title: 840_ PAXgene RNA tube Replicate 1

description: Biological replicate 1 of 2. RNA extracted from whole blood preserved in PAXgene RNA blood tubes.


title: WT_24h_S.meliloti_rep4

status: Public on Sep 20 2019

type: SRA

city: Cologne

first: Tak

last: Lee

address: Carl-von-Linne weg 10

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description:
wt_inoc_rpkm.txt
NG-135_0008

library_source: transcriptomic

data_processing:
The quality of the fastq files were validated with fastqc
Sequence reads were trimmed for adapter and repetitive sequences with Cutadept
The resulting reads from the raw fastq data were quality controlled and and mapped to the M. truncatula reference genome version 4.0  using R package STAR
The FPKM (Fragments per kilobase per million mapped reads) and RPKM (Reads per kilobase per million mapped reads) values were calculated with featureCounts in R package Rsubread
Genome_build: Mt4.0v1

molecule: total RNA

organism: Medicago truncatula

source_name: 2-3mm segment of root

growth_protocol: Seeds were scarified, surface sterilized with 10% (v/v) bleach solution, stratified for 3 days at 4 °C and germinated on water agar plates. Plants were grown in sterile conditions in controlled environment rooms at 22 °C (80% humidity, 16 h light/8 h dark, 300 μmol m2 s-1 light intensity) on filter paper-lined agar media in sealed plates

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, Germantown, USA), the RNase free DNase kit (Qiagen, Germantown, USA) was used to remove genomic DNA.
RNA-Seq libraries were prepared with the Illumina TruSeq® Stranded mRNA HT kit

tag: time

tag: tissue

value: 2-3mm segment of root

tag: genotype

value: wild type ecotype jemalong cultivar Jester

tag: treatments

value: Sinorhizobium meliloti strain 2011


title: 840_ RNAgard tube Replicate 3

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

description: Biological replicate 3 of 3. RNA extracted from whole blood preserved in RNAgard blood tubes.

hyb_protocol: cRNA was hybridized to SurePrint G3 Human GE v2 8x60K microarrays (Agilent Technologies) following manufacturer's instructions

scan_protocol: Slides were scanned on a Agilent Technologies Scanner G2600D Images were quantified using Agilent Feature Extraction Software

data_processing: Agilent Feature Extraction Software (v 11.5.1.1) was used for background subtraction and R script v3.3 software was used to conduct the preliminary data filtration and statistical analysis.

organism: Homo sapiens

source_name: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues

label_protocol: Total RNA (200ng) was used as starting material, which was amplified using the Low Input Quick Amp Two-Color Kit (Agilent Technologies).The labelled cRNA was purified using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and eluted, labelled cRNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA).

growth_protocol: growth protocol is not applicable

extract_protocol:
Blood was collected and preserved in PAXgene™ RNA tubes, RNAgard® Blood Tubes and CPT tubes from eight healthy volunteers. In parallel, PBMCs were isolated from the CPT tubes following the manufacturer’s instructions.
Total RNA was extracted using PAXgene™ RNA blood miRNA kit (Qiagen, Hilden, Germany) from blood preserved in PAXgene™ RNA tubes and RNAgard® Blood Tubes following manufacturer's instructions. RNA from PBMC in Trizol (from CPT tubes) was extracted following manufacturer's instructions

tag: reference

source_name: Whole blood

tag: test


title: 15.2 WDLPS - resection

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

country: Netherlands

institute: Erasmus University Medical Center

description:
well differentiated liposarcoma
WDLPS - resection

data_processing: The expression of a specific miRNA in a sample was normalized to the median CT of all detectable miRNAs in that sample (ΔCT = CT miR-X – median CT all miRNAs in a sample). The normalized expression (ΔCT) was subsequently used to calculate the relative expression values (2^-ΔCT) for each specific miRNA. The normalized miRNA expression data were median centered to acquire relative expression values that were eventually used for clustering analyses. In the matrix templates blue cells designate flagged wells whereas green cells indicate wells with undetermined values which were arbitrarily set at Ct39.99.

label: FAM

source_name: formalin-fixed paraffin embedded tumor material

label_protocol: MicroRNA expression was determined using TaqMan® Low Density Array (TLDA) cards (A card v2.0, B card v3.0, Applied Biosystems/Thermo Fisher Scientific). Megaplex™ RT Primers (Human Pool, pool A v2.1, pool B v3.0, Applied Biosystems/Thermo Fisher Scientific) were used for cDNA synthesis, followed by a standard pre-amplification protocol using Megaplex™ PreAmp Primers (Human Pool, pool A v2.1, pool B v3.0, Applied Biosystems/Thermo Fisher Scientific). The TLDA cards were analysed using a 7900HT Real-Time PCR system (Applied Biosystems). The paired samples were processed in three batches for logistical and technical reasons, with each primary and its matching recurrent tumour being placed within the same batch.

extract_protocol: Total RNA was isolated using the RecoverAll™ Total Nucleic Acid Isolation Kit (Ambion/Life Technologies) according to manufacturer's instructions.

treatment_protocol: Patients with available tumour samples of a primary and matching first recurrent WDLPS who were treated with surgery only were included. The formalin-fixed and paraffin-embedded (FFPE) tissue blocks were obtained through PALGA, the Dutch nationwide pathology registry, and the pathology department of the Maria Skłodowska-Curie Institute-Oncology Center together with anonymized clinicopathological information. The archival tumour samples were examined by an expert pathologist to confirm the initial histopathological diagnosis and to determine the percentage of tumour cells. Only sections containing approximately 100% tumour cells were used for isolation.

value: recurrent tumor


title: WT_24h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
NG-135_0006


title: 14.2 WDLPS - resection


title: 840_ RNAgard tube Replicate 1

description: Biological replicate 1 of 3. RNA extracted from whole blood preserved in RNAgard blood tubes.

value: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues


title: AML with normal karyotype (NK) AML45_nk

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

description: AML with normal karyotype (NK)

hyb_protocol: Fifteen ug mRNA was hybridized to the ABI Human Genome Survey Microarray v1

scan_protocol: DIG-labeled targets hybridize to the probes on the arrays and anti-digoxigenin-alkaline phosphatase is added to bind digoxigenin in cDNA targets. The ABI 1700 Expression Array System (ABI, U.S) was used to scan the arrays for chemiluminescence

data_processing: Signal intensity, S/N ratio (signal to noise ratio), and flags values were extracted for each array. The S/N ratio value of 3.0 and flags value of 5000 were used to exclude false positives and/or missing data. For those probes that passed the filtering criterion, the signal values were log2 transformed and normalized across arrays with quantile normalization method after control probes were removed.

label: digoxigenin (DIG)

source_name: peripheral blood

label_protocol: Labeling was done with the Applied Biosystems Chemiluminescent RT-IVT Labeling Kit  (P/N 4340472) using 2 ug high quality total RNA

growth_protocol: Patients’ samples (peripheral blood or bone marrow) were stored in the tissue bank of the St Bartholomew’s Hospital after informed written consent was obtained.

extract_protocol: Total RNA of AML patient samples was extracted from a total of 10 - 20 x 106 thawed cells using Trizol (Gibco-BRL) purification method. RNA quality  was evaluated on the 2100 Bioanalyzer (Agilent Technologies) and the concentration was measured using a NanoDrop spectrophotometer (NanoDrop Technologies).

value: Normal Karyotype (NK)

value: peripheral blood

tag: disease state

value: Acute Myeloid Leukaemia


title: 840_ CPT tube Replicate 1

description: Biological replicate 1 of 3. RNA extracted from PBMCs isolated from whole blood preserved in CPT tubes.


title: WT_24h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
NG-135_0005


title: 839_ CPT tube Replicate 3

description: Biological replicate 3 of 3. RNA extracted from PBMCs isolated from whole blood preserved in CPT tubes.


title: 13.2 WDLPS - resection


title: AML with inv(16) AML44_inv16

description: AML with inv(16)


title: WT_24h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
NG-135_0007


title: AML with other karyotype AML43_other

description: AML with other karyotype

value: Other


title: WT_24h_mock_rep4

description:
wt_mock_rpkm.txt
NG-135_0004

value: mock


title: 11.2 WDLPS - resection


title: WT_24h_mock_rep3

description:
wt_mock_rpkm.txt
NG-135_0003


title: AML with normal karyotype (NK) AML46_nk

description: AML with normal karyotype (NK)


title: AML with t(15;17) AML42_1517

description: AML with t(15;17)


title: 839_ CPT tube Replicate 2

description: Biological replicate 2 of 3. RNA extracted from PBMCs isolated from whole blood preserved in CPT tubes.


title: 839_ RNAgard tube Replicate 3

value: RNA extracted from whole blood preserved in RNAgard blood tubes.


title: 839_ RNAgard tube Replicate 2

description: Biological replicate 2 of 3. RNA extracted from whole blood preserved in RNAgard blood tubes.


title: WT_24h_mock_rep2

description:
wt_mock_rpkm.txt
NG-135_0002


title: 839_ PAXgene RNA tube Replicate 2

description: Biological replicate 2 of 2. RNA extracted from whole blood preserved in PAXgene RNA blood tubes.


title: AML with normal karyotype (NK) AML40_nk

description: AML with normal karyotype (NK)


title: 10.2 WDLPS - resection


title: AML with t(8;21) AML38_821

description: AML with t(8;21)


title: 839_ PAXgene RNA tube Replicate 1

value: RNA extracted from whole blood preserved in PAXgene RNA blood tubes.


title: AML with normal karyotype (NK) AML41_nk

description: AML with normal karyotype (NK)


title: WT_24h_mock_rep1

description:
wt_mock_rpkm.txt
NG-135_0001


title: 839_ RNAgard tube Replicate 1


title: AML with normal karyotype (NK) AML36_nk

description: AML with normal karyotype (NK)


title: WT_16h_S.meliloti_rep5

description:
wt_inoc_rpkm.txt
NG-112_0048


title: WT_16h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
NG-112_0047


title: 8.2 WDLPS - resection


title: 6.2 WDLPS - resection


title: 9.2 WDLPS - resection


title: AML with other karyotype AML35_other

description: AML with other karyotype


title: AML with t(8;21) AML34_821

description: AML with t(8;21)


title: AML with 11q23 AML33_11q23

description: AML with 11q23


title: 444_ CPT tube Replicate 3

value: RNA extracted from PBMCs isolated from whole blood preserved in CPT tubes.


title: 4.2 WDLPS - resection


title: 3.2 WDLPS - resection


title: WT_16h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
NG-112_0045


title: 444_ PAXgene RNA tube Replicate 2


title: 839_ CPT tube Replicate 1


title: WT_16h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
NG-112_0044


title: 2.2 WDLPS - resection


title: 1.2 WDLPS - resection


title: 5.2 WDLPS - resection


title: WT_16h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
NG-112_0046


title: 30.1 WDLPS - resection

value: primary tumor


title: AML with normal karyotype (NK) AML31_nk

description: AML with normal karyotype (NK)


title: WT_16h_mock_rep5

description:
wt_mock_rpkm.txt
NG-112_0043


title: 444_ CPT tube Replicate 2


title: WT_16h_mock_rep3

description:
wt_mock_rpkm.txt
NG-112_0041


title: AML with other karyotype AML28_other

description: AML with other karyotype


title: 29.1 WDLPS - resection


title: AML with other karyotype AML37_other

description: AML with other karyotype


title: AML with normal karyotype (NK) AML30_nk

description: AML with normal karyotype (NK)


title: WT_16h_mock_rep2

description:
wt_mock_rpkm.txt
NG-112_0040


title: 444_ PAXgene RNA tube Replicate 1


title: 444_ CPT tube Replicate 1


title: 444_ RNAgard tube Replicate 1


title: AML with t(15;17) AML29_1517

description: AML with t(15;17)


title: WT_16h_mock_rep4

description:
wt_mock_rpkm.txt
NG-112_0042


title: AML with other karyotype AML32_other

description: AML with other karyotype


title: 28.1 WDLPS - resection


title: 444_ RNAgard tube Replicate 2


title: 444_ RNAgard tube Replicate 3


title: WT_16h_mock_rep1

description:
wt_mock_rpkm.txt
NG-112_0039


title: 27.1 WDLPS - resection


title: AML with other karyotype AML27_other

description: AML with other karyotype


title: WT_14h_S.meliloti_rep5

description:
wt_inoc_rpkm.txt
16090-0028


title: WT_14h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
16090-0027


title: 423_ CPT tube Replicate 3


title: WT_14h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
16090-0025


title: 26.1 WDLPS - resection


title: WT_14h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
16090-0026


title: 25.1 WDLPS - resection


title: 24.1 WDLPS - resection


title: 23.1 WDLPS - resection


title: WT_14h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
16090-0024


title: WT_14h_mock_rep4

description:
wt_mock_rpkm.txt
16090-0023


title: 22.1 WDLPS - resection


title: 21.1 WDLPS - resection


title: AML with other karyotype AML25_other

description: AML with other karyotype


title: 423_ PAXgene RNA tube Replicate 2


title: 423_ CPT tube Replicate 2


title: AML with inv(16) AML24_inv16

description: AML with inv(16)


title: 423_ RNAgard tube Replicate 3


title: AML with 11q23 AML23_11q23

description: AML with 11q23


title: AML with other karyotype AML26_other

description: AML with other karyotype


title: 423_ RNAgard tube Replicate 2


title: WT_14h_mock_rep2

description:
wt_mock_rpkm.txt
16090-0021


title: AML with other karyotype AML20_other

description: AML with other karyotype


title: AML with t(8;21) AML19_821

description: AML with t(8;21)


title: AML with normal karyotype (NK) AML18_nk

description: AML with normal karyotype (NK)


title: AML with normal karyotype (NK) AML21_nk

description: AML with normal karyotype (NK)


title: 423_ RNAgard tube Replicate 1


title: 361_ CPT tube Replicate 3


title: AML with other karyotype AML22_other

description: AML with other karyotype


title: 423_ PAXgene RNA tube Replicate 1


title: 20.1 WDLPS - resection


title: 19.1 WDLPS - resection


title: 17.1 WDLPS - resection


title: WT_14h_mock_rep1

description:
wt_mock_rpkm.txt
16090-0019


title: 16.1 WDLPS - resection


title: WT_14h_mock_rep3

description:
wt_mock_rpkm.txt
16090-0022


title: AML with normal karyotype (NK) AML16_nk

description: AML with normal karyotype (NK)


title: 423_ CPT tube Replicate 1


title: AML with other karyotype AML15_other

description: AML with other karyotype


title: WT_12h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
16090-0016


title: 361_ RNAgard tube Replicate 3


title: 361_ PAXgene RNA tube Replicate 2


title: 361_ CPT tube Replicate 2


title: WT_12h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
16090-0014


title: 15.1 WDLPS - resection


title: WT_12h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
16090-0015


title: AML with normal karyotype (NK) AML14_nk

description: AML with normal karyotype (NK)


title: WT_12h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
16090-0017


title: WT_12h_mock_rep5

description:
wt_mock_rpkm.txt
16090-0013


title: 361_ RNAgard tube Replicate 2


title: 13.1 WDLPS - resection


title: AML with other karyotype AML17_other

description: AML with other karyotype


title: 14.1 WDLPS - resection


title: 361_ PAXgene RNA tube Replicate 1


title: 361_ CPT tube Replicate 1


title: 10.1 WDLPS - resection


title: AML with other karyotype AML11_other

description: AML with other karyotype


title: AML with other karyotype AML13_other

description: AML with other karyotype


title: WT_12h_mock_rep3

description:
wt_mock_rpkm.txt
16090-0011


title: 361_ RNAgard tube Replicate 1


title: 360_ PAXgene RNA tube Replicate 2


title: 360_ CPT tube Replicate 3


title: 9.1 WDLPS - resection


title: 11.1 WDLPS - resection


title: WT_12h_mock_rep2

description:
wt_mock_rpkm.txt
16090-0010


title: WT_12h_mock_rep1

description:
wt_mock_rpkm.txt
16090-0009


title: 8.1 WDLPS - resection


title: AML with other karyotype AML12_other

description: AML with other karyotype


title: 6.1 WDLPS - resection


title: WT_10h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
16090-0008


title: AML with inv(16) AML10_inv16

description: AML with inv(16)


title: 5.1 WDLPS - resection


title: WT_10h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
16090-0007


title: 360_ RNAgard tube Replicate 3


title: AML with other karyotype AML8_other

description: AML with other karyotype


title: 3.1 WDLPS - resection


title: 4.1 WDLPS - resection


title: WT_10h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
16090-0006


title: AML with t(8;21) AML9_821

description: AML with t(8;21)


title: WT_10h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
16090-0005


title: 360_ CPT tube Replicate 2


title: 360_ RNAgard tube Replicate 2


title: WT_10h_mock_rep4

description:
wt_mock_rpkm.txt
16090-0004


title: 2.1 WDLPS - resection


title: AML with 11q23 AML6_11q23

description: AML with 11q23


title: 1.1 WDLPS - resection


title: 21D-6mg_Rep5

city: New York

first: Christopher

middle: L

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

data_processing:
Sequencing data was quality checked using FastQC, aligned to the reference genome (Rn6) with the STAR software package
Differential expression based on counts per million mapped reads was performed using edgeR.
Genome_build: Rn6
Supplementary_files_format_and_content: edgeR

organism: Rattus norvegicus

source_name: Plantaris tendon

extract_protocol:
Tendons were finely minced, and then placed into 2mL tubes containing 2.3mm steel beads and TRI Reagent (Molecular Research Center, Cincinnati, OH, USA), homogenized for 15 sec, and isolated following product directions. The subsequent RNA pellet was then further cleaned up using miRNeasy kit (Qiagen, Valencia, CA, USA), supplemented with DNase I (Qiagen). RNA concentration was determined using a NanoDrop (ThermoFisher Scientific, Waltham, MA, USA), and quality was assessed using a TapeStation D1000 System (Agilent, Santa Clara, CA, USA). All RNA samples used for sequencing had RIN values > 8.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Sprague Dawley

tag: surgical repair time

value: 21 days

tag: gsk2894631a treatment dose


title: AML with other karyotype AML7_other

description: AML with other karyotype


title: 360_ PAXgene RNA tube Replicate 1


title: 360_ CPT tube Replicate 1


title: AML with normal karyotype (NK) AML5_nk

description: AML with normal karyotype (NK)


title: AML with t(8;21) AML2_821

description: AML with t(8;21)


title: 21D-6mg_Rep4


title: 360_ RNAgard tube Replicate 1


title: 21D-6mg_Rep2


title: 21D-6mg_Rep3


title: WT_10h_mock_rep1

description:
wt_mock_rpkm.txt
16090-0001


title: WT_10h_mock_rep3

description:
wt_mock_rpkm.txt
16090-0003


title: AML with t(8;21) AML1_821

description: AML with t(8;21)


title: 208_ PAXgene RNA tube Replicate 2


title: WT_8h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
NG-112_0038


title: 3280.F2.C3.I9.R1

city: São Paulo

first: Glaucia

middle: Mendes

last: Souza

state: SP

address: Av Prof Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: Instituto de Quimica da Universidade de São Paulo

description: Internode 9 from 11-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings

data_processing: Raw and background corrected data

organism: Saccharum hybrid cultivar (mixed)

label_protocol: CyScribe Post-Labelling Kit Protocol - GE Healthcare

growth_protocol: Field in Araras

extract_protocol: Trizol, DNase treatment and Qiagen RNeasy purification

value: internode 9

tag: variety

tag: collect

value: internodes


title: 21D-6mg_Rep1


title: WT_8h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
NG-112_0037

value: 2-3mm segment of root

value: wild type ecotype jemalong cultivar Jester


title: 21D-2mg_Rep5


title: WT_10h_mock_rep2

description:
wt_mock_rpkm.txt
16090-0002


title: AML with t(15;17) AML3_1517

description: AML with t(15;17)


title: WT_8h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
NG-112_0036

value: Sinorhizobium meliloti strain 2011


title: 208_ CPT tube Replicate 3

value: Agilent's Universal Human Reference RNA composed of pooled total RNA from ten cell lines representing different human tissues


title: 21D-2mg_Rep4


title: WT_8h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
NG-112_0035


title: 208_ RNAgard tube Replicate 3


title: 21D-2mg_Rep3


title: WT_8h_mock_rep4

description:
wt_mock_rpkm.txt
NG-112_0034


title: 3280.F2.C4.I5.R1

description: Internode 5 from 13-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages

value: internode 5


title: 208_ CPT tube Replicate 1


title: 3280.F2.C4.I1.R1

description: Internode 1 from 13-month old plants T1 and T2 from Plot 1 compared with pool from internodes from all developmental stages

value: internode 1


title: 208_ PAXgene RNA tube Replicate 1


title: WT_8h_mock_rep3

description:
wt_mock_rpkm.txt
NG-112_0033


title: 208_ CPT tube Replicate 2


title: 21D-2mg_Rep2


title: 208_ RNAgard tube Replicate 1


title: 208_ RNAgard tube Replicate 2


title: 21D-2mg_Rep1


title: 3280.F2.C4.I9.R2

description: Internode 9 from 13-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: 21D-0mg_Rep5


title: WT_8h_mock_rep2

description:
wt_mock_rpkm.txt
NG-112_0032


title: 3280.F2.C4.I9.R1

description: Internode 9 from 13-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: 3280.F2.C3.I9.R2

description: Internode 9 from 11-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: 3280.F2.C2.I9.R2

description: Internode 9 from 8-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: 207_ PAXgene RNA tube Replicate 2


title: 207_ CPT tube Replicate 2


title: 3280.F2.C2.I9.R1

description: Internode 9 from 8-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: 207_ CPT tube Replicate 3


title: 3280.F2.C4.I5.R2

description: Internode 5 from 13-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: 207_ RNAgard tube Replicate 3

description: Biological replicate 3 of 3. RNA extracted from whole blood preserved in RNAgard blood tubes.


title: WT_8h_mock_rep1

description:
wt_mock_rpkm.txt
NG-112_0031


title: 207_ RNAgard tube Replicate 2


title: 21D-0mg_Rep4


title: WT_4h_S.meliloti_rep5

description:
wt_inoc_rpkm.txt
NG-112_0030


title: 21D-0mg_Rep3


title: 21D-0mg_Rep2


title: WT_4h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
NG-112_0029


title: WT_4h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
NG-112_0028


title: 21D-0mg_Rep1


title: mNPC_S16_BrdU

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Department of Biological Science

institute: Florida State University

library_source: genomic

data_processing:
Library strategy: Repli-Seq
The fastq reads for G1 WGS control and BrdU pull down libraries for S1-S16 are aligned to hg38 for 3 human cell lines and mm10 for 2 mouse cell lines. The resulting sam files are dduplicated. The log2 ratio between RPM of BrdU pull-down and that of G1 WGS was calculated for each S phase fraction, which was subsequently used to construct a matrix consisting of 16 rows where each row represented an S phase fraction ranging from S1 to S16 and each column represented a 50kb genomic bin. The matrix is subsequently Gaussian smoothed with a lambda of 1 and scaled such that the column sum for each bin amounts to 100.
Genome_build: hg38,mm10
Supplementary_files_format_and_content: The final data matrix consists of 3 rows indicating genomic bins and 16 rows where each row represents a S phase fraction from S1 to S16 and the values represent percentage of replication for the corresponding bin during the corresponding S phase fraction.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse neural progenitor cells

growth_protocol: H1 and H9 cells were cultured in mTeSR1 (StemCell Technologies #85850) on hESC-qualified Matrigel (Corning #354277) -coated dishes according to WiCell instruction. For the maintenance and expansion, cells were detached using ReLeSR (StemCell Technologies #95872). When the cell reached approximately 70% confluent, cells were pulse-labeled with 400uM BrdU for 30 minutes. To obtain single-cell suspension easily, the BrdU-labeled WA01 and WA09 cells were harvested using Gentle Cell Dissociating Reagent (StemCell Technologies #07174). HCT116 cells were cultured in McCoy’s 5A  medium supplemented with 10% FBS according to ATCC’s instruction.  F121-9 mouse mouse embryonic stem cell was cultured in 2i media on gelatin-coated dish as described in (PMID:29735606). F121-9 differentiation to NPC was performed using RHB-A (TakaraBio #Y40001) as described in (PMID:29735606) for 10 days. F121-9 ESC and NPC were pulse-labeled with 400uM BrdU for 30 minutes and harvested using ESGRO Complete Accutase (Millipore Sigma #SF006). NPC differentiation was confirmed by 1) cell morphology, 2) qPCR for marker genes; Oct4 (ESC marker), Sox1 (NPC marker), Ptn (NPC marker), Nestin (NPC marker).

extract_protocol: DNA from G1 fraction was made into whole-genome sequencing library to normalize any bias during library preparation, sequencing and sequence read mapping. DNA from S1-S16 fractions were made into repli-seq library basically as described in (PMID: 29599440) but from 80K sorted cells instead of 20K sorted cells.

treatment_protocol: When the cell reached approximately 70% confluent, asynchronously growing cells were pulse-labeled with 400uM BrdU for 30 minutes, harvested and ethanol fixed, then retroactively synchronized by FACS sorting according to the DNA content.

tag: cell type

value: F121-9 mNPC

tag: developmental stage

value: neural progenitor cells


title: WT_4h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
NG-112_0027


title: mNPC_S15_BrdU


title: WT_4h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
NG-112_0026


title: 207_ PAXgene RNA tube Replicate 1

description: Biological replicate 1 of 2. RNA extracted from whole blood preserved in PAXgene RNA blood tubes.


title: 07D-6mg_Rep4

value: 7 days


title: WT_4h_mock_rep5

description:
wt_mock_rpkm.txt
NG-112_0025

value: mock


title: 3280.F2.C3.I5.R2

description: Internode 5 from 11-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: 3280.F2.C3.I5.R1

description: Internode 5 from 11-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: 207_ RNAgard tube Replicate 1

description: Biological replicate 1 of 3. RNA extracted from whole blood preserved in RNAgard blood tubes.


title: 3280.F2.C1.I5.R2

description: Internode 5 from 4-month-old plants T17 and T18 from Plot R2 compared with pool from internodes from all developmental stages


title: 3280.F2.C2.I5.R1

description: Internode 5 from 8-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: 3280.F2.C1.I5.R1

description: Internode 5 from 4-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: mNPC_S13_BrdU


title: 3280.F2.C2.I5.R2

description: Internode 5 from 8-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: 207_ CPT tube Replicate 1

description: Biological replicate 1 of 3. RNA extracted from PBMCs isolated from whole blood preserved in CPT tubes.


title: WT_4h_mock_rep4

description:
wt_mock_rpkm.txt
NG-112_0024


title: WT_12h_mock_rep4

description:
wt_mock_rpkm.txt
16090-0012


title: 3280.F2.C4.I1.R2

description: Internode 1 from 13-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: 3280.F2.C3.I1.R2

description: Internode 1 from 11-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: mNPC_S12_BrdU


title: 3280.F2.C3.I1.R1

description: Internode 1 from 11-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: mNPC_S14_BrdU


title: mNPC_S11_BrdU


title: 07D-6mg_Rep5


title: mNPC_S10_BrdU


title: 07D-2mg_Rep4


title: 07D-2mg_Rep5


title: WT_4h_mock_rep3

description:
wt_mock_rpkm.txt
NG-112_0023


title: 07D-2mg_Rep3


title: 07D-6mg_Rep1


title: WT_4h_mock_rep1

description:
wt_mock_rpkm.txt
NG-112_0021


title: 07D-2mg_Rep2


title: mNPC_S9_BrdU


title: WT_4h_mock_rep2

description:
wt_mock_rpkm.txt
NG-112_0022


title: WT_2h_S.meliloti_rep6

description:
wt_inoc_rpkm.txt
NG-112_0020


title: mNPC_S8_BrdU


title: 07D-0mg_Rep5


title: mNPC_S7_BrdU


title: 07D-0mg_Rep4


title: WT_2h_S.meliloti_rep5

description:
wt_inoc_rpkm.txt
NG-112_0019


title: 3280.F2.C2.I1.R2

description: Internode 1 from 8-month-old plants T9 and T10 from Plot R2 compared with pool from internodes from all developmental stages


title: 3280.F2.C2.I1.R1

description: Internode 1 from 8-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: 07D-0mg_Rep3


title: 3280.F2.C1.I1.R2

description: Internode 1 from 4-month-old plants T17 and T18 from Plot R2 compared with pool from internodes from all developmental stages


title: 3280.F2.C1.I1.R1

description: Internode 1 from 4-month-old plants T1 and T2 from Plot R1 compared with pool from internodes from all developmental stages


title: 07D-0mg_Rep2


title: WT_2h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
NG-112_0017


title: WT_2h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
NG-112_0016


title: 07D-0mg_Rep1


title: WT_2h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
NG-112_0015


title: mNPC_S4_BrdU


title: 00-Rep4

value: 0 days


title: WT_2h_mock_rep6

description:
wt_mock_rpkm.txt
NG-112_0014


title: mNPC_S3_BrdU


title: mNPC_S5_BrdU


title: 00-Rep3


title: WT_2h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
NG-112_0018


title: WT_2h_mock_rep5

description:
wt_mock_rpkm.txt
NG-112_0013


title: 00-Rep2


title: mNPC_S1_BrdU


title: mNPC_G1_WGS


title: WT_2h_mock_rep3

description:
wt_mock_rpkm.txt
NG-112_0011


title: 3280.F2.C3.L1.R1

description: Leaves +1 from 11-month-old plants T1 and T2 from Plot R1 from Fild 2 compared with pool from leaves +1 from all developmental stages

value: Leaf +1


title: 3280.F2.C4.L1.R1

description: Leaves +1 from 13-month-old plants T1 and T2 from Plot R1 from Field 2 compared with pool from leaves +1 from all developmental stages


title: 3280.F2.C3.L1.R2

description: Leaves +1 from 11-month-old plants T9 and T10 from Plot R2 from Field 2 compared with pool from leaves +1 from all developmental stages


title: 3280.F2.C2.L1.R1

description: Leaves +1 from 8-month-old plants T1 and T2 from Plot R1 from Field 2 compared with pool from leaves +1 from all developmental stages


title: 3280.F2.C1.L1.R2

description: Leaves +1 from 3-month-old plants T17 and T18 from Plot R2 from Field 2 compared with pool from leaves +1 from all developmental stages


title: mESC_S16_BrdU

source_name: mouse embryonic stem cells

value: F121-9 mESC

value: embryonic stem cells


title: WT_2h_mock_rep2

description:
wt_mock_rpkm.txt
NG-112_0010


title: mNPC_S2_BrdU


title: 3280.F2.C1.L1.R1

description: Leaves +1 from 3-month-old plants T1 and T2 from Plot R1 from Field 2 compared with pool from leaves +1 from all developmental stages

value: leaf +1


title: WT_0h_S.meliloti_rep4

description:
wt_inoc_rpkm.txt
NG-112_0008


title: WT_2h_mock_rep1

description:
wt_mock_rpkm.txt
NG-112_0009


title: 3280.F2.C4.L1.R2

description: Leaves +1 from 13-month-old plants T9 and T10 from Plot R2 from Field 2 compared with pool from leaves +1 from all developmental stages


title: WT_2h_mock_rep4

description:
wt_mock_rpkm.txt
NG-112_0012


title: Cdk8-ko control, replicate 4

city: Vienna

first: Veronika

last: Sexl

address: Veterinaerplatz 1

department: Pharmacology / Toxikology

country: Austria

institute: University of Veterinary Medicine Vienna

description: expression profile of BCR/ABLp185+ bone marrow Cdk8-ko cell lines DMSO control, replicate 4

data_processing:
Alignment to genome version GRCm38 using STAR
Adapter trimming and removing of low quality bases was performed using Trimmomatic
Counting of reads was done using featureCounts
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: raw count file (tab delimited)

source_name: BCR-ABL1p185+ bone marrow Cdk8∆/∆ cell lines

growth_protocol: Cells were cultured in RPMI incl. 10% FCS,50 μmol/l 2-mercaptoethanol, 100 u/ml penicillin and 100 μg/ml streptomycin

extract_protocol:
QIAGEN RNeasy extraction kit
RNA-seq: SENSE mRNA-Seq Library Prep kit, 50 bp single-end

treatment_protocol: cells were treated with 1µM SenexinB or 0,01% DMSO for 48h prior RNA isolation

value: bone marrow

value: Cdk8 KO

tag: treatment

value: control


title: Cdk8-ko control, replicate 3

description: expression profile of BCR/ABLp185+ bone marrow Cdk8-ko cell lines DMSO control, replicate 3


title: mESC_S14_BrdU


title: mESC_S13_BrdU


title: Cdk8-ko senexin B, replicate 4

description: expression profile of BCR/ABLp185+ bone marrow Cdk8-ko cell lines Senexin B, replicate 4

value: senexin B


title: Cdk8-ko senexin B, replicate 3

description: expression profile of BCR/ABLp185+ bone marrow Cdk8-ko cell lines Senexin B, replicate 3


title: mESC_S15_BrdU


title: LKO_3_Liver

city: Tsukuba

first: Takashi

last: Matsuzaka

state: Ibaraki

address: 1-1-1 Tennodai

department: Internal Medicine

country: Japan

institute: University of Tsukuba

description: Gene expression after 14 days high-sucrose diet feeding

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Liver from LKO mouse fed a high-sucrose diet

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA Kit (TaKaRa Bio, Shiga, Japan) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop Lite spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Liver-specific Elovl6 knockout (LKO) and control mice (n=3 per group) were fed high-sucrose diet (D11725, Research Diets) for 14 days, fasted for 4 hr, then sacrificed. Livers were removed and flash frozen in liquid nitrogen.

value: Liver-specific Elovl6 knockout (LKO)

value: liver

tag: gender

value: male


title: Cdk8-ko senexin B, replicate 2

description: expression profile of BCR/ABLp185+ bone marrow Cdk8-ko cell lines Senexin B, replicate 2


title: WT_0h_S.meliloti_rep3

description:
wt_inoc_rpkm.txt
NG-112_0007

value: 2-3mm segment of root

value: wild type ecotype jemalong cultivar Jester

value: Sinorhizobium meliloti strain 2011


title: LKO_1_Liver


title: LKO_2_Liver


title: Cdk8-ko control, replicate 2

description: expression profile of BCR/ABLp185+ bone marrow Cdk8-ko cell lines DMSO control, replicate 2


title: Flox_2_Liver

source_name: Liver from control mouse fed a high-sucrose diet


title: Cdk8-ko senexin B, replicate 1

description: expression profile of BCR/ABLp185+ bone marrow Cdk8-ko cell lines Senexin B, replicate 1


title: mESC_S11_BrdU


title: mESC_S12_BrdU


title: 3280.F2.C2.L1.R2

description: Leaves +1 from 8-month-old plants T9 and T10 from Plot R2 from Field 2 compared with pool from leaves +1 from all developmental stages


title: Cdk8-ko control, replicate 1

description: expression profile of BCR/ABLp185+ bone marrow Cdk8-ko cell lines DMSO control, replicate 1


title: WT_0h_S.meliloti_rep2

description:
wt_inoc_rpkm.txt
NG-112_0006


title: mESC_S10_BrdU


title: WT_0h_mock_rep2

description:
wt_mock_rpkm.txt
NG-112_0002


title: WT_0h_mock_rep4

description:
wt_mock_rpkm.txt
NG-112_0004


title: mESC_S7_BrdU


title: wild-type control, replicate 4

description: expression profile of BCR/ABLp185+ bone marrow wt cell lines DMSO control, replicate 4

source_name: BCR-ABL1p185+ bone marrow wt cell lines

value: wildtype


title: mESC_S6_BrdU


title: WT_0h_mock_rep1

description:
wt_mock_rpkm.txt
NG-112_0001

value: mock


title: WT_0h_mock_rep3

description:
wt_mock_rpkm.txt
NG-112_0003


title: wild-type control, replicate 3

description: expression profile of BCR/ABLp185+ bone marrow wt cell lines DMSO control, replicate 3


title: wild-type senexin B, replicate 4

description: expression profile of BCR/ABLp185+ bone marrow wt cell lines Senexin B, replicate 4


title: Flox_1_Liver


title: mESC_S9_BrdU


title: WT_0h_S.meliloti_rep1

description:
wt_inoc_rpkm.txt
NG-112_0005


title: mESC_S5_BrdU


title: wild-type senexin B, replicate 2

description: expression profile of BCR/ABLp185+ bone marrow wt cell lines Senexin B, replicate 2


title: wild-type control, replicate 2

description: expression profile of BCR/ABLp185+ bone marrow wt cell lines DMSO control, replicate 2


title: NI-4h-R3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description: total RNA (rRNA depleted)

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
Bowtie version 0.12.7 (parameters --chunkmbs 400 -m 1) was used for alignment on the reference genome (Mycobacterium abscessus strain ATCC19977 or Mycobacteroides chelonae CCUG 47445, from NCBI).
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -s 1).
Count data were analyzed using R version 3.4.1 and the Bioconductor package DESeq2 version 1.18.1. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm.
Genome_build: Mycobacterium abscessus souche ATCC19977, and Mycobacteroides chelonae CCUG 47445, from NCBI

organism: Mycobacteroides abscessus

source_name: 43 clinical strain (smooth)

growth_protocol: Amoebae and macrophages were infected with mid-log phase bacteria. Amoeba infections were performed in a nutrient poor medium called mowat while macropha infections were performed in DMEM medium supplemented with10% Fetal Bovine Serum.

extract_protocol:
Bacterial RNA were isolated with TRIzol reagent and extracted with chloroform isoamyl.
RNA samples were treated with DNases (AMBION) to remove DNA contaminants, purified with the RNA MEGAclear kit (Thermofisher), and depleted of ribosomal RNA with the riboZero kit (Illumina). RNA (total, depleted, purified) is checked on the Bioanalyser system (Agilent) for its quality and integrity. cDNA libraries were prepared with samples displaying a RIN above 7. Libraries were prepared with the TruSeq Stranded RNA LT prep kit cDNA synthesis, set A (Illumina).

treatment_protocol: Phagocytic cells were lysed with Guanidium thiocyanate, N-Lauryl-sarcosine, Sodium citrate +/- Tween 80 plus β-mercaptoethanol to release intracellular bacteria.

tag: source

value: 4 h M. abscessus culture in mowat medium

value: 43 clinical strain (smooth)

value: wild type


title: mESC_S4_BrdU

value: F121-9 mESC

value: embryonic stem cells


title: U937-collagen_SE HIV+Drug+_rep2

city: Stony Brook

first: Hussein

last: Kaddour

address: 100 Nicolls Road

department: Pharmacological Sciences

institute: Stony Brook University

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-infected ART-naïve people who use illicit drugs
SAMPLE 14_D2

hyb_protocol: The samples were hybridized overnight (16 hours) to Clariom™ S Human Arrays (Applied Biosystems™) in a GeneChip™ Hybridization Oven 645 (Applied Biosystems™)

scan_protocol: The arrays were washed and stained using the GeneChip™ Hybridization, Wash and Stain Kit, (Applied Biosystems™) in a GeneChip™ Fluidics Station 450, according to manufacturer’s protocol. The arrays were scanned in a GeneChip™ Scanner 3000 7G (Applied Biosystems™)

data_processing:
QC analysis and initial analysis were performed using Transcriptome Analysis Console (TAC) V 4.0.0.25 (Applied Biosystems™)
The expression analysis settings were as follow: Gene-Level Fold Change < -2 or > 2, Gene-Level P-Value < 0.05, and ebayes ANOVA Method

label: Biotin

source_name: promonocytes-collagen_SE HIV+Drug+

label_protocol: 150 ng of total RNA was prepared for microarray analysis using the GeneChip™ WT PLUS Reagent Kit (Applied Biosystems) according to manufacturer’s protocol.

growth_protocol: Promonocytic U937 cells were maintained in RPMI media, supplemented with 10% FBS, 1% penicillin streptomycin, 1µg/mL Amphetoricin B, 2 mM sodium pyruvate, 1% of glutamate, and 10 mM HEPES buffer pH 8, in a 37°C, 5% CO2 incubator

extract_protocol: total RNA was extracted from cells using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's protocol. An on-column DNAse digestion step (RNase-Free DNase set, Qiagen, Germany) was added after the first wash buffer step of the kit. RNA quality and quantity was measured determined in duplicate with ND-1000 NanoDrop Spectrophotometer (Thermofisher) and 2100 Bioanalyzer (Agilent)

treatment_protocol: Three Biological replicates of U937 cells (2 million) were treated with vehicle PBS (P) or with 100 µg semen exosomes from four different clinical groups (A: HIV-Drug-, B: HIV-Drug+, C: HIV+Drug-, and D: HIV+Drug+) and plated in collagen-coated tissue culture 6 well plates. The culture was incubated in a 37°C, 5% CO2 incubator for 18 hours.

tag: cell line

value: semen exosomes from HIV+Drug+

tag: incubation condition

value: atop collagen_18 hours, 37°C, 5% CO2


title: U937-collagen_SE HIV+Drug-_rep3

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-infected ART-naïve people who do not use illicit drugs
SAMPLE 12_C3

source_name: promonocytes-collagen_SE HIV+Drug-

value: semen exosomes from HIV+Drug-


title: NI-4h-R2

description: total RNA (rRNA depleted)

tag: genotype


title: mESC_S8_BrdU


title: wild-type senexin B, replicate 3

description: expression profile of BCR/ABLp185+ bone marrow wt cell lines Senexin B, replicate 3

tag: tissue

value: bone marrow

value: senexin B


title: NI-4h-R1

description: total RNA (rRNA depleted)


title: mESC_S3_BrdU


title: U937-collagen_SE HIV+Drug-_rep2

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-infected ART-naïve people who do not use illicit drugs
SAMPLE 11_C2


title: U937-collagen_SE HIV+Drug+_rep3

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-infected ART-naïve people who use illicit drugs
SAMPLE 15_D3


title: wild-type senexin B, replicate 1

description: expression profile of BCR/ABLp185+ bone marrow wt cell lines Senexin B, replicate 1


title: NI-16h-R3

description: total RNA (rRNA depleted)

value: 16 h M. abscessus culture in mowat medium


title: mESC_S1_BrdU


title: NI-16h-R2

description: total RNA (rRNA depleted)


title: mESC_S2_BrdU


title: U937-collagen_SE HIV+Drug+_rep1

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-infected ART-naïve people who use illicit drugs
SAMPLE 13_D1


title: U937-collagen_SE HIV-Drug+_rep3

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-unifected (Healthy) people who use illicit drugs
SAMPLE 9_B3

source_name: promonocytes-collagen_SE HIV-Drug+

value: semen exosomes from HIV-Drug+


title: U937-collagen_SE HIV-Drug+_rep2

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-unifected (Healthy) people who use illicit drugs
SAMPLE 8_B2


title: Mlkl -/-

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Illumina v1.8 software used for basecalling
A gene-barcode matrix was generated for each sample using  the Cell Ranger pipeline v3.0.2 from 10X Genomics. For Mlkl -/- sample,  cells were included if the number of unique genes detected per cell were between 500 and 3500 and  percentage of mitochondrial reads <= 4%. For  Casp8 C362A/C362A Mlkl -/- sample, cells were included if number of unique genes detected per cell were  between 300 and 3000 and percentage of mitochondrial reads <= 4%.
We used integration method in Seurat v3.0 to identify cell types that are common  and unique to both samples. Dimensionality reduction was then performed on the normalized and  scaled data, followed by clustering and visualization using Unified Manifold Approximation and  Projection (UMAP).
For each sample the R1 file provides the barcode representing the cell and the R2 file provides the insert sequence
Genome_build: mm10

source_name: small intestine

extract_protocol:
Whole intestines were harvested from E18.5 embryos and dissociated using the Worthington Papain Dissociation System (LK003150). Used 0.5 mL papain solution per sample with a 30 minute incubation time. Approximately 10,000 cells injected for single-cell RNA-seq with the Chromium Single Cell 3’ Library and Gel bead kit v2 (10x Genomics).
cDNAs and libraries were prepared according to manufacturer instructions (10× Genomics)

tag: background

tag: age

value: Mlkl -/-


title: Casp8 C362A/C362A Mlkl -/-

value: Casp8 C362A/C362A Mlkl -/-


title: mESC_G1_WGS


title: NI-16h-R1

description: total RNA (rRNA depleted)


title: pTATA-loz1GFP_MinusZn_input2

city: Columbus

first: Stevin

last: Wilson

state: Ohio

department: Molecular Genetics

institute: The Ohio State University

data_processing:
Sequencing reads were analyzed using the HOMER suite (Heinz et al., 2010).
Tag directories were created using HOMER makeTagDirectory with -fragLength parameter set for each sample.
UCSC bedgraph files were generated for each sample using HOMER makeUCSCfile
Genome_build: Schizosaccharomyces_pombe.ASM294v2
Supplementary_files_format_and_content: UCSC bedgraph files generated using HOMER makeUCSCfile

organism: Schizosaccharomyces pombe

source_name: cells

growth_protocol: 75 ml of the strain loz1Δ pgk1(ΔTATA)-Loz1GFP were grown to an OD600 of ~6.0 in ZL-EMM supplemented with or without 100 mM Zn2+ and were treated with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched by the addition of 250 mM glycine.

extract_protocol:
Cells were then washed, resuspended in the lysis buffer (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% (v/v) Triton X-100, 0.1% (w/v) sodium deoxycholate, 0.4mM DTT, and protease inhibitors) and lysed by vortexing for 7 x 1 min in the presence of zirconium beads.  To obtain cross-linked chromatin, cell lysates were centrifuged at 14,000 rpm for 5 min and the supernatant discarded.  After centrifugation, cross-linked chromatin was resuspended in lysis buffer, DNA sheared to an average length of 500 bp by sonication using Covaris Evolution, and cell debris removed by centrifugation at 14000 rpm for 5 min.   For immunoprecipitations, chromatin solutions were incubated with anti-GFP antibodies (Abcam Ab290) and protein A magnetic beads (Invitrogen™ Dynabeads™ Protein A) overnight at 4°C.   After Immuno-complexes were harvested the crosslinks were reversed by heating at 65°C for 5-7 hrs.
The ChIP-seq library preparation and sequencing were performed by the Institute for Genomic Medicine at Nationwide Children’s Hospital. ChIP-seq libraries were constructed from 5 ng of fragmented ChIP DNA using NEB Ultra II FS library prep kit (New England Biolabs, Ipswhich MA).  Briefly, DNA fragment ends were 5´ Phosphorylated, dA-tailed, and ligated with a unique, dual UMI indexed adaptor (Integrated DNA Technologies, Iowa). Following purification, using a magnetic-bead based approach (AMPure XP System), adaptor-ligated DNA was amplified by 8-9 PCR cycles.  Quality of libraries were determined via Agilent 2200 TapeStation using High Sensitivity D1000 reagents, and quantified using Kappa SYBR®Fast qPCR kit (KAPA Biosystems, Inc, MA).

tag: chip antibody

tag: zinc supplementation

value: no


title: K-mac-16h-R2

description: total RNA (rRNA depleted)

value: M.abscessus infection of J774.2 macrophages for 16  h

tag: strain


title: L-mac-16h-R3

description: total RNA (rRNA depleted)


title: mNPC_S6_BrdU

value: F121-9 mNPC

value: neural progenitor cells


title: pTATA-loz1GFP_MinusZn_input1


title: wild-type control, replicate 1

description: expression profile of BCR/ABLp185+ bone marrow wt cell lines DMSO control, replicate 1

value: wildtype

value: control


title: J-mac-16h-R1

description: total RNA (rRNA depleted)

value: 43 clinical strain (smooth)

value: wild type


title: pTATA-loz1GFP_MinusZn_repeat4


title: I-ni-16h-R3

description: total RNA (rRNA depleted)

value: 16 h M. abscessus culture in DMEM 10%


title: pTATA-loz1GFP_MinusZn_repeat3


title: I-4h-R3

description: total RNA (rRNA depleted)

value: M.abscessus infection of A. castellanii for 4 h


title: T-NI-R4

description: total RNA (rRNA depleted)

organism: Mycobacteroides chelonae

value: 16 h M. chelonae culture in mowat medium


title: I-4h-R2

description: total RNA (rRNA depleted)


title: R-NI-R2

description: total RNA (rRNA depleted)


title: S-NI-R3

description: total RNA (rRNA depleted)


title: pTATA-loz1GFP_MinusZn_repeat2


title: pTATA-loz1GFP_MinusZn_repeat1


title: I-4h-R1

description: total RNA (rRNA depleted)


title: U937-collagen_SE HIV-Drug-_rep3

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-unifected (Healthy) people who do not use illicit drugs
SAMPLE 6_A3

source_name: promonocytes-collagen_SE HIV-Drug-

value: semen exosomes from HIV-Drug-

value: atop collagen_18 hours, 37°C, 5% CO2


title: U937-collagen_SE HIV-Drug-_rep2

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-unifected (Healthy) people who do not use illicit drugs
SAMPLE 5_A2


title: pTATA-loz1GFP_PlusZn_input2

value: yes


title: Flox_3_Liver

description: Gene expression after 14 days high-sucrose diet feeding

value: liver

value: male


title: I-16h-R3

description: total RNA (rRNA depleted)

value: M.abscessus infection of A. castellanii for 16 h


title: Q-NI-R1

description: total RNA (rRNA depleted)


title: U937-collagen_SE HIV-Drug+_rep1

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-unifected (Healthy) people who use illicit drugs
SAMPLE 7_B1

value: semen exosomes from HIV-Drug+


title: U937-collagen_SE HIV-Drug-_rep1

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-unifected (Healthy) people who do not use illicit drugs
SAMPLE 4_A1


title: U937-collagen_PBS_rep2

description:
gene expression data of promonocytic U937 cells treated with vehicle PBS
SAMPLE 2_P2

value: vehicle PBS (P)


title: persister cell polysome pools_rep3

city: Villejuif

first: Shensi

last: SHEN

address: 114 Rue Edouard Vaillant

institute: Gustave Roussy Institute

description:
polysome RNA
A375 persister cell on Day 1

hyb_protocol: Accoding to Affymetrix protocol

scan_protocol: Accoding to Affymetrix protocol

data_processing:
The data were analyzed with Affymetrix default analysis settings and global scaling as normalization method.
Clariom_D_Human.r1.pgf
Clariom_D_Human.na36.hg38.transcript.csv

label: biotin

source_name: A375 persister cell

label_protocol: Accoding to Affymetrix protocol

growth_protocol: A375 melanoma cells were cultured according to the ATCC protocol

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

treatment_protocol: One day after spliting A375 cells were treated for 3 days with DMSO or Vemurafenib and combimetinib

value: melanoma


title: U937-collagen_PBS_rep1

description:
gene expression data of promonocytic U937 cells treated with vehicle PBS
SAMPLE 1_P1


title: pTATA-loz1GFP_PlusZn_input1


title: parental cell polysome pools_rep2

description:
polysome RNA
A375 parental cell on Day 1

source_name: A375 parental cell


title: persister cell polysome pools_rep2


title: P-I-R4

description: total RNA (rRNA depleted)

value: M. chelonae infection of A. castellanii for 16 h


title: U937-collagen_PBS_rep3

description:
gene expression data of promonocytic U937 cells treated with vehicle PBS
SAMPLE 3_P3


title: parental cell polysome pools_rep1


title: parental cell polysome pools_rep3


title: parental cell mRNA total input_rep3

description: A375 parental cell on Day 1


title: pTATA-loz1GFP_PlusZn_repeat4


title: I-16h-R1

description: total RNA (rRNA depleted)


title: pTATA-loz1GFP_PlusZn_repeat3


title: persister cell polysome pools_rep1


title: I-16h-R2

description: total RNA (rRNA depleted)


title: O-I-R3

description: total RNA (rRNA depleted)


title: N-I-R2

description: total RNA (rRNA depleted)


title: G-ni-16h-R1

description: total RNA (rRNA depleted)


title: H-ni-16h-R2

description: total RNA (rRNA depleted)


title: M-I-R1

description: total RNA (rRNA depleted)


title: pTATA-loz1GFP_PlusZn_repeat2


title: pTATA-loz1GFP_PlusZn_repeat1


title: Negative Control 10

status: Public on Sep 19 2019

city: Siena

first: Mohsen

last: Navari

state: SI

address: Via delle Scotte 6

department: Medical Biotechnology

country: Italy

institute: University of Siena

description:
normal T-cells
SAMPLE 13

data_processing: The expression level of miRNAs was normalized to house keeping miRNAs and the data was further processed in GeneSpring version GX 12  based on the following criteria: threshold: 1.0; logbase: 2; normalization: shift to 75 percentile; baseline transformation: median of all samples.

source_name: Healthy Donor

label_protocol: Briefly, 350 ng of total RNA for each samples was reversed transcribed using the Megaplex RT stem-loop primers in a 7.5 μl reaction volume through the protocol’s default 40 cycles run; 2.5 μl of each RT product were pre-amplified in a 25 μl reaction volume with Megaplex Pre-Amp primers to increase detection sensitivity according to manufacturer specifications. Nine μl of 4-fold diluted pre-amplified RT product were 100 fold diluted in the PCR reaction mix and amplified using TaqMan Low Density Arrays (TLDAs) on a TaqMan Real Time 7900HT (Life Technologies, Carlsbad, CA USA) according to the standard protocol.

extract_protocol: For FFPE samples, RecoverAll™ Total Nucleic Acid Isolation Kit (Thermofisher, Waltham, MA, USA) was used to extract total RNA from FFPE samples. Up to five 10 μm-thick sections were processed per reaction. The samples were rehydrated using a series of xylene and ethanol washes. Next, they were subjected to a rigorous protease digestion with an incubation time tailored for recovery of total RNA. RNA was purified using a rapid glass-fibre filter methodology that includes an on-filter DNase treatment and were eluted into the low salt buffer provided. A NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA) was used to quantify RNA content and assess its purity in terms of 260/280 and 260/230 absorbance.  Extraction of RNA from normal CD4+ samples was achieved by means of TRIZOL (Thermofisher, Waltham, MA, USA) reagent, according to the manufacturer’s protocol.

tag: disease state

value: normal T-cells

tag: sample type

value: Fresh Cells


title: Negative Control 12

description:
normal T-cells
SAMPLE 15

value: control


title: persister cell mRNA total input_rep3

description: A375 persister cell on Day 1


title: Negative Control 5

description:
normal T-cells
SAMPLE 8


title: Negative Control 8

description:
normal T-cells
SAMPLE 11


title: Negative Control 7

description:
normal T-cells
SAMPLE 10


title: Negative Control 6

description:
normal T-cells
SAMPLE 9


title: Negative Control 4

description:
normal T-cells
SAMPLE 7


title: 21: PC-3M-Pro4 cells in culture 3

city: Leiden

first: Lanpeng

last: Chen

state: South Holland

address: Einsteinweg 55, GW3.19

department: Institute of Biology

institute: Leiden University

description: Cell lines in culture

data_processing:
All RNAseq libraries (150–750 bp inserts) were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single-end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample.
Illumina reads were aligned against the human (GRCh38.p3) and zebrafish (GRCz10.80) reference genome sequences using TopHat (version 2.0.5). Secondary alignments of reads were excluded by filtering the files using SAMtools (version 0.1.18)
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9).
To make comparisons across samples possible, these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor, library size estimates determined using the R/Bioconductor (release 2.11) package DESeq were employed
Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools.
Supplementary_files_format_and_content: tab-delimited text files include gene name, ID, reads and normalized comparision between each groups

source_name: PC-3M-Pro4 cells

growth_protocol: PC-3M-Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200-400 PC-3M-Pro4 cells were injected into the duct of cuvier (DoC) of the zebrafish embryos using a Pneumatic Picopump and a manipulator (WPI). After transplantation, 120 well-engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.

extract_protocol:
Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area (80 fish per group randomly chosen from >100 engrafted fish) at 6dpi (8dpf) with a micro dissection scissor (WPI). The samples were immediately washed with cold PBS and stored in TRIzol (Sigma) at -80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at  -80 ˚C. RNA isolation was further performed using RNeasy mini kit (qiagen)
then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina, San Diego CA, USA).

value: PC-3M-Pro4 cells

tag: FISH strain


title: PTCL3

description:
peripheral T-cell lymphoma
SAMPLE 3

source_name: Tumor Sample

value: peripheral T-cell lymphoma

value: Tumor

value: Formalin-Fixed, Paraffin-Embedded


title: Negative Control 1

description:
normal T-cells
SAMPLE 4

tag: cell type


title: Negative Control 11

description:
normal T-cells
SAMPLE 14


title: Negative Control 3

description:
normal T-cells
SAMPLE 6


title: 19: PC-3M-Pro4 cells in culture 1

description: Cell lines in culture


title: Negative Control 9

description:
normal T-cells
SAMPLE 12


title: PTCL2

description:
peripheral T-cell lymphoma
SAMPLE 2


title: Negative Control 2

description:
normal T-cells
SAMPLE 5


title: 20: PC-3M-Pro4 cells in culture 2

description: Cell lines in culture


title: parental cell mRNA total input_rep1

description: A375 parental cell on Day 1


title: persister cell mRNA total input_rep2

description: A375 persister cell on Day 1


title: parental cell mRNA total input_rep2

description: A375 parental cell on Day 1


title: persister cell mRNA total input_rep1

description: A375 persister cell on Day 1


title: Day 15_CD47+_B_re-analyzed

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

description:
sample name in processed data file:
day15_CD47_B
GSM2537137

data_processing:
Fastq files were align to the hg19 reference genome using STAR and default parameters
Ensembl v67 gene annotations were used for gene counts, gene counts were obtain using STAR
Raw gene counts were transformed using 'LIMMA-Voom' method
Genome_build: Hg19
Supplementary_files_format_and_content: Voom transformed abundance measurement, log2 scaled.

source_name: RUES2 ESCs

growth_protocol: Fetal lung tissue (weeks 16-21) was obtained in the Guttentag laboratory under protocols originally reviewed by the Institutional Review Board at the Children’s Hospital of Philadelphia and subsequently reviewed by Vanderbilt University. The cell stocks used in the present studies were donated to the Kotton laboratory for the purpose of providing reference data. Samples were isolated by the overnight culture of lung explants in Waymouth media; a technique that generally yields 86 ± 2% epithelial cells with the remaining cells consisting of fibroblasts with <1% endothelial cells

extract_protocol:
Tissue was digested using dispase, collagenase I, and DNase using the gentle MACS 63 dissociator (Miltenyi) for 30 minutes at 37°C. The cell suspension was passed over 70uM and 40uM filters to generate a single cell suspension. Magnetic bead sorting using MACS LS columns (Miltenyi) and the following antibodies: HTII-280 (anti-human AEC2 antibody, IgM, Terrace Biotechnologies) and anti-IgM magnetic beads (Miltenyi) was used to obtain purified human AEC2 cells and were subsequently collected into trizol
Sequencing libraries were prepared from the total RNA extracts of the above 13 samples using Illumina TruSeq RNA Sample Preparation Kit v2. The mRNA was isolated using magnetic beads-based poly(A) selection, fragmented, and randomly primed for reverse transcription, followed by second-strand synthesis to create double-stranded cDNA fragments. These cDNA fragments were then end-repaired, added with a single ‘A’ base, and ligated to Illumina® 64 Paired-End sequencing adapters. The products were purified and PCR-amplified to create the final cDNA library. The libraries from individual samples were pooled in groups of four for cluster generation on the Illumina cBot using Illumina TruSeq Paired-End Cluster Kit. Each sample was sequenced four per lane on the Illumina HiSeq 2500 to generate more than 30 million single end 100-bp reads

value: RUES2 ESCs

tag: developmental stage

value: Day 15 in-vitro differentiation

tag: culture media

value: 9 days Chir, Bmp4, retinoic acid (CBRa)

tag: isolation method

value: sorted CD47hi/CD26lo, enriched for NKX2-1+ cells


title: 21 wk fetal_D_re-analyzed

description:
sample name in processed data file:
late_HFL_D
GSM2537135

source_name: lung explant

value: lung explant

value: gestational week 21

value: overnight in Waymouth's media

value: enriched for epithelial cells by overnight culture


title: 21 wk fetal_C_re-analyzed

description:
sample name in processed data file:
late_HFL_C
GSM2537134


title: 21 wk fetal_B_re-analyzed

description:
sample name in processed data file:
late_HFL_B
GSM2537133


title: Day 15_CD47+_C_re-analyzed

description:
sample name in processed data file:
day15_CD47_C
GSM2537138


title: Day 15_CD47+_A_re-analyzed

description:
sample name in processed data file:
day15_CD47_A
GSM2537136


title: PTCL1

description:
peripheral T-cell lymphoma
SAMPLE 1


title: 20 wk fetal_A

description:
sample name in processed data file:
late_HFL_A

value: gestational week 20


title: week 16 fetal_A

description:
sample name in processed data file:
early_HFL_A

value: gestational week 16


title: Adult AEC2_A_re-analyzed

description:
sample name in processed data file:
adult_lung_A
GSM2537127

source_name: lung

value: lung

value: 43 years

value: sorted HT2-280 antibody positive cells


title: week 17.5 fetal_B

description:
sample name in processed data file:
early_HFL_B

value: gestational week 17.5


title: Adult AEC2_C_re-analyzed

description:
sample name in processed data file:
adult_lung_C
GSM2537129

value: 77 years


title: PDIS9061-763

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

data_processing:
FASTQ files were generated using bcl2fastq (v2.16.0.10).
For RamDA-seq data with living cells, fastq-mcf (version 1.04.807) was used for adapter trimming with the parameters '-l 36 --lowcomplex-pct 74 --homopolymer- pct 74 -k 4' for RamDA-seq and '-L 75 -l 46 -k 4 -q 30' for C1-RamDA-seq. The reads were mapped to the mouse genome (mm10) using HISAT2 with the parameters '--dta-cufflinks -p 4 -k 5 -X 800 --sp 1000,1000'. Uniquely mapped reads were selected using the bamtools ‘filter’ command with the parameters '-isMapped true -tag NH:1' and samtools ‘view’ command with the parameter ‘-q 40’. BigWig files were generated using deepTools (version 2.2.4). The transcript-level expression levels were quantified using sailfish (version 0.9.2). The transcript-level expression levels were also calculated using Bowtie2 (version 2.2.6) with the parameters '-k 100 -X 800' and eXpress (version 1.5.1) with the parameter '--no-bias-correct'.
Genome_build: mm10
Supplementary_files_format_and_content: txt, bigWig

growth_protocol: 5G6GR mouse ES cells were used for bulk and single-cell RNA-seq. The cells were cultured in a feeder-free gelatin-coated dish in 10% fetal calf serum containing Glasgow minimal essential medium (GMEM; Sigma-Aldrich), 1000 U/mL leukemia inhibitory factor (ESGRO; Invitrogen), 100 µmol/l 2-mercaptoethanol (Nacalai Tesque), 1× non-essential amino acids (Life Technologies), 1 mmol/L sodium pyruvate (Life Technologies), 2 mmol/L L-glutamine (Nacalai Tesque), 0.5× penicillin/streptomycin (Life Technologies), 0.5 ug/ml puromycin (Sigma) and 10 µg/mL blasticidin (Life Technologies).

extract_protocol:
For single-cell RamDA-seq, single cells were directly sorted into the cell lysis buffer containing RNasein plus (Promega), Cell Lysis Buffer (Roche), NP40 (Thermo), and RNase free water (TaKaRa). The cell lysate solution was stored at -80ºC until use.
For library construction of RamDA-seq, refer to the protocol in "Single-cell full-length total RNA sequencing uncovers dynamics of non-polyadenylated RNAs, recursive splicing and enhancer RNAs".

treatment_protocol: For the assessment of PrE differentiation, 5G6GR ES cells were cultured in differentiation medium containing 100 mmol/l dexamethasone rather than blasticidin. The cells are cultured for 72 hours.

value: Neural stem cell derived from human induced pluripotent stem

value: MoFlo sorted cell

tag: method subtype

value: RamDA-seq


title: PDIS9061-766


title: PDIS9061-768


title: PDIS9061-767


title: PDIS9061-765


title: PDIS9061-764


title: PDIS9061-761


title: PDIS9061-762


title: PDIS9061-760


title: PDIS9061-758


title: PDIS9061-759


title: PDIS9061-757


title: PDIS9061-756


title: PDIS9061-755


title: PDIS9061-754


title: U937-collagen_SE HIV+Drug-_rep1

description:
gene expression data of promonocytic U937 cells treated with semen exosomes from HIV-infected ART-naïve people who do not use illicit drugs
SAMPLE 10_C1

tag: cell line

tag: treatment

value: semen exosomes from HIV+Drug-

value: atop collagen_18 hours, 37°C, 5% CO2


title: PDIS9061-751


title: PDIS9061-749


title: PDIS9061-752


title: PDIS9061-750


title: week 17.5 fetal_C

description:
sample name in processed data file:
early_HFL_C


title: Adult AEC2_B_re-analyzed

description:
sample name in processed data file:
adult_lung_B
GSM2537128

value: 62 years


title: PDIS9061-742


title: PDIS9061-746


title: PDIS9061-741


title: PDIS9061-739


title: PDIS9061-743


title: PDIS9061-733


title: PDIS9061-734


title: PDIS9061-738


title: PDIS9061-744


title: PDIS9061-736


title: PDIS9061-729


title: PDIS9061-732


title: PDIS9061-730


title: PDIS9061-727


title: PDIS9061-731


title: PDIS9061-728


title: PDIS9061-735


title: PDIS9061-724


title: PDIS9061-726


title: PDIS9061-747


title: PDIS9061-753


title: PDIS9061-740


title: PDIS9061-721


title: PDIS9061-717


title: PDIS9061-718


title: PDIS9061-719


title: PDIS9061-716


title: PDIS9061-714


title: PDIS9061-715


title: PDIS9061-720


title: PDIS9061-737


title: PDIS9061-713


title: PDIS9061-722


title: PDIS9061-705


title: PDIS9061-712


title: PDIS9061-708


title: PDIS9061-707


title: PDIS9061-709


title: PDIS9061-704


title: PDIS9061-699


title: PDIS9061-697


title: PDIS9061-703


title: PDIS9061-700


title: PDIS9061-694


title: PDIS9061-692


title: PDIS9061-693


title: PDIS9061-691


title: PDIS9061-690


title: PDIS9061-689


title: PDIS9061-688


title: PDIS9061-687


title: PDIS9061-686


title: PDIS9061-683


title: PDIS9061-711


title: PDIS9061-682


title: PDIS9061-681


title: PDIS9061-695


title: PDIS9061-680


title: PDIS9061-679


title: PDIS9061-672


title: PDIS9061-673


title: PDIS9061-674


title: PDIS9061-677


title: PDIS9061-671


title: PDIS9061-668


title: PDIS9061-670


title: PDIS9061-666


title: PDIS9061-665


title: PDIS9061-662


title: PDIS9061-669


title: PDIS9061-660


title: PDIS9061-658


title: PDIS9061-661


title: PDIS9061-664


title: PDIS9061-657


title: PDIS9061-685


title: PDIS9061-654


title: PDIS9061-678


title: PDIS9061-653


title: PDIS9061-655


title: PDIS9061-650


title: PDIS9061-652


title: PDIS9061-649


title: PDIS9061-648


title: PDIS9061-656


title: PDIS9061-647


title: PDIS9061-646


title: PDIS9061-676


title: PDIS9061-644


title: PDIS9061-638


title: PDIS9061-641


title: PDIS9061-639


title: PDIS9061-642


title: PDIS9061-634


title: PDIS9061-633


title: PDIS9061-636


title: PDIS9061-637


title: PDIS9061-630


title: PDIS9061-632


title: PDIS9061-629


title: PDIS9061-631


title: PDIS9061-625


title: PDIS9061-626


title: PDIS9061-627


title: PDIS9061-628


title: PDIS9061-622


title: PDIS9061-623


title: PDIS9061-620


title: PDIS9061-619


title: PDIS9061-621


title: PDIS9061-617


title: PDIS9061-645


title: PDIS9061-618


title: PDIS9061-643


title: PDIS9061-616


title: PDIS9061-635


title: PDIS9061-640


title: PDIS9061-615


title: PDIS9061-614


title: PDIS9061-613


title: PDIS9061-610


title: PDIS9061-611


title: PDIS9061-606


title: PDIS9061-609


title: PDIS9061-607


title: PDIS9061-605


title: PDIS9061-599


title: PDIS9061-602


title: PDIS9061-601


title: PDIS9061-600


title: PDIS9061-604


title: PDIS9061-597


title: PDIS9061-595


title: PDIS9061-593


title: PDIS9061-594


title: PDIS9061-612


title: PDIS9061-586


title: PDIS9061-590


title: PDIS9061-591


title: PDIS9061-587


title: PDIS9061-608


title: PDIS9061-582


title: PDIS9061-581


title: PDIS9061-583


title: PDIS9061-585


title: PDIS9061-580


title: PDIS9061-592


title: PDIS9061-579


title: PDIS9061-575


title: PDIS9061-577


title: PDIS9061-576


title: PDIS9061-578


title: PDIS9061-568


title: PDIS9061-566


title: PDIS9061-571


title: PDIS9061-572


title: PDIS9061-565


title: PDIS9061-563


title: PDIS9061-567


title: PDIS9061-560


title: PDIS9061-557


title: PDIS9061-555


title: PDIS9061-556


title: PDIS9061-554


title: PDIS9061-549


title: PDIS9061-562


title: PDIS9061-561


title: PDIS9061-558


title: PDIS9061-573


title: PDIS9061-552


title: PDIS9061-551


title: PDIS9061-548


title: PDIS9061-553


title: PDIS9061-569


title: PDIS9061-547


title: PDIS9061-546


title: PDIS9061-541


title: PDIS9061-536


title: PDIS9061-543


title: PDIS9061-538


title: PDIS9061-544


title: PDIS9061-539


title: PDIS9061-537


title: PDIS9061-534


title: PDIS9061-532


title: PDIS9061-542


title: PDIS9061-698


title: PDIS9061-529


title: PDIS9061-530


title: PDIS9061-528


title: PDIS9061-531


title: PDIS9061-527


title: PDIS9061-526


title: PDIS9061-521


title: PDIS9061-517


title: PDIS9061-523


title: PDIS9061-519


title: PDIS9061-520


title: PDIS9061-516


title: PDIS9061-515


title: PDIS9061-514


title: PDIS9061-513


title: PDIS9061-535


title: PDIS9061-511


title: PDIS9061-510


title: PDIS9061-509


title: PDIS9061-512


title: PDIS9061-508


title: PDIS9061-507


title: PDIS9061-524


title: PDIS9061-500


title: PDIS9061-502


title: PDIS9061-506


title: PDIS9061-505


title: PDIS9061-503


title: PDIS9061-501


title: PDIS9061-499


title: PDIS9061-504


title: PDIS9061-494


title: PDIS9061-498


title: PDIS9061-495


title: PDIS9061-489


title: PDIS9061-497


title: PDIS9061-496


title: PDIS9061-490


title: PDIS9061-487


title: PDIS9061-484


title: PDIS9061-482


title: PDIS9061-480


title: PDIS9061-483


title: PDIS9061-488


title: PDIS9061-479


title: PDIS9061-473


title: PDIS9061-474


title: PDIS9061-475


title: PDIS9061-476


title: PDIS9061-472


title: PDIS9061-486


title: PDIS9061-469


title: PDIS9061-467


title: PDIS9061-468


title: PDIS9061-470


title: PDIS9061-465


title: PDIS9061-457


title: PDIS9061-463


title: PDIS9061-459


title: PDIS9061-461


title: PDIS9061-454


title: PDIS9061-464


title: PDIS9061-460


title: PDIS9061-453


title: PDIS9061-451


title: PDIS9061-452


title: PDIS9061-449


title: PDIS9061-478


title: PDIS9061-450


title: PDIS9061-446


title: PDIS9061-466


title: PDIS9061-445


title: PDIS9061-444


title: PDIS9061-438


title: PDIS9061-440


title: PDIS9061-441


title: PDIS9061-439


title: PDIS9061-437


title: PDIS9061-442


title: PDIS9061-435


title: PDIS9061-436


title: PDIS9061-434


title: PDIS9061-432


title: PDIS9061-430


title: PDIS9061-431


title: PDIS9061-448


title: PDIS9061-423


title: PDIS9061-424


title: PDIS9061-427


title: PDIS9061-433


title: PDIS9061-426


title: PDIS9061-422


title: PDIS9061-471


title: PDIS9061-425


title: PDIS9061-420


title: PDIS9061-419


title: PDIS9061-417


title: PDIS9061-418


title: PDIS9061-443


title: PDIS9061-416


title: PDIS9061-414


title: PDIS9061-413


title: PDIS9061-410


title: PDIS9061-409


title: PDIS9061-408


title: PDIS9061-429


title: PDIS9061-407


title: PDIS9061-406


title: PDIS9061-596


title: PDIS9061-405


title: PDIS9061-399


title: PDIS9061-404


title: PDIS9061-398


title: PDIS9061-401


title: PDIS9061-393


title: PDIS9061-397


title: PDIS9061-392


title: PDIS9061-391


title: PDIS9061-395


title: PDIS9061-389


title: PDIS9061-388


title: PDIS9061-415


title: PDIS9061-385


title: PDIS9061-384


title: PDIS9061-411


title: PDIS9061-383


title: PDIS9061-381


title: PDIS9061-380


title: PDIS9061-379


title: PDIS9061-382


title: PDIS9061-378


title: PDIS9061-372


title: PDIS9061-377


title: PDIS9061-370


title: PDIS9061-369


title: PDIS9061-371


title: PDIS9061-365


title: PDIS9061-368


title: PDIS9061-390


title: PDIS9061-364


title: PDIS9061-360


title: PDIS9061-359


title: PDIS9061-361


title: PDIS9061-373


title: PDIS9061-362


title: PDIS9061-386


title: PDIS9061-387


title: PDIS9061-358


title: PDIS9061-357


title: PDIS9061-355


title: PDIS9061-353


title: PDIS9061-356


title: PDIS9061-375


title: PDIS9061-354


title: PDIS9061-347


title: PDIS9061-348


title: PDIS9061-352


title: PDIS9061-351


title: PDIS9061-346


title: PDIS9061-344


title: PDIS9061-343


title: PDIS9061-366


title: PDIS9061-340


title: PDIS9061-345


title: PDIS9061-336


title: PDIS9061-339


title: PDIS9061-341


title: PDIS9061-335


title: PDIS9061-337


title: PDIS9061-329


title: PDIS9061-338


title: PDIS9061-333


title: PDIS9061-330


title: PDIS9061-328


title: ATAC_Eutrema_10days_leaf_Input

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

data_processing:
RNA-seq: analysis was performed using Tophat v2.1.1 and cufflinks v2.2.1
ChIP-seq: analysis was performed using bowtie1.1.1
ATAC-seq:analysis was performed using bowtie1.1.1, macs2
Genome_build: Arabidopsis thaliana, Eutrema salsugineum, Phaseolus vulgaris,  Glycine max, Brachypodium distachyon, Oryza sativa, Setaria viridis, Populus trichocarpa, Sorghum bicolor genomes were from JGI (phytozome version 11) ; Zea mays from maizeGDB AGP_v4; Hordeum vulgare from ensemble (version 42) ; Asparagus officinalis from Asparagus genome project (http://asparagus.uga.edu/tripal/);  Spirodela polyrhiza from Michael et al..
Supplementary_files_format_and_content: *BED file, the identified regulatory regions, tab delimited text file, see ACR_column_header.txt for column headers
Supplementary_files_format_and_content: *BIGWIG , the genome coverage of each sample

organism: Eutrema salsugineum

source_name: DNA

growth_protocol: Arabidopsis thaliana (accession Col-0) were grown on 1/2MS plates under 25°C and continues light for 7 days. Leaves were collected for the experiments. Spirodela polyrhiza (accession 7498) were grown in liquid bases (Schenk and Hilldebrandt basak salt mixture) under 25°C and continuous light. Whole seedlings were collected 3 days after transferring to a new basis. Eutrema salsugineum (accession Shandong) and Asparagus officinalis (accession Gijnlim) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). All the young leaves were collected for the experiments. Phaseolus vulgaris (accession G19833) and Glycine max (accession William82) were grown in the soil for approximately 10 days under 25°C and photoperiodic lighting (16 hours of light:8 hours of dark). The 2nd and 3rd leaves were collected for the experiments. Brachypodium distachyon (accession Bd21), Oryza sativa (accession Nipponbare), Setaria viridis (accession A10), Sorghum bicolor, Zea mays (accession B73), and Hordeum vulgare (accession Morex) were grown in soil for ~6-7days under 25°C, 16 hours of light/8 hours of dark. The inner second leaves—which contains the third and fourth leaves sheathed inside—were used for experiments. Populus trichocarpa leaves were collected from the tree and flash-frozen with liquid N2 immediately for the following experiments.

extract_protocol: ATAC-seq libraries were prepared following the ATAC-seq protocol  as previously described in (Lu et al. 2016).

tag: accession

value: Shandong

value: leaf


title: PDIS9061-323


title: PDIS9061-350


title: PDIS9061-326


title: ATAC_Eutrema_10days_leaf_rep1

tag: tissue


title: PDIS9061-327


title: PDIS9061-322


title: ChIP_Eutrema_10days_leaf_H2A.Z

extract_protocol: ChIP-seq: ChiP-seq was performed following the methods of Zhang et al (2007) (https://www.ncbi.nlm.nih.gov/pubmed/17439305).  Tissues were cross-linked with 1% formaldehyde and chromatin was sonicated, followed by immunoprecipitation.


title: PDIS9061-342


title: PDIS9061-321


title: ChIP_Eutrema_10days_leaf_Input


title: ChIP_Eutrema_10days_leaf_H3K4me1


title: PDIS9061-456


title: PDIS9061-319


title: ChIP_Eutrema_10days_leaf_H3K4me3


title: PDIS9061-318


title: ChIP_Eutrema_10days_leaf_H3K56ac


title: ChIP_Eutrema_10days_leaf_H3K27me3


title: ChIP_Eutrema_10days_leaf_H3K36me3


title: PDIS9061-316


title: PDIS9061-317


title: PDIS9061-315


title: PDIS9061-314


title: ATAC_Eutrema_10days_leaf_rep2


title: RNA_Eutrema_10days_leaf_rep1

source_name: mRNA

extract_protocol: RNA-seq: 1.3 ug of total RNA was prepared for sequencing with the Illumina Truseq mRNA Stranded Library Kit, following the manufacturer's protocol


title: RNA_Eutrema_10days_leaf_rep2


title: PDIS9061-312


title: PDIS9061-313


title: BIBO_6y_genomic DNA [201533610046_R08C01]

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

description:
201533610046_R08C01
sample: 454
Normal buccal epithelial cells.

hyb_protocol: gDNA was bisulphite converted using the Zymo EZ DNA methylation kit. Hybridized to the Infinium MethylationEPIC array.

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

data_processing:
GenomeStudio software V2-0-3.
Average Beta (after background-subtraction and colour-correction in GenomeStudio software according to standard Illumina protocol).

label: Cy5 and Cy3

source_name: buccal swab genomic DNA

label_protocol: Standard Illumina Protocol.

extract_protocol: QIAamp DNA Mini Kit.

value: buccal epithelial cells

tag: gender

value: Female

tag: age (days)


title: BIBO_6y_genomic DNA [201530460051_R07C01]

description:
201530460051_R07C01
sample: 458
Normal buccal epithelial cells.

value: Male


title: BIBO_6y_genomic DNA [201533610046_R01C01]

description:
201533610046_R01C01
sample: 453
Normal buccal epithelial cells.


title: PDIS9061-310


title: PDIS9061-309


title: BIBO_6y_genomic DNA [201516320049_R02C01]

description:
201516320049_R02C01
sample: 449
Normal buccal epithelial cells.


title: PDIS9061-320


title: PDIS9061-311


title: BIBO_6y_genomic DNA [201516320024_R06C01]

description:
201516320024_R06C01
sample: 448
Normal buccal epithelial cells.


title: PDIS9061-307


title: PDIS9061-306


title: BIBO_6y_genomic DNA [201530460051_R02C01]

description:
201530460051_R02C01
sample: 446
Normal buccal epithelial cells.


title: PDIS9061-308


title: BIBO_6y_genomic DNA [201533610046_R05C01]

description:
201533610046_R05C01
sample: 444
Normal buccal epithelial cells.


title: PDIS9061-305


title: PDIS9061-304


title: ChIP_Eutrema_10days_leaf_H3

tag: age


title: BIBO_6y_genomic DNA [201530460051_R04C01]

description:
201530460051_R04C01
sample: 442
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320024_R02C01]

description:
201516320024_R02C01
sample: 441
Normal buccal epithelial cells.


title: PDIS9061-302


title: BIBO_6y_genomic DNA [201516320005_R08C01]

description:
201516320005_R08C01
sample: 439
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320024_R04C01]

description:
201516320024_R04C01
sample: 437
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201533610046_R07C01]

description:
201533610046_R07C01
sample: 436
Normal buccal epithelial cells.


title: PDIS9061-297


title: PDIS9061-299


title: BIBO_6y_genomic DNA [201530460007_R02C01]

description:
201530460007_R02C01
sample: 435
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320018_R03C01]

description:
201516320018_R03C01
sample: 432
Normal buccal epithelial cells.


title: PDIS9061-301


title: PDIS9061-296


title: BIBO_6y_genomic DNA [201530460044_R03C01]

description:
201530460044_R03C01
sample: 433
Normal buccal epithelial cells.


title: PDIS9061-294


title: PDIS9061-291


title: BIBO_6y_genomic DNA [201516320024_R08C01]

description:
201516320024_R08C01
sample: 431
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320055_R06C01]

description:
201516320055_R06C01
sample: 447
Normal buccal epithelial cells.


title: PDIS9061-292


title: BIBO_6y_genomic DNA [201516320024_R03C01]

description:
201516320024_R03C01
sample: 428
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320055_R05C01]

description:
201516320055_R05C01
sample: 445
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320005_R03C01]

description:
201516320005_R03C01
sample: 424
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320018_R01C01]

description:
201516320018_R01C01
sample: 422
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201533610043_R02C01]

description:
201533610043_R02C01
sample: 421
Normal buccal epithelial cells.


title: PDIS9061-287


title: PDIS9061-288


title: PDIS9061-285


title: PDIS9061-303


title: PDIS9061-286


title: BIBO_6y_genomic DNA [201533610043_R01C01]

description:
201533610043_R01C01
sample: 420
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320055_R08C01]

description:
201516320055_R08C01
sample: 415
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201533620002_R07C01]

description:
201533620002_R07C01
sample: 413
Normal buccal epithelial cells.


title: PDIS9061-283


title: PDIS9061-298


title: BIBO_6y_genomic DNA [201530460044_R07C01]

description:
201530460044_R07C01
sample: 410
Normal buccal epithelial cells.


title: PDIS9061-282


title: BIBO_6y_genomic DNA [201530460007_R07C01]

description:
201530460007_R07C01
sample: 409
Normal buccal epithelial cells.


title: PDIS9061-280


title: PDIS9061-278


title: PDIS9061-277


title: BIBO_6y_genomic DNA [201530440001_R05C01]

description:
201530440001_R05C01
sample: 407
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320055_R07C01]

description:
201516320055_R07C01
sample: 408
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320017_R02C01]

description:
201516320017_R02C01
sample: 406
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320017_R01C01]

description:
201516320017_R01C01
sample: 404
Normal buccal epithelial cells.


title: PDIS9061-276


title: BIBO_6y_genomic DNA [201516320018_R02C01]

description:
201516320018_R02C01
sample: 403
Normal buccal epithelial cells.


title: PDIS9061-279


title: BIBO_6y_genomic DNA [201516320005_R04C01]

description:
201516320005_R04C01
sample: 400
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201533620002_R06C01]

description:
201533620002_R06C01
sample: 399
Normal buccal epithelial cells.


title: PDIS9061-284


title: PDIS9061-275


title: PDIS9061-272


title: BIBO_6y_genomic DNA [201530460044_R05C01]

description:
201530460044_R05C01
sample: 397
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320049_R06C01]

description:
201516320049_R06C01
sample: 398
Normal buccal epithelial cells.


title: PDIS9061-273


title: PDIS9061-274


title: PDIS9061-271


title: BIBO_6y_genomic DNA [201516320055_R04C01]

description:
201516320055_R04C01
sample: 392
Normal buccal epithelial cells.


title: PDIS9061-269


title: PDIS9061-270


title: PDIS9061-268


title: BIBO_6y_genomic DNA [201516320005_R07C01]

description:
201516320005_R07C01
sample: 391
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530440001_R06C01]

description:
201530440001_R06C01
sample: 388
Normal buccal epithelial cells.


title: PDIS9061-281


title: BIBO_6y_genomic DNA [201533610046_R06C01]

description:
201533610046_R06C01
sample: 387
Normal buccal epithelial cells.


title: PDIS9061-266


title: BIBO_6y_genomic DNA [201530440009_R08C01]

description:
201530440009_R08C01
sample: 385
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530460051_R01C01]

description:
201530460051_R01C01
sample: 384
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530440034_R01C01]

description:
201530440034_R01C01
sample: 383
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320005_R01C01]

description:
201516320005_R01C01
sample: 382
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530440034_R02C01]

description:
201530440034_R02C01
sample: 381
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530460006_R01C01]

description:
201530460006_R01C01
sample: 376
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530460006_R02C01]

description:
201530460006_R02C01
sample: 386
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201533620002_R03C01]

description:
201533620002_R03C01
sample: 393
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530440009_R07C01]

description:
201530440009_R07C01
sample: 375
Normal buccal epithelial cells.


title: PDIS9061-265


title: PDIS9061-264


title: PDIS9061-263


title: PDIS9061-262


title: BIBO_6y_genomic DNA [201516320017_R03C01]

description:
201516320017_R03C01
sample: 373
Normal buccal epithelial cells.


title: PDIS9061-261


title: BIBO_6y_genomic DNA [201530440001_R04C01]

description:
201530440001_R04C01
sample: 370
Normal buccal epithelial cells.


title: PDIS9061-259


title: PDIS9061-256


title: PDIS9061-255


title: PDIS9061-257


title: BIBO_6y_genomic DNA [201533620002_R01C01]

description:
201533620002_R01C01
sample: 369
Normal buccal epithelial cells.


title: PDIS9061-254


title: PDIS9061-267


title: BIBO_6y_genomic DNA [201530460044_R02C01]

description:
201530460044_R02C01
sample: 367
Normal buccal epithelial cells.


title: PDIS9061-253


title: PDIS9061-251


title: PDIS9061-252


title: BIBO_6y_genomic DNA [201530440060_R08C01]

description:
201530440060_R08C01
sample: 366
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320049_R08C01]

description:
201516320049_R08C01
sample: 365
Normal buccal epithelial cells.


title: PDIS9061-249


title: PDIS9061-250


title: BIBO_6y_genomic DNA [201533610046_R03C01]

description:
201533610046_R03C01
sample: 354
Normal buccal epithelial cells.


title: PDIS9061-246


title: BIBO_6y_genomic DNA [201533610046_R04C01]

description:
201533610046_R04C01
sample: 355
Normal buccal epithelial cells.


title: PDIS9061-248


title: BIBO_6y_genomic DNA [201533610043_R08C01]

description:
201533610043_R08C01
sample: 360
Normal buccal epithelial cells.


title: PDIS9061-244


title: PDIS9061-243


title: BIBO_6y_genomic DNA [201516320001_R02C01]

description:
201516320001_R02C01
sample: 349
Normal buccal epithelial cells.


title: PDIS9061-247


title: BIBO_6y_genomic DNA [201530460044_R01C01]

description:
201530460044_R01C01
sample: 345
Normal buccal epithelial cells.


title: PDIS9061-241


title: BIBO_6y_genomic DNA [201530440001_R08C01]

description:
201530440001_R08C01
sample: 347
Normal buccal epithelial cells.


title: PDIS9061-240


title: BIBO_6y_genomic DNA [201533610046_R02C01]

description:
201533610046_R02C01
sample: 340
Normal buccal epithelial cells.


title: PDIS9061-242


title: PDIS9061-238


title: BIBO_6y_genomic DNA [201530460007_R04C01]

description:
201530460007_R04C01
sample: 336
Normal buccal epithelial cells.


title: PDIS9061-234


title: PDIS9061-236


title: BIBO_6y_genomic DNA [201530440034_R06C01]

description:
201530440034_R06C01
sample: 338
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530440034_R05C01]

description:
201530440034_R05C01
sample: 337
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320024_R05C01]

description:
201516320024_R05C01
sample: 358
Normal buccal epithelial cells.


title: PDIS9061-231


title: BIBO_6y_genomic DNA [201516320024_R07C01]

description:
201516320024_R07C01
sample: 334
Normal buccal epithelial cells.


title: PDIS9061-245


title: BIBO_6y_genomic DNA [201530440034_R04C01]

description:
201530440034_R04C01
sample: 332
Normal buccal epithelial cells.


title: PDIS9061-227


title: BIBO_6y_genomic DNA [201530440009_R05C01]

description:
201530440009_R05C01
sample: 331
Normal buccal epithelial cells.


title: PDIS9061-226


title: PDIS9061-225


title: PDIS9061-230


title: PDIS9061-222


title: BIBO_6y_genomic DNA [201516320005_R06C01]

description:
201516320005_R06C01
sample: 323
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320001_R08C01]

description:
201516320001_R08C01
sample: 351
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530460006_R07C01]

description:
201530460006_R07C01
sample: 327
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320049_R07C01]

description:
201516320049_R07C01
sample: 343
Normal buccal epithelial cells.


title: PDIS9061-224


title: BIBO_6y_genomic DNA [201530460044_R08C01]

description:
201530460044_R08C01
sample: 324
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530460007_R08C01]

description:
201530460007_R08C01
sample: 333
Normal buccal epithelial cells.


title: PDIS9061-219


title: BIBO_6y_genomic DNA [201516320018_R04C01]

description:
201516320018_R04C01
sample: 330
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530440009_R02C01]

description:
201530440009_R02C01
sample: 319
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530460007_R06C01]

description:
201530460007_R06C01
sample: 322
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530440001_R07C01]

description:
201530440001_R07C01
sample: 320
Normal buccal epithelial cells.


title: PDIS9061-218


title: PDIS9061-217


title: PDIS9061-216


title: BIBO_6y_genomic DNA [201530440009_R01C01]

description:
201530440009_R01C01
sample: 318
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201533620002_R02C01]

description:
201533620002_R02C01
sample: 317
Normal buccal epithelial cells.


title: PDIS9061-214


title: PDIS9061-213


title: BIBO_6y_genomic DNA [201516320012_R03C01]

description:
201516320012_R03C01
sample: 314
Normal buccal epithelial cells.


title: PDIS9061-211


title: PDIS9061-220


title: PDIS9061-210


title: PDIS9061-212


title: BIBO_6y_genomic DNA [201530440001_R01C01]

description:
201530440001_R01C01
sample: 310
Normal buccal epithelial cells.


title: PDIS9061-209


title: PDIS9061-207


title: ATAC_Sorghum_7days_leaf_rep1

organism: Sorghum bicolor


title: PDIS9061-206


title: BIBO_6y_genomic DNA [201530460007_R05C01]

description:
201530460007_R05C01
sample: 308
Normal buccal epithelial cells.


title: PDIS9061-208


title: ATAC_Sorghum_7days_leaf_rep2


title: BIBO_6y_genomic DNA [201530440060_R04C01]

description:
201530440060_R04C01
sample: 306
Normal buccal epithelial cells.


title: PDIS9061-205


title: ChIP_Sorghum_7days_leaf_Input


title: PDIS9061-203


title: PDIS9061-202


title: ChIP_Sorghum_7days_leaf_H2A.Z


title: PDIS9061-201


title: BIBO_6y_genomic DNA [201530460006_R04C01]

description:
201530460006_R04C01
sample: 304
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530460006_R06C01]

description:
201530460006_R06C01
sample: 316
Normal buccal epithelial cells.


title: ATAC_Sorghum_7days_leaf_Input


title: PDIS9061-200


title: BIBO_6y_genomic DNA [201530460006_R05C01]

description:
201530460006_R05C01
sample: 311
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201516320049_R03C01]

description:
201516320049_R03C01
sample: 303
Normal buccal epithelial cells.


title: ChIP_Sorghum_7days_leaf_H3K4me3


title: PDIS9061-198


title: PDIS9061-197


title: BIBO_6y_genomic DNA [201516320018_R08C01]

description:
201516320018_R08C01
sample: 302
Normal buccal epithelial cells.


title: PDIS9061-195


title: PDIS9061-196


title: ChIP_Sorghum_7days_leaf_H3K56ac


title: PDIS9061-194


title: BIBO_6y_genomic DNA [201516320018_R07C01]

description:
201516320018_R07C01
sample: 300
Normal buccal epithelial cells.


title: PDIS9061-192


title: ChIP_Sorghum_7days_leaf_H3K27me3


title: BIBO_6y_genomic DNA [201516320017_R06C01]

description:
201516320017_R06C01
sample: 299
Normal buccal epithelial cells.


title: ChIP_Sorghum_7days_leaf_H3K36me3


title: PDIS9061-190


title: PDIS9061-193


title: ChIP_Sorghum_7days_leaf_H3


title: PDIS9061-189


title: PDIS9061-191


title: BIBO_6y_genomic DNA [201530440001_R03C01]

description:
201530440001_R03C01
sample: 297
Normal buccal epithelial cells.


title: ChIP_Sorghum_7days_leaf_H3K4me1


title: PDIS9061-188


title: PDIS9061-187


title: PDIS9061-199


title: RNA_Sorghum_7days_leaf_rep2


title: BIBO_6y_genomic DNA [201516320001_R06C01]

description:
201516320001_R06C01
sample: 292
Normal buccal epithelial cells.


title: BIBO_6y_genomic DNA [201530440060_R07C01]

description:
201530440060_R07C01
sample: 288
Normal buccal epithelial cells.


title: PDIS9061-186


title: RNA_Sorghum_7days_leaf_rep1


title: BIBO_6y_genomic DNA [201530460006_R03C01]

description:
201530460006_R03C01
sample: 298
Normal buccal epithelial cells.


title: ATAC_Rice_7days_leaf_Input

organism: Oryza sativa

value: Nipponbare


title: PDIS9061-184


title: PDIS9061-183


title: PDIS9061-182


title: ATAC_Rice_7days_leaf_rep2


title: PDIS9061-181


title: PDIS9061-180


title: BIBO_6y_genomic DNA [201530460044_R06C01]

description:
201530460044_R06C01
sample: 285
Normal buccal epithelial cells.


title: ATAC_Rice_7days_leaf_rep1


title: PDIS9061-178


title: BIBO_6y_genomic DNA [201530440060_R01C01]

description:
201530440060_R01C01
sample: 283
Normal buccal epithelial cells.


title: PDIS9061-176


title: PDIS9061-177


title: PDIS9061-175


title: BIBO_6y_genomic DNA [201516320018_R06C01]

description:
201516320018_R06C01
sample: 281
Normal buccal epithelial cells.