary tumor

description:
2255-T-T+lin-
processed data column: 2255-T


title: A427PIM_SAR10_3

value: pimasertib + SAR405840

value: 10 nM


title: Overexpression GFP-KSRP polyA RNA


title: purified Tomato-positive PDAC cancer cells from mouse 0758 primary tumor - technical replicate1

description:
0758-T1-T+lin-_46_1
read count merged with file "0758-T1-T+lin-_46_2"
processed data column: 0758-T1

value: primary PDAC

value: no


title: A427PIM_SAR10_2

value: pimasertib + SAR405839


title: A427PIM_SAR10_1

value: pimasertib + SAR405838


title: purified Tomato-positive PDAC cancer cells from mouse 0758 LN metastasis - technical replicate2

description:
0758-LNM-T+lin-_48_2
read count merged with file "0758-LNM-T+lin-_48_1"
processed data column: 0758-LNM

value: LN met (PDAC)


title: purified Tomato-positive PDAC cancer cells from mouse 0758 LN metastasis - technical replicate1

description:
0758-LNM-T+lin-_48_1
read count merged with file "0758-LNM-T+lin-_48_2"
processed data column: 0758-LNM


title: A427PIM_SAR100_3

value: Non-Small Cell Lung Cancer (NSCLC)

value: pimasertib + SAR405843


title: Hypoxia Blimp1 KD rep1

source_name: PDAC

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

tag: condition

value: Hypoxia

value: Blimp1 knockdown


title: Hypoxia Blimp1 KD rep2


title: Alzheimer's Brain Sample68

city: New York

first: Shahar

last: Barbash

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Reference genome alignment: sequence reads in fastq format were aligned to the reference genome GRCh38 from Ensembl, repeat-masked version, complete genome, using the bowtie2 aligner version 2.2.3 and the –end-to-end and –sensitive options, to insure global alignments of the query sequences.
Alignment conversion: sequence alignment conversion from textual .sam to binary .bam files was performed with samtools version 0.1.19
Sequence trimming and primer removal was performed with the bbduk.sh utility from the BBMap project (http://sourceforge.net/projects/bbmap/). Reference file were a long polyA tail and the sequences of the Illumina truseq primer. Options: ktrim=r (trim right end), useshortkmers=t (look for shorter kmers at read tips), mink=5 (minimum length of short kmers), trimq = 10 (regions with average quality below this value will be trimmed), qtrim=t (trim reads to remove bases below both ends).
Genome_build: GRCh38

source_name: NCI - HIGH

extract_protocol:
RNA was extracted with the SPLIT RNA extraction kit (Lexogen GmbH, Vienna, Austria) yielding the large RNA fraction with a lower cut-off size of 150 nt. Evaluation on a Bioanalyzer RNA Nano chip (Agilent Technologies) showed medium to high RNA quality (RIN of 6.2 – 8.3). 4 µg RNA was incubated with Terminator 5´-phosphate-dependent exonuclease (Epicentre, Madison, WI, USA) to remove degraded RNA while leaving the capped, full-length mRNA intact
Per sample, 20 ng of the purified full-length total RNA were used for performing the 3’ QuantSeq Reverse protocol (Lexogen GmbH, Vienna, Austria) resulting in NGS libraries which originate from the 3’ end of polyadenylated RNA. Library generation was started by oligo(dT) priming with primers already containing the Illumina-compatible linker sequence for Read 1. After first strand synthesis the RNA was removed before the second strand synthesis was initiated by random primers which contained the corresponding Illumina-compatible linker sequence. 3’ QuantSeq generated just one fragment per transcript at the very 3’ end. The libraries were PCR amplified and barcoded in 18 cycles. Equal amounts of the 72 libraries were combined to one lane mixture.

tag: diagnosis

value: Alzheimer's disease

value: brain


title: Alzheimer's Brain Sample70


title: Alzheimer's Brain Sample66

source_name: DEM - MED


title: Alzheimer's Brain Sample67

source_name: MCI - HIGH


title: Alzheimer's Brain Sample71


title: Alzheimer's Brain Sample69

source_name: MCI - MED


title: Alzheimer's Brain Sample65

source_name: NCI - MED


title: Alzheimer's Brain Sample63


title: Alzheimer's Brain Sample72

source_name: MCI - LOW


title: Normoxia control KD rep2

value: Normoxia

value: wildtype


title: Normoxia control KD rep1


title: Normoxia Blimp1 KD rep2


title: Hypoxia control KD rep1


title: Alzheimer's Brain Sample62


title: Alzheimer's Brain Sample64

source_name: NCI - LOW


title: Hypoxia control KD rep2


title: Alzheimer's Brain Sample60


title: Alzheimer's Brain Sample61


title: BAT_Cold_2

data_processing:
Illumina Casava1.9 software used for basecalling for sample S5BAT_WT_1/2/3 and S5BAT_WT_COLD_1/2/3, Illumina Casava1.5 software used for basecalling for sample S2CNT_1/2, S2BETA_1/2, S2COLD_1/2, S2SWIM_1/2, S3CNT_1/2 and S330oC_1/2.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using tophat-2.0.9 with parameters --bowtie-n
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks-2.1.1 with parameters -b -u --max-bundle-frags 100000000
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: brown fat

growth_protocol: Adipose tissue depots were digested in 0.2% collagenase at 37°C for 25–30 min. Digested tissues were filtered through a 100-mm membrane, and SVF cells were collected by centrifugation at 1,500 rpm for 5 min. After centrifugation, the mature adipocytes floating on top were collected for genotyping analysis. The freshly iso- lated SVF cells were seeded and cultured in DMEM con- taining 10% newborn calf serum and 0.5% penicillin/ streptomycin at 37°C with 5% CO2. On confluence, the cells were induced to differentiate for 2 days with DMEM containing 10% FBS, 850 nmol/L insulin, 0.5 mmol/L dexamethasone (Sigma-Aldrich), 250 mmol/L of 3-isobutyl- methylxanthine (Sigma-Aldrich) and 1 mmol/L rosiglita- zone (Sigma-Aldrich) in DMEM. The induction medium was replaced with DMEM containing 10% FBS and 160 nmol/L insulin for 2 days. Then cells were incubated in DMEM with 10% FBS

extract_protocol:
Total RNA from primary cells or mouse tissues were extracted with miRNeasy Mini Kit (Qiagen).
NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: Mice swimming protocol  started at 10 min two times daily, with 10 min increase each day until 90 min, two times per day was reached. Then, the training will last for 2 weeks; For CL316243 treatment, mice were IP injected with 1mg/Kg/Day for 7 days.

tag: developmental stage

value: 8 weeks old

value: brown fat

value: 4oC 7 days


title: BAT_Cold_3


title: Normoxia Blimp1 KD rep1

tag: cell line


title: BAT_control for Cold_3

value: room termperature


title: BAT_control for Cold_2


title: Alzheimer's Brain Sample58

source_name: DEM - HIGH


title: BAT_control for Cold_1


title: Alzheimer's Brain Sample57


title: Alzheimer's Brain Sample56


title: Alzheimer's Brain Sample55


title: Alzheimer's Brain Sample54


title: BAT_Cold_1


title: BAT_control_1


title: iWAT_swimming_1

source_name: inguinal WAT fat

value: 16 weeks old

value: inguinal WAT fat


title: BAT_30oC7days_1

value: 30oC for 7 days


title: BAT_control_2


title: iWAT_4oC7day_1


title: iWAT_swimming_2


title: Alzheimer's Brain Sample59


title: Alzheimer's Brain Sample52

source_name: DEM - LOW


title: iWAT_Control_1


title: Alzheimer's Brain Sample51


title: Alzheimer's Brain Sample50


title: iWAT_Control_2


title: Alzheimer's Brain Sample48


title: iWAT_4oC7day_2


title: Alzheimer's Brain Sample46


title: Alzheimer's Brain Sample47


title: Input_Myc_sgMll3/Cas9_2

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences using Trim Galore. Reads were aligned to mouse genome assembly mm9 using bowtie2 (v2.1) with default parameters. Duplicate reads were collapsed using Picard. To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
The bigwig files have been normalized to 10 million mapped reads.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: bigWig

source_name: Liver tumor cell line, sgMll3/Cas9, input

growth_protocol: Derived primary proliferating cells were cultured in complete DMEM (10% FBS, 1x Penicillin/Streptomycin), maintained on collagen-coated plates (PurCol, Advanced Biomatrix), and passaged until visibly free from fibroblasts.

extract_protocol:
0.5 million liver tumor cells were crosslinked for 10 minutes using 1% formaldehyde, followed by quenching with 0.125M glycine for 10 minutes. To prepare chromatin from crosslinked cells, aliquots of cells were kept in individual eppendorf tubes for sonication to maximize the chromatin fragmentation efficiency.
After purifying immunoprecipitated DNA, a TruSeq ChIP Sample Prep Kit (Illumina) was used to construct the ChIP-Seq library following the manufacturer's protocol except for amplifying the adaptor-ligated library for 15 cycles.
ChIP-Seq libraries were sequenced using an Illumina HiSeq 2000 platform with single-end reads of 50 bases. Four libraries at equal molarity were pooled to aim for a sequencing depth of 20-40 million aligned reads per sample.

tag: strain/background

value: Liver tumor cell line

tag: chip antibody


title: Alzheimer's Brain Sample49


title: BAT_30oC7days_2


title: Alzheimer's Brain Sample45


title: Alzheimer's Brain Sample44


title: Alzheimer's Brain Sample43


title: Alzheimer's Brain Sample53


title: Input_Myc_sgp53/Cas9_2

source_name: Liver tumor cell line, sgp53/Cas9, input

tag: cell type


title: Alzheimer's Brain Sample42


title: Input_Myc_sgp53/Cas9_1


title: iWAT_Cl316243_1

value: CL316243 treatment, 1mg/Kg/24hrs


title: iWAT_Cl316243_2


title: Alzheimer's Brain Sample41


title: H3K27Ac_Myc_sgMll3/Cas9_3

source_name: Liver tumor cell line, sgMll3/Cas9, H3K27Ac ChIP


title: Alzheimer's Brain Sample40


title: H3K27Ac_Myc_sgMll3/Cas9_1


title: Alzheimer's Brain Sample38


title: H3K27Ac_Myc_sgMll3/Cas9_2


title: H3K27Ac_Myc_sgp53/Cas9_1

source_name: Liver tumor cell line, sgp53/Cas9, H3K27Ac ChIP


title: Alzheimer's Brain Sample39


title: H3K27Ac_Myc_sgp53/Cas9_3


title: Alzheimer's Brain Sample36


title: Alzheimer's Brain Sample34


title: Alzheimer's Brain Sample35


title: H3K27Ac_Myc_sgp53/Cas9_2


title: H3K4me1_Myc_sgMll3/Cas9_3

source_name: Liver tumor cell line, sgMll3/Cas9, H3K4me1 ChIP


title: Alzheimer's Brain Sample37


title: Input_Myc_sgMll3/Cas9_1


title: H3K4me1_Myc_sgMll3/Cas9_1


title: Alzheimer's Brain Sample32


title: H3K4me1_Myc_sgp53/Cas9_3

source_name: Liver tumor cell line, sgp53/Cas9, H3K4me1 ChIP


title: Alzheimer's Brain Sample33


title: H3K4me1_Myc_sgp53/Cas9_2


title: Alzheimer's Brain Sample30


title: H3K4me1_Myc_sgp53/Cas9_1


title: Alzheimer's Brain Sample29


title: H3K4me3_Myc_sgMll3/Cas9_2

source_name: Liver tumor cell line, sgMll3/Cas9, H3K4me3 ChIP


title: Alzheimer's Brain Sample28


title: Alzheimer's Brain Sample27


title: Alzheimer's Brain Sample25


title: H3K4me1_Myc_sgMll3/Cas9_2


title: H3K4me3_Myc_sgMll3/Cas9_1


title: H3K4me3_Myc_sgp53/Cas9_2

source_name: Liver tumor cell line, sgp53/Cas9, H3K4me3 ChIP


title: Alzheimer's Brain Sample24


title: H3K4me3_Myc_sgp53/Cas9_3


title: Alzheimer's Brain Sample26


title: Alzheimer's Brain Sample21


title: Alzheimer's Brain Sample22

source_name: DEM - MED


title: Alzheimer's Brain Sample31


title: Alzheimer's Brain Sample19


title: Alzheimer's Brain Sample20


title: overexpression-control

tag: age

value: post natal day 21

value: primary brown adipocytes cultures

value: overexpression-control

tag: post-treatment

value: cells were differentiated for 5 days


title: overexpression-lncBATE10

tag: strain

tag: tissue


title: H3K4me3_Myc_sgp53/Cas9_1


title: Alzheimer's Brain Sample18

value: Alzheimer's disease


title: Alzheimer's Brain Sample16

source_name: MCI - HIGH

value: brain


title: Alzheimer's Brain Sample17


title: H3K4me3_chIP-seq

city: Nijmegen

first: Andreas

last: Kompatscher

state: Gelderland

address: Geert Grooteplein Zuid 30

department: Physiology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description: Sample 2

data_processing:
Base calling was performed with CASAVA version 1.4
burrows-wheeler transformation, 0.710 -r789 , default
Peak calling was executed with Macs2, q-value (False discovery rate, FDR) 0.001
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were generated using a custom bam to bigwig script

growth_protocol: mpkDCT cells were cultured on 14 cm petri-dishes. Convulent plates (15 x10^6 cells) were used for chromatin isolation. Cells were cultured in DMEM/HAMF12 medium supplemented with 2% FCS, glutamine, insulin, dexamethasone, selenium, transferrin, Triiodothyronine, HEPES pH 7.5, D-Glucose, EGF.

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

value: immortalized mouse DCT cells

tag: passages

value: rabbit H3K4me3 (Abcam, AB8580)


title: Alzheimer's Brain Sample23


title: Alzheimer's Brain Sample15

source_name: NCI - HIGH


title: H3K4me3_Myc_sgMll3/Cas9_3


title: Input_chIP-seq

description: Sample 3


title: Alzheimer's Brain Sample14


title: sh-lncBATE10

tag: treatment


title: Alzheimer's Brain Sample11


title: Alzheimer's Brain Sample13


title: Alzheimer's Brain Sample12


title: Alzheimer's Brain Sample9


title: Alzheimer's Brain Sample10

source_name: NCI - MED


title: Alzheimer's Brain Sample6


title: Alzheimer's Brain Sample5


title: sh-control

value: sh-control


title: Alzheimer's Brain Sample3


title: Alzheimer's Brain Sample8


title: Alzheimer's Brain Sample7

source_name: MCI - MED


title: Alzheimer's Brain Sample4


title: Alzheimer's Brain Sample1

source_name: MCI - LOW


title: Alzheimer's Brain Sample2


title: KO11

city: Paris

first: Laina

last: Freyer

address: 25-28 rue du Dr Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur

data_processing:
Alignment of raw reads to mm10 using STAR aligner
Quality control using RSeQC and Picard (%GC, %duplicates, gene body coverage, unsupervised clustering, library complexity, etc)
Picard MarkDuplicates
Gene quantification using featureCounts
Gene annotation using Gencode
Normalize count matrix with DESeq2
Differential expression with DESeq2
Transcript quantification with Kallisto
Genome_build: mm10
Supplementary_files_format_and_content: Excel worksheet of normalized counts

source_name: Apela KO NEO-OUT embryo

extract_protocol:
RNA was isolated from whole embryos using the RNeasy Plus Mini Kit (Qiagen 74134).
Libraries were constructed by the New York Genome Center using TruSeq Stranded mRNA library prep (Illumina).

value: C57Bl6/CD-1 mix

value: whole embryo

tag: genotype

value: Apela KO NEO-OUT


title: KO12


title: KO10


title: KO9


title: KO8


title: KO6

source_name: Apela KO NEO-IN embryo

value: Apela KO NEO-IN


title: KO7


title: KO5


title: KO3


title: KO4


title: KO1


title: KO2


title: Abdomen_SP+_3h_rep2

city: Oxford

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing: 3' adapter of sequences was trimmed by looking for a perfect match to the first 8 nucleotides of the 3' adapter. Sequences composed of a single nucleotide, containing less than 16 or more than 26 nucleotides were filtered out.

organism: Drosophila melanogaster

source_name: Abdomen tissues

growth_protocol: Parents of experimental flies were 4 days old when eggs were collected. All flies were grown at a low standard density (18µL eggs / 70mL SYA medium). Virgin Dahomey females were collected on ice within 6 hours of eclosion windows and stored in single sex groups of 10. SP0 and SP+ males were collected in within 24 hours of eclosion using ice or CO2 anaesthesia and stored in single sex groups of 10. Mating assays were performed when females were 6 days old and males were 5-6 days old. The day before matings, two males were aspirated into each mating vial. On the day of the assay, a single female was aspirated into each vial. Females were allowed to mate once. Females that mated for less than 10 minutes were discarded. The time point for profiling was 180 mins after the start of mating (ASM) for each pair.

extract_protocol:
At 180 minutes ASM, the females were frozen in liquid N2. After freezing but before RNA extraction, the abdomens were separated from the head and thorax without defrosting. Body parts (HT or Abd) of females within each SP treatment were combined into a single microcentrifuge tube. The experiment was replicated, using exactly the same procedure, four times (2 replicates of which were subjected to illumina sequencing). The final sample size of body parts within each of these tubes was N = 61-74. Total RNA was isolated, using the mirVana kit (Ambion).
miR array assays were performed using a service provider (BaseClear). Each assay was started using 2 to 5 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore). The small RNAs (< 300 nt) isolated were 3'-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining. cDNA libraries of the short RNA fractions were generated as described in Szittya et al. 2008, (High-throughput sequencing of Medicago truncatula short RNAs identifies eight new miRNA families. BMC Genomics, 9, 593) and then sequenced on the Illumina GA2 platform (Solexa, BaseClear provider).

tag: female strain

value: Dahomey wild type females

tag: strain of males to which females were mated

value: SP+ control (SP+, SP0 construct in Dahomey wt background)


title: Wt2

source_name: wild-type embryo

value: wild-type


title: Wt1


title: Wt3


title: HeadThorax_SP0_3h_rep4

source_name: Head + Thorax tissues

value: SP0 knockout males in Dahomey wt background


title: ZY821_24hpi_3

city: Winnipeg

first: Mark

last: Belmonte

state: Manitoba

address: 50 Sifton Road

department: Biological Sciences

country: Canada

institute: University of Manitoba

data_processing:
Read calling performed in-house at Genome Québec using Illumina software (gqinnovationcenter.com)
Fastq files were trimmed using Trimmomatic (Bolger et al., 2014), trimming adapter sequences, headcrop of 6 bases, bases with an average quality score of less than 30 in a sliding window of 4 bases, and dropping remaining reads shorter than 50nt.
TopHat (v2.0.13, Trapnell et al., 2012, http://ccb.jhu.edu/software/tophat/index.shtml) was used to align and map the trimmed reads in high sensitivity mode using the reference assembly (v5) as a guide.
Identification of novel transcripts was performed using cufflinks v2.2.1 (Trapnell et al., 2012) and transcript sequences were extracted from this annotation using BedTools.
Cuffquant, CuffNorm and Cuffdiff were used to generate normalized counts in FPKM and to identify differentially expressed genes (pooled dispersion method). Genes were considered significantly differentially expressed with a corrected p-value of < 0.05 (false discovery rate = 0.05).
Genome_build: Brassica napus v4.1
Supplementary_files_format_and_content: XLSX file - FPKMs and putative annotation based on blast+ hits to Arabidopsis for all samples

organism: Brassica napus

source_name: Mature Leaf

growth_protocol: Westar seeds stored at 4˚C were planted in Sunshine Mix No.1 soil and grown at 22˚C with 50-70% humidity with long day conditions (16 hours light, 8 hours dark 150-200 µE/m2/s). ZY821 plants were treated similarly, however 1 month after planting they were subjected to a four-week vernalization treatment (8 hours light, 16 hours dark, 40% humidity, 8-10˚C and 100 µE/m2/s), before being transferred back to long day conditions. Both cultivars were inoculated at 30-50% bloom stage.

extract_protocol:
RNA was isolated using Invitrogen Plant RNA Purification Reagent, and subsequently treated with the Ambion Turbo DNA-free DNase Kit according to the manufacturer’s protocol. Quantity and purity were assessed spectrophotometrically and quality of RNA samples was verified with electropherogram profiles and RNA Integrity Numbers (RIN) using an Agilent 2100 Bioanalyzer and RNA Nano Chip
RNA-sequencing libraries were prepared according to alternative HTR protocol (C2) established by R. Kumar et al. (2012) with the exception of library PCR enrichment that was carried out using 11 PCR cycles. RNA sequencing libraries were validated using the Agilent Bioanalyzer DNA chips (Agilent Technologies) and quantified using the Quant-iT dsDNA Assay kit (ThermoFisher Scientific).

treatment_protocol: Field-collected Sclerotinia ascospores were suspended at a concentration of 8 x10E4 spores per mL in a 0.02% Tween80 solution. 30µL of the solution was pipetted onto senescing petals placed in a perti plate. Ascospores were allowed to germinate into hyphae and grow for 72 hours prior to being placed on B. napus leaves and grown under normal conditions for 24 hours.

value: Zhongyou 821

value: 24 hours post-inoculation


title: ZY821_Ctl_3

value: Mock-inoculated


title: ZY821_24hpi_1


title: ZY821_Ctl_2


title: Control no GVHD PSGL-1loCD4+ T, 2

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
Control no GVHD PSGL-1loCD4+ T
11258_WT-extra2

data_processing:
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings. Aligned reads were used to generate pileup for each base with Samtools v0.1.18.
Read counts for each refseq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the TMM method implemented in Bioconductor package "edgeR" .
Genome_build: mm9
Supplementary_files_format_and_content: Normalized counts for each refseq genes

source_name: Control no GVHD mice

growth_protocol: in vivo alloreactive T cell expansion

extract_protocol:
Using miRNeasy Mini Kit purchased from Qiagen (Valencia, USA)
Ribozero RNA-seq

value: Speen

value: CD4 T cells

tag: cell subtype

value: PSGL-1loCD4+ T


title: Control no GVHD PSGL-1loCD4+ T, 1

description:
Control no GVHD PSGL-1loCD4+ T
11257_WT-extra1


title: ZY821_Ctl_1


title: ZY821_24hpi_2


title: IrradNesCFP3

city: new york

first: alexandre

last: wojcinski

address: 430 E. 67th Street

institute: memorial sloan kettering cancer center

data_processing:
The output data (FASTQ files) were mapped to the target genome using the rnaStar aligner that maps reads genomically and resolves reads across splice junctions.
HTSeq (www-huber.embl.de/users/anders/HTSeq) was used to compute the expression count matrix from the mapped reads.
The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analyze differential expression between sample groups.
A heatmap was generated using the heatmap.2 function from the gplots R package. The data plot was the mean centered normalized log2 expression of the top 100 significant genes with adjusted p-value cutoff 0.05, and mean coverage of at least 15. Hierarchical clustering was generated with the Pearson correlation on the normalized log2 expression values.
Genome_build: mm10
Supplementary_files_format_and_content: xls file,  normalized count tables

source_name: Nes-CFP positive cells in P5 mouse cerebellum Irradiated at P1

extract_protocol:
Mouse cerebella were freshly dissected, dissociated using papain dissociation system (Worthington biochem) into single-cell suspension, and Nes-CFP positive cells were isolated using fluorescence activated cell sorting (FACS). RNA was extracted using Trizol reagent.
Samples were sent to MSKCC Integrated Genomics Operation (IGO). PolyA selection protocol was used and 100ng starting amount of RNA was used for the construction of sequencing libraries.

value: Swiss webster

value: cerebellum irradiated at P1

value: Nes-CFP/+


title: HeadThorax_SP+_3h_rep4


title: Westar_24hpi_3

value: Westar


title: Westar_24hpi_2


title: Abdomen_SP0_3h_rep4


title: chronic GVHD PSGL-1loCD4+ T, 1

description:
chronic GVHD PSGL-1loCD4+ T
11255_WTCD-extra1

source_name: chronic GVHD mice


title: Westar_24hpi_1


title: IrradNesCFP2


title: IrradNesCFP1


title: Westar_Ctl_3


title: Abdomen_SP0_3h_rep2


title: HeadThorax_SP0_3h_rep3


title: controlNesCFP3

source_name: Nes-CFP positive cells in P5 Non-Irradiated mouse cerebellum

value: cerebellum


title: HeadThorax_SP+_3h_rep3


title: controlNesCFP1


title: Westar_Ctl_2


title: lacZ2-ChIRP-seq

city: Leipzig

first: Stefanie

last: Binder

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description:
oligos for CAPTURE: 6x 25mers with 3´-BIO-TEG (100pol/ml)
library strategy: ChIRP-seq
negative control for STAiR1, STAiR2, and STAiR6

data_processing:
Adapters were trimmed with software cutadapt
Reads were aligned to hg19 with software tophat (tophat v2.0.11, bowtie 2.2.1.0, samtools 0.1.18.0)
Gene expression was counted with software cufflinks
Differential gene expression was analysed with software cuffdiff (cuffdiff --library-type fr-secondstrand)
Genome_build: hg19
Supplementary_files_format_and_content: genes.fpkm_tracking and isoforms.fpkm_tracking

source_name: multiple myeloma cell line

growth_protocol: INA-6 cells were cultured in RPMI+Glutamax supplemented with 1% penecillin/streptomycin, 10% FBS and 1ng/ml IL-6 in medium sized cell culture flasks

extract_protocol:
For Capture-RNA-seqs (identification of STAiR transcript architecture) RNA was isolated from 2x10^7 INA-6 cells by adding 1ml TRIzol (Thermo Fischer), followed by a standard RNA preparation as indicated by the manufacturer, including an RNA-precipitation by 2-propanol. Total prepared RNA was incubated in 0.5ml lysis and 1ml hybridization buffer (for buffers see the publication on ChIRP by Chu et al. 2011) and 100pmol/ml biotinylated oligo mixture (oligos designed against each STAiR target using singlemoleculefish.com and ordered via MWG Eurofins) using  for 4h at 37°C. For ChIRP-RNA-seqs (identification of STAiR RNA-binding partners) 2x10^7 INA-6 cells were crosslinked with 1% formaldehyde. Cell lysis and chromatin fragmentation was conducted in 0.5ml lysis buffer (for buffers and protocols see Chu et al 2011) by 20min sonication resulting in RNA fragments of 200-500nt. After adding 1ml hybridization buffer, 100pmol/ml biotinylated oligo mixture was added and incubated for 4h at 37°C. The particular oligo mixture for Capture and ChIRP contained 12 different oligos targeting one STAiR lncRNA. A negative control oligo mixture targeting the bacterial RNA lacZ was also used. Streptavidin Dynabeads Myone C1 magnetic beads (Thermo Fischer) were added and incubated for another 30min. After magnetic separation and four washing steps in washing buffer, RNA was released by a proteinaseK-digestion. RNA was isolated by a standard TRIzol preparation and DNase digested (Turbo-DNA-free, Thermo Fischer).
Libraries were prepared using scriptseq™ v2 RNA-Seq Library Preparation Kit (Epicenter) according to the manufacturer´s instructions

treatment_protocol: INA-6 cells were cultured in the presence of 1ng/ml IL-6


title: Abdomen_SP+_3h_rep4


title: Neg2

city: Williamsburg

first: Maria Cristina

last: Picardo

state: VA

address: 540 Landrum Dr

department: Applied Science, ISC 3

institute: College of William and Mary

data_processing:
The sequences and quality scores in the form of FASTQ files were aligned to the mm10 murine genomic database from the University of California at Santa Cruz (http://hgdownload.soe.ucsc.edu/downloads.html) using Tophat2 software with the parameters specified in “TophatParameters.txt”, running on the Galaxy cluster computer at Johns Hopkins University (https://usegalaxy.org/). Average mapping rate was 85%.
BAM files were sorted using Samtools (http://www.htslib.org/download/),and then HTSeq-count was applied to map reads to genes with the command: htseq-count -f bam -s no -i gene_name BAMFILE.bam genes.gtf > BAMFILE.txt where genes.gtf is the gene annotation from the Ensembl mouse gene annotation database (http://www.ensembl.org/Mus_musculus/Info/Index)
Custom Python scripts were implemented to compute reads per kilobase of transcript per million mapped reads (RPKM) for each gene in each sample by normalizing for exon length according to the Ensembl mouse gene annotation database. These scripts read the Ensembl mouse gene annotation database (http://www.ensembl.org/Mus_musculus/Info/Index), and then apply the gtf-to-genes-1.40 package (https://pypi.python.org/pypi/gtf_to_genes) to extract the total exon length for each gene.
Genome_build: mm10 murine genomic database

source_name: preBötC in the brainstem

growth_protocol: To identify Dbx1-derived preBötC neurons, we crossed female Dbx1 Cre-driver mice (Dbx1CreERT2; Hirata et al., 2009; stock no. 028131, The Jackson Laboratory, Bar Harbor, ME) with male reporter mice whose Rosa26 locus was modified by targeted insertion of a loxP-flanked STOP cassette followed by a gene for the fluorescent protein tdTomato (Rosa26tdTomato, stock no. 007905; The Jackson Laboratory). In their offspring, Dbx1CreERT2; Rosa26tdTomato mice, Cre-mediated recombination resulted in cytosolic tdTomato expression in cells derived from Dbx1-expressing progenitors.

extract_protocol:
Dbx1 preBötC neurons were identified using epifluorescence and removed under bright-field imaging (specifically, a version of differential interference contrast microscopy called ‘Dodt’ by Zeiss) on a fixed-stage microscope. Non-Dbx1 neurons were identified as neuronal somata without tdTomato fluorescence. We fabricated and heat-sterilized micropipettes from borosilicate capillary glass (1.50 mm outer diameter, 0.86 mm inner diameter). Micropipettes were devoid of solution prior to the isolating cells. After forming a seal with the plasma membrane, we applied negative pressure to draw single neurons into the tip of the micropipette. Tips containing the sampled neurons were immediately broken in sterile RNase/DNase-free tubes submersed in liquid nitrogen until a total of 15 neurons were collected. Each sample of 15 neurons was collected from a different animal.
RNA libraries were prepared for sequencing using standard Illumina protocols. Full-length cDNA was processed with the Nextera Library Preparation Kits

value: postnatal day 2

value: non Dbx1-derived interneuron (Dbx1 -)

tag: number of cells

value: 15 neurons


title: Pos2

value: Dbx1-derived interneuron (Dbx1 +)


title: lacZ-ChIRP-seq

description:
oligos for CAPTURE: 6x 25mers with 3´-BIO-TEG (100pol/ml)
library strategy: ChIRP-seq
negative control for STAiR15 and STAiR18


title: Pos1


title: Etv2-high.screen

city: St. Louis

first: Kyunghee

last: Choi

state: MO

address: 660 S Euclid Ave

institute: Washington University in St. Louis, School of Medicine

description: gene.expression.and.screen_sgRNA_reads_counting_for_screen.txt

data_processing:
Library strategy: CRISPR screen
RNA-seq reads were aligned to the mouse mm9 assembly from the UCSC Genome Browser with Tophat2.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5(Liao et al., 2013). All gene-level counts were then imported into the R/Bioconductor package EdgeR normalized to adjust for differences in library size.
CRISPR screen sequencing data processing was performed faithfully following the previously described protocol of Feng Zhang lab (Shalem et al., 2014). Briefly, after trimming of the adaptor sequences, the reads were mapped to the sgRNA library (http://genome-engineering.org/gecko/?page_id=15, the designed sgRNA sequences from the library were assembled  into a index file using the Bowtie build-index function). The summarized reads counting of each sgRNA for each sample is presented in the processed data file "sgRNA reads counting for screen".
Genome_build: mm9
Supplementary_files_format_and_content: gene-level counts for RNA-seq samples and summarized reads counting of each sgRNA for CRISPR screening samples

source_name: ES cells

extract_protocol:
based on the manufacturer's protocol for DNeasy Blood & Tissue Kit (Qiagen)
Genomic DNA extraction and sgRNA library amplification were performed faithfully following the previously described protocol (Shalem et al., 2014).

value: wildtype

tag: reporter

value: ES cells

tag: protocol

value: sorted Etv2-tdTomato expression cells  from day 4 EBs


title: STAiR18-ChIRP-seq

description:
oligos for CAPTURE: 12x 20mers with 3´-BIO-TEG (100pol/ml)
library strategy: ChIRP-seq
to identify RNA-binding partners of STAiR18

tag: cell line


title: Neg3

tag: developmental stage


title: STAiR6-ChIRP-seq

description:
oligos for CAPTURE: 12x 20mers with 3´-BIO-TEG (100pol/ml)
library strategy: ChIRP-seq
to identify RNA-binding partners of STAiR6


title: STAiR15-ChIRP-seq

description:
oligos for CAPTURE: 12x 20mers with 3´-BIO-TEG (100pol/ml)
library strategy: ChIRP-seq
to identify RNA-binding partners of STAiR15


title: Pos3


title: STAiR2-ChIRP-seq

description:
oligos for CAPTURE: 12x 20mers with 3´-BIO-TEG (100pol/ml)
library strategy: ChIRP-seq
to identify RNA-binding partners of STAiR2


title: lacZ2-CAPTURE-seq

description:
oligos for CAPTURE: 6x 25mers with 3´-BIO-TEG (100pol/ml)
library strategy: CAPTURE-seq
negative control for STAiR1, STAiR2, and STAiR6


title: lacZ-CAPTURE-seq

description:
oligos for CAPTURE: 6x 25mers with 3´-BIO-TEG (100pol/ml)
library strategy: CAPTURE-seq
negative control for STAiR15 and STAiR18


title: Neg1


title: STAiR1-ChIRP-seq

description:
oligos for CAPTURE: 12x 20mers with 3´-BIO-TEG (100pol/ml)
library strategy: ChIRP-seq
to identify RNA-binding partners of STAiR1


title: Westar_Ctl_1


title: controlNesCFP2


title: STAiR18-CAPTURE-seq

description:
oligos for CAPTURE: 12x 20mers with 3´-BIO-TEG (100pol/ml)
library strategy: CAPTURE-seq
to identify STAiR18 splice variants


title: pr.screen

value: sorted PDGFR-alpha positive cells  from day 4 EBs


title: STAiR15-CAPTURE-seq

description:
oligos for CAPTURE: 12x 20mers with 3´-BIO-TEG (100pol/ml)
library strategy: CAPTURE-seq
to identify STAiR15 splice variants


title: lib.screen

value: 24 hours post-infection of ES cells with the GeCKO lentivirus library, reflecting the library complexity


title: STAiR2-CAPTURE-seq

description:
oligos for CAPTURE: 12x 20mers with 3´-BIO-TEG (100pol/ml)
library strategy: CAPTURE-seq
to identify STAiR2 splice variants


title: Foxh1-ko-pr

description: gene.expression.and.screen_integrated_RNA-seq_data.txt

data_processing:
RNA-seq reads were aligned to the mouse mm9 assembly from the UCSC Genome Browser with Tophat2.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5(Liao et al., 2013). All gene-level counts were then imported into the R/Bioconductor package EdgeR normalized to adjust for differences in library size.
CRISPR screen sequencing data processing was performed faithfully following the previously described protocol of Feng Zhang lab (Shalem et al., 2014). Briefly, after trimming of the adaptor sequences, the reads were mapped to the sgRNA library (http://genome-engineering.org/gecko/?page_id=15, the designed sgRNA sequences from the library were assembled  into a index file using the Bowtie build-index function). The summarized reads counting of each sgRNA for each sample is presented in the processed data file "sgRNA reads counting for screen".
Genome_build: mm9
Supplementary_files_format_and_content: gene-level counts for RNA-seq samples and summarized reads counting of each sgRNA for CRISPR screening samples

extract_protocol:
based on the manufacturer's protocol for RNeasy Mini kit (Qiagen)
Library preparation was performed with 10 ng of total RNA (GTAC core facility, Washington University in St. Louis): Total RNA integrity was validated using an Agilent bioanalyzer. All samples were prepared using the Ribozero (Epicentre) kit per manufacturer’s protocol. cDNA was then blunt ended, an A base added to the 3’ ends, and then Illumina sequencing adapters were ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags.

value: sorted PDGFR-alpha positive cells  from day 5 EBs


title: STAiR6-CAPTURE-seq

description:
oligos for CAPTURE: 12x 20mers with 3´-BIO-TEG (100pol/ml)
library strategy: CAPTURE-seq
to identify STAiR6 splice variants


title: STAiR1-CAPTURE-seq

description:
oligos for CAPTURE: 12x 20mers with 3´-BIO-TEG (100pol/ml)
library strategy: CAPTURE-seq
to identify STAiR1 splice variants


title: Etv2-high/Scl-int

value: sorted cells with high Etv2-tdTomato expression and intermediate level  Scl-GFP expression  from day 4 Ebs


title: dp

value: sorted PDGFR-alpha/FLK1 double positive cells  from day 3.5 EBs


title: HCT8-500nM-1

city: Boston

first: David

middle: T

last: Ting

address: 149 E 13th street

institute: Massachusetts General Hospital

data_processing:
The paired-end reads were aligned to the human_g1k_v37.fasta reference genome from http://www.1000genomes.org using BSMAP version 2.74 with default settings.
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and were removed.
BSMAP’s methratio.py script was used to extract methylation ratio data from the mapped reads with the --zero-meth, --remove-duplicate, and --combine-CpG options.
CpG-specific methylation data was extracted by taking the rows of the methratio.py output that had a value of “+” in the strand field and had a sequence context that began with “..CG”.
Each CpG in the CpG methylation data table was annotated with repeat masker information (ucsc_repeatmasker_2014-06-23.txt from the UCSC genome browser (https://genome.ucsc.edu) and its distance from the nearest Gencode annotation (gencode.v19.annotation.gtf from http://www.gencodegenes.org).
CpG methylation fractions for specific repeat types were averaged over all repeats of the given type. Distances to the nearest annotated genes were binned in 5,000-base increments from 0 to 100,000 bases, and CpG methylation fractions were averaged by distance bin within each repeat class.
Genome_build: hg19
Supplementary_files_format_and_content: CSV file of average percent CpG methylation for repeats annotated in repeat masker

source_name: Colon Cancer Cell line HCT8

growth_protocol: RPMI-1640 + 10% FBS + 1% Pen/Strep

extract_protocol:
DNA extracted using Qiagen DNA micro kit
Methyl sequencing with the EZ DNA Methylation-Lightning Kit (Zymo Research) followed by Illumina library construction using the EpiGnome Methyl-Seq Kit (Epicentre/Illumina) .  Sequencing on MiSeq 75 bp pair-end

treatment_protocol: AZA as indicated

tag: aza concentration


title: HCT8-0nM-2

value: 0 nM


title: Etv2-int

tag: cell type

value: sorted cells with intermediate level Etv2-tdTomato expression from day 4 EBs


title: HCT8-1uM-2


title: HCT116-1uM-1

source_name: Colon cancer Cell line HCT116


title: HCT8-1uM-1


title: HCT116-1uM-2


title: HCT116-500nM-1


title: es.screen

value: 2 weeks post-infection and cells were selected with puromycin, enriched infected cells serve as "input" for screening


title: pr

value: sorted PDGFR-alpha single positive cells  from day 3.5 EBs


title: RNAseq_Myc_sgMll3/Cas9_2

description:
Myc Mll3 2A
Processed data file: deseq2_mll3li_p53.txt

data_processing:
Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (Bolger et al. 2014). RNA-seq reads were then aligned to GRCm38.75/mm10 with STAR (Dobin et al. 2012). Genome-wide transcript counting was performed by HTSeq to generate RPKM matrix. Differentially expressed genes were identified by DESeq2 (v.1.8.2 ,package in R).
Genome_build: GRCm38.75/mm10
Supplementary_files_format_and_content: rpkm.txt: Tab-delimited text file includes RPKMs from each experiment.
Supplementary_files_format_and_content: deseq2_mll3li_p53.txt: Tab-delimited text file includes differentially expressed genes.

source_name: Liver tumor cell line, Myc;sgMll3/Cas9

growth_protocol: Derived primary proliferating cells were cultured in complete DMEM (10% FBS, 1x Penicillin/Streptomycin), maintained on collagen-coated plates (PurCol, Advanced Biomatrix), and passaged until visibly free from fibroblasts. RNA from independent triplicates was extracted.

extract_protocol:
Cells were lysed by adding RLT buffer directly to the culture dish. RNA was extracted using RNeasy Qiagen Kit.
RNA samples were used for HiSeq library construction with the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer's instructions. Samples are barcoded with TruSeq SBS Kit v3 (Illumina).

tag: strain/background

value: Liver tumor cell line

tag: viral transduction

value: in vivo hydrodynamic transfection with px330_sgMll3


title: HCT116-0nM-2


title: RNAseq_Myc_sgp53/Cas9_2

description:
Myc p53 2
Processed data file: deseq2_mll3li_p53.txt

source_name: Liver tumor cell line, Myc;sgp53/Cas9

value: in vivo hydrodynamic transfection with px330_sgp53


title: RNAseq_Myc_sgp53/Cas9_3

description:
Myc p53 3
Processed data file: deseq2_mll3li_p53.txt


title: Etv2-high/Scl-negative

value: sorted cells with high Etv2-tdTomato expression and negative Scl-GFP expression  from day 4 Ebs


title: RNAseq_Myc_sgMll3/Cas9_1

description:
Mll3 1
Processed data file: deseq2_mll3li_p53.txt


title: HCT116-0nM-1


title: RNAseq_Myc_sgp53/Cas9_1

description:
Myc p53 1
Processed data file: deseq2_mll3li_p53.txt


title: Scl-high

value: sorted cells with high Scl-GFP expression  from day 4 Ebs


title: DLD1-1uM-2

source_name: Colon cancer Cell line DLD1


title: HCT8-0nM-1


title: DLD1-1uM-1


title: DLD1-500nM-1