title: 21yr_male_cell181

description: Single cell from human pancreas


title: 21yr_male_cell178

status: Public on Sep 28 2017

type: SRA

city: Stanford

first: Martin

last: Enge

state: CA

address: James H. Clark Center, 318 Campus Drive,

department: Bioengineering

country: USA

institute: Stanford University

description: Single cell from human pancreas

library_source: transcriptomic

data_processing:
Sequencing reads were trimmed, adapter sequences removed and the reads aligned using STAR with default parameters.
Duplicate reads were removed using picard. Transcript counts were obtained using HT-Seq and hg19 UCSC exon/transcript annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Pancreatic islet

extract_protocol:
Single-cells were collected  in lysis buffer in 96-well plates, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analyzed on an automated Fragment Analyzer (Advanced Analytical).
Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (FC-131-1024; Illumina) according to the manufacturer’s instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq instrument.

tag: gender

value: male

value: alpha


title: 21yr_male_cell179

description: Single cell from human pancreas


title: 21yr_male_cell176

description: Single cell from human pancreas

value: unsure


title: 21yr_male_cell175

description: Single cell from human pancreas


title: 21yr_male_cell174

description: Single cell from human pancreas


title: 21yr_male_cell171

description: Single cell from human pancreas


title: 21yr_male_cell170

description: Single cell from human pancreas


title: 21yr_male_cell173

description: Single cell from human pancreas


title: 21yr_male_cell188

description: Single cell from human pancreas


title: 21yr_male_cell172

description: Single cell from human pancreas


title: 21yr_male_cell168

description: Single cell from human pancreas


title: 21yr_male_cell166

description: Single cell from human pancreas


title: 21yr_male_cell162

description: Single cell from human pancreas


title: 21yr_male_cell163

description: Single cell from human pancreas


title: 21yr_male_cell160

description: Single cell from human pancreas


title: 21yr_male_cell157

description: Single cell from human pancreas


title: 21yr_male_cell154

description: Single cell from human pancreas


title: 21yr_male_cell164

description: Single cell from human pancreas


title: 21yr_male_cell161

description: Single cell from human pancreas


title: 21yr_male_cell156

description: Single cell from human pancreas


title: 21yr_male_cell153

description: Single cell from human pancreas


title: 21yr_male_cell177

description: Single cell from human pancreas


title: 21yr_male_cell180

description: Single cell from human pancreas


title: 21yr_male_cell155

description: Single cell from human pancreas


title: 21yr_male_cell150

description: Single cell from human pancreas


title: 21yr_male_cell152

description: Single cell from human pancreas


title: 21yr_male_cell149

description: Single cell from human pancreas


title: 21yr_male_cell151

description: Single cell from human pancreas


title: 21yr_male_cell167

description: Single cell from human pancreas


title: 21yr_male_cell169

description: Single cell from human pancreas


title: 21yr_male_cell165

description: Single cell from human pancreas


title: 21yr_male_cell146

description: Single cell from human pancreas


title: 21yr_male_cell147

description: Single cell from human pancreas


title: 21yr_male_cell144

description: Single cell from human pancreas


title: 21yr_male_cell142

description: Single cell from human pancreas


title: 21yr_male_cell141

description: Single cell from human pancreas


title: 21yr_male_cell143

description: Single cell from human pancreas


title: 21yr_male_cell148

description: Single cell from human pancreas


title: 21yr_male_cell158

description: Single cell from human pancreas


title: 21yr_male_cell139

description: Single cell from human pancreas


title: 21yr_male_cell137

description: Single cell from human pancreas


title: 21yr_male_cell138

description: Single cell from human pancreas


title: 21yr_male_cell135

description: Single cell from human pancreas

value: acinar


title: 21yr_male_cell136

description: Single cell from human pancreas


title: 21yr_male_cell133

description: Single cell from human pancreas


title: 21yr_male_cell132

description: Single cell from human pancreas


title: 21yr_male_cell131

description: Single cell from human pancreas


title: 21yr_male_cell134

description: Single cell from human pancreas


title: 21yr_male_cell130

description: Single cell from human pancreas


title: 21yr_male_cell129

description: Single cell from human pancreas


title: 21yr_male_cell127

description: Single cell from human pancreas


title: 21yr_male_cell126

description: Single cell from human pancreas


title: 21yr_male_cell125

description: Single cell from human pancreas


title: 21yr_male_cell145

description: Single cell from human pancreas


title: 21yr_male_cell120

description: Single cell from human pancreas


title: 21yr_male_cell121

description: Single cell from human pancreas


title: 21yr_male_cell124

description: Single cell from human pancreas


title: 21yr_male_cell118

description: Single cell from human pancreas


title: 21yr_male_cell117

description: Single cell from human pancreas


title: 21yr_male_cell123

description: Single cell from human pancreas


title: 21yr_male_cell115

description: Single cell from human pancreas


title: 21yr_male_cell122

description: Single cell from human pancreas


title: 21yr_male_cell113

description: Single cell from human pancreas


title: 21yr_male_cell140

description: Single cell from human pancreas


title: 21yr_male_cell114

description: Single cell from human pancreas


title: 21yr_male_cell116

description: Single cell from human pancreas


title: 21yr_male_cell112

description: Single cell from human pancreas


title: 21yr_male_cell111

description: Single cell from human pancreas


title: 21yr_male_cell110

description: Single cell from human pancreas


title: 21yr_male_cell108

description: Single cell from human pancreas


title: 21yr_male_cell109

description: Single cell from human pancreas


title: 21yr_male_cell159

description: Single cell from human pancreas


title: 21yr_male_cell128

description: Single cell from human pancreas


title: 21yr_male_cell105

description: Single cell from human pancreas


title: 21yr_male_cell107

description: Single cell from human pancreas


title: 21yr_male_cell106

description: Single cell from human pancreas


title: 21yr_male_cell102

description: Single cell from human pancreas


title: 21yr_male_cell104

description: Single cell from human pancreas


title: 21yr_male_cell100

description: Single cell from human pancreas


title: 21yr_male_cell101

description: Single cell from human pancreas


title: 21yr_male_cell103

description: Single cell from human pancreas


title: 21yr_male_cell99

description: Single cell from human pancreas


title: 21yr_male_cell119

description: Single cell from human pancreas


title: 21yr_male_cell98

description: Single cell from human pancreas


title: 21yr_male_cell97

description: Single cell from human pancreas


title: 21yr_male_cell95

description: Single cell from human pancreas


title: 21yr_male_cell92

description: Single cell from human pancreas


title: 21yr_male_cell91

description: Single cell from human pancreas


title: 21yr_male_cell93

description: Single cell from human pancreas


title: 21yr_male_cell90

description: Single cell from human pancreas


title: 21yr_male_cell94

description: Single cell from human pancreas


title: 21yr_male_cell89

description: Single cell from human pancreas


title: 21yr_male_cell88

description: Single cell from human pancreas


title: 21yr_male_cell86

description: Single cell from human pancreas


title: 21yr_male_cell85

description: Single cell from human pancreas


title: 21yr_male_cell83

description: Single cell from human pancreas


title: 21yr_male_cell84

description: Single cell from human pancreas


title: 21yr_male_cell87

description: Single cell from human pancreas


title: 21yr_male_cell81

description: Single cell from human pancreas


title: 21yr_male_cell80

description: Single cell from human pancreas


title: 21yr_male_cell78

description: Single cell from human pancreas


title: 21yr_male_cell75

description: Single cell from human pancreas


title: 21yr_male_cell76

description: Single cell from human pancreas


title: 21yr_male_cell74

description: Single cell from human pancreas


title: 21yr_male_cell77

description: Single cell from human pancreas


title: 21yr_male_cell71

description: Single cell from human pancreas


title: 21yr_male_cell73

description: Single cell from human pancreas


title: 21yr_male_cell68

description: Single cell from human pancreas


title: 21yr_male_cell79

description: Single cell from human pancreas


title: 21yr_male_cell72

description: Single cell from human pancreas


title: 21yr_male_cell69

description: Single cell from human pancreas


title: 21yr_male_cell67

description: Single cell from human pancreas


title: 21yr_male_cell65

description: Single cell from human pancreas


title: 21yr_male_cell63

description: Single cell from human pancreas


title: 21yr_male_cell64

description: Single cell from human pancreas


title: 21yr_male_cell62

description: Single cell from human pancreas


title: 21yr_male_cell61

description: Single cell from human pancreas


title: 21yr_male_cell60

description: Single cell from human pancreas


title: 21yr_male_cell59

description: Single cell from human pancreas


title: 21yr_male_cell58

description: Single cell from human pancreas


title: 21yr_male_cell82

description: Single cell from human pancreas


title: 21yr_male_cell56

description: Single cell from human pancreas


title: 21yr_male_cell96

description: Single cell from human pancreas


title: 21yr_male_cell53

description: Single cell from human pancreas


title: 21yr_male_cell70

description: Single cell from human pancreas


title: 21yr_male_cell52

description: Single cell from human pancreas


title: 21yr_male_cell51

description: Single cell from human pancreas


title: 21yr_male_cell50

description: Single cell from human pancreas


title: 21yr_male_cell46

description: Single cell from human pancreas


title: 21yr_male_cell49

description: Single cell from human pancreas


title: 21yr_male_cell48

description: Single cell from human pancreas


title: 21yr_male_cell43

description: Single cell from human pancreas


title: 21yr_male_cell45

description: Single cell from human pancreas


title: 21yr_male_cell66

description: Single cell from human pancreas


title: 21yr_male_cell41

description: Single cell from human pancreas


title: 21yr_male_cell44

description: Single cell from human pancreas


title: 21yr_male_cell40

description: Single cell from human pancreas


title: 21yr_male_cell39

description: Single cell from human pancreas


title: 21yr_male_cell54

description: Single cell from human pancreas


title: 21yr_male_cell38

description: Single cell from human pancreas


title: 21yr_male_cell37

description: Single cell from human pancreas


title: 21yr_male_cell57

description: Single cell from human pancreas

value: delta


title: 21yr_male_cell35

description: Single cell from human pancreas


title: 21yr_male_cell55

description: Single cell from human pancreas


title: 21yr_male_cell34

description: Single cell from human pancreas


title: 21yr_male_cell31

description: Single cell from human pancreas


title: 21yr_male_cell36

description: Single cell from human pancreas


title: 21yr_male_cell30

description: Single cell from human pancreas


title: 21yr_male_cell32

description: Single cell from human pancreas


title: 21yr_male_cell29

description: Single cell from human pancreas


title: 21yr_male_cell28

description: Single cell from human pancreas


title: 21yr_male_cell47

description: Single cell from human pancreas


title: 21yr_male_cell33

description: Single cell from human pancreas


title: 21yr_male_cell25

description: Single cell from human pancreas


title: 21yr_male_cell27

description: Single cell from human pancreas


title: 21yr_male_cell42

description: Single cell from human pancreas


title: 21yr_male_cell23

description: Single cell from human pancreas


title: 21yr_male_cell24

description: Single cell from human pancreas


title: 21yr_male_cell21

description: Single cell from human pancreas


title: 21yr_male_cell22

description: Single cell from human pancreas


title: 21yr_male_cell19

description: Single cell from human pancreas


title: 21yr_male_cell17

description: Single cell from human pancreas


title: 21yr_male_cell20

description: Single cell from human pancreas


title: 21yr_male_cell16

description: Single cell from human pancreas


title: 21yr_male_cell18

description: Single cell from human pancreas


title: 21yr_male_cell15

description: Single cell from human pancreas


title: 21yr_male_cell13

description: Single cell from human pancreas


title: 21yr_male_cell14

description: Single cell from human pancreas


title: 21yr_male_cell11

description: Single cell from human pancreas


title: 21yr_male_cell7

description: Single cell from human pancreas


title: 21yr_male_cell10

description: Single cell from human pancreas


title: 21yr_male_cell8

description: Single cell from human pancreas


title: 21yr_male_cell5

description: Single cell from human pancreas


title: 21yr_male_cell6

description: Single cell from human pancreas


title: 21yr_male_cell4

description: Single cell from human pancreas


title: 21yr_male_cell2

description: Single cell from human pancreas


title: 21yr_male_cell1

description: Single cell from human pancreas


title: 21yr_male_cell26

description: Single cell from human pancreas


title: Input DNA rep3

city: Boston

first: Jingwei

last: Cheng

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

library_source: genomic

data_processing:
Images analysis and base calling was done using the solexa pipeline
For all samples reads were aligned to their indicated build usiwng bowtie2 (version 2.2.1) with parameters -k 1
Normalized read density of a ChIP-seq dataset in any genomic region was calculated using Bamliquidator (version 1.0) read density calculator (https://github.com/BradnerLab/pipeline/wiki/bamliquidator).
MACS version 1.4.2 (Model based analysis of ChIP-seq) peak finding algorithm was used to identify regions of ChIP-seq enrichment over background and to generate .wig files for visualization. A p-value threshold of enrichment of 1e-9 was used for all datasets
genome build: hg19
processed data files format and content: : .wig files of genomic ChIP-seq density

molecule: genomic DNA

source_name: Merkel cell carcinoma cell line

growth_protocol: MKL-1 cells grow as suspension clumps in RPMI medium supplemented with 10% FBS, Penicillin-Streptomycin, and glutamax

extract_protocol:
Lysates were clarified from sonicated nuclei as described in 'ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. 2009 Methods 48, no. 3: 240-248.'
10 ng of DNA from ChIP experiments or input DNA were prepared for sequencing with NEBNext ChIP-seq Library Prep Reagent Set for Illumina (New England Biolabs). Diluted libraries were used for 50 cycles single-end sequencing on HiSeq2000 system (Illumina) at the Center for Cancer Computational Biology (CCCB) at Dana-Farber Cancer Institute following the manufacturer’s protocol.

tag: cell line

tag: cell type

value: Merkel cell carcinoma

tag: merkel cell polyomavirus

value: positive

tag: chip antibody


title: H3K4me3_ChIP-seq

value: H3k4me3 (Millipore, 07-473)


title: tg-5

city: Bethesda

first: Minh

middle: Q

last: Nguyen

state: MARYLAND

address: 9000, Rockville Pike

institute: NIDCR/NIH

data_processing:
bcl2fastq (v2.17) was used for basecalling
Sequence reads were processed using the Drop-seq cookbook (v 1.12) from the McCarroll lab (http://mccarrolllab.com/dropseq/)
Reads were aligned using STAR (v 2.5.3a) to mm10 genome
Seurat package (v 1.4.0.16) was used for downstream data analysis in R as described by the Satija lab (http://satijalab.org/seurat/)
Genome_build: mm10
Supplementary_files_format_and_content: csv file with cell barcodes and corresponding gene expression counts; only cells with at least 1000 transcripts are included for analysis

molecule: polyA RNA

organism: Mus musculus

source_name: trigeminal neurons

extract_protocol:
Trigeminal neurons were isolated using the postnatal neural tissue dissociation kit (Miltenyi Biotec), followed by a 12.5%/20% percoll gradient.  Glia and other non-neuronal cells were then depleted using the mouse neuron isolation kit (Milteny Biotec).
Libraries construction were performed as described by the Drop-seq protocol from the McCarroll lab

tag: strain

value: FVB/N

tag: age

value: 3-6 wks

tag: genotype/variation

value: wild type

value: trigeminal neuron


title: tg-8


title: tg-7


title: tg-9


title: tg-6


title: tg-4


title: tg-3


title: tg-1


title: 21yr_male_cell9

description: Single cell from human pancreas


title: 21yr_male_cell12

description: Single cell from human pancreas


title: 21yr_male_cell3

description: Single cell from human pancreas


title: 84HPP_Poly

city: Barcelona

first: Marta

last: Sese

state: Barcelona

address: Pg. Vall Hebron, 119

department: Translational Molecular Pathology

country: Spain

institute: Vall Hebron Institute of Research (VHIR)

description:
Hypoxia_PP242_Polysomes_Replicate2
COUNTS_POLYSOME_02_new_pipeline

data_processing:
RNA-seq reads were mapped against human reference genome with STAR
Genes were quantified with RSEM
We used gene annotation file from gencode (version 19)
differential expression analysis was performed with edgeR robust
Genome_build: GRCh37
Supplementary_files_format_and_content: txt tables with expected counts estimated by RSEM

source_name: Breast Tissue

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) (Invitrogen) supplemented with 10% heat-inactivated foetal bovine serum (FBS) (Life Technologies) and antibiotics (100 U/mL penicillin, 100 μg/mL streptomycin) (Life Technologies). MCF10A cells were maintained in DMEM supplemented with 10% FBS, 20 ng/mL EGF (#E9644; Sigma), 0.5 μg/mL hydrocortisone, 100 ng/mL cholera toxin (#C9903; Sigma) and 10 μg/mL insulin (#I9278; Sigma).

extract_protocol:
Polysomal mRNA was obtained by 10%–50% sucrose gradient sedimentation. Upon hypoxia or normoxia, with and without PP242 treatments, cells were washed twice with cold 1× phosphate-buffered saline (PBS) and lysed by incubation for 10 minutes on ice in polysome buffer: 1.5 mM KCl, 5 mM Tris-HCl pH 7.4, 2.5 mM MgCl2, 1% Triton X-100, 1% Na-deoxycholate, 100 μg/ml cycloheximide, 2.5 μl/mL RNAaseOut and 1× Complete Roche Protease Inhibitor. The cell lysate was centrifuged at 12,000 × g for 15 minutes at 4°C. One microgram of total protein from the supernatant was loaded onto a 10%–50% sucrose gradient, made with the BioComp Gradient Maker, and ultracentrifuged at 37,000 rpm (SW40 rotor) for 150 minutes at 4°C. The sucrose gradient was fractionated with the ISCP UV gradient fractionation system (BioComp), connected to a UV detector to monitor absorbance at 254 nm, and the polysome profile was recorded. Twelve fractions of 900 μl each were isolated and RNA was extracted using phenol:chloroform and ethanol precipitation followed by an RNeasy Mini Kit (Qiagen) for DNase treatment according to the manufacturer's instructions. Both total RNA and polysome-bound mRNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity.
The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,).

treatment_protocol: Cells were maintained at 37°C in a 5% CO2 humidified incubator. To establish hypoxic conditions, cells were subjected to 0.5% O2 in 5% CO2/95% N2 and 100% humidity for 24 hours in a hypoxic chamber (INVIVO2 200; Ruskinn Technology, UK). PP242 was purchased from Selleckchem (#S2218), reconstituted in dimethyl sulfoxide (DMSO) and used at a final concentration of 2.5 μM for 3 hours

tag: treatment

tag: fraction

value: Polysomal mRNA

tag: barcode

tag: replicate

value: Biological replicate 2


title: 83NPP_Poly

description:
Normoxia_PP242_Polysomes_Replicate2
COUNTS_POLYSOME_02_new_pipeline


title: mouse1_input

city: Munich

first: Francisca

last: Rojas Ringeling

address: Feodor-Lynen-Straße 25, 81377

department: Biochemistry

country: Germany

institute: Ludwig Maximilian University of Munich

description: anti-m6A antibody (212B11, Synaptic Systems)

data_processing:
Pre-processing of reads was performed using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), namely adapters were clipped, poor quality reads were filtered out and identical reads were collapsed
Pre-processed reads from E13.5 mouse forebrains were aligned to the mouse genome (build GRCm38/mm10), and reads from the human organoids and fetal brain to the human genome (build GRCh37/hg19), using Tophat2 (Kim et al., 2013) with default settings.
m6A-tagged regions were identified using the MACS2 peak calling algorithm (Zhang et al., 2008), with the input library as background.
Genome_build: mm10 for mouse. hg19 for human.
Supplementary_files_format_and_content: narrowPeak files from MACS2 output, containing m6A peaks

source_name: Forebrain tissue

extract_protocol:
For m6A profiling of mouse developing brain, forebrains from wild type E13.5 embryos were dissected and total RNA was extracted from them. mRNA was then isolated using the Dynabeads mRNA Purification Kit (Ambion). m6A pull-down was performed using a rabbit polyclonal anti-m6A antibody (Synaptic systems), and immunoprecipitation with protein G dynabeads (Novex). For m6A profiling of 47 day organoids, the same procedure was followed.
cDNA libraries from pulled-down RNA and input RNA were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina®.

tag: tissue

value: Forebrain tissue

tag: genotype

value: Wild type


title: 81N_Poly

description:
Normoxia_Polysomes_Replicate2
COUNTS_POLYSOME_02_new_pipeline

value: Normoxia


title: 84HPP_Total

description:
Hypoxia_PP242_Total_Replicate2
COUNTS_POLYSOME_02_new_pipeline

value: Total mRNA


title: 82H_Poly

description:
Hypoxia_Polysomes_Replicate2
COUNTS_POLYSOME_02_new_pipeline

value: Hypoxia


title: 83NPP_Total

description:
Normoxia_PP242_Total_Replicate2
COUNTS_POLYSOME_02_new_pipeline


title: mouse3_input


title: mouse2_input


title: mouse2_m6A


title: mouse1_m6A


title: 82H_Total

description:
Hypoxia_Total_Replicate2
COUNTS_POLYSOME_02_new_pipeline


title: 68HPP_Poly

description:
Hypoxia_PP242_Polysomes_Replicate1
COUNTS_POLYSOME_02_new_pipeline

value: Biological replicate 1


title: 81N_Total

description:
Normoxia_Total_Replicate2
COUNTS_POLYSOME_02_new_pipeline


title: tg-2


title: mouse3_m6A


title: 65N_Poly

description:
Normoxia_Polysomes_Replicate1
COUNTS_POLYSOME_02_new_pipeline


title: 66H_Poly

description:
Hypoxia_Polysomes_Replicate1
COUNTS_POLYSOME_02_new_pipeline


title: 67NPP_Poly

description:
Normoxia_PP242_Polysomes_Replicate1
COUNTS_POLYSOME_02_new_pipeline


title: 66H_Total

description:
Hypoxia_Total_Replicate1
COUNTS_POLYSOME_02_new_pipeline


title: 68HPP_Total

description:
Hypoxia_PP242_Total_Replicate1
COUNTS_POLYSOME_02_new_pipeline


title: 67NPP_Total

description:
Normoxia_PP242_Total_Replicate1
COUNTS_POLYSOME_02_new_pipeline


title: 41NormPoly

description:
Normoxia_Polysomes_Replicate2
COUNTS_POLYSOME_01_new_pipeline


title: 44HipPPPoly

description:
Hypoxia_PP242_Polysomes_Replicate2
COUNTS_POLYSOME_01_new_pipeline


title: 42HipPoly

description:
Hypoxia_Polysomes_Replicate2
COUNTS_POLYSOME_01_new_pipeline


title: 43NormPPPoly

description:
Normoxia_PP242_Polysomes_Replicate2
COUNTS_POLYSOME_01_new_pipeline


title: 44HipPPTotal

description:
Hypoxia_PP242_Total_Replicate2
COUNTS_POLYSOME_01_new_pipeline


title: 65N_Total

description:
Normoxia_Total_Replicate1
COUNTS_POLYSOME_02_new_pipeline


title: 43NormPPTotal

description:
Normoxia_PP242_Total_Replicate2
COUNTS_POLYSOME_01_new_pipeline


title: 42HipTotal

description:
Hypoxia_Total_Replicate2
COUNTS_POLYSOME_01_new_pipeline


title: 41NormTotal

description:
Normoxia_Total_Replicate2
COUNTS_POLYSOME_01_new_pipeline


title: 40HipPPPoly

description:
Hypoxia_PP242_Polysomes_Replicate1
COUNTS_POLYSOME_01_new_pipeline


title: 39NormPPPoly

description:
Normoxia_PP242_Polysomes_Replicate1
COUNTS_POLYSOME_01_new_pipeline


title: 38HipPoly

description:
Hypoxia_Polysomes_Replicate1
COUNTS_POLYSOME_01_new_pipeline


title: 38HipTotal

description:
Hypoxia_Total_Replicate1
COUNTS_POLYSOME_01_new_pipeline


title: 40HipPPTotal

description:
Hypoxia_PP242_Total_Replicate1
COUNTS_POLYSOME_01_new_pipeline


title: 37NormTotal

description:
Normoxia_Total_Replicate1
COUNTS_POLYSOME_01_new_pipeline


title: THP-1, GABPA 24 h EtOH

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description: Chromatin IP against GABPA

data_processing:
Alignment to hg19 using Bowtie v1.0 parameters: -n 1 – k 1 -m 1 -l 32 -t -q –best
Peak discovery using MACS2 parameters: -m 5 50 –bw 150
Genome_build: hg19
Supplementary_files_format_and_content: tdf

source_name: human monocytic cell line THP-1

growth_protocol: THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol:
Proteins were crosslinked with formaldehyde to DNA, then GABPA-bound fragments were pulled down by chromatin immunoprecipitation
ChIP-seq library was prepared from 5-10 ng ChIP DNA with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) per manufacturer's protocol

treatment_protocol: Treated with EtOH or 24 h 100 nM 1,25(OH)2D3

value: monocytic leukemia cells

value: GABP-a (Santa Cruz sc-28312 X)

tag: treatment protocol

value: 24 h EtOH


title: THP-1, GABPA 24 h 1,25(OH)2D3

description: Chromatin IP against GABPA


title: 39NormPPTotal

description:
Normoxia_PP242_Total_Replicate1
COUNTS_POLYSOME_01_new_pipeline


title: 37NormPoly

description:
Normoxia_Polysomes_Replicate1
COUNTS_POLYSOME_01_new_pipeline


title: 3058035

city: Seattle

first: Carl

last: Murie

state: Washington

address: 1100 Fairview Ave. N

department: VIDD

institute: Fred Hutch Cancer Research Center

data_processing:
Quality control of the fastq files was performed using FastQC (Braham Bioinformatics).
hg38 reference genome was built with RSEM using the STAR option. UCSC annotations were downloaded Dec. 2016.
Sequences were aligned with STAR 2.4.2a using default parameters
Reads were quanitified with RSEM 1.2.22 with default parameters
Genes with zero or low counts (< 0.5cpm across all libraries) were removed from the dataset and the counts TMM normalized using edgeR.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Each row is a gene and each column is a sample.

source_name: Whole blood

extract_protocol:
Poly(A)+ RNA was prepared from whole blood in PAXgene Blood RNA tubes that had been stored at -80 oC. Following the manufacturer’s protocols, RNA was extracted using the PAXgene Blood Kit (PreAnalytiX) and quantified by spectrophotometry. A total of 1.2 µg of total RNA per sample was processed using the GLOBINclear Human kit (Ambion) in order to remove globin mRNA. The quantity and quality of the RNA was analyzed on a Bioanalyzer Eukaryote Total RNA Nano chip.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: collection day (post chmi)

tag: individual

value: volunteer 10


title: 5157163


title: 3059106

value: volunteer 9


title: 8058040


title: 3059052


title: 8059120

value: volunteer 8


title: 9157176


title: 1059050


title: 4058036


title: 9059049

value: volunteer 7


title: 7157165


title: 7059119


title: 7058039

value: volunteer 6


title: 5157172


title: 4059107


title: 6059118


title: 4059116

value: volunteer 5


title: 4157162


title: 1157168


title: 5059054


title: 5059063

value: volunteer 4


title: 6059064


title: 2059051


title: 7059056


title: 8157166


title: 7058048


title: 6059055

value: volunteer 3


title: 5059117


title: 6058047


title: 8059031


title: 7157174


title: 3058044


title: 4059053

value: volunteer 2


title: 2059114


title: 4157177


title: 5058037


title: 6059109

value: volunteer 1


title: WI-38 cells, unstranded polyA RNA-seq, 15h HSV-1 infection, Replicate 1, unlabeled RNA

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description:
no processed data due to technical reasons
UnStranded RNA-seq

data_processing:
Data was mapped onto the hg19 reference using Tophat2 (Kim et al. 2013).
Antisense transcripts were defined on the coverage tracks using a custom running sum algorithm, followed by extensive filtering.
Antisense transcripts were classified into divergent, convergent and intal, based on the location of the TSS in respect to the sense transcript.
Expression values for the different samples (columns X-X) are presented as log(2) transformed RPKM values of averages from biological replicates.
Expression values are shown for the stranded RNA-sequencing data provided here (columns X-X). In addition, published RNA-sequencing data was reanalyzed the same way (columns X-X, as indicated by first author name and GSM identifiers).
The following datasets were reanalyzed: HSV-1 infected HFF cells (Rutkowski et al. 2015, PMID: 25989971, GEO: GSE59717), RNA-sequencing from VZV keratinocytes (Jones et al. 2014, PMID: 24497829, SRA: E-MTAB-1717) and CMV infected fibroblast (Tirosh et al. 2015, PMID: 26599541, GEO: GSE69906), and NET-seq data from HeLa cells (Schlackow et al. 2017, PMID: 28017589, GEO: GSE81662)
Column names contain first author name, SRA identifiers for VZV data and GEO identifiers for all others. Several identifiers indicate that replicates were available and averaged.
Nearest FANTOM transcripts (Hon et al. 2017) are provided.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text

source_name: WI-38 cells

growth_protocol: WI38 fibroblasts were cultured in Minimal Essential Medium (MEM) supplemented with 10% Fetal Bovine Serum (FBS) and with 100 units/ml penicillin, 100 µg/ml streptomycin. HeLa cells were cultured in Dulbecco's Modified Eagle Medium (DMEM)  supplemented with 10% Fetal Bovine Serum (FBS) and with 100 units/ml penicillin, 100 µg/ml streptomycin.

extract_protocol:
Illumina TruSeq RNA Library Prep Kit v2
Cells were resuspended in Trizol and, following Chloroform-mediate phase separation, RNA extracted from the aqueous phase using the CC-25 kit (Zymo).

treatment_protocol: For RNA labeling, 4SU at a concentration of 500 µM was added one hour before harvesting. Cells were infected with Herpes simplex virus 1 as indicated.

tag: 4su treatment

value: 1h before harvesting

tag: hsv-1 infection

value: Infected 15h before harvesting

tag: rna isolation

value: unlabeled RNA (flowthrough)

tag: adapter sequence

value: GATCGGAAGAGCACACGT

value: AGTTCCG


title: WI-38 cells, unstranded polyA RNA-seq, 15h HSV-1 infection, Replicate 2, unlabeled RNA

tag: cell line

value: GTGAAAC


title: 2059060


title: 9058032


title: WI-38 cells, unstranded polyA RNA-seq, 9h HSV-1 infection, Replicate 2, unlabeled RNA

value: Infected 9h before harvesting

value: GTCCGCA


title: WI-38 cells, unstranded polyA RNA-seq, 4h HSV-1 infection, Replicate 2, unlabeled RNA

value: Infected 4h before harvesting

value: ACGTCCC


title: WI-38 cells, unstranded polyA RNA-seq, uninfected, Replicate 2, unlabeled RNA

value: Uninfected

value: ATGTCAG


title: WI-38 cells, unstranded polyA RNA-seq, 9h HSV-1 infection, Replicate 1, unlabeled RNA

value: AGTCAAC


title: WI-38 cells, unstranded polyA RNA-seq, 4h HSV-1 infection, Replicate 2, labeled RNA

value: labeled RNA (eluate)

value: CTTGTAA


title: WI-38 cells, unstranded polyA RNA-seq, 9h HSV-1 infection, Replicate 2, labeled RNA


title: WI-38 cells, unstranded polyA RNA-seq, 9h HSV-1 infection, Replicate 1, labeled RNA

value: ACAGTGA


title: WI-38 cells, unstranded polyA RNA-seq, 15h HSV-1 infection, Replicate 2, labeled RNA


title: WI-38 cells, unstranded polyA RNA-seq, uninfected, Replicate 2, labeled RNA

value: CAGATCA


title: WI-38 cells, unstranded polyA RNA-seq, 4h HSV-1 infection, Replicate 1, unlabeled RNA

value: 1h before harvesting


title: WI-38 cells, unstranded polyA RNA-seq, uninfected, Replicate 1, labeled RNA

value: CGATGTA


title: WI-38 cells, unstranded polyA RNA-seq, 15h HSV-1 infection, Replicate 1, labeled RNA

value: Infected 15h before harvesting

value: GCCAATA


title: WI-38 cells, unstranded polyA RNA-seq, 15h HSV-1 infection, Replicate 2, total RNA

value: total RNA

value: GATCGGAAGAGCACACGT

value: AGTTCCG


title: WI-38 cells, unstranded polyA RNA-seq, 4h HSV-1 infection, Replicate 1, labeled RNA

value: TGACCAA


title: WI-38 cells, unstranded polyA RNA-seq, 15h HSV-1 infection, Replicate 1, total RNA


title: WI-38 cells, unstranded polyA RNA-seq, 9h HSV-1 infection, Replicate 1, total RNA

value: Infected 9h before harvesting


title: WI-38 cells, unstranded polyA RNA-seq, 4h HSV-1 infection, Replicate 2, total RNA

value: Infected 4h before harvesting


title: WI-38 cells, unstranded polyA RNA-seq, uninfected, Replicate 1, unlabeled RNA

value: Uninfected

value: unlabeled RNA (flowthrough)


title: WI-38 cells, unstranded polyA RNA-seq, 4h HSV-1 infection, Replicate 1, total RNA


title: 9157167

value: volunteer 1


title: WI-38 cells, unstranded polyA RNA-seq, uninfected, Replicate 1, total RNA


title: WI-38 cells, stranded polyA RNA-seq, 15h HSV-1 infection, Replicate 2

description:
processed data file: HSV1_antisensetranscripts.tsv
Stranded RNA-seq

extract_protocol:
Bioo Scientific NEXTflex Directional RNA-Seq Kit (dUTP Based)
Cells were resuspended in Trizol and, following Chloroform-mediate phase separation, RNA extracted from the aqueous phase using the CC-25 kit (Zymo).

value: AGATCGGAAGAGCACACGT

value: GATCAGA


title: WI-38 cells, stranded polyA RNA-seq, 9h HSV-1 infection, Replicate 2

value: ACTTGAA


title: WI-38 cells, stranded polyA RNA-seq, 15h HSV-1 infection, Replicate 1


title: WI-38 cells, unstranded polyA RNA-seq, 9h HSV-1 infection, Replicate 2, total RNA

value: AGTCAAC


title: WI-38 cells, stranded polyA RNA-seq, 9h HSV-1 infection, Replicate 1

value: ACAGTGA


title: WI-38 cells, stranded polyA RNA-seq, 4h HSV-1 infection, Replicate 2

value: CTTGTAA


title: WI-38 cells, unstranded polyA RNA-seq, uninfected, Replicate 2, total RNA

value: 1h before harvesting

value: CAGATCA


title: WI-38 cells, stranded polyA RNA-seq, uninfected, Replicate 1

value: total RNA

value: CGATGTA


title: WI-38 cells, stranded polyA RNA-seq, uninfected, Replicate 2


title: WI-38 cells, stranded polyA RNA-seq, 4h HSV-1 infection, Replicate 1


title: THP-1, PU.1 24 h EtOH rep1

description: THP-1 PU1 EtOH repl 1

extract_protocol:
proteins were crosslinked with formaldehyde to DNA, then PU1-bound fragments were pulled down by chromatin immunoprecipitation
ChIP-seq library was prepared from 5-10 ng ChIP DNA with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) per manufacturer's protocol

tag: cell type

value: human monocytic cell line

tag: treated with

value: EtOH (vehicle) for 24hrs

tag: chip antibody

value: PU.1 (Santa Cruz sc-22805 X)


title: THP-1, PU.1 24 h EtOH rep3

description: THP-1 PU1 EtOH repl 3


title: THP-1, PU.1 24 h EtOH rep2

description: THP-1 PU1 EtOH repl 2


title: THP-1, PU.1 24 h 1,25(OH)2D3 rep1

description: THP-1 PU1 V repl 1

value: 100nM VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)


title: LN-CRISPR-plasmid

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street

department: Bioinformatics and Computational Biology

institute: University of Texas MD Anderson Cancer Center

description: CRISPR plasmid

data_processing:
Library strategy: CRISPR
Illumina Casava1.7 software used for basecalling.
Genome_build: hg19

source_name: Prostate cancer cell line

growth_protocol: LNCaP cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
PCR was performed on genomic DNA to construct the sequencing library.
PCR was performed on genomic DNA to construct the sequencing library to read the barcode.

treatment_protocol: LNCaP cells were infected with the pooled lentiviral GeCKO v2 library at an MOI of 0.5. After three days of puromycin selection, half of the surviving cells were stored as 0 day control samples, and the rest of cells were cultured for an additional 2 weeks.

value: LNCaP


title: LN-CRISPR-DHT

description: CRISPR DHT


title: RNAseq: si-HNRNPL rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA-seq reads were aligned against the hg19 human reference genome with the UCSC known gene transcript annotation using TopHat v2.0.9. The RNA-seq read count of each gene was calculated using HTSeq-0.5.4p3 and differential gene expression analysis was performed using DESeq v1.9.12 (FDR≤0.05, fold change≥1.5). The differential alternative splicing analysis was performed using rMATS (Shen et al., 2014), a computational tool that allows for the analysis of replicate RNA-seq data.
Genome_build: hg19

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were constructed with TruSeq Stranded mRNA Library Prep Kit from Illumina according to the manufacturer’s manual.

treatment_protocol: LNCaP cells were transfected with 20 nM siRNA oligos of si-Ctrl, si-HNRNPL, si-LARP, respectively using RNAiMax reagent (Life Technology).


title: RNAseq: si-LARP rep1


title: RNAseq: si-HNRNPL rep3


title: RNAseq: si-HNRNPL rep2


title: RNAseq: si-Ctrl rep3


title: RNAseq: si-Ctrl rep2


title: RNAseq: si-LARP rep2


title: RNAseq: si-LARP rep3


title: LN-CRISPR-0d

description: CRISPR day 0


title: RNAseq: si-Ctrl rep1


title: circ-RNAseq: si-LARP rep2

description: circRNA-Seq

data_processing:
Illumina Casava1.7 software used for basecalling.
The circular RNA was identified using the CIRCexplorer (Zhang et al., 2014). Briefly, RNA-seq reads were first mapped using TopHat 2.0.9 (parameters: -a 6 --microexon-search -m 2) against the hg19 human reference genome with the UCSC known gene transcript annotation. Unmapped reads were then extracted and mapped onto the relevant reference genome using TopHat-Fusion (TopHat 2.0.9, parameters:--fusion-search --keep-fasta-order --bowtie1 --no-coverage-search). Back-spliced junction reads were extracted and further realigned against existing gene annotations to determine the precise positions of donor or acceptor splice site for each back-spliced event. Junction reads with shifted alignments against canonical splice sites were adjusted to the correct positions and reads with alignments on different genes or non-canonical splice sites were discarded.
Genome_build: hg19

extract_protocol:
Total RNA was extracted with Trizol reagent (Life Technology). The Ribominus kit (Life Technology) was employed to remove rRNA. RNase R treatment was performed with 20U RNase R (Epicenter) per μg RNA at 37°C for 15 min. RNAs with or without RNase R treatment were purified and subjected to library preparation and next generation sequencing.
RNA-seq libraries were constructed with TruSeq Stranded mRNA Library Prep Kit from Illumina according to the manufacturer’s manual.


title: circ-RNAseq: si-LARP rep1

description: circRNA-Seq


title: circ-RNAseq: si-Ctrl rep2

description: circRNA-Seq


title: circ-RNAseq: si-HNRNPL rep2

description: circRNA-Seq


title: circ-RNAseq: si-HNRNPL rep1

description: circRNA-Seq


title: circ-RNAseq: si-Ctrl rep1

description: circRNA-Seq


title: ST_ChIP-seq

description: Peaks also called using both replicates  = ST.peaks_bothreps.bed, ST.peaks_bothreps.txt. These files are available on the series record.

data_processing:
FASTQ data were mapped to human hg19 genome using Bowtie (bowtie-0.12.7)
Duplicate peaks were removed (macs2 filterdup function) and the reads were normalized (macs2 randsample) so that the input and the ChIP sample have the same number of reads using MACS2 (MACS-2.0.10.20130306).
Peaks were called using MACS2 with hs as the genome size (macs2 callpeak ).
Using BETA(1.0.5), the ChIP-seq peaks were incorporated with the differential expression data (diffexp.txt file from RNA-seq analysis) to find the direct targets and predict motifs.   Parameters: BETA plus --peakfile STHA_1.peaks_peaks.bed --diff_expr diffexp.txt --kind O --genome hg19
genome build: hg19
processed data files format and content:  bed files of called peaks and macs output

value: Merkel cell carcinoma

tag: merkel cell polyomavirus

value: positive

value: Ab5 (James DeCaprio Lab)


title: THP-1, PU.1 24 h 1,25(OH)2D3 rep3

description: THP-1 PU1 V repl 3


title: THP-1, PU.1 24 h 1,25(OH)2D3 rep2

description: THP-1 PU1 V repl 2


title: EP400_ChIP-seq rep2

description: Peaks also called using both replicates  = p400.peaks_bothreps.bed, p400.peaks_bothreps.txt. These files are available on the series record.


title: Input DNA rep2


title: Max_ChIP-seq rep1

description: Peaks also called using both replicates  = MAX.peaks_bothreps.bed, MAX.peaks_bothreps.txt. These files are available on the series record.

value: Max (Santa Cruz, SC-197)


title: ST-HA_ChIP-seq

value: HA (Abcam, ab9110)


title: EP400 shRNA rep3

data_processing:
The reads were mapped to hg19 with tophat-2.0.4
"FPKM_tracking" files were produced by Cufflinks
the reads were sorted using samtools (samtools-0.1.19)
Using HTSeq-0.6.1_python-2.7.3, Transcript parts per million (TPM) counts were calculated and assigned to genes  A. Mortazavi, B. A. Williams, K. McCue, L. Schaeffer, and B. Wold, “Mapping and quantifying mammalian transcriptomes by RNA-Seq,” Nature Methods, vol. 5, no. 7, pp. 621–628, 2008.
Differentially expressed genes were called using DEseq2 with the Benjamini-Hochberg (BH) adjusted p-value of 0.1
Genome_build: hg19
Supplementary_files_format_and_content: "FPKM tracking" files include FPKM values for each sample, count.txt files include TPM counts for each sample, results.csv and diffexp.text files summarize all 6 samples.

source_name: MKL-1 line with Dox inducible EP400 shRNA

extract_protocol:
Total RNA was purified from MKL-1 cells using RNeasy plus mini kit (Qiagen). mRNA was isolated with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
Sequencing libraries were prepared with NEBNext mRNA library Prep Master Mix Set for Illumina (New England Biolabs). 50 cycles single-end sequencing was performed on HiSeq2000 system at CCCB.

treatment_protocol: Cells were treated with or without doxycycline to induce expression of EP400 shRNA.

tag: dox treatment

tag: ep400 shrna expression


title: EP400 shRNA rep2


title: untreated rep3


title: EP400 shRNA rep1


title: untreated rep2


title: neg4b

city: San Diego

first: John

last: Welsh

state: California

address: 3030 Bunker Hill Street

institute: Vaccine Research Institute of San Diego

description: RNA-seq

data_processing:
read alignment: bowtie2
transcript assembly: cufflinks
normalization: quantile normalization using R
Genome_build: GRCm38/mm10 using mouse.rna.fna downloaded from ncbi: 3/2014:
Supplementary_files_format_and_content: expression_table_genes.txt
Supplementary_files_format_and_content: expression_table_isoforms.txt
Supplementary_files_format_and_content: Plumbagin.DHT.RMA.table.xls: Removed RNAs lacking poly-A tail and RNAs with average FPKM < 1 across all samples, quantile normalized

source_name: PTEN-P2 cells

growth_protocol: PTEN-P2 cells were maintained in DMEM with phenol red (Dulbecco's Modified Eagle's Medium) containing 4.5 g/L glucose, 10% FBS (Omega Scientific, Tarzana, CA, USA), 100 U/ml penicillin, 100 μg/ml streptomycin, insulin-selenium-transferrin (5 μg/ml insulin). G418 (100 μg/ml) was included to maintain stable expression of H2B-GFP. For experiments, PTEN-P2 cells were grown in DMEM free of phenol red (Dulbecco's Modified Eagle's Medium) containing 4.5 g/L glucose, 10% FBS which was treated with charcoal dextran to remove hormones (Omega Scientific, Tarzana, CA, USA), 2mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, insulin-selenium-transferrin (5 μg/ml insulin), without G418.

extract_protocol:
Cells in culture were treated for 1 hour with 0, 0.5, or 4 M plumbagin dissolved in DMSO, with or without overnight and continued treatment with 10-8M DHT in DMSO, or mock treatment with DMSO. The DMSO concentration was constant between treatment conditions. After treatment, cells were harvested and RNA was purified using RNeasy (Qiagen, Germantown, MD, USA). NGS sequencing libraries were prepared from using NEBNext for Illumina® using index primers (New England Biolabs, Ipswich, MA, USA). These libraries were sequenced, 6 index primers per lane, using the Illumina HiSeq platform at the UCSD sequencing facility (http://igm.ucsd.edu/genomics). Reads were from 252-269 reads per lane.
NEBNext for Illumina® using index primers (New England Biolabs, Ipswich, MA, USA
Pools of 6 samples per lane using index primers

treatment_protocol: +/- plumbagin +/- DHT'

value: PTEN-P2 cells

tag: treatment

value: 1hr  4.0microM plumbagin, no DHT

tag: tag

value: ATTGGC


title: pos0.5b

description: RNA-seq

tag: tissue

value: 1hr  0.5microM plumbagin with continued 10^-8M DHT

value: GCCTAA


title: pos4a

description: RNA-seq

value: 1hr  4.0microM plumbagin with continued 10^-8M DHT

value: ATCAGT


title: pos0b

description: RNA-seq

value: 24hr 10^-8M DHT treatment

value: CGTGAT


title: neg0b

description: RNA-seq

value: No treatment control

value: ACATCG


title: neg0.5b

description: RNA-seq

value: 1hr  0.5microM plumbagin, no DHT

value: TGGTCA


title: Max_ChIP-seq rep2

value: Merkel cell carcinoma

value: positive


title: pos4b

description: RNA-seq

value: CACTGT


title: neg4a

description: RNA-seq

value: AGGAAT


title: pos0.5a

description: RNA-seq

value: PTEN-P2 cells

value: CGTACG


title: neg0a

description: RNA-seq


title: neg0.5a

description: RNA-seq

value: CCACTC


title: pos0a

description: RNA-seq

value: GGCCAC


title: 240a

description: RNA-seq

value: 240min 10^-8M DHT treatment

value: ATTGGC


title: 30b

description: RNA-seq

value: 30min 10^-8M DHT treatment

value: GATCTG


title: EP400_ChIP-seq rep1


title: 240b

description: RNA-seq

value: CTGATC


title: 30a

description: RNA-seq


title: 60a

description: RNA-seq

value: 60min 10^-8M DHT treatment


title: Input DNA rep1


title: 15a

description: RNA-seq

value: 15min 10^-8M DHT treatment

value: ACATCG


title: 15b

description: RNA-seq

value: GCCTAA


title: untreated rep1

value: Merkel cell carcinoma


title: 0b

description: RNA-seq

value: No treatment control

value: barcode


title: Ecc_16hr

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

description:
Poly(A) mRNA
16hrs post-infection with Ecc15.
Processed data file: Processed_data.txt

data_processing:
Illumina CASAVA1.8.2 software used for basecalling.
Sequenced reads were filtered for low-quality sequence, trimmed for adaptor sequence, trimmed 3' ends of the resulting reads for which PHRED quality scores were lower than 20 using Cutadapt v.1.6, and then mapped to Drosophila melanogaster reference genome (NCBI build 5.3) using TopHat v.2.0.7 with parameters -p 16 --bowtie-n --b2-sensitive --mate-inner-dist 70 --mate-std-dev 90 --no-coverage-search --library-type fr-unstranded --no-novel-juncs.
After removing duplicate reads, the FPKM values for each gene were calculated using Cufflinks v.2.0.2.
The FPKM values were converted to log2-FPKM after adding one to the FPKM values. The log2-FPKM for the samples were then normalized using the quantile normalization method (MATLAB R2011b).
Genome_build: NCBI build 5.3 (Release 5)
Supplementary_files_format_and_content: Processed_data.txt: Tab-delimited text file includes normalized log2-FPKM values for each sample.

organism: Drosophila melanogaster

source_name: Drosophila anterior midgut, Ecc, 16h

extract_protocol:
Total RNA was extracted from each of midguts using the Qiagen RNeasy mini kit (Qiagen). Poly(A) mRNA isolation from total RNAs (5 µg) and fragmentation were performed using the Illumina TruSeq RNA Sample Prep Kit with poly-T oligo-attached magnetic beads, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina TruSeq RNA sample prep kit v2, according to the manufacturer’s protocol.

treatment_protocol: Sucrose treatment or infection with Ecc15 for 2h, 4h, or 16h.

value: anterior midgut

value: infection with Ecc15

tag: time post-treatment


title: Ecc_2hr

description:
Poly(A) mRNA
2hrs post-infection with Ecc15.
Processed data file: Processed_data.txt

source_name: Drosophila anterior midgut, Ecc, 2h


title: 60b

description: RNA-seq

value: PTEN-P2 cells

value: TCAAGT


title: RNA-seq_grp7-1 LL36-rep3

city: Bielefeld

last: Lewinski

address: Universitätsstraße 25

department: RNA Biology and Molecular Physiology

institute: Bielefeld University

description: Sample 3

data_processing:
Only the 100 bp R1-reads coming from the original paired-end reads were used for further analysis. Only the R1 reads were submitted to SRA.
Raw RNA-seq reads were subjected to quality trimming and filtering by Sickle v1.2 (https://github.com/najoshi/sickle) using parameters -l 50 -q 30.
The trimmed and filtered reads were mapped to the Arabidopsis thaliana transcriptome defined by atRTD.gff using  STAR v2.5.2a with the parameter --quantMode TranscriptomeSAM
Estimated read counts per transcript were obtained by Salmon v0.8.2 and summarized into estimated read counts per gene by tximport
rRNA, mitochondrial and chloroplast genes were excluded from the analysis
Differentially expressed genes (DEGs) Enriched transcripts between RIP samples and RNA-seq samples were detected by edgeR as described in the tximport vignette (https://github.com/mikelove/tximport/blob/master/vignettes/tximport.md).
Genes with a FDR<0.05 and a TPM>1 in at least one of the genotypes were considered putative DEGs.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including TPM values in a matrix for each sample as columns

organism: Arabidopsis thaliana

source_name: aerial tissue

growth_protocol: Aerial parts of Col-2 wt plants, AtGRP7-ox plants and the grp7-1 8i lines were grown grown in 12 h light-12 h dark cycles for 16 days, subsequently shifted to continuous light and harvested at LL36 or LL24.

extract_protocol:
Total RNA was isolated using the Universal RNA purification Kit (EURx, Roboklon) including DNase digestion. Total RNA integrity was analyzed on Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano Kit and RNA showing an RIN >8 were further processed.
Libraries were prepared from three biological replicates using the TruSeq RNA sample prep kit v2. Sequencing was carried out using an Illumina HiSeq2000 at the Genomics Center of the Max-Planck-Institute for Developmental Biology, Tuebingen, with 100 nt paired-end reads.

treatment_protocol: Harvesting at timepoint LL24 and L36 in three lines (Col-2, AtGRP7-ox and grp7-1 8i)

value: aerial tissue

tag: genotype

value: grp7-1 8i

tag: time point


title: RNA-seq_grp7-1 LL36-rep2

description: Sample 2


title: RNA-seq_grp7-1 LL36-rep1

description: Sample 1


title: RNA-seq_grp7-1 LL24-rep3

description: Sample 3


title: Suc_2hr

description:
Poly(A) mRNA
2hrs after treatment with sucrose.
Processed data file: Processed_data.txt

source_name: Drosophila anterior midgut, sucrose, 2h

value: sucrose


title: RNA-seq_AtGRP7ox-LL24-rep2

description: Sample 2

value: AtGRP7 ox


title: RNA-seq_AtGRP7ox-LL24-rep1

description: Sample 1


title: RNA-seq_AtGRP7ox-LL36-rep2

description: Sample 2


title: RNA-seq_grp7-1 LL24-rep1

description: Sample 1


title: RNA-seq_AtGRP7ox-LL36-rep3

description: Sample 3


title: RNA-seq_Col2-LL36-rep1

description: Sample 1

value: Columbia 2, wt


title: RNA-seq_Col2-LL36-rep3

description: Sample 3


title: RNA-seq_AtGRP7ox-LL24-rep3

description: Sample 3


title: 7GFP LL36 rep3

description: harvested at LL36

data_processing:
Raw RIP-seq reads were subjected to quality trimming and filtering by Sickle v1.2 (https://github.com/najoshi/sickle) using parameters -l 50 -q 20.
The trimmed and filtered reads were mapped to the Arabidopsis thaliana transcriptome defined by atRTD.gff using  STAR v2.5.2a with the parameter --quantMode TranscriptomeSAM
Estimated read counts per transcript were obtained by Salmon v0.8.2 and summarized into estimated read counts per gene by tximport
rRNA, mitochondrial and chloroplast genes were excluded from the analysis
Differentially expressed genes (DEGs) Enriched transcripts between RIP samples and RNA-seq samples were detected by edgeR as described in the tximport vignette (https://github.com/mikelove/tximport/blob/master/vignettes/tximport.md).
Genes with a FDR <0.001 and a log2-fold change > 0.5 were considered putative RIP targets
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including TPM values in a matrix for each sample as columns

growth_protocol: Plants grown in 12 h light-12 h dark cycles for 16 days and subsequently shifted to continuous light were vacuum-infiltrated with 1 % formaldehyde for 15 min at LL36 or LL24, followed by quenching with 125 mM glycine.

extract_protocol:
A whole-cell extract was prepared in RIP-lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 4 mM MgCl2, 0.1 % Igepal, 1 % SDS, 5 mM DTT, 10 mM Vanadylribonucleosid complex, 100 U RiboLockTM/ml (Fermentas), 1 mM phenylmethylsulfonylfluorid and protease inhibitor tablets (Roche)). The extract was pre-cleared with Sepharose beads and subjected to immunoprecipitation with GFP-Trap® beads (Chromotek, Martinsried, Germany), hereafter called IP+. After extensive washing with RIP-washing buffer (50 mM Tris-HCl pH 7.5, 500 mM NaCl, 4 mM MgCl2, 5 mM DTT, 0.5 % Igepal, 1 % SDS, 0.5 % Na-deoxycholate, 2 M urea), coprecipitated RNAs were eluted with TriReagent and treated with DNase (Promega).
Libraries were prepared of three biological replicates using the Illumina TrueSeq Sample preparation kit v2, except for omitting the two rounds of poly(A) selection commonly used for total RNA as a starting material. Sequencing was carried out using an Illumina HiSeq2000 at the Genomics Center of the Max-Planck-Institute for Developmental Biology, Tuebingen, with 100 nt single-end reads.

treatment_protocol: Harvesting at timepoint LL24 and L36

value: AtGRP7::AtGRP7-GFP in grp7-1


title: RNA-seq_AtGRP7ox-LL36-rep1

description: Sample 1


title: RNA-seq_Col2-LL24-rep3

description: Sample 3


title: RNA-seq_Col2-LL24-rep1

description: Sample 1


title: RNA-seq_grp7-1 LL24-rep2

description: Sample 2


title: 7GFP LL24 rep3

description: harvested at LL24


title: 7GFP LL36 rep1

description: harvested at LL36


title: 7GFP LL36 rep2

description: harvested at LL36


title: 7GFP LL24 rep2

description: harvested at LL24


title: Ecc_4hr

description:
Poly(A) mRNA
4hrs post-infection with Ecc15.
Processed data file: Processed_data.txt

source_name: Drosophila anterior midgut, Ecc, 4h


title: Suc_4hr

description:
Poly(A) mRNA
4hrs after treatment with sucrose.
Processed data file: Processed_data.txt

source_name: Drosophila anterior midgut, sucrose, 4h


title: 7GFP LL24 rep1

description: harvested at LL24


title: 2848T

city: Guangzhou

first: Jingping

last: Yun

state: Guangdong

address: 651 Dongfeng East Road

department: Pathology

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequencing reads were firstly filtered for adapters and ribosomal RNA. Reads containing five or more low quality (quality score < 20) bases were also removed. The remained high-quality reads were then aligned to human genome (hg19) by using Tophat (v2.0.9) with default parameters.
Gene expression level measured by FPKM (fragments per kilobase per million) was calculated by Cufflinks (v2.1.1), the GTF file was povided by Illumina iGenomes UCSC hg19(ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz)
Genome_build: hg19
Supplementary_files_format_and_content: expression: tab-delimited text files include: #(unique id) and FPKM values for each sample

source_name: Liver

extract_protocol:
Sequencing libraries were prepared by using prepared by using TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to standard protocols. Briefly, total RNA was firstly randomly fragmented and poly-A-selected. Secondly, the RNA fragments were reverse transcribed to cDNA, end-repaired and ligated with adapters. The libraries then underwent size selection, PCR and purification. The quality of libraries was assessed by using Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). Sequencing was then performed on an Illumina HiSeq 2500 sequencer with 125 bp pair-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: HCC

tag: individual

value: patient No.2848

value: tumor

tag: differentiation status

value: well differentiated

tag: liver cirrhosis

value: without Liver Cirrhosis

tag: hbv infection

value: HBV infection-free


title: 2801N

value: patient No.2801

value: non-tumor

value: poorly differentiated

value: with Liver Cirrhosis


title: 2801T


title: RNA-seq_Col2-LL36-rep2

description: Sample 2


title: 2858N

value: patient No.2858

value: HBV-infected


title: 2809T

value: patient No.2809


title: RNA-seq_Col2-LL24-rep2

description: Sample 2

value: aerial tissue


title: 2796N

value: patient No.2796


title: 2777T

value: patient No.2777


title: 2777N


title: 2762T

value: patient No.2762


title: 2766T

value: HCC

value: patient No.2766


title: 2634N

value: patient No.2634


title: 2591N

value: patient No.2591


title: 2701N

value: patient No.2701

value: without Liver Cirrhosis


title: 2634T

value: tumor


title: 2701T


title: 2429N

value: patient No.2429

value: non-tumor

value: well differentiated


title: 2429T


title: LELS_ChIP-seq_p300_stage9_replicate1

city: Nijmegen

first: Simon

last: van Heeringen

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Radboud University

description: ChIP-seq of p300 in stage 10.5 Xenopus laevis embryos

data_processing:
ChIP-seq and genomic DNA reads were aligned to the genome using bwa version 0.7.10-r789 with default parameters
Duplicates in genomic DNA were marked using Picard MarkDuplicates version 2.7.1
ChIP-seq peaks were called using macs2 version 2.0.10 with qvalue cutoff=1e-03 relative to respective ChIP input track.
RNA-seq reads were mapped to genome Xla.v91 + transcriptome v1.8 (http://www.xenbase.org) using STAR version 2.4.2a with --quantMode TranscriptomeSAM. Quantification was performed on the reads mapped to the transcriptome by STAR using eXpress v1.5.1.
Genome_build: Xenopus tropicalis: xt9.0; Xenopus laevis: Xla.v91; Xenopus tropicalis x Xenopus laevis: xt9.0 + Xla.v91 (merged)
Supplementary_files_format_and_content: Results from eXpress (.xprs); peak files in BED format.

organism: Xenopus laevis

source_name: whole embryo

growth_protocol: Embryos were generated using IVF (in vitro fertilization) with outbred animals.

extract_protocol:
Protein-DNA complexes were isolated with antibody from whole embryo lysates that were fixed, sonicated and yolk depleted.
Libraries were prepared with the Kapa Hyper Prep kit (Kapa Biosystems)

tag: developmental stage

value: NF stage 10.5

tag: cell type

value: whole embryo

value: p300 (C-20, Santa Cruz sc-585)


title: LELS_ChIP-seq_input_stage9_replicate2

description: ChIP-seq input in stage 9 Xenopus laevis embryos

value: NF stage 9

tag: chip antibody

value: None (Input)


title: LELS_ChIP-seq_p300_stage9_replicate2


title: LELS_ChIP-seq_input_stage9_replicate1


title: LELS_ChIP-seq_H3K4me3_stage9_replicate2

description: ChIP-seq of H3K4me3 in stage 9 Xenopus laevis embryos

value: H3K4me3  (Abcam ab8580)


title: 2858T

value: patient No.2858

value: with Liver Cirrhosis

value: HBV-infected


title: 2591T

value: HCC

value: poorly differentiated


title: LELS_ChIP-seq_H3K4me3_stage9_replicate1


title: Xenopus_laevis_RNAseq_stage10.5_replicate2

description: Total RNA (rRNA depleted) of stage 10.5 Xenopus laevis embryos

extract_protocol:
Total RNA was extracted from 20 Nieuwkoop-Faber stage 10.5 embryos (two biological replicates) using Trizol and Qiagen columns. 4-5 ug of total RNA was treated with DNase I on column and depleted of rRNA (ribosomal RNA) using Magnetic gold RiboZero RNA kit (Illumina) resulting in a yield of 45 - 52 ng of rRNA depleted total RNA.
2 ng of rRNA-depleted total RNA was reserved for Experion (Bio-Rad) quality assessment run for rRNA depletion and the remaining was used for first and second strand synthesis (strand-specific protocol). Total yield of dscDNA was between 14.5-15.8 ng and out of this 1.2 - 5 ng was used for sample preparation for high high-throughput sequencing (according to manufacturer's protocol).


title: Xenopus_laevis_RNAseq_stage10.5_replicate1


title: RPMI_liquid_37_e

city: Omaha

first: Jill

middle: R

last: Blankenship

state: NE

address: 6001 Dodge St, AH114

department: Biology

institute: University of Nebraska at Omaha

data_processing:
All eight Candida chromosomes were downloaded from NCBI, and annotation was downloaded into a gff3 file, and transformed into a gtf file using gffread
Fastq files were generated using the bcl2fastq software, version 1.8.4. The fastq files for each sample were analyzed using the Tuxedo pipeline in order to find differentially expressed genes.
Read alignment was performed using tophat version 2.0. FPKM values were calculated with cufflinks 2.2.
Genome_build: ASM18296v3
Supplementary_files_format_and_content: tab-delimited text files include average FPKM values for each Sample. Average is across replicates.

organism: Candida albicans

growth_protocol:
SC5314 cells were grown overnight in YPD media at 30˚C with shaking. Cells were washed twice and resuspended with equal volumes of PBS. Cells were added to liquid or solid media as described below.
100 µl of washed cells were incubated in 50 ml of pre-warmed media in a 250 ml flask. Cells grown at 37˚C in liquid RPMI-MOPS with shaking for 3 hours

extract_protocol:
cell harvesting: Cells were harvested by filtration and then frozen at -80˚C.
RNA was collected from frozen cell pellets using the RNeasy kit (Qiagen) with minor modifications. Cell pellets were resuspended in the supplied resuspension buffer with 10 µl/ml beta-mecaptoethanol and moved to a 2 ml screw-cap tube. Cells were mechanically disrupted using 450 nm glass beads in a mini-bead beater (RPI), with three 1-minute bead beating pulses and 2 minute rests. The resulting supernatant was cleared of cell debris and RNA was precipitated with 70% EtOH. The cell supernatant/EtOH mix was placed into the purification column, washed, and eluted with 100 µl nuclease-free water. Residual genomic DNA was removed from the RNA samples during washing using a Qiagen RNase-free DNase on-column removal kit.
RNASeq libraries were generated beginning with 1.8 ng of total RNA following standardized protocols with the TruSeq RNA v2 kit

tag: strain

tag: media substrate

value: liquid

tag: temperature


title: Xenopus_laevis_genomic

description: Genomic DNA of Xenopus laevis embryos

extract_protocol:
Genomic DNA was isolated.
DNA was sonicated to 200-700bp fragments, 300bp fragments were size-selected.

value: NF stage 12


title: RPMI_liquid_37_a


title: RPMI_liquid_37_c


title: Lees_liquid_37_e

growth_protocol:
SC5314 cells were grown overnight in YPD media at 30˚C with shaking. Cells were washed twice and resuspended with equal volumes of PBS. Cells were added to liquid or solid media as described below.
100 µl of washed cells were incubated in 50 ml of pre-warmed media in a 250 ml flask. Cells grown at 37˚C in liquid Lee's with shaking for 3 hours


title: Lees_liquid_37_c


title: Lees_liquid_37_a


title: FBS_liquid_37_c

growth_protocol:
SC5314 cells were grown overnight in YPD media at 30˚C with shaking. Cells were washed twice and resuspended with equal volumes of PBS. Cells were added to liquid or solid media as described below.
100 µl of washed cells were incubated in 50 ml of pre-warmed media in a 250 ml flask. Cells grown at 37˚C in liquid YPD+10% FBS with shaking for 3 hours


title: FBS_liquid_37_e


title: cAMP_ChIP-IgG

city: Charleston

first: Makoto

last: Taniguchi

state: SC

address: 173 Ashley Ave

institute: Medical University of South Carolina

data_processing:
SoLiD sequencing of ChIP-seq libraries were performed on Applied Biosystems SoLiD
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie
peaks were called using analysis package HOMER.
Genome_build: mm9

source_name: Cultured Striatal neuron

growth_protocol: Primary cultured striatal neuron were prepared from mouse E15-16.  Striatal neurons were plated at a density of 1.0 * 10^7 cells/10 cm and cultured in the Neurobasal/B27 containing Penicillin, streptomycin, and glutamine at 37 degree/5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Seqencing library construction from immunoprecipitated DNA was performed as described (Kim et al., 2010; Koike et al.,2012)

treatment_protocol: Primary cultured striatal neurons were stimulated with forskilin 10 microM for 3 hours at DIV6.

value: Cultured striatal neuron prepared from E15-16 mouse pups

tag: passages

value: Primary cultured neuron

tag: treated with

value: 10uM forskilin for 3 hours

value: normal rabbit IgG (Invitrogen, cat#10500C, lot#503140C)


title: Control_Input


title: Control_ChIP-IgG


title: Spider_liquid_37_e

growth_protocol:
SC5314 cells were grown overnight in YPD media at 30˚C with shaking. Cells were washed twice and resuspended with equal volumes of PBS. Cells were added to liquid or solid media as described below.
100 µl of washed cells were incubated in 50 ml of pre-warmed media in a 250 ml flask. Cells grown at 37˚C in liquid spider with shaking for 3 hours


title: FBS_liquid_37_a


title: Control_ChIP-HD5

value: HDAC5 (Cell Signaling Technology, cat#2082, lot#2)


title: WT rep1

city: Beijing

first: Xueying

last: Mai

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing:
Use cutadapt v1.11 to remove the low quality bases and trimmed the sequence in 50nt length.
Use TopHat v2.1.1 to aligned the reads with default parameter.
Use Cufflinks 2.2.1 to calculate the gene expression level.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM for each sample in text.

source_name: mouse liver

extract_protocol:
RNA was extracted using the Direct-zol™ RNA MiniPrep Kit (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

value: Wild Type


title: cAMP_ChIP-HD5


title: YPD_liquid_30_a

growth_protocol:
SC5314 cells were grown overnight in YPD media at 30˚C with shaking. Cells were washed twice and resuspended with equal volumes of PBS. Cells were added to liquid or solid media as described below.
100 µl of washed cells were incubated in 50 ml of pre-warmed media in a 250 ml flask. Cells grown at 30˚C in liquid YPD media with shaking  for 3 hours


title: YPD_liquid_30_c


title: Spider_liquid_37_a


title: RPMI_solid_37_e

growth_protocol:
SC5314 cells were grown overnight in YPD media at 30˚C with shaking. Cells were washed twice and resuspended with equal volumes of PBS. Cells were added to liquid or solid media as described below.
140 µl of washed cells and 200 µl of H2O were spread on the surface of pre-warmed agar plates using 3.5 mm glass beads. Plates were incubated at 37˚

extract_protocol:
cell harvesting: 2 ml of sterile, autoclaved nanopure water was added to the top of the agar plate. A sterile, disposable cell scraper was scraped across the surface of the plates to liberate cells from the agar surface and to collect the water/cell slurry at a collection point on the plate. The water/cell slurry was pipetted into microcentrifuge tubes and quickly spun down at full speed in a microcentrifuge. The supernatant was poured off and the cell pellets were frozen at -80˚C.
RNA was collected from frozen cell pellets using the RNeasy kit (Qiagen) with minor modifications. Cell pellets were resuspended in the supplied resuspension buffer with 10 µl/ml beta-mecaptoethanol and moved to a 2 ml screw-cap tube. Cells were mechanically disrupted using 450 nm glass beads in a mini-bead beater (RPI), with three 1-minute bead beating pulses and 2 minute rests. The resulting supernatant was cleared of cell debris and RNA was precipitated with 70% EtOH. The cell supernatant/EtOH mix was placed into the purification column, washed, and eluted with 100 µl nuclease-free water. Residual genomic DNA was removed from the RNA samples during washing using a Qiagen RNase-free DNase on-column removal kit.
RNASeq libraries were generated beginning with 1.8 ng of total RNA following standardized protocols with the TruSeq RNA v2 kit

value: solid


title: SunTag rep1

value: SunTag


title: Suc_16hr

description:
Poly(A) mRNA
16hrs after treatment with sucrose.
Processed data file: Processed_data.txt

source_name: Drosophila anterior midgut, sucrose, 16h

value: anterior midgut

tag: treatment

value: sucrose

tag: time post-treatment


title: RPMI_solid_37_c


title: Lees_solid_37_e


title: RPMI_solid_37_a


title: FBS_solid_37_e


title: Lees_solid_37_a


title: FBS_solid_37_c


title: cAMP_Input


title: FBS_solid_37_a


title: Spider_solid_37_c


title: org2_m6A

description: anti-m6A antibody (212B11, Synaptic Systems)

data_processing:
Pre-processing of reads was performed using the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), namely adapters were clipped, poor quality reads were filtered out and identical reads were collapsed
Pre-processed reads from E13.5 mouse forebrains were aligned to the mouse genome (build GRCm38/mm10), and reads from the human organoids and fetal brain to the human genome (build GRCh37/hg19), using Tophat2 (Kim et al., 2013) with default settings.
m6A-tagged regions were identified using the MACS2 peak calling algorithm (Zhang et al., 2008), with the input library as background.
Genome_build: mm10 for mouse. hg19 for human.
Supplementary_files_format_and_content: narrowPeak files from MACS2 output, containing m6A peaks

source_name: organoid tissue

extract_protocol:
For m6A profiling of mouse developing brain, forebrains from wild type E13.5 embryos were dissected and total RNA was extracted from them. mRNA was then isolated using the Dynabeads mRNA Purification Kit (Ambion). m6A pull-down was performed using a rabbit polyclonal anti-m6A antibody (Synaptic systems), and immunoprecipitation with protein G dynabeads (Novex). For m6A profiling of 47 day organoids, the same procedure was followed.
cDNA libraries from pulled-down RNA and input RNA were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina®.

value: organoid tissue

tag: age

value: 47 days


title: Spider_liquid_37_c


title: Spider_solid_37_e


title: control-2

city: beltsville

first: Tianbao

last: Yang

state: MD

address: 10300 BALTIMORE AVENUE

department: BARC

institute: USDA-ARS

description: control sample

data_processing:
The paired-end raw reads were filtered with Illumina Pipeline (CASAVA) v1.8.2 with the default parameter.
The raw reads after filtered were separately aligned to the Solanum lycopersicum (ITAG 2.3) genome and CDS with RNA-Seq analysis algorithm included in the CLC Genomics Workbench 7.0.4 (CLC bio, Boston, USA) using the default parameters.
Genome_build: SL 2.4
Supplementary_files_format_and_content: xls, rpkm value

organism: Solanum lycopersicum

source_name: fruit

growth_protocol: Tomato plants (S. lycopersicum cv ‘microtom’) were grown in greenhouse at 28 °C and 16 h/8 h (light/dark).

extract_protocol:
RNA was extracted using the RNeasy plant mini kit (Qiagen); on-column DNase digestion with the RNase-Free DNase set (Qiagen) was performed to remove contaminating DNA
Illumina TruSeq RNA sample preparation kit

treatment_protocol: CaCl2 and H2O were injected in the mature green tomato fruit, and havested at 0h, 8h, and 24h after injeciton

value: fruit

value: mature green stage

value: control sample


title: Water 24h-2

description: injected with water, and harvested at 24 hours after injection


title: YPD_solid_30_e


title: YPD_liquid_30_e

value: liquid


title: control-1

description: control sample


title: HSD tissue, replicate 4

city: Monroe

first: Wayne

last: Hemphill

state: Louisiana

address: 700 University Ave

institute: University of Louisiana at Monroe

description: nm-vs-hs rna-seq raw data Fall 2016.csv

data_processing:
Base calling and quality scoring were performed with Illumina Real Time Analysis Software v2.4.6.0
Sequence results were mapped to the dm6 genome with Bowtie 2 v2.3.0
Mapped reads were assembled using Cufflinks and Cuffmerge v2.2.0
Differential expression of the mapped reads and assembled transcriptome was performed using Cuffdiff; Reads Per Kilobase per Million reads (RPKM) and fold change values were calculated.
Genome_build: dm6
Supplementary_files_format_and_content: comma separated value files contain RPKM, fold change, p, and q values for each experimental diet group, as well as RPKM values from the normal/control diet group.

source_name: Head

growth_protocol: All flies used in the experiment were wild-type, Oregon R-C (Bloomington stock #5) genotype.  Upon eclosing, female virgins were collected and housed on low calorie media at approximately equal densities of 30 flies/vial until in excess of 450 flies were obtained. Females were then synchronously mated with males of the same genotype in a 2:1 ratio for 2 days.  After mating, males were removed, and the females were divided equally into three groups and placed on one of the three corresponding media types (ND, HSD, HFD).  The fly groups were kept on their respective media for seven days, being transferred to new media every three to four days.  Flies were kept in an incubator at 25℃ on a 12-hour light/dark cycle with consistent humidity, until decapitation, excluding any handling without anesthesia for media transfers.

extract_protocol:
Flies were transferred from their media briefly into empty vials and anesthetized using FlyNap® (Carolina®).  The flies were then submerged in a petri dish with 1 mL TRIzol® reagent, and their heads were pulled off with forceps in rapid succession.  The heads (N=20) were then immediately placed in 200 µL of TRI Reagent® in a 1.5mL microcentrifuge tube.  There were six biological replicates (tubes) for each media group, with each replicate/tube containing 20 heads.  The head tissue in each tube was then homogenized using an electric pestle.  RNA extraction and purification was performed using a Direct-zol™ RNA MicroPrep kit (Zymo Research).  The RNA was eluted with sterile water, after which purity and concentration were confirmed via 260/280 and 260/230 ratios measured using a NanoDrop® 2000c (Thermo Scientific).  N=6 per experimental condition.
Libraries were prepared according to the specifications accompanying the Illumina TruSeq Stranded mRNA Library Prep Kit High Throughput (RS-122-2103).

treatment_protocol: The ND acted as our control diet, and consisted of 2.6% w/v cornmeal, 4% w/v dry inactivated yeast, 0.8% w/v agar, 3% w/v sucrose, 1.5% v/v Tegosept (20% w/v in 70% ethanol), and 0.3% v/v propionic acid.  The HFD and HSD were identical to the ND, except for an addition of 20% w/v coconut oil in the HFD, and the use of 20% w/v sucrose instead of 3% in the HSD.  The low calorie (LC) diet briefly used for collections and mating contains 5.2% w/v cornmeal, 5% w/v dry inactivated yeast, 1% w/v agar, 3% w/v sugar, 1.5% v/v Tegosept (20% w/v in 70% ethanol), 0.3% v/v tetracycline (10mg/mL), and 0.3% v/v propionic acid.

value: head tissues

tag: diet

value: High sugar


title: YPD_solid_30_c


title: Water 24h-1

value: injected with water, and harvested at 24 hours after injection


title: F. fujikuroi NCIM1100 in planta

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

data_processing:
RNA-seq reads were mapped on the reference genomes using tophat2 (v2.0.8).
The interval for allowed intron lengths were set to min 20 nt and max 1 kb (Kim, 2013, Trapnell et al., 2009).
Cufflinks was used  to determine the abundance of transcripts in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) and calculated differentially expressed genes using cuffdiff (Trapnell et al., ,2012, Trapnell et al., 2010).
The gene models were included as raw junctions. Genes with a minimum of fourfold increase or decrease in expression (|log2 of the FPKM values +1| ≥ 2) between the two experimental conditions were considered as regulated.
Genome_build: F. fujikuroi IMI58289 : http://www.ebi.ac.uk/ena/data/view/PRJEB185; Further 9 strains: http://www.ebi.ac.uk/ena/data/view/PRJEB14872
Supplementary_files_format_and_content: tab-delimited text files holding FPKM values for each sample

organism: Fusarium fujikuroi

source_name: in planta, rice, 7 dpi

growth_protocol: RNA was isolated from lyophilized mycelia grown before in liqid synthetic media with 6 mM or 60 mM glutamine for 3 days or from lyophilized infected rice roots after 7 days post infection.

extract_protocol:
Total RNA was extracted using Trizol reagent. The DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).
Illumina TruSeq RNA Library
Total RNA was sequenced using Illumina HiSeq 2000 technology by BGI Tech Solutions (Hong Kong) Co., Limited.

tag: genotype

value: wild type

tag: dpi

tag: culture condition

value: in planta, rice, 7 dpi


title: F. fujikuroi FSU48 in planta


title: HeLa koBBC3as 59F8 cells, stranded polyA RNA-seq, 6h uninfected, Replicate 1

description:
Stranded RNA-seq
processed data file: HSV1_antisensetranscripts.tsv

data_processing:
Data was mapped onto the hg19 reference using Tophat2 (Kim et al. 2013).
Antisense transcripts were defined on the coverage tracks using a custom running sum algorithm, followed by extensive filtering.
Antisense transcripts were classified into divergent, convergent and intal, based on the location of the TSS in respect to the sense transcript.
Expression values for the different samples (columns X-X) are presented as log(2) transformed RPKM values of averages from biological replicates.
Expression values are shown for the stranded RNA-sequencing data provided here (columns X-X). In addition, published RNA-sequencing data was reanalyzed the same way (columns X-X, as indicated by first author name and GSM identifiers).
The following datasets were reanalyzed: HSV-1 infected HFF cells (Rutkowski et al. 2015, PMID: 25989971, GEO: GSE59717), RNA-sequencing from VZV keratinocytes (Jones et al. 2014, PMID: 24497829, SRA: E-MTAB-1717) and CMV infected fibroblast (Tirosh et al. 2015, PMID: 26599541, GEO: GSE69906), and NET-seq data from HeLa cells (Schlackow et al. 2017, PMID: 28017589, GEO: GSE81662)
Column names contain first author name, SRA identifiers for VZV data and GEO identifiers for all others. Several identifiers indicate that replicates were available and averaged.
Nearest FANTOM transcripts (Hon et al. 2017) are also provided.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text

source_name: HeLa koBBC3as 59F8 cells

extract_protocol:
TruSeq Stranded mRNA Library Prep Kit
Cells were resuspended in Trizol and, following Chloroform-mediate phase separation, RNA extracted from the aqueous phase using the CC-25 kit (Zymo).

tag: 4su treatment

tag: hsv-1 infection

value: Infected 6h before harvesting

tag: rna isolation

value: total RNA

tag: adapter sequence

value: GATCGGAAGAGCACACGT

tag: barcode

value: TTTCGGA


title: org1_m6A


title: Ca 24h-2

description: injected with CaCl2, and harvested at 24 hours after injection

tag: developmental stage


title: F. fujikuroi MRC2276 in planta

tag: strain


title: F. fujikuroi E282 in planta


title: HSD tissue, replicate 3

description: nm-vs-hs rna-seq raw data Fall 2016.csv


title: HSD tissue, replicate 1

description: nm-vs-hs rna-seq raw data Fall 2016.csv


title: Ca 8h-1

description: injected with CaCl2, and harvested at 8 hours after injection


title: HeLa koBBC3as 59F8 cells, stranded polyA RNA-seq, 2h uninfected, Replicate 2

value: Infected 2h before harvesting

value: AGTGGAT


title: Water 8h-2

description: injected with water, and harvested at 8 hours after injection


title: YPD_solid_30_a

tag: media substrate

value: solid

tag: temperature


title: Lees_solid_37_c


title: HSD tissue, replicate 2

description: nm-vs-hs rna-seq raw data Fall 2016.csv

tag: tissue


title: Water 8h-1

tag: treatment

value: injected with water, and harvested at 8 hours after injection


title: HeLa koBBC3as 59F8 cells, stranded polyA RNA-seq, 6h uninfected, Replicate 2

value: TTCCTTT


title: F. fujikuroi m567 in planta


title: Ca 8h-2

value: fruit

value: mature green stage

value: injected with CaCl2, and harvested at 8 hours after injection


title: org_input

value: organoid tissue

value: 47 days


title: F. fujikuroi NCIM1100 high nitrogen

source_name: liquid culture, 60 mM Gln

value: liquid culture, 60 mM Gln


title: HFD tissue, replicate 1

description: nm-vs-hf rna-seq raw data Fall 2016.csv

value: head tissues

value: High fat


title: F. fujikuroi IMI58289 in planta

value: wild type

value: in planta, rice, 7 dpi


title: NMD tissue, replicate 4

description:
nm-vs-hf rna-seq raw data Fall 2016.csv
nm-vs-hs rna-seq raw data Fall 2016.csv

value: Normal media


title: Spider_solid_37_a


title: HeLa koBBC3as 59F8 cells, stranded polyA RNA-seq, 2h uninfected, Replicate 1

value: total RNA

value: GATCGGAAGAGCACACGT

value: TGAAACG


title: HFD tissue, replicate 4

description: nm-vs-hf rna-seq raw data Fall 2016.csv


title: HeLa koBBC3as 59F8 cells, stranded polyA RNA-seq, 4h uninfected, Replicate 2

value: Infected 4h before harvesting

value: CTGATAT


title: Ca 24h-1

value: injected with CaCl2, and harvested at 24 hours after injection


title: HeLa koBBC3as 59F8 cells, stranded polyA RNA-seq, 4h uninfected, Replicate 1

value: TGGCCTT


title: HFD tissue, replicate 3

description: nm-vs-hf rna-seq raw data Fall 2016.csv


title: F. fujikuroi B20 in planta


title: F. fujikuroi B14 in planta


title: HFD tissue, replicate 2

description: nm-vs-hf rna-seq raw data Fall 2016.csv


title: NMD tissue, replicate 2


title: HeLa koBBC3as 59F8 cells, stranded polyA RNA-seq, uninfected, Replicate 2

value: Uninfected

value: GTACGTA


title: NMD tissue, replicate 1


title: F. fujikuroi FSU48 high nitrogen


title: HeLa koBBC3as 56D2 cells, stranded polyA RNA-seq, 4h HSV-1 infection, Replicate 2

source_name: HeLa koBBC3as 56D2 cells

value: TGTCAGA


title: NMD tissue, replicate 3


title: 2796T

tag: disease state

value: HCC

tag: individual

value: patient No.2796

value: tumor

tag: differentiation status

value: well differentiated

tag: liver cirrhosis

value: without Liver Cirrhosis

tag: hbv infection

value: HBV infection-free


title: HeLa koBBC3as 59F8 cells, stranded polyA RNA-seq, uninfected, Replicate 1

value: TCCGCAC


title: input3_pcw11

source_name: PCW11 human brain cortex

extract_protocol:
total RNA was extracted using RNeasy Mini Kit (Qiagen) and next, mRNA was isolated using the Dynabeads mRNA Purification Kit (Invitrogen)
cDNA libraries from pulled-down RNA and input RNA were prepared using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina®.

value: brain cortex

tag: age

value: post conceptional week 11


title: HeLa koBBC3as 56D2 cells, stranded polyA RNA-seq, 2h HSV-1 infection, Replicate 2

tag: 4su treatment

value: Infected 2h before harvesting

value: total RNA

value: GATCGGAAGAGCACACGT

value: GTTCCGT


title: HeLa koBBC3as 56D2 cells, stranded polyA RNA-seq, 4h HSV-1 infection, Replicate 1

tag: hsv-1 infection

value: Infected 4h before harvesting

value: GCTACAT


title: F. fujikuroi C1995 in planta

tag: genotype

value: wild type

tag: dpi

tag: culture condition

value: in planta, rice, 7 dpi


title: F. fujikuroi MRC2276 high nitrogen

value: liquid culture, 60 mM Gln


title: F. fujikuroi B14 high nitrogen


title: F. fujikuroi m567 high nitrogen


title: HeLa koBBC3as 56D2 cells, stranded polyA RNA-seq, 6h HSV-1 infection, Replicate 2

value: Infected 6h before harvesting

tag: rna isolation

tag: adapter sequence

tag: barcode

value: CGTCCCG


title: F. fujikuroi E282 high nitrogen

tag: strain


title: input1_pcw11

tag: tissue


title: HeLa koBBC3as 56D2 cells, stranded polyA RNA-seq, 2h HSV-1 infection, Replicate 1

value: AGCTTAT


title: F. fujikuroi IMI58289 high nitrogen


title: JJC1392_LB_BR1

city: Edinburgh

first: David

last: Leach

address: KIng's Building

country: United Kingdom

institute: University of Edinburgh

data_processing:
files in fastq format were converted to fasta format - Example: fastq_to_fasta -i [FILE_NAME].sanfastq -o [FILE_NAME].fasta
reads were mapped to the E. coli K12 MG1655 (NC000913.3) genome using Novoalign version 2.07  (www.novocraft.com) - Example: (novoalign -f [FILE_NAME].fasta -d NC000913.3.nix -r Random > [FILE_NAME].novo)
pyCRAC software (http://sandergranneman.bio.ed.ac.uk/Granneman_Lab/pyCRAC_software.html) was used to convert the novo file into a GTF file and hit tables - Example:  pyReadCounters.py -f [FILE_NAME].novo --gtf=Ecoli_K12.gtf --ignorestrand
bedtools version 2.26.0 (http://bedtools.readthedocs.io/en/latest/) were used to generate bedgraph files that were viewed in IGB version 9.0.0 (bioviz.org/igb) - Example: bedtools genomecov -bg -i [FILE_NAME]_count_output_reads.gtf -g chromosome.txt > [FILE_NAME].bedgraph
Genome_build: Escherichia coli K12 MG1655 NC000913.3
Supplementary_files_format_and_content: bedgraph files including count data for the whole genome

organism: Escherichia coli

source_name: Bacterial Cell Lysates

growth_protocol: Cells were grown in either M9 minimal medium supplemented with 0.4% glucose, 5 μM, CaCl2 and 1 mM MgSO4 or LB medium supplemented with 0.5% glucose at 37 °C to an OD600nm of 0.2-0.25

extract_protocol:
Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1/100 anti-RecA antibody (Abcam, ab63797). IP samples were then incubated with Protein G Dynabeads® (Life Technologies) for 2 h at room temperature. All samples were washed 3 times with 1 X PBS + 0.02% Tween-20 before re-suspending the Protein G dynabeads in 200 μl of TE buffer (10 mM Tris (pH 7.4), 1 mM EDTA) + 1% SDS. 100 μl of TE buffer was added to the input samples and all samples were then incubated at 65°C for 10 h to reverse formaldehyde crosslinks. DNA was isolated using the MinElute PCR purification kit (Qiagen). DNA was eluted in 50 μl of TE buffer using a 2-step elution. Samples were stored at -20°C.
All samples were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit.

treatment_protocol: Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M

tag: growth medium

value: LB

tag: chip antibody

value: anti-RecA antibody (Abcam, ab63797)


title: input2_pcw11

city: Munich

last: Rojas Ringeling

address: Feodor-Lynen-Straße 25, 81377

institute: Ludwig Maximilian University of Munich


title: F. fujikuroi C1995 high nitrogen


title: HeLa koBBC3as 56D2 cells, stranded polyA RNA-seq, 6h HSV-1 infection, Replicate 1

growth_protocol: WI38 fibroblasts were cultured in Minimal Essential Medium (MEM) supplemented with 10% Fetal Bovine Serum (FBS) and with 100 units/ml penicillin, 100 µg/ml streptomycin. HeLa cells were cultured in Dulbecco's Modified Eagle Medium (DMEM)  supplemented with 10% Fetal Bovine Serum (FBS) and with 100 units/ml penicillin, 100 µg/ml streptomycin.

value: TTGTAAC


title: F. fujikuroi B20 high nitrogen


title: JJC1392_LB_BR2


title: HeLa koBBC3as 56D2 cells, stranded polyA RNA-seq, uninfected, Replicate 1

value: Uninfected

value: ATCAGAA


title: m6A3_pcw11

value: brain cortex

value: post conceptional week 11


title: HeLa cells, stranded polyA RNA-seq, 6h HSV-1 infection, Replicate 2

source_name: HeLa cells

tag: cell line

value: HeLa

value: total RNA

value: GATCGGAAGAGCACACGT

value: CTTGAAT


title: F. fujikuroi NCIM1100 low nitrogen

source_name: liquid culture, 6 mM Gln

value: wild type

value: liquid culture, 6 mM Gln


title: LETS_ChIP-seq_p300_stage9_replicate1

description: ChIP-seq of p300 in stage 10.5 Xenopus tropicalis x Xenopus laevis embryos

organism: Xenopus tropicalis x Xenopus laevis

tag: developmental stage

value: NF stage 10.5

tag: cell type

value: whole embryo

value: p300 (C-20, Santa Cruz sc-585)


title: m6A2_pcw11


title: LETS_ChIP-seq_input_stage9_replicate2

description: ChIP-seq input in stage 9 Xenopus tropicalis x Xenopus laevis embryos

value: NF stage 9

value: None (Input)


title: LETS_ChIP-seq_p300_stage9_replicate2


title: m6A1_pcw11


title: xt_xl_st10.5_MethylC-seq

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

description:
MethylC-seq
A single sample was sequenced across multiple flow cells.

data_processing:
MethylC-seq libraries were sequenced in single-end mode on the Illumina HiSeq 1500 platform. The sequenced reads in FASTQ format were mapped to the in silico bisulfite-converted reference genome (Xenopus laevis: J-Strain v9.1 / Xenopus tropicalis JGI.7.1) using the Bowtie alignment algorithm with the following parameters: -e 120 -l 20 -n 0 as described before (Bogdanovic et al., 2016 Nature Genetics).
Genome_build: Xenopus tropicalis x Xenopus laevis (xla.v91_xt7.1)
Supplementary_files_format_and_content: xt_xl_st10.5.allC.txt: Tab-delimited text file includes the DNA methylation calls. The column headers are as follows: Column 1 - assembly (chromosome); Column 2 - position: coordinate for the cytosine position on the chromosome (first base of chromosome = 0); Column 3 - strand: + or - strand; Column 4 - class: context of the cytosine and the two following bases from the same strand; Column 5 - mc: number of reads supporting a methylated cytosine; Column 6 - h: total number of reads at that position.

source_name: whole embryos, st.10.5 (gastrula)

extract_protocol:
Embryos were homogenized in 3 volumes STOP buffer (15 mM EDTA, 10 mM Tris-HCl pH7.5, 1% SDS, 0.5 mg/mL proteinase K), after which two phenol:chloroform:isoamylalcohol (PCI, 25:24:1) extractions were performed. DNA was then precipitated in 1/5 volume NH4AC 4M and 3 volumes EtOH and dissolved in 100 uL, treated with RNase and purified by a PCI extraction. The precipitation was done with EtOH and the DNA was resuspended in 50 uL H2O.
MethylC-seq library generation was performed as described previously (Ulrich et al., 2015 Nature Protocols). Briefly, the genomic DNA was sonicated to an average size of 200 bp using a Covaris sonicator. Sonicated DNA was then purified and end-repaired, followed by the ligation of methylated Illumina TruSeq sequencing adapters. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 6 cycles of amplification.

value: 10.5 (gastrula)


title: HeLa koBBC3as 56D2 cells, stranded polyA RNA-seq, uninfected, Replicate 2

value: GTCAACA


title: HeLa cells, stranded polyA RNA-seq, 4h HSV-1 infection, Replicate 2

value: Infected 4h before harvesting

value: AGATCAT


title: TETS_ChIP-seq_p300_stage9_replicate1

description: ChIP-seq of p300 in stage 10.5 Xenopus tropicalis embryos

organism: Xenopus tropicalis


title: F. fujikuroi E282 low nitrogen


title: TETS_ChIP-seq_p300_stage9_replicate2


title: TETS_ChIP-seq_input_stage9_replicate2

description: ChIP-seq input in stage 9 Xenopus tropicalis embryos


title: F. fujikuroi FSU48 low nitrogen


title: F. oxysporum V64-1 in planta

organism: Fusarium oxysporum

value: in planta, rice, 7 dpi


title: HeLa cells, stranded polyA RNA-seq, 2h HSV-1 infection, Replicate 1

value: Infected 2h before harvesting

value: GATGTAT


title: F. fujikuroi MRC2276 low nitrogen


title: LETS_ChIP-seq_H3K4me3_stage9_replicate2

description: ChIP-seq of H3K4me3 in stage 9 Xenopus tropicalis x Xenopus laevis embryos

value: H3K4me3  (Abcam ab8580)


title: F. fujikuroi C1995 low nitrogen


title: HeLa cells, stranded polyA RNA-seq, 2h HSV-1 infection, Replicate 2

value: HeLa

value: total RNA

value: GATCGGAAGAGCACACGT

value: CCAATAT


title: HeLa cells, stranded polyA RNA-seq, 6h HSV-1 infection, Replicate 1

value: Infected 6h before harvesting

value: GACCAAT


title: TETS_ChIP-seq_H3K4me3_stage9_replicate2

description: ChIP-seq of H3K4me3 in stage 9 Xenopus tropicalis embryos

value: whole embryo


title: LETS_ChIP-seq_H3K4me3_stage9_replicate1

value: NF stage 9


title: HeLa cells, stranded polyA RNA-seq, 4h HSV-1 infection, Replicate 1

value: TAGGCAT


title: LETS_ChIP-seq_input_stage9_replicate1

value: None (Input)


title: TETS_ChIP-seq_H3K4me3_stage9_replicate1


title: HeLa cells, stranded polyA RNA-seq, uninfected, Replicate 1

value: Uninfected

value: TCACGAT


title: F. fujikuroi B20 low nitrogen

value: wild type

value: liquid culture, 6 mM Gln


title: F. fujikuroi B14 low nitrogen


title: F. oxysporum V64-1 high nitrogen

value: liquid culture, 60 mM Gln


title: HeLa cells, stranded polyA RNA-seq, uninfected, Replicate 2

value: CAGTGAT


title: F. fujikuroi IMI58289 low nitrogen


title: F. fujikuroi m567 low nitrogen


title: F. oxysporum V64-1 low nitrogen


title: untreated-Input

status: Public on Sep 27 2017

city: Shanghai

first: Meng-Meng

last: Ji

address: Ruijin No.2 Road

institute: Shanghai Ruijin Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were adaptor-trimmed and mapped to human genome (hg19) by bowtie2 software with default parameters.
Peak calling was performed with MACS software (v1.4.3).
Differentially enriched regions were identified by diffReps software (v1.55.4).
The  enriched peaks were then annotated with the latest UCSC RefSeq database to connect the peak information with the gene annotation.
Genome_build: hg19
Supplementary_files_format_and_content: bed format: enriched peaks

source_name: Jurkat cell

growth_protocol: Cells were grown in RPMI-1640 medium, supplemented with 10% heat-inactivated fetal bovine serum in a humidified atmosphere containing 95% air-5% CO2 at 37°C.

extract_protocol:
DNA extraction protocol
Chromatin Immunoprecipitation was performed according to Wamstad et al. (2012). The yield of ChIPed DNA was determined via Quant IT fluorescence assay (Life Technologies) and enrichment efficiencies of ChIP reactions were evaluated by qPCR. Illumina sequencing libraries were generated with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs) by following the manufacturer’s manual.
The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent), and then, subjected to high-throughput 150 base paired-end sequencing on Illumina Hiseq sequencer according to the manufacturer’s recommended protocol.

treatment_protocol: Jurkat (KMT2D V5486M) cells were treated with Chidamide (5nm)，Decitabine (5μm)，Chidamide (5nm)+Decitabine (5μm)，respectively.

value: Jurkat cell (KMT2D V5486M)

tag: antibody