title: LI324.7

description:
Sample name: LI324.7_CAGATC
Column header name in processed data file: LI324-7_CAGATC
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: mRNA C2C12-H3.1-G

status: Public on Jul 20 2015

type: SRA

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi, Higashi-ku, Fukuoka

department: Medical Institute of Bioregulation, Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description: Tet-On-C2C12 cells that harbor the N-terminal-GFP-tagged H3.1 gene under a doxycycline (Dox)-inducible promoter.

library_source: transcriptomic

data_processing:
Illumina RTA 1.17 software used for basecalling.
Sequenced reads were mapped onto the mouse genome (mm9) using Tophat (version 2.0.8) (Trapnell et al., 2012) with the software's default parameter.
Gene expression levels (FPKM; Fragments per kilobase of exon per million mapped sequence reads) were estimated using the cuffdiff program in Cufflinks (version 2.0.1) (Trapnell et al., 2012) using mapped reads and the software’s default parameters.
genome build: mm9
processed data files format and content: tab-delimited text file include FPKM values for each Sample
processed data file: mRNASeq_FPKMTable.txt.gz

molecule: total RNA

organism: Mus musculus

source_name: C2C12 cells_H3.1_Growth

growth_protocol: Cells  were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 20% fetal bovine serum. Undifferentiated cells were harvested at 60–70% confluence.

extract_protocol:
Total RNA was isolated and reversed-transcribed with Takara Prime Script Reverse Transcriptase and an oligo dT primer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Differentiated cells were transferred to DMEM containing 2% horse serum upon reaching confluence and harvested 48 h later.

tag: cell type

value: myoblast

tag: cell line

tag: culture status

value: growth (G)


title: HiSeq_E6

city: Montreal

first: Juan Pablo

last: Lopez

state: Quebec

address: 6875 La Salle Blvd

department: Human Genetics

country: Canada

institute: McGill University

description: processed_data: ncRNA_Expression.txt

data_processing:
All sequencing data were processed using CASAVA 1.8+ and extracted from FASTQ files
Fastx_toolkit was used to trim the Illumina adapter sequences
Additional filtering based on defined cutoffs was applied in order to obtain high quality data. These filters included: 1) Phred quality (Q) score higher than 30, 2) reads between 15-40nt in length, 3) adapter detection based on perfect-10nt match, and 4) removal of reads without detected adapter
We used Bowtie to align reads to the human genome (GRCh37)
We used ncPRO-seq in combination with miRBase (V20) to match them to known miRNA sequences
We used the Rfam and NCBI's piRNA databases to map other small RNA sequences
All sequencing data was normalized with the Bioconductor - DESeq2 package, using a detection threshold of 1 count per miRNA (present at least once in each of the libraries tested)
Genome_build: Human genome (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include small RNA count values for each sample

organism: Homo sapiens

source_name: Brain

extract_protocol:
Peripheral blood samples were collected in PAXgene blood RNA tubes (PreAnalytix, Switzerland). PAXgene tubes were frozen using a sequential freezing process. This involves storing tubes at room temperature for 3h, transferring to 4°C overnight, followed by 6-8h at -20°C and then final storage at -80°C. Total RNA (including the miRNA fraction) was isolated from whole-blood using the PAXgene Blood miRNA Kit (Qiagen, Canada), according to manufacturer's instructions. Furthermore, total RNA was isolated from frozen brain, heart and liver tissues using the miRNeasy Mini Kit protocol (Qiagen, Canada) with no modifications. RNA and miRNA yield and quality were determined using the Nanodrop 1000 (Thermo Scientific, USA) and Agilent 2100 Bioanalizer (Agilent Technologies, USA).
All libraries were prepared using the Illumina TruSeq Small RNA protocol following the manufacturer's instructions with 12 cycles of PCR amplification after ligation of the 3' and 5' adapters.  Individual libraries were prepared using a unique index primer in order to allow for pooling of multiple samples prior to sequencing. Libraries were validated and quantified using an Agilent 2100 Bioanalyzer High Sensitivity DNA chip and qRT-PCR with the KAPA library quantification kit (Kapa Biosystems, USA). Sample C1 (control - human brain) was not sequenced. All additional samples (A1-A10), as well as sample AC (control - no purification method), were sequenced.
Purification Method: In order to compare three different small RNA library purification methods, we prepared 11 libraries starting with 1µg of good quality total RNA (RIN>8). All libraries were prepared using total RNA extracted from peripheral blood of a single individual. The RNA was split into 11 aliquots and each was used as a technical replicate. In addition, we used total RNA from commercially available human brain as a library preparation control. Libraries were purified as follows: 1) Purification by Novex TBE PAGE gel: 50µl of amplified cDNA from samples A1-A3 and C1 were loaded into a 6% Novex gel and run for 80 minutes at 130-135 V. After cleaning the gel with RNase free water, a band was manually cut to contain all fragments sized 145-160nt, corresponding to mature miRNAs and other regulatory small RNA molecules;  2) Purification by Pippin Prep automated gel system (Sage 3%): The Pippin Prep system (PPS) allows automatic selection of specified cDNA products. 25µl of amplified cDNA from samples A4-A7 were loaded into a Pippin Prep machine. Furthermore, in order to test variability between machines, samples A4 and A5 were loaded into PPS1, while samples A6 and A7 were loaded into PPS2. Size selection was automated for products between 125 and 180nt; 3) Purification by AMPure XP beads: Biotinylated magnetic AMPure beads allow for selection of specified cDNA products bound to streptavidin. 50µl of amplified cDNA from samples A8-A10 were mixed and purified two times with AMPure XP beads at a 1.8:1 ratio (beads:sample). This ratio allows for optimal selection of all products higher than 100nt.

tag: tissue

value: Brain

tag: input amount (rna)

value: 1 ug

tag: purification method

value: AMPure XP beads

tag: rin value


title: mRNA C2C12-WT-G

description: C2C12 cells that non harbor the N-terminal or C-terminal -GFP-tagged H3 gene

source_name: C2C12 cells_WT_Growth


title: LI25.6

city: Davis

first: Dario

last: Cantu

state: CA

address: One Shields Ave

department: Viticulture & Enology

country: USA

institute: University of California, Davis

description:
Sample name: LI25.6_GCCAAT
Column header name in processed data file: LI25-6_GCCAAT
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

data_processing:
raw data files were adapter and quality trimmed with Sickle v 1.2.1 (Q>20) and Scythe v0.991 (prior 0.4) programs. Respectively.
Bowtie2 (v. 2.2.3) with options (-q --end-to-end --sensitive --no-unal -p 20) was run with the custom built bowtie2 index (bowtie2-build) from concatenated transcripts from the V. vinifera cv. PN40024 (transcriptome version V1 obtained from CRIBI - http://genomes.cribi.unipd.it/grape/) and the E. necator C-strain reference genomes
Ambiguously mapped reads were excluded from further analysis using the sam2counts.py script (v0.9.1; -q30 option)
Genome_build: e.necator.transcripts.fasta and v.vinifera.transcripts.fasta are linked as supplementary files on the Series record.
Supplementary_files_format_and_content: processed(sam2counts.py -q30) tab-delimited file of raw bowtie2 counts from quality filtered (sickle Q>20/scythe prior 0.4) data; contains 97 columns (one gene identifier, 96 samples) and 36505 rows with one header row, 29971 rows referencing grapevine genes, and 6533 rows representing E. necator genes

molecule: polyA RNA

organism: Vitis vinifera

source_name: whole plant

growth_protocol: green cuttings were prepared in June 2013 and established in the greenhouse. After four months, three plants of each accession were transferred to two Conviron PGR15 growth chambers in the UC Davis Controlled Environment Facility. The growing conditions in both chambers were identical and set to conditions that favor E. necator infections (23°C during the day, 15°C at night, 16-hour photoperiod, 60% humidity).

extract_protocol:
Leaves from each plant were collected at two time points (1 day and 5 days after inoculation) and immediately frozen in liquid nitrogen. RNA was extracted using a CTAB extraction protocol followed by a cleanup step with the Qiagen RNeasy Plant Mini Kit. High quality RNA samples were obtained from all accessions, time points (1 and 5 days post inoculation), and treatments (healthy and PM infected).
cDNA libraries were sequenced in single-end mode with 50 cycles at the DNA Technology core at the UC Davis Genome Center using an Illumina HiSeq2500 sequencer.
A total of 8 HiSeq2500 lanes were sequenced with each individual lane loaded with a 12 libraries comprising all replicates (3 biological replicates) of each infection time point (1 and 5 dpi) and treatment (powdery mildew infected and healthy controls) of a specific genotype

treatment_protocol: A suspension of E. necator (strain C-strain) conidia was prepared. Conidia were collected from detached leaf cultures, suspended in 0.001% Tween 20 solution, and adjusted to a concentration of 5 x 105 conidia/mL. In one chamber, E. necator conidia were applied to grapevine leaves using a portable paint sprayer. Grapevines in the other chamber were mock inoculated with 0.001% Tween solution only.

tag: ecotype

value: sativa

tag: cultivar

value: Late Vavilov

tag: timepoint

value: 5 DPI

tag: infection

value: inoculated with Erysiphe necator c-strain

tag: resistant to powdery mildew

value: yes

value: whole plant


title: LI224.5

description:
Sample name: LI224.5_ACAGTG
Column header name in processed data file: LI224-5_ACAGTG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI

value: 1 DPI


title: mRNA C2C12-H3mm12-G

description: Tet-On-C2C12 cells that harbor the N-terminal-GFP-tagged H3mm12 gene under a doxycycline (Dox)-inducible promoter.

source_name: C2C12 cells_H3mm12_Growth


title: HiSeq_E5

description: processed_data: ncRNA_Expression.txt


title: HiSeq_E4

description: processed_data: ncRNA_Expression.txt

source_name: Whole-blood

value: Whole-blood


title: CES3_12N

city: Kunming

first: Tianqing

last: Li

address: No. Boda Road, Yuhua Area, Chenggong New Town

country: China

institute: Primate Translational Medicine Research Center, Kunming University of Science and Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: ftp.ensembl.org/pub/release-76/fasta/macaca_mulatta/dna/Macaca_mulatta.MMUL_1.dna.toplevel.fa.gz
Supplementary_files_format_and_content: RPKM data for genes.

organism: Macaca fascicularis

source_name: dome-shaped monkey ESCs

growth_protocol: Primed ESCs were cultured in the CESM, which is composed of PSGro® Human iPSC/ESC Growth Medium (StemRD) and conventional monkey ESC culture media according to the 1: 3 ratio; Dome-shaped ESCs are cultured in the NHSMV media, which of 500 ml are including the following the components: 475 ml knockout DMEM, 5 g AlbuMAXI, 5 ml N2 supplement, recombinant human insulin (12.5 μg/ml), 10 ng/ml human LIF, 8 ng/ml recombinant bFGF and 1 ng/ml TGF-β1, 1mM glutamine, 1% nonessential amino acids, 0.1mM β-mercaptoethanol, PD0325901 (1 μM), CHIR99021 (3 μM), SB202190 (5 μM), SP600125 (10 μM), SB203580 (10 μM) and 50μg/ml Vitamin C.

extract_protocol:
500 ng mRNA of each sample was used to produce its respective sequence library.
mRNA was fragmented using the fragmentation Buffer (Ambion) and double-stranded cDNA was then synthesized using SuperScript II (Invitrogen) RT and random primers. Libraries were prepared according to Illumina's instructions. Sequencing was then performed in a HiSeq 2500 apparatus (Illumina) according to the TruSeq RNA Sample Preparation Guide (Illumina).

tag: colony morphology

value: dome-shaped

tag: culture media

value: NHSMV

tag: single cell passage

value: strong


title: LI15.4

description:
Sample name: LI15.4_TGACCA
Column header name in processed data file: LI15-4_TGACCA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI


title: LI124.2

description:
Sample name: LI124.2_CGATGT
Column header name in processed data file: LI124-2_CGATGT
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: CES1_P26N


title: HiSeq_E2

description: processed_data: ncRNA_Expression.txt


title: HiSeq_E11

description: processed_data: ncRNA_Expression.txt

source_name: Heart

value: Heart


title: HiSeq_E3

description: processed_data: ncRNA_Expression.txt


title: KhU35.19

description:
Sample name: KhU35.19_GTGAAA
Column header name in processed data file: KhU35-19_GTGAAA
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI

value: Khalchili

value: Mock Innoculated


title: LU224.15

description:
Sample name: LU224.15_ATGTCA
Column header name in processed data file: LU224-15_ATGTCA
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI


title: CES1_P15N


title: KhU324.18

description:
Sample name: KhU324.18_GTCCGC
Column header name in processed data file: KhU324-18_GTCCGC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI


title: KhU25.16

description:
Sample name: KhU25.16_CCGTCC
Column header name in processed data file: KhU25-16_CCGTCC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: LI35.12

description:
Sample name: LI35.12_CTTGTA
Column header name in processed data file: LI35-12_CTTGTA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI


title: HiSeq_D12

description: processed_data: HiSeq2500.txt


title: CES3_12P

source_name: primed monkey ESCs

value: flat

value: CESM

value: weak


title: CES_3Pr


title: KhU224.15

description:
Sample name: KhU224.15_ATGTCA
Column header name in processed data file: KhU224-15_ATGTCA
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI

value: sativa


title: HiSeq_D11

description: processed_data: HiSeq2500.txt

value: AMPure XP beads


title: CES_1Pr


title: HiSeq_D10

description: processed_data: HiSeq2500.txt


title: CES_2-N


title: HiSeq_D8

description: processed_data: HiSeq2500.txt


title: HiSeq_D9

description: processed_data: HiSeq2500.txt


title: d6BVSC+#2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description:
SC3seq amiplified from 10 ng total RNA extracted from cells sorted with BVSC
processed data file: expression_mouse.txt

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-c -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the genome and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”, “—no-length-correction” and “—library-type fr-secondstrand” options and reference gene annotations with extended TTSs. We also set the cufflinks option “—max-mle-iterations” to 50,000, because default iterations (5,000) resulted in “FAILED” when estimating the expression levels of some genes. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: mm10
Genome_build: hg19
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample.

source_name: d6 BVSC+ cells

growth_protocol:
hiPSCs were maintained under a feeder-free condition [StemFitTM (Ajinomoto, Tokyo, Japan) medium on recombinant LAMININ511 (rLN511E8) (iMatrix-511, Nippi, Tokyo, Japan)-coated cell culture plates] (Nakagawa et al., 2014).  The iMeLCs were induced by plating 1.0-2.0 × 10^5 hiPSCs maintained in StemFitTM onto a well of a human plasma fibronectin (Millipore, FC010)-coated 12-well plate in GK15 medium [GMEM (Life Technologies) with 15% KSR, 0.1 mM NEAA, 2 mM L-glutamine, 1 mM sodium pyruvate and 0.1 mM 2-mercaptoethanol] containing 50 ng/ml of Activin A, 3 µM of CHIR99021 and 10 µM of a ROCK inhibitor (Y-27632; Wako Pure Chemical Industries).  The hPGCLCs were induced by plating 3.0 × 10^3 iMeLCs or iPSCs into a well of a low-cell-binding V-bottom 96-well plate (Thermo, 81100574) in GK15 supplemented with 1000 U/ml of LIF (Millipore, #LIF1005), 200 ng/ml of BMP4, 100 ng/ml of SCF (R&D Systems, 455-MC), 50 ng/ml of EGF (R&D Systems, 236-EG), and 10 µM of the ROCK inhibitor.  In some experiments, PD173074 (StemGent, #04-0008) or LDN193189 (StemGent, #04-0074) were added for iMeLCs or hPGCLC induction, respectively.  In other experiments, WNT3A (R&D Systems, 5036-WN) was used in place of CHIR99021, and BMP2 (R&D Systems, 355-BM), BMP7 (R&D Systems, 354-BP), or BMP8A (R&D Systems, 1073-BP) was used in place of BMP4.
mESCs were cultured in a 2i+LIF, feeder-free culture condition. mEpiLCs and mPGCLCs (d2, d4, and d6) were induced as described previously (Hayashi et al., 2011).
cyESCs (CMK9) were cultured with conventional hESC medium [DMEM/F12 (Life Technologies) supplemented with 20% (vol/vol) of KSR (Life Technologies), 1 mM of sodium pyruvate (Life Technologies), 2 mM of GlutaMax (Life Technologies), 0.1 mM of nonessential amino acids (Life Technologies), 0.1 mM of 2-mercaptoethanol (Sigma-Aldrich), 1000 U/mL of ESGRO mouse LIF (Millipore), 4 ng/ml of recombinant human bFGF (Wako Pure Chemical Industries)] on mouse embryonic feeders (MEFs).

extract_protocol:
Total RNA was extracted from hiPSCs, iMeLCs, and hPGCLCs or mESCs, mEpiLCs, and mPGCLCs by using an RNeasy Micro Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.  Synthesis and amplification of cDNAs using 1 ng of purified total RNA, and construction of cDNA libraries for RNA sequencing (ABI SOLiD 5500XL system; Life Technologies) were performed as described in (Nakamura et al., 2015).
For isolating single cells of cyESCs for the SC3-seq analysis [Nakamura et.al., Nuceic Acids Res. (2015)], cells were first detached as clumps by the CTK solution [0.25% of Trypsin (Life Technologies), 0.1 mg/mL of Collagenase Ⅳ (Life Technologies), 1 mM of CaCl2 (Nacalai Tesque)], were incubated in 0.25% of trypsin/PBS (Sigma-Aldrich) for around 10 min at 37℃, and were then dispersed into single cells in 1% (vol/vol) KSR/PBS. Genital ridges were dissected out and were dissociated into single cells by incubating with 0.25% trypsin/PBS for around 10 min at 37℃ followed by repeated pipetting. The resulting single cells were dispersed in 0.1 mg/ml of PVA/PBS (Sigma-Aldrich) and were processed for the SC3-seq analysis (Nakamura et al., 2015).
cDNA synthesis and amplification from isolated RNAs/single cells were perfomed essentially as reported in [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.]. Library constructions for SOLiD System were performed as reported in [Nakamura et.al., Nuceic Acids Res. (2015)].

tag: strain background

value: BVSC R8

value: d6 BVSC+ cells


title: KhI35.12

description:
Sample name: KhI35.12_CTTGTA
Column header name in processed data file: KhI35-12_CTTGTA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

value: 5 DPI

value: inoculated with Erysiphe necator c-strain

value: yes


title: HiSeq_D6

description: processed_data: HiSeq2500.txt

value: Whole-blood


title: KhI324.7

description:
Sample name: KhI324.7_CAGATC
Column header name in processed data file: KhI324-7_CAGATC
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI

value: 1 DPI

value: whole plant


title: d6BVSC+#1


title: KhU124.13

description:
Sample name: KhU124.13_AGTCAA
Column header name in processed data file: KhU124-13_AGTCAA
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI


title: d4BVSC+#2

source_name: d4 BVSC+ cells

value: d4 BVSC+ cells


title: HiSeq_D5

description: processed_data: HiSeq2500.txt


title: HiSeq_E1

description: processed_data: ncRNA_Expression.txt

value: 1 ug


title: d4BVSC+#1


title: d2BV+#2

description:
SC3seq amiplified from 1 ng total RNA extracted from cells sorted with BV
processed data file: expression_mouse.txt

source_name: d2 BV+ cells

value: d2 BV+ cells


title: KhI224.5

description:
Sample name: KhI224.5_ACAGTG
Column header name in processed data file: KhI224-5_ACAGTG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI

value: Khalchili


title: KhI25.6

description:
Sample name: KhI25.6_GCCAAT
Column header name in processed data file: KhI25-6_GCCAAT
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI


title: HiSeq_D4

description: processed_data: HiSeq2500.txt


title: CES_2Pr

value: flat


title: KhI15.4

description:
Sample name: KhI15.4_TGACCA
Column header name in processed data file: KhI15-4_TGACCA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI


title: KhI124.2

description:
Sample name: KhI124.2_CGATGT
Column header name in processed data file: KhI124-2_CGATGT
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: EpiLC#2

description:
SC3seq amiplified from 10 ng total RNA extracted from cells
processed data file: expression_mouse.txt

source_name: EpiLC

value: EpiLC


title: d2BV+#1


title: KhU15.14

description:
Sample name: KhU15.14_AGTTCC
Column header name in processed data file: KhU15-14_AGTTCC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI

value: Mock Innoculated


title: HiSeq_D3

description: processed_data: HiSeq2500.txt


title: KU35.27

description:
Sample name: KU35.27_ATTCCT
Column header name in processed data file: KU35-27_ATTCCT
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI

value: sativa

value: Karadzhandal


title: EpiLC#1

value: BVSC R8


title: HiSeq_C15

description: processed_data: RNA_Degradation.txt

value: AMPure XP beads


title: mESC#2

source_name: mESC

value: mESC


title: KU25.1

description:
Sample name: KU25.1_ATCACG
Column header name in processed data file: KU25-1_ATCACG
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI

value: 5 DPI


title: KU324.25

description:
Sample name: KU324.25_ACTGAT
Column header name in processed data file: KU324-25_ACTGAT
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI

value: yes


title: mESC#1


title: HiSeq_C14

description: processed_data: RNA_Degradation.txt

value: Whole-blood


title: HiSeq_C13

description: processed_data: RNA_Degradation.txt


title: KU15.10

description:
Sample name: KU15.10_TAGCTT
Column header name in processed data file: KU15-10_TAGCTT
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: KI35.8

description:
Sample name: KI35.8_ACTTGA
Column header name in processed data file: KI35-8_ACTTGA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

value: inoculated with Erysiphe necator c-strain


title: HiSeq_C12

description: processed_data: RNA_Degradation.txt


title: HiSeq_C11

description: processed_data: RNA_Degradation.txt


title: HiSeq_D2

description: processed_data: HiSeq2500.txt


title: KU124.9

description:
Sample name: KU124.9_GATCAG
Column header name in processed data file: KU124-9_GATCAG
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI

value: 1 DPI

value: whole plant


title: HiSeq_C10

description: processed_data: RNA_Degradation.txt


title: KI324.3

description:
Sample name: KI324.3_TTAGGC
Column header name in processed data file: KI324-3_TTAGGC
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: HiSeq_C9

description: processed_data: RNA_Degradation.txt


title: control_villi_Myc_ChIP-exo-seq

city: Columbus

first: Gustavo

middle: W.

last: Leone

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

description: ChIP-exo-seq

library_source: genomic

data_processing:
Map raw fastq files with Bowtie2 aligner (version 2.2.1).
Only the reads uniquely mapped to the genome were utilized for further analysis.
Identify peaks with Genome wide Event finding and Motif discovery algorithm GEM (version 2.4.1) with a false discovery rate (FDR) less than 1% as well as Model-based Analysis of ChIP-Seq algorithm MACS2 (version 2.0.10) with a FDR less than 5%.
The intersection of GEM and MACS2 results were used for all downstream analysis.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Processed data files are BED files.

molecule: genomic DNA

source_name: Intestinal villus cells, wild type, Myc ChIP

growth_protocol: Mice were housed under standard conditions.

extract_protocol:
DNA-protein complexes were sonicated and precipitated with indicated antibodies.
The sequencing libraries were constructed as described in: Development of an Illumina-based ChIP-exonuclease method provides insight into FoxA1-DNA binding properties. Serandour AA, Brown GD, Cohen JD, Carroll JS. Genome Biol. 2013 Dec 27;14(12):R147. doi: 10.1186/gb-2013-14-12-r147 (PMID 24373287).

treatment_protocol: Intestinal-specific inducible Cre (Ah-cre) was used to delete Rb.

tag: strain/background

value: mixed (C57BL/6 X 129 X FVB/N)

tag: genotype/variation

value: wild type

value: intestinal villus cells

tag: chip antibody

value: Myc (Santa Cruz; sc-764 X, lot# D2314)


title: control_villi_E2f3_ChIP-exo-seq

description: ChIP-exo-seq

source_name: Intestinal villus cells, wild type, E2f3 ChIP

tag: cell type

value: E2f3 (Santa Cruz; sc-878 X, lot# E1712)


title: RbKO_villi_E2f3_ChIP-exo-seq

description: ChIP-exo-seq

source_name: Intestinal villus cells, Rb KO, E2f3 ChIP

value: Rb KO


title: control_crypts_E2f3_ChIP-exo-seq

description: ChIP-exo-seq

source_name: Intestinal crypt cells, wild type, E2f3 ChIP

value: intestinal crypt cells


title: control_crypts_Myc_ChIP-exo-seq

description: ChIP-exo-seq

source_name: Intestinal crypt cells, wild type, Myc ChIP


title: HiSeq_C8

description: processed_data: RNA_Degradation.txt

tag: tissue


title: HiSeq_D1

description: processed_data: HiSeq2500.txt

tag: input amount (rna)


title: KI224.22

description:
Sample name: KI224.22_CGTACG
Column header name in processed data file: KI224-22_CGTACG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI

value: sativa

value: Karadzhandal


title: RbKO_crypts_Myc_ChIP-exo-seq

description: ChIP-exo-seq

source_name: Intestinal crypt cells, Rb KO, Myc ChIP


title: HiSeq_C7

description: processed_data: RNA_Degradation.txt

tag: purification method

value: AMPure XP beads


title: KI15.21

description:
Sample name: KI15.21_GTTTCG
Column header name in processed data file: KI15-21_GTTTCG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

source_name: whole plant


title: KU224.11

description:
Sample name: KU224.11_GGCTAC
Column header name in processed data file: KU224-11_GGCTAC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI

value: Mock Innoculated


title: RbKO_crypts_E2f3_ChIP-exo-seq

description: ChIP-exo-seq

source_name: Intestinal crypt cells, Rb KO, E2f3 ChIP


title: HiSeq_C6

description: processed_data: RNA_Degradation.txt

source_name: Whole-blood

tag: rin value


title: KI124.20

description:
Sample name: KI124.20_GTGGCC
Column header name in processed data file: KI124-20_GTGGCC
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI

tag: ecotype


title: HU324.18

description:
Sample name: HU324.18_GTCCGC
Column header name in processed data file: HU324-18_GTCCGC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI

tag: cultivar

value: Husseine


title: RbKO_villi_Myc_ChIP-exo-seq

description: ChIP-exo-seq

source_name: Intestinal villus cells, Rb KO, Myc ChIP


title: Mes_TNF_12hr_rep2

city: Galveston

first: Allan

last: Brasier

state: TX

address: 301 Univ. Blvd

department: Medicine

institute: University Texas Medical Branch

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Reads were mapped with Tophat v2.0.10 with options -p 10 -r 170 --mate-std-dev 40. Reference was hg19.
Reads mapping to genes were counted with HTSeq0.5.4p5/htseq-count
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: excel file with raw read counts per gene

source_name: small airway epithelial cell line

extract_protocol:
Total cellular RNA was extracted using either RNAqueous™ phenol-free total RNA isolation kits (Life Technologies, CA) or Quick-RNA MiniPrep kits (ZYMO Research) according to the manufacture's recommendations
RNA libraries were prepared for sequencing using the Illumina TruSeq RNA Sample Preparation kit under conditions prescribed by the manufacturer (Illumina).

tag: tgf-beta treatment

value: Yes

tag: tnf-alpha treatment

value: 12 hour


title: Mes_TNF_12hr_rep1


title: HU25.16

description:
Sample name: HU25.16_CCGTCC
Column header name in processed data file: HU25-16_CCGTCC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI

tag: timepoint

value: 5 DPI

tag: infection

tag: resistant to powdery mildew

value: yes


title: HiSeq_C3

description: processed_data: RNA_Degradation.txt

value: Whole-blood


title: HiSeq_C4

description: processed_data: RNA_Degradation.txt


title: Mes_TNF_12hr_rep3


title: KI25.23

description:
Sample name: KI25.23_GAGTGG
Column header name in processed data file: KI25-23_GAGTGG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

value: inoculated with Erysiphe necator c-strain

value: whole plant


title: Mes_TNF_1hr_rep2

value: 1 hour


title: Mes_TNF_1hr_rep1


title: HU224.15

description:
Sample name: HU224.15_ATGTCA
Column header name in processed data file: HU224-15_ATGTCA
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI

value: 1 DPI


title: HiSeq_C1

description: processed_data: RNA_Degradation.txt


title: Mes_TNF_1hr_rep3


title: HiSeq_A15

description: processed_data: RNA_Input.txt

value: Pippin Prep automated gel system (Sage 3%)


title: Mes_Control_rep3


title: HiSeq_C2

description: processed_data: RNA_Degradation.txt


title: HiSeq_A14

description: processed_data: RNA_Input.txt


title: HU124.13

description:
Sample name: HU124.13_AGTCAA
Column header name in processed data file: HU124-13_AGTCAA
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI


title: HI324.7

description:
Sample name: HI324.7_CAGATC
Column header name in processed data file: HI324-7_CAGATC
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: HU35.19

description:
Sample name: HU35.19_GTGAAA
Column header name in processed data file: HU35-19_GTGAAA
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: Mes_Control_rep2


title: HiSeq_A12

description: processed_data: RNA_Input.txt


title: HiSeq_A13

description: processed_data: RNA_Input.txt


title: Mes_Control_rep1


title: HiSeq_C5

description: processed_data: RNA_Degradation.txt


title: Epi_TNF_12hr_rep3


title: HU15.14

description:
Sample name: HU15.14_AGTTCC
Column header name in processed data file: HU15-14_AGTTCC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: HI224.5

description:
Sample name: HI224.5_ACAGTG
Column header name in processed data file: HI224-5_ACAGTG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: HiSeq_AC

description: processed_data: Library_Preparation.txt

value: 1 ug

value: No Purification Control


title: HiSeq_A11

description: processed_data: RNA_Input.txt


title: Epi_TNF_12hr_rep2


title: HI25.6

description:
Sample name: HI25.6_GCCAAT
Column header name in processed data file: HI25-6_GCCAAT
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

value: sativa


title: Epi_TNF_12hr_rep1


title: HI124.2

description:
Sample name: HI124.2_CGATGT
Column header name in processed data file: HI124-2_CGATGT
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: Epi_TNF_1hr_rep3


title: HI15.4

description:
Sample name: HI15.4_TGACCA
Column header name in processed data file: HI15-4_TGACCA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI


title: HI35.12

description:
Sample name: HI35.12_CTTGTA
Column header name in processed data file: HI35-12_CTTGTA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI


title: CU324.25

description:
Sample name: CU324.25_ACTGAT
Column header name in processed data file: CU324-25_ACTGAT
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI

value: Carignane

value: no


title: Epi_TNF_1hr_rep1


title: SyU324.18

description:
Sample name: SyU324.18_GTCCGC
Column header name in processed data file: SyU324-18_GTCCGC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI

organism: Vitis vinifera subsp. sylvestris

value: Mock Innoculated


title: HiSeq_A9

description: processed_data: Library_Preparation.txt

value: AMPure XP beads


title: HiSeq_A8

description: processed_data: Library_Preparation.txt


title: SyU25.16

description:
Sample name: SyU25.16_CCGTCC
Column header name in processed data file: SyU25-16_CCGTCC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: HiSeq_A10

description: processed_data: Library_Preparation.txt


title: Epi_TNF_1hr_rep2


title: SyU35.19

description:
Sample name: SyU35.19_GTGAAA
Column header name in processed data file: SyU35-19_GTGAAA
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: HiSeq_A7

description: processed_data: Library_Preparation.txt


title: CU25.23

description:
Sample name: CU25.23_GAGTGG
Column header name in processed data file: CU25-23_GAGTGG
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: Epi_Control_rep3


title: SyU224.15

description:
Sample name: SyU224.15_ATGTCA
Column header name in processed data file: SyU224-15_ATGTCA
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI


title: HiSeq_A6

description: processed_data: Library_Preparation.txt


title: Epi_Control_rep2


title: HiSeq_A5

description: processed_data: Library_Preparation.txt


title: CU35.27

description:
Sample name: CU35.27_ATTCCT
Column header name in processed data file: CU35-27_ATTCCT
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: CU224.22

description:
Sample name: CU224.22_CGTACG
Column header name in processed data file: CU224-22_CGTACG
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI


title: CU15.21

description:
Sample name: CU15.21_GTTTCG
Column header name in processed data file: CU15-21_GTTTCG
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: Epi_Control_rep1


title: HiSeq_A4

description: processed_data: Library_Preparation.txt


title: SyI324.7

description:
Sample name: SyI324.7_CAGATC
Column header name in processed data file: SyI324-7_CAGATC
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: SyI35.12

description:
Sample name: SyI35.12_CTTGTA
Column header name in processed data file: SyI35-12_CTTGTA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI


title: CI35.11

description:
Sample name: CI35.11_GGCTAC
Column header name in processed data file: CI35-11_GGCTAC
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI


title: SyU124.13

description:
Sample name: SyU124.13_AGTCAA
Column header name in processed data file: SyU124-13_AGTCAA
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI


title: HiSeq_A1

description: processed_data: Library_Preparation.txt

value: Novex TBE PAGE gel


title: HiSeq_A2

description: processed_data: Library_Preparation.txt


title: CU124.20

description:
Sample name: CU124.20_GTGGCC
Column header name in processed data file: CU124-20_GTGGCC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI


title: CI25.9

description:
Sample name: CI25.9_GATCAG
Column header name in processed data file: CI25-9_GATCAG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI


title: SyI224.5

description:
Sample name: SyI224.5_ACAGTG
Column header name in processed data file: SyI224-5_ACAGTG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: CI224.8

description:
Sample name: CI224.8_ACTTGA
Column header name in processed data file: CI224-8_ACTTGA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: SyI25.6

description:
Sample name: SyI25.6_GCCAAT
Column header name in processed data file: SyI25-6_GCCAAT
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI


title: CI324.10

description:
Sample name: CI324.10_TAGCTT
Column header name in processed data file: CI324-10_TAGCTT
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: FTO3C3_me6A

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: anti-me6A antibody (Synaptic Systems)

data_processing:
Illumina TruSeq adapters were removed with cutadapt; reads with remaining length 16-28 were kept as potential miRNAs, full length reads as potential other RNAs
Potential miRNAs were mapped against miRbase v20 (July 2013)  using mamaslemonpy (in-house software, available on Python Package Index PyPI), counts were tabulated
Whole workflow is implemented in Snakemake and is available as a Snakefile
Genome_build: mirBase v20
Supplementary_files_format_and_content: Two excel files showing the read counts of miRNAs in FTO ko and RNA immunoprecipitation experiments

source_name: HEK293 derivative

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% FCS and 1% PenStrep in a humidified incubator at 37°C supplied with 5% CO2.

extract_protocol:
The large and small RNA fractions from FTO knockdown was prepared using RNeasy Plus Universal mini kit (Qiagen, Hilden, Germany) following the instructions of the manufacturer. The small RNA fraction was eluted with the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany).
Illumina TruSeq Small RNA Sample Preparation Guide was used for cDNA synthesis and library preparation. The protocol was strictly followed. Briefly, 3’ and 5’ adapters were ligated to the samples, followed by reverse transcription and amplification with primers containing the unique indices for different samples. Amplified cDNA constructs were purified using Ampure XP beads. DNA was loaded into two lanes at 5 pM and 10 pM concentrations and subjected to Illumina sequencing. Demultiplexing was done using Illumina CASAVA 1.8.2.

treatment_protocol: Cells were transfected following the standard protocol at 10 nM concentration of siRNAs using lipofectamine 2000 as a transfection reagent. Briefly, cells were plated in 6-well plate one day before transfection. On day of transfection, the medium was changed, and 2 h later the formed complexes of siRNAs and lipofectamine were added to cells in a drop-like manner. RNA and protein were extracted after 48 h of transfection from both, FTO siRNA and scrambled siRNA transfected cells.

tag: rna type

value: small RNA

tag: treatment of cells

value: no treatment

tag: antibody

value: anti-me6A antibody (Synaptic Systems)

tag: cell line

value: HEK293 derivative


title: CI15.3

description:
Sample name: CI15.3_TTAGGC
Column header name in processed data file: CI15-3_TTAGGC
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

value: 5 DPI

value: inoculated with Erysiphe necator c-strain


title: FTO3C3_IgG

description: IgG isotop (Cell Signaling Technology)

value: IgG isotop (Cell Signaling Technology)


title: SyI15.4

description:
Sample name: SyI15.4_TGACCA
Column header name in processed data file: SyI15-4_TGACCA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

value: yes

value: whole plant


title: SyI124.2

description:
Sample name: SyI124.2_CGATGT
Column header name in processed data file: SyI124-2_CGATGT
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI

value: 1 DPI


title: FTO3C3_Input


title: SyU15.14

description:
Sample name: SyU15.14_AGTTCC
Column header name in processed data file: SyU15-14_AGTTCC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: siRNA RC3H1/2, 2h ActD, Replicate 2

city: Berlin

first: Markus

last: Landthaler

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrück-Center for Molecular Medicine

data_processing:
Demultiplexing was performed using Flexbar 2.4 (http://sourceforge.net/projects/flexbar/files/2.4/)
Supplementary_files_format_and_content: Raw reads were  mapped to the human genome version hg18 and D. melanagoster genome version dm3 using tophat2. Non-redundant reads per gene were counted using quasR. For decay determination, read counts were divided by the sum of the reads matching to the Drosophila transcriptome and by transcript length, and log2-transformed. Decay rates were estimated using linear least-squares regression on the data of two biological replicates. We used quantile normalization of the two sets of decay rates to remove potential biases from normalization. Differences in decay rates were computed by subtracting decay rates of siRNA treated samples from the decay rates of the mock treated samples. 4SU-based measurement of mRNA half-lives was performed as described (Dolken, L. et al., RNA 14, 1959-72 (2008))

source_name: HEK293 cell culture

extract_protocol: RNA was harvested using Trizol reagent and supplemented with 5% D. melanogaster total RNA. Illumina TruSeq RNA Sample Preparation Kit v2 (Cat#FC-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries. Adapter sequence: AGATCGGAAGAGCACACGT

value: HEK 293

tag: culture medium

value: DMEM

tag: treatment

value: Co-RNAi against RC3H1 and RC3H2, addition of 50 ug/ml ActD 2h before harvesting

tag: barcode

value: GTGAAAC


title: X03416U35.27

description:
Sample name: X03416U35.27_ATTCCT
Column header name in processed data file: 03416U35-27_ATTCCT
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI

value: Mock Innoculated

tag: tissue


title: FTO2D4_IgG

description: IgG isotop (Cell Signaling Technology)


title: MiSeq_D12

description: processed_data: MiSeq.txt

value: Whole-blood

tag: input amount (rna)

tag: purification method

value: AMPure XP beads


title: HiSeq_A3

description: processed_data: Library_Preparation.txt

value: 1 ug

value: Novex TBE PAGE gel

tag: rin value


title: HiSeq_D7

description: processed_data: HiSeq2500.txt


title: FTO2D4_me6A

description: anti-me6A antibody (Synaptic Systems)

value: small RNA

value: no treatment

value: anti-me6A antibody (Synaptic Systems)


title: siRNA RC3H1/2, 0h ActD, Replicate 2

value: Co-RNAi against RC3H1 and RC3H2, no addition of ActD

value: CCGTCCC


title: FTO2D4_Input

value: HEK293 derivative


title: MiSeq_D11

description: processed_data: MiSeq.txt


title: MiSeq_D10

description: processed_data: MiSeq.txt


title: siRNA RC3H1/2, 2h ActD, Replicate 1

value: CTTGTAA


title: X03416U224.22

description:
Sample name: X03416U224.22_CGTACG
Column header name in processed data file: 03416U224-22_CGTACG
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI

tag: cultivar

value: 1 DPI

value: yes

value: whole plant


title: FTO1C1_IgG

description: IgG isotop (Cell Signaling Technology)

value: IgG isotop (Cell Signaling Technology)


title: siRNA RC3H1/2, 1h ActD, Replicate 1

value: HEK 293

value: DMEM

value: Co-RNAi against RC3H1 and RC3H2, addition of 50 ug/ml ActD 1h before harvesting

value: CAGATCA


title: FTO1C1_me6A

description: anti-me6A antibody (Synaptic Systems)


title: MiSeq_D9

description: processed_data: MiSeq.txt

value: Whole-blood

value: AMPure XP beads


title: siRNA RC3H1/2, 1h ActD, Replicate 2

value: GTCCGCA


title: X03416U15.21

description:
Sample name: X03416U15.21_GTTTCG
Column header name in processed data file: 03416U15-21_GTTTCG
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI

value: 5 DPI

value: Mock Innoculated


title: CI124.1

description:
Sample name: CI124.1_ATCACG
Column header name in processed data file: CI124-1_ATCACG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI

value: Carignane

value: inoculated with Erysiphe necator c-strain

value: no


title: MiSeq_D8

description: processed_data: MiSeq.txt


title: X03416U124.20

description:
Sample name: X03416U124.20_GTGGCC
Column header name in processed data file: 03416U124-20_GTGGCC
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI


title: siRNA RC3H1/2, 0h ActD, Replicate 1

value: Co-RNAi against RC3H1 and RC3H2, no addition of ActD

value: GCCAATA


title: MiSeq_D7

description: processed_data: MiSeq.txt


title: Mock treatment, 2h ActD, Replicate 2

value: Mock treatment, addition of 50 ug/ml ActD 2h before harvesting

value: ATGTCAG


title: FTO1C1_Input

value: small RNA

value: no treatment

value: HEK293 derivative


title: FTO3C3_FTO kd

value: FTO specific siRNA

tag: time of harvesting


title: MiSeq_D6

description: processed_data: MiSeq.txt


title: X03416U324.25

description:
Sample name: X03416U324.25_ACTGAT
Column header name in processed data file: 03416U324-25_ACTGAT
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 1DPI

value: 1 DPI

value: yes

value: whole plant


title: X03416I324.10

description:
Sample name: X03416I324.10_TAGCTT
Column header name in processed data file: 03416I324-10_TAGCTT
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI


title: X03416U25.23

description:
Sample name: X03416U25.23_GAGTGG
Column header name in processed data file: 03416U25-23_GAGTGG
plants were placed in growth chambers and mock-innoculated. Whole plant data was collected 5DPI


title: Mock treatment, 1h ActD, Replicate 2

value: HEK 293

value: DMEM

value: Mock treatment, addition of 50 ug/ml ActD 1h before harvesting

value: AGTTCCG


title: FTO3C3_scr

value: scrambled siRNA


title: Mock treatment, 2h ActD, Replicate 1

value: ACAGTGA


title: X03416I25.9

description:
Sample name: X03416I25.9_GATCAG
Column header name in processed data file: 03416I25-9_GATCAG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

value: 5 DPI

value: inoculated with Erysiphe necator c-strain


title: FTO2D4_FTO kd


title: MiSeq_D3

description: processed_data: MiSeq.txt

value: Whole-blood

value: AMPure XP beads


title: MiSeq_D2

description: processed_data: MiSeq.txt


title: FTO1C1_FTO kd

value: small RNA


title: 100_FCX

status: Public on Jul 19 2015

city: Rochester

first: Hu

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
alignment TopHat v2.0.6
htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited gene counts

source_name: brain

extract_protocol:
RNA was extracted from frozen human postmortem samples of cerebellum and frontal cortex using 20-30 mg of tissue. A two-step tissue homogenization method was performed using pestle tips and 21G syringes. Total RNA was extracted using the RNAeasy Plus Mini Kit (QIAGEN, Germantown, MD, USA), as per manufacturer’s instructions. RNA integrity (RIN) was verified on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and 100-200 ng of RNA (RIN ≥ 7.0) in a 5 μl volume was used for library preparation and RNA sequencing (RNAseq).
Paired-end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit (Illumina) by the Mayo Clinic sequencing core facilities (Rochester, MN) followed by quality control, cluster generation and sequencing on the Illumina HiSeq 2000 platform. The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina (by the Mayo Clinic core).

value: Frontal Cortex

tag: genotype

value: Healthy


title: X03416I15.3

description:
Sample name: X03416I15.3_TTAGGC
Column header name in processed data file: 03416I15-3_TTAGGC
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

tag: timepoint


title: Mock treatment, 1h ActD, Replicate 1

value: TGACCAA


title: MiSeq_D1

description: processed_data: MiSeq.txt


title: X03416I124.1

description:
Sample name: X03416I124.1_ATCACG
Column header name in processed data file: 03416I124-1_ATCACG
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI

value: 1 DPI

tag: infection


title: 97_cereb

value: Cerebellum


title: FTO2D4_scr

value: HEK293 derivative


title: FTO1C1_scr


title: MiSeq_D5

description: processed_data: MiSeq.txt


title: 95_cereb


title: 95_FCX


title: Mock treatment, 0h ActD, Replicate 2

value: HEK 293

value: Mock treatment, no addition of ActD

value: AGTCAAC


title: Mock treatment, 0h ActD, Replicate 1

value: DMEM

value: CGATGTA


title: 94_FCX


title: 94_cereb


title: 93_FCX


title: X03416I224.8

description:
Sample name: X03416I224.8_ACTTGA
Column header name in processed data file: 03416I224-8_ACTTGA
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 1DPI

tag: resistant to powdery mildew

value: yes

value: whole plant


title: X03416I35.11

description:
Sample name: X03416I35.11_GGCTAC
Column header name in processed data file: 03416I35-11_GGCTAC
plants were placed in growth chambers innoculated with grapevine powdery mildew. Whole plant data was collected 5DPI

value: 5 DPI

value: inoculated with Erysiphe necator c-strain


title: 91_FCX


title: 93_cereb


title: 91_cereb


title: 90_cereb


title: 86_FCX


title: 90_FCX


title: 86_cereb


title: 24_FCX


title: 24_cereb


title: 75_FCX

value: sALS


title: 75_cereb


title: 74_FCX


title: 73_FCX


title: 71_cereb


title: 72_cereb


title: 97_FCX


title: 71_FCX


title: 14_cereb


title: 70_cereb


title: 70_FCX


title: 13_FCX


title: 14_FCX


title: 13_cereb


title: 72_FCX


title: 12_cereb


title: 12_FCX


title: 7_FCX


title: 11_cereb


title: 63_FCX


title: 62_FCX


title: 11_FCX


title: 63_cereb


title: 7_cereb_b


title: 6_FCX


title: 62_cereb


title: 73_cereb_a


title: 74_cereb


title: 57_cereb


title: 57_FCX


title: 1_FCX


title: 34_cereb


title: 2_cereb


title: Floret_ON_rep2

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

institute: Shanghai Center for Plant Stress Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and a ‘CATG’ tag was electronically added to the 5’ end. Only clean reads that contained no ambiguous nucleotide (‘N’), were exactly 21nt long, and had a read count of at least 2 in a library were retained for further analysis.
Counts of tags were normalized to transcript per million (TPM) according to total number of clean tags in each library
Genome_build: n/a
Supplementary_files_format_and_content: Tab-delimited text files include tag sequences,copy number and normalized count (transcript per million, TPM)

organism: Zea mays

source_name: ear

growth_protocol: maize hybrid DH3719 were over-seeded at the beginning of May and then thinned at the seedling stage to a stand of 100,000 plants per ha. The inter-row distance was 50cm for wide rows and 20cm for narrow rows. The intra-row distance was 28cm. Seeds were planted interlacingl only in two neighboring narrow rows for maximal light interception and nutrient uuptake. Border plots were set on all sides of the field to eliminate margin effects. Weed growth was controlled by the pre-emergence herbicide and cultivation.Before planting, 90 kg P2O5 ha-1 (Ca(H2PO4)2·H2O), 80 kg K2O ha-1 (K2SO4), and 30 kg ZnSO4·7H2O ha-1 were applied in all plots, with additional 45 kg P2O5 ha-1 and 40 kg K2O ha-1 at the V12 stage (68 d after sowing when the twelfth ligule emerged).

extract_protocol:
The cob (the central white tissue of the ear) and florets (the peripheral light yellow tissue of the ear) of maize ear were harvested separately, flash frozen and stored at -80℃. Total RNA was extracted from cob and florets with TRIZOL reagent (Invitrogen).
6 µg of total RNA from each sample was used in library construction according to the standard DGE protocol. Briefly, mRNA was purified by oligo(dT) magnetic beads adsorption (Invitrogen) and reverse transcribed into cDNAs. The cDNAs were digested with an anchoring restriction enzyme (NlaIII or DpnII) and ligated to an Illumina-specific adapter, Adapter 1, containing a recognition site for the type IIS restriction enzyme MmeI. Following MmeI digestion, cDNAs were purified and a second Illumina adapter, Adapter 2, was ligated to the 3' ends. After 15 cycles of linear PCR amplification, 95bp fragments were purified by 6% TBE PAGE Gel electrophoresis and then sequenced by an Illumina HiSeq 2000 sequencer for 49 cycles.

treatment_protocol: Field experiments were conducted at the Shangzhuang Experimental Station, China Agricultural University, Beijing. Eight adjacent plots with the same fertility were used for control (optimal N fertilization: 250 kg ha-1; ON) and Low N (zero N fertilization) treatments with four replicates . ON was determined by N absorbed by the plants minus soil mineral N (Nmin) and N deposition. The physical and chemical properties of the calcareous soil were as follows: soil density 1.4 g cm-3, pH (H2O) 7.9, organic matter 7.3 g kg-1; total N 0.7 g kg-1, Nmin 60.0 kg ha-1, Olsen-P 7.1 mg kg-1, and NH4OAc- extracted K 97.6 mg kg-1.

tag: strain

value: maize hybrid DH3719

value: floret

tag: age

value: silking stage

value: low nitrogen supply


title: Floret LN_rep3

value: optimal nitrogen supply


title: TMED9 rep1

city: West Haven

first: Francesc

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The first 6 and last 12 nucleotides for each read were trimmed to remove lower-scoring base reads. Trimming was performed using the FASTX toolkit. Sequences were aligned using Tophat v.2.0.8  to the latest reference UCSC human genome and transcript annotation (hg19), and only reads that mapped to a unique location within the genome were considered for further analysis.
Tophat alignments were processed using Cufflinks v2.1.1 software to calculate differential gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. Cuffdiff output format.

source_name: HEK293 Flp-In_TMED9

growth_protocol: standard cell culture conditions, in DMEM supplemented with 10% FBS supplemented with antibiotics (100 U/mL penicillin and 100 μg/mL streptomycin)

extract_protocol:
Qiagen RNeasy kit with on-column DNAse digestion (Qiagen, #79254)
RNA libraries were prepared for sequencing using strand specific Illumina protocols

treatment_protocol: Infected with pLKO.1 lentivirus, as indicated, and selected with Puromycin (1 μg/mL). Collected at Day 6 post-infection.

value: HEK293 Flp-In

tag: cell line vendor/cat. #

value: Invitrogen #R750-07

tag: RNAi treatment

value: TMED9 shRNA

tag: trc contruct id

tag: shRNA info

value: shRNAs targeting Chr5q35 loci; TMED9 at  Chr5:177,019,213

tag: stable exogenous dna

value: Promega pGL4.29


title: TMED9 rep2

tag: cell line


title: TSPAN17 rep1

source_name: HEK293 Flp-In_TSPAN-17

value: TSPAN-17 shRNA

value: shRNAs targeting Chr5q35 loci; TSPAN17 at Chr5:176,074,388


title: Floret_ON_rep1

tag: tissue

tag: treatment


title: N4BP3 rep2

source_name: HEK293 Flp-In_N4BP3

value: N4BP3 shRNA

value: shRNAs targeting Chr5q35 loci; N4BP3 at Chr5:177,540,556


title: Floret_ON_rep3


title: Floret LN_rep1


title: 1_cereb

value: Cerebellum


title: TSPAN17 rep2


title: N4BP3 rep1


title: 2_FCX

value: Frontal Cortex


title: TSPAN17 rep3


title: 34_FCX


title: ASNA1 rep3

source_name: HEK293 Flp-In_ASNA1

value: ASNA1 shRNA

value: control shRNA for engagement of the RNAi pathway; ASNA1 encoded on Chr19


title: 6_cereb


title: Cob_ON_rep3

value: maize hybrid DH3719

value: cob


title: Cob_ON_rep1

value: silking stage

value: low nitrogen supply


title: Cob_ON_rep2


title: ASNA1 rep2

value: HEK293 Flp-In


title: SMC_miRNA

city: Xuzhou

first: Yanhong

last: Wang

address: shanghai road number101

institute: Jiangsu Normal University

data_processing:
After getting rid of reads with 5' primer contaminants and without 3' primer, removal of redundancy and reads smaller than 18nt, the clean reads were mapped to the latest caprine genome assembly [http://goat.kiz.ac.cn/GGD/download.htm] using the program SOAP
Then, the reads were searched against the Sanger miRBase (version 19.0) to identify the miRNAs.
Genome_build: Capra hircus CHIR_1.0
Supplementary_files_format_and_content: Text files include count values for each identified miRNAs

organism: Capra hircus

source_name: Adult caprine skeletal muscle

extract_protocol:
On day 90(d90), caprine embryos (gestation period 150 days) were collected into sterile physiological saline immediately after removal from the reproductive tract of slaughtered goats at a local abattoir. These tissues were snap-frozen in liquid nitrogen and stored at −80°C until use. And RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.Low molecular weight RNAs were separated by 15% polyacrylamide gel electrophoresis (PAGE), and RNA molecules in the range of 18–30nt were enriched and ligated with proprietary adapters to the 5′ and 3′ termini. A reverse transcription reaction followed by low-cycle PCR was performed to obtain sufficient product for Solexa technology

value: skeletal muscle

value: 6 months old

tag: breed

value: Chinese Xuhuai Goat


title: FC_miRNA

source_name: Fetal caprine skeletal muscle

value: On day 90, caprine embryos


title: Na_PDS_2

city: Cambridge

first: Giovanni

last: Marsico

address: Robinson Way

country: United Kingdom

institute: CRUK Cambridge Institute

description: library strategy: G4-seq

data_processing:
Fastq files (Read-1) containing 150 bp single-end reads were aligned to the humang genome (hg19) using bwa mem. Read-2 files were assigned to the same genomic location of the corresponding Read-1 files.
Bam alignment files were converted to bed files and processed with bedtools: 1) bamToBed conersion; 2) bed file expansion (slopBed -s -r 30); 3) grouping to keep only best alignments (groupBy -g 4 -c 5 -o max); 4) fasta sequence extraction (bedtools getfasta -s)
fasta sequence files and original fastq file were processed in R to compare Read-1 to Read-2 files: sequence tails beyond poly-A (>9) were trimmed; difference in quality score and base mismatches was calculated for each pair of reads; single-base mismatch values were averaged for all reads overlapping each aligned genomic location.
Genome_build: hg19

extract_protocol:
not applicable, DNA purchased from Coriell Institute for Medical Research
Illumina TruSeq DNA sample prep kit was used to prepare all samples

tag: cell type

tag: sample type

value: Read-1:Na+ sequencing; Read-2:PDS+Na+ sequencing


title: Floret LN_rep2

value: floret

value: optimal nitrogen supply


title: N4BP3 rep3

value: Invitrogen #R750-07

value: N4BP3 shRNA

value: shRNAs targeting Chr5q35 loci; N4BP3 at Chr5:177,540,556

value: Promega pGL4.29


title: Na_PDS_1

description: library strategy: G4-seq

source_name: DNA purchased from Coriell Institute for Medical Research


title: ASNA1 rep1

value: ASNA1 shRNA

value: control shRNA for engagement of the RNAi pathway; ASNA1 encoded on Chr19


title: nonH rep2

source_name: HEK293 Flp-In_non-hairpin 18-mer

value: non-hairpin 18-mer

value: negative control shRNA (Addgene #10879)


title: SMC

data_processing:
After remove reads with adapters, reads in which unknown bases are more than 5% and low quality reads, the clean reads were aligned to the the lastest bovine genome assembly [ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/bigZips/bosTau6.fa.gz] using SOAPaligner/SOAP2
Genome_build: bosTau6
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

source_name: Six months old goat skeletal muscle

growth_protocol: All animal protocols were approved by the Review Committee for the Use of Animal Subjects of Northwest A&F University.

extract_protocol:
On day 90(d90), caprine embryos (gestation period 150 days) were collected into sterile physiological saline immediately after removal from the reproductive tract of slaughtered goats at a local abattoir. These tissues were snap-frozen in liquid nitrogen and stored at −80°C until use. And RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: longissimus thoracis

value: 6 months old goat


title: Na_K_2

description: library strategy: G4-seq

value: Read-1:Na+ sequencing; Read-2:K+ sequencing


title: FC

source_name: Fetal goat skeletal muscle

value: On day 90 goat, embryos


title: Cob_LN_rep2

value: maize hybrid DH3719

value: cob

value: silking stage


title: nonH rep1

value: HEK293 Flp-In


title: Na_K_1

description: library strategy: G4-seq


title: Cob_LN_rep3

value: optimal nitrogen supply


title: Cob_LN_rep1


title: wt_mRNA  [Sample 2]

status: Public on Jul 18 2015

city: Dallas

first: Yunkun

last: Dang

address: 5323 Harry Hines Blvd

department: Physiology

institute: University of Texas Southwestern Medical Center

description: reference file: NCv12T0_ORF.fa

data_processing:
removal of adaptor sequences with a customized Perl script. Unless indicated, all the following steps were carried out with customized Perl scripts.
removal of rRNA and tRNA contamination, following the instruction of the Kit (ARTseq)
aligned to the non-redundant ORF sequences with bowtie (ver 1.0.0) using following options: -l 18 -n 0 -m 1 –best –strata. Corresponding alignment reference sequences (fasta) were indicated above and were created with bowtie-build.
For RPF sequencing, pick read with desired length (28-32), determine the A site (16-18nt from 5' end). For mRNA seq, calculate the RPKM of each ORF by counted the short reads from mRNA seq that at least have one nucleotide overlapped with ORFs.  Processed result s were converted with “bedtools genomecov” to generate bedgraph file, whose score are normalized to RPM and converted to wig. Results were visualized the result on IGV2., with corresponding references created by choosing “Create  .genome file” in IGV “Genomes” manu and choosing corresponding fasta file.
Only reads mapped to plus strand were calculated. In order to compare different samples, normalization factors were introduced based on the ribosomal contamination for in vitro experiments, which account for about 90% of the library size for each sample and is assumed to be equivalent for all samples due to equal amount of lysate used, or total reads mapped to the references (for in vivo experiments).  The RCDT of each sense codons was derived as follows: For a gene with RPKM ≥ 1, if a specific codon has at least 1 RPF read covered and is not located within the first or last 20 amino acids from N and C terminus, respectively, its normalized RPF readings (i.e. RPM) was divided by the mRNA density (RPKM) determined by RNA-seq. We summed all quotients of this codon from the genome and divided by the total number of the codon in this analysis, which is referred as codon decoding time (CDT) for each sense codon. To calculate RCDT, the CDT of each codon was normalized to the highest occupied codon (CCA, proline).
Genome_build: Non-redundant whole ORF sequences (v12) were obtained from Neurospora crassa database at Broad Institute (http://www.broadinstitute.org/annotation/genome/neurospora/MultiDownloads.html). We added 100nt upstream and downstream UTR sequences to each ORF to facilitate mapping. If gene has multiple variants, which acount for 5% of all genes, we only keep the first one, i.e. NCUXXXXXT0)
Supplementary_files_format_and_content: wig file, scores represent the RPM at given site. contains 4 columns: Gene, start position, end position, score (RPM)
Bed file Contaisn 6 columns: Gene, start, end, read ID, score, strand. This file record the position of each short reads on reference, which was used to calculate RPKM
Fasta files are the references for alignment (the corresponding reference file for each sample was indicated in the sample description field)

organism: Neurospora crassa

source_name: mycelia

growth_protocol: For the in vivo ribosome profiling, fresh conidia (2x107 conidia/ml) were germinated in 200 mL growth medium (Vogel's minimal medium + 2% glucose) at room temperate with orbital shaking (200 rpm) under constant light for 12 hr.

extract_protocol:
ribosomal protected fragments (RPFs) were isolated by harvesting monosome through sucrose cushion (in vitro) or through size exclusion column (in vivo) followed by phenol extraction
Libraries are constructed by following the instruction of ARTseq Ribosomal Profiling Kit (Epicenter)

tag: genotype/variation

value: wild type

value: mycelia

tag: seq type

value: mRNA seq

tag: molecule subtype

value: mRNA


title: MOP-4_in.vitro [Sample 7]

description:
four in vitro sample are independently processed and data are merged into one file (in.vitro.luc.wig.gz)
reference file: MOP-4 in luc-ref.fa

source_name: cell extracts reacted with synthesized mRNA

tag: optimized region of luciferase

value: Luciferase codons of 224-423 are fully optimized

value: ribosomal profiling

value: Ribosome-protected fragments


title: Control3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using STAR software v2.4 to hg19. Data were converted and sorted by samtools 0.1.19 and reads per gene were counted via htseq version 0.6.1. Data analysis was performed using R/Bioconductor (3.2/2.12) using DESeq2 (v 1.8).
Candidate genes were filtered to a minimum of 2x fold change and FDR-corrected pvalue<0.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; normalized text file and raw data txt files

source_name: PC-3 cells

extract_protocol:
RNA wasisolated using a Peq-Gold kit
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000  following the manufacturer's protocols.

treatment_protocol: PC-3 cells (Prostatecarcinoma cells) were treated with 160 micromolar S-adenosylmethionine or vehicle

value: PC-3 prostate carcinoma cells

value: PBS

tag: treatment period


title: Cwt-Opt_in.vivo [Sample 4]

description: reference file: NCv12T0-luc-cwt-opt.fa

tag: strain

value: harboring WT-OPT luciferase @ his locus

value: Luciferase codons of 424-550 are de-optimized to WT


title: Opt_in.vivo [Sample 3]

description: reference file: NCv12T0-luc-opt.fa

value: harboring OPT-luciferase @ his locus

value: all codons of luciferase are fully optimized (i.e. most frequent codon)


title: OPT-2_in.vitro [Sample 5]

description:
four in vitro sample are independently processed and data are merged into one file (in.vitro.luc.wig.gz)
reference file: OPT-2 in luc-ref.fa

value: full gene optimized to 1

value: cell extracts reacted with synthesized mRNA


title: COP-5_in.vitro [Sample 8]

description:
four in vitro sample are independently processed and data are merged into one file (in.vitro.luc.wig.gz)
reference file: COP-5 in luc-ref.fa

value: Luciferase codons of  424-550 are fully optimized


title: wt_RPF [Sample 1]

description:
reads of 28-32 nt are used for analyses. For each read, only the first position of A site codon are counted.
reference file: NCv12T0_ORF.fa


title: SAM1

value: S-adenosylmethionine 160 micromolar


title: Control2


title: SAM2


title: SAM3


title: Control1


title: T. minima in-vitro growing in PDA rep1

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

institute: Joint Genome Institute

description: Sample 7

data_processing:
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 30 (Q>30).
Quality filtering was done with Scythe v.0.991 with a prior of 0.4
Bowtie2 v.2.1.0  was used to map the processed reads to the combined references with the following options: -q --end-to-end --sensitive --no-unal -p20.
Read counts were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Togninia minima strain UCRPA7, assembly UCRPA7V03 and WGS project AORD01000000.
Supplementary_files_format_and_content: PA7-augustus-counts-q30.txt: tab delimited text file, raw read counts determined by mapping the trimmed sequencing reads

organism: Phaeoacremonium minimum

source_name: T. minima in-vitro growing in PDA

growth_protocol: A plug (1cm x 1cm) of active growing mycelia was used to inoculate a new Petri dish with media, mycelia was grown at room temperature.

extract_protocol:
Total RNA was extracted using a CTAB based protocol with a chloroform denaturation step. RNA was cleaned with RNeasy kit (Qiagen, US) including the Dnase treatment on column.
Illumina TruSeq RNA Sample Prep Kit v2 protocol

treatment_protocol: Different growth media: Potato Dextrose Agar, minimal media agar with ground dormant canes of Vitis vinifera L. cv. Cabernet Sauvignon and Vitis vinifera L. cv. Merlot

tag: enviromental conditions

value: In-vitro

tag: culture media

value: Potato dextrose agar

value: Mycelia


title: T. minima in-vitro growing in PDA rep2

description: Sample 8


title: T. minima in-vitro growing in Merlot wood rep3

description: Sample 6

value: minimal media agar with dormant canes of V. vinifera L. cv. Merlot


title: T. minima in-vitro growing in Cabernet wood rep3

description: Sample 3

value: minimal media agar with dormant canes of V. vinifera L. cv. Cabernet Sauvignon


title: T. minima in-vitro growing in Merlot wood rep2

description: Sample 5


title: NOP-3_in.vitro [Sample 6]

description:
four in vitro sample are independently processed and data are merged into one file (in.vitro.luc.wig.gz)
reference file: NOP-3 in luc-ref.fa

value: Luciferase codons of  1-223 are fully optimized

value: ribosomal profiling


title: T. minima in-vitro growing in Cabernet wood rep1

description: Sample 1


title: T. minima in-vitro growing in Merlot wood rep1

description: Sample 4


title: Light exposure plus minocycline rep 1

status: Public on Jul 17 2015

city: Cologne

first: Thomas

last: Langmann

address: Kerpener Strasse 62

department: Department of Ophthalmology

institute: University of Cologne

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The analyses were performed with the Illumina RNA Express software that aligns RNA-Seq reads with STAR aligner, assigns reads to genes and performs differential gene expression with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes Dseq2-normalized counts.

extract_protocol:
Retinas were removed and RNA was harvested using Qiagen RNeasy Kit.
Library preparation and RNAseq were carried out as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide, the Illumina HiSeq 1000 System User Guide (Illumina, Inc., San Diego, CA, USA), and the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Kapa Biosystems, Inc., Woburn, MA, USA).

value: 10.000 Lux light exposure for 1h + 45 mg/kg minocycline injection i.p. daily for 4 days, analysis after four days

value: retina


title: Light exposure rep 1

value: 10.000 Lux light exposure for 1h, analysis after four days


title: T. minima in-vitro growing in PDA rep3

description: Sample 9


title: Light exposure rep 2


title: Light exposure plus minocycline rep 2


title: Control rep 2

value: no treatment


title: Control rep 1


title: 24dd_TRA_pos_DOX_minus_INP_Rep1

city: Boston

first: Shannan

last: Ho Sui

state: Massachusetts

address: 401 Park Drive, Level 3 East

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

data_processing:
ChIP-Seq data was aligned to the hg19 reference genome using bwa version 0.5.7 with default parameter settings. Subsequently, reads were filtered for duplicates and extended by 200bp. Visualization of read count data was performed by converting raw bam files to .tdf files using IGV tools (Thorvaldsdóttir et al., 2013) and normalizing to 1 million reads.
For H3K4me2 and H3K27ac histone marks, the Irreproducible Discovery Rate (IDR) framework with a cutoff of 0.05 in combination with the MACS2 peak caller version 2.1 was used to identify peaks taking advantage of both replicates (if available) for each condition. For MACS2 peak calling, we used an initial p-value cutoff of 0.01 and the corresponding whole cell extract (WCE) control library as background.
Genome_build: hg19
Supplementary_files_format_and_content: All coordinates are based on hg19. ENCODE narrowPeak Format: chromosome,chromstart,chromend,peak name,macs2 integer score, strand, fold change over background,-log10pvalue,-log10qvalue,relative summit position to peak star. For the K4me1 and K36me3: .tdf files can be displayed in the IGV.

source_name: reprogramming intermediates of hiF-T cells

growth_protocol: Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript. http://www.cell.com/cell/abstract/S0092-8674%2815%2900700-X

extract_protocol:
Total RNA, including the small RNA fraction, was obtained by organic extraction followed by miRNeasy purification (Qiagen).
ChIP-seq Illumina libraries were prepared and analyzed as previously described (Mikkelsen et al., 2010) starting from one million cells crosslinked in 1% PFA. ChIP-Seq libraries were sequenced with approximately 20 million 50-bp single end reads each.

tag: antibody epitope, vendor, catalog number, lot

tag: surface antigen enrichment

value: DOX days 0-20


title: 24dd_TRA_pos_DOX_plus_H3K27ace_Rep1

value: DOX days 0-24


title: 24dd_TRA_pos_DOX_plus_H3K36me3_Rep1


title: 24dd_TRA_pos_DOX_plus_H3K4me2_Rep2

description: FinalIDR_TRA60_Pos_H3K4me2_macs2.regionPeak


title: 24dd_TRA_pos_DOX_minus_H3K36me3_Rep1


title: 24dd_TRA_pos_DOX_plus_H3K4me2_Rep1


title: 24dd_TRA_pos_DOX_plus_Rep1


title: 24dd_TRA_pos_DOX_minus_H3K4me3_Rep1


title: 24dd_TRA_pos_DOX_minus_H3K27ace_Rep1


title: 24dd_TRA_pos_DOX_plus_H3K4me3_Rep1


title: 24dd_TRA_pos_DOX_minus_H3K4me2_Rep1


title: 24dd_TRA_pos_DOX_plus_H3K27me3_Rep1


title: T. minima in-vitro growing in Cabernet wood rep2

description: Sample 2


title: 24dd_TRA_pos_DOX_minus_H3K27me3_Rep1


title: 24dd_TRA_pos_DOX_minus_H3K4me1_Rep1


title: 10dd_DOX_plus_SSEA3_pos_H3K4me3_Rep1

value: DOX days 0-10


title: 10dd_DOX_plus_SSEA3_pos_H3K4me2_Rep1


title: 10dd_DOX_plus_SSEA3_pos_H3K4me1_Rep1


title: 10dd_DOX_plus_SSEA3_pos_H3K27ace_Rep1


title: 5dd_DOX_plus_H3K36me3_Rep1

value: DOX days 0-5


title: 5dd_DOX_plus_INP_Rep1


title: MiSeq_D4

city: Montreal

first: Juan Pablo

address: 6875 La Salle Blvd

institute: McGill University

description: processed_data: MiSeq.txt

data_processing:
All sequencing data were processed using CASAVA 1.8+ and extracted from FASTQ files
Fastx_toolkit was used to trim the Illumina adapter sequences
Additional filtering based on defined cutoffs was applied in order to obtain high quality data. These filters included: 1) Phred quality (Q) score higher than 30, 2) reads between 15-40nt in length, 3) adapter detection based on perfect-10nt match, and 4) removal of reads without detected adapter
We used Bowtie to align reads to the human genome (GRCh37)
We used ncPRO-seq in combination with miRBase (V20) to match them to known miRNA sequences
We used the Rfam and NCBI's piRNA databases to map other small RNA sequences
All sequencing data was normalized with the Bioconductor - DESeq2 package, using a detection threshold of 1 count per miRNA (present at least once in each of the libraries tested)
Genome_build: Human genome (GRCh37)
Supplementary_files_format_and_content: Tab-delimited text files include small RNA count values for each sample

source_name: Whole-blood

extract_protocol:
Peripheral blood samples were collected in PAXgene blood RNA tubes (PreAnalytix, Switzerland). PAXgene tubes were frozen using a sequential freezing process. This involves storing tubes at room temperature for 3h, transferring to 4°C overnight, followed by 6-8h at -20°C and then final storage at -80°C. Total RNA (including the miRNA fraction) was isolated from whole-blood using the PAXgene Blood miRNA Kit (Qiagen, Canada), according to manufacturer's instructions. Furthermore, total RNA was isolated from frozen brain, heart and liver tissues using the miRNeasy Mini Kit protocol (Qiagen, Canada) with no modifications. RNA and miRNA yield and quality were determined using the Nanodrop 1000 (Thermo Scientific, USA) and Agilent 2100 Bioanalizer (Agilent Technologies, USA).
All libraries were prepared using the Illumina TruSeq Small RNA protocol following the manufacturer's instructions with 12 cycles of PCR amplification after ligation of the 3' and 5' adapters.  Individual libraries were prepared using a unique index primer in order to allow for pooling of multiple samples prior to sequencing. Libraries were validated and quantified using an Agilent 2100 Bioanalyzer High Sensitivity DNA chip and qRT-PCR with the KAPA library quantification kit (Kapa Biosystems, USA). Sample C1 (control - human brain) was not sequenced. All additional samples (A1-A10), as well as sample AC (control - no purification method), were sequenced.
Purification Method: In order to compare three different small RNA library purification methods, we prepared 11 libraries starting with 1µg of good quality total RNA (RIN>8). All libraries were prepared using total RNA extracted from peripheral blood of a single individual. The RNA was split into 11 aliquots and each was used as a technical replicate. In addition, we used total RNA from commercially available human brain as a library preparation control. Libraries were purified as follows: 1) Purification by Novex TBE PAGE gel: 50µl of amplified cDNA from samples A1-A3 and C1 were loaded into a 6% Novex gel and run for 80 minutes at 130-135 V. After cleaning the gel with RNase free water, a band was manually cut to contain all fragments sized 145-160nt, corresponding to mature miRNAs and other regulatory small RNA molecules;  2) Purification by Pippin Prep automated gel system (Sage 3%): The Pippin Prep system (PPS) allows automatic selection of specified cDNA products. 25µl of amplified cDNA from samples A4-A7 were loaded into a Pippin Prep machine. Furthermore, in order to test variability between machines, samples A4 and A5 were loaded into PPS1, while samples A6 and A7 were loaded into PPS2. Size selection was automated for products between 125 and 180nt; 3) Purification by AMPure XP beads: Biotinylated magnetic AMPure beads allow for selection of specified cDNA products bound to streptavidin. 50µl of amplified cDNA from samples A8-A10 were mixed and purified two times with AMPure XP beads at a 1.8:1 ratio (beads:sample). This ratio allows for optimal selection of all products higher than 100nt.

value: Whole-blood

tag: input amount (rna)

tag: purification method

value: AMPure XP beads

tag: rin value


title: 24dd_TRA_pos_DOX_plus_H3K4me1_Rep1

tag: treatment


title: 8dd_DOX_plus_H3K4me2_Rep1

value: DOX days 0-8


title: 5dd_DOX_plus_H3K4me2_Rep2

description: FinalIDR_Rep_Day5_H3K4me2_macs2.regionPeak


title: 5dd_DOX_plus_H3K4me2_Rep1


title: 5dd_DOX_plus_H3K4me1_Rep1


title: 5dd_DOX_plus_H3K27me3_Rep1


title: hIPSC-T_P10_INP_Rep1

source_name: hIPSCs from reprogrammed hiF-T cells (hIPSC-T)

tag: passage (pre-reprogramming)


title: 5dd_DOX_plus_H3K27ace_Rep1


title: hIPSC-T_P10_H3K36me3_Rep1


title: hIPSC-T_P10_H3K4me3_Rep1


title: hIPSC-T_P10_H3K4me2_Rep1


title: hIPSC-T_P10_H3K27me3_Rep1


title: hiF-T_P15_INP_Rep1

source_name: immortalized human inducible fibroblasts-like cells (hiF-T)


title: hiF-T_P15_H3K4me2_Rep2

description: FinalIDR_HIFT_Fib_H3K4me2_macs2.regionPeak


title: hiF-T_P15_H3K4me3_Rep1


title: hiF-T_P15_H3K4me1_Rep1


title: hiF-T_P15_H3K4me2_Rep1


title: 5dd_DOX_plus_H3K4m3_Rep1


title: hiF-T_P15_H3K27ace_Rep1


title: hIPSC-T_P10_H3K4me1_Rep1


title: hIPSC-T_P10_H3K27ace_Rep1


title: Rph1- Old (S2O, Exp 1) Input

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Base-Calling: CASAVA was used to call bases for experiment 1 and BCL2FASTQ v2 was used to call bases for experiment 2.
Merge: experiment 2 data are merged from four lanes and two flowcells, or eight lanes each. Raw files correspond to merged data with internal labeling in tag headers.
Alignment: ChIP-seq data were aligned using bowtie v0.12.7 and v0.12.5 in the case of the first and second replicate of H3K36me3 data respectively. ChIP-seq data were aligned with parameters -m 1 --best, to guarantee a single optimal alignment for each tag and to remove tags mapping optimally to multiple loci.
Track Generation: aligned tags were expressed as bedGraphs using the BEDtools utility genomeCoverageBed (-bg) and adjusted for total tags sequenced. H3 bedGraphs were subtracted from H3K36me3 bedGraphs to normalize for sonication efficiency, then tracks for the two replicates were combined by unweighted average.
Genome_build: sacCer2
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Standard YPD medium was used in all experiments.

extract_protocol:
Chromatin immunoprecipitation was performed as described previously from 4 X 10^8 cells (W. Dang et al., Nature 459, 802 (Jun 11, 2009)). Briefly, cross-linked cells were lyzed by bead beating in FA lysis buffer (50mM HEPES-KOH, pH 7.5, 500mM NaCl, 1mM EDTA, 0.1% Triton X-100) and the chromatin sheared using a Diagenode Bioruptor or Covaris Ultrasonicator to achieve an average size of <500bp. Equal aliquots of sonicated chromatin were used per immunoprecipitation (IP) reaction (H3K36me3 (Active Motif 61101) and H3 (Abcam ab1791)) and 10% of the amount was saved as input. IP was performed using protein A Dynabeads (Life Technologies). ChIP-qPCR was performed against standards made from a dilution series of an input DNA mix. Enrichment was ascertained by calculating signal over IgG. To ensure that we were getting H3K4me3 and H3K36me3 enrichment at 5’ ends and 3’ ends respectively, ChIP-qPCR validation was performed with 5’ and 3’ end primer sets over long genes before library preparation for ChIP-seq. Primer sequences are available upon request.
For ChIP-seq, 1ng of DNA from IP and input was used to prepare libraries using the Microplex library preparation kit (Diagenode). Twelve multiplexed libraries were sequenced in a single lane on the Illumina HiSeq or NextSeq 500 platform.

treatment_protocol: Up to 4 X 10^8 replicatively aged yeast mother cells (20-25 generations old on average) for RNA-seq were purified as described in S. Tsuchiyama, E. Kwan, W. Dang, A. Bedalov, B. K. Kennedy, Methods in molecular biology 1077, 11 (2013).

tag: ChIP

value: Input

tag: experiment

tag: age

value: Old

tag: sort

tag: genotype

tag: antibody


title: Rph1- Old (S3O, Exp 1) H3

value: Abcam ab1791


title: Rph1- Old (S3O, Exp 1) Input


title: Rph1- Old (S2O, Exp 1) H3


title: Rph1- Young (S2Y, Exp 1) Input

value: Young


title: hiF-T_P15_H3K27me3_Rep1


title: hiF-T_P15_H3K36me3_Rep1


title: Rph1- Old (S2O, Exp 1) H3K36me3

value: Active Motif 61101


title: Rph1- Young (S2Y, Exp 1) H3


title: WT Young (S2Y, Exp 1) Input

value: WT


title: Rph1- Young (S2Y, Exp 1) H3K36me3


title: WT Old (S3O, Exp 1) Input


title: SHL

first: Martin

middle: G

last: Frasch

state: QC

address: 3175, Côte-Sainte-Catherine

department: Dépt. obstétrique-gynécologie

institute: Université de Montréal

data_processing:
Raw data were mapped to the reference genome of the sheep Ovis aris v3.1 from NCBI and Ensembl (GCA_000298735.1) as transcriptome reference.
Index of the reference fasta file were built with Bowtie2, we then trimmed the adaptor of the fastQ files with TrimGalore, and mapped reads to the reference with Tophat2.
The number of reads per gene were counted with HTseq and assembled into a matrix containing the read count of each gene per sample.
Genome_build: Ovis aris v3.1 from NCBI and Ensembl (GCA_000298735.1)
Supplementary_files_format_and_content: Tab delimited file included read count for each sample

organism: Ovis aries

source_name: Second hit microglia

extract_protocol:
Total RNA was extracted from cultured microglia using TRIzol Reagent. RNAseq libraries were prepared by using Illumina TruSeq RNA Sample Preparation v2 kit (Illumina) and quality control was performed on the BioAnalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: microglia

value: 130 days ± 1.3 dGA

value: exposed to LPS in vivo and in vitro


title: WT Old (S3O, Exp 1) H3K36me3


title: WT Old (S2O, Exp 1) H3K36me3


title: WT Young (S2Y, Exp 1) H3


title: WT Old (S3O, Exp 1) H3


title: WT Young (S2Y, Exp 1) H3K36me3


title: NL3

source_name: Naive microglia

value: exposed to saline in vivo and LPS in vitro


title: SHC

source_name: Second hit control

value: exposed to LPS in vivo and saline in vitro


title: Rph1- Old (S3O, Exp 1) H3K36me3


title: NL2


title: Rph1- Old (S4O, Exp 9)

data_processing:
Base-Calling: bases were called using CASAVA
Trimming: tags were trimmed to 35bp before alignment.
Alignment: RNA-seq tags were aligned using tophat v2.0.5 and bowtie indices for the sacCer2 assembly. RNA spike-in sequences were included in the assembly (see sacCer2.SPIKE.fa, available on series record). Libraries were stranded and tophat was run using the parameter --library-type fr-firststrand to reflect this. Additionally, only the optimal alignment for each tag was recorded (-g 1).
Masking: tags mapping to rDNA loci were filtered out.
Track Generation: masked BED files were split into two files containing tags aligned to the + reference strand and the - reference strand. Each was passed through the BEDtools utility genomeCoverageBed (-bg) to make bedGraphs. These were then normalized to the RPKM coefficient for the sample and then run through bedGraphToBigWig from the UCSC Genome Browser utilities package. Tags on the + strand are in *.P.bw and tags on the - strand are in *.M.bw.
Genome_build: sacCer2
Supplementary_files_format_and_content: bigWig

extract_protocol:
mRNA was purified from 5ug total RNA using the Dynabeads mRNA Direct kit (Ambion).
Since yeast genes are relatively short (average gene size ~1.3Kb), we chose to fragment the mRNA to ~40-50bp rather than the conventional 200-300bp size using RNA fragmentation reagents from Ambion. We believe that this gives better resolution over gene bodies to quantify 5’ and 3’ reads for estimation of cryptic transcripts. To do this, the fragmented RNA was phosphorylated by T4 PNK (NEB) and then size selected on a 15% polyacrylamide gel containing urea. Following size selection, the entire RNA was used as input in the TruSeq small RNA sample preparation protocol (Illumina). Final size selection of amplified library was done using 6% polyacrylamide gels.

tag: strategy

value: Normal Fragment


title: Rph1- Old (S3O, Exp 9)


title: NL1


title: Rph1- Old (S2O, Exp 9)


title: NC3

source_name: Naive microglia control

value: exposed to saline in vivo


title: WT Old (S2O, Exp 1) Input


title: WT Old (S4O, Exp 9)


title: Rph1- Young (S1Y, Exp 9)


title: NC2


title: WT Old (S3O, Exp 9)


title: WT Old (S2O, Exp 1) H3


title: WT Old (S2O, Exp 9)


title: NC1


title: Rph1- Old (S3O, Exp 8)


title: WT Young (S1Y, Exp 9)


title: h1ESC dorsomorphin induced 24h_BS-seq

first: Gang

address: 320 Yueyang Rd, Shanghai

institute: Shanghai Institutes for Biological Sciences

data_processing:
quality control, trim base quality less than 20 with fastx-tool-kit, remove reads less than 10bp
mapping with bismark v0.07, with default parameters
extract methylated and unmethylated reads with bismark v0.07
Genome_build: ucsc hg18
Supplementary_files_format_and_content: BED format; with chromosome, start, end, methylated counts, unmethylated counts

source_name: H1 cell line

growth_protocol: growth protocol is described in our previous study (PMCID: PMC3322377)

extract_protocol:
Qiagen DNeasy mini kit, performed as per manufacturer's instructions
For end repair and add dATP, add 7.25 ml EA mix1 and 1.75 ml EA mix 2 to the 16 ml PCR product. Then PCR with the system: 12℃ 15 min; 37℃ 15 min; 72℃ 20 min, and hold in 4℃. Add 2 ml water, 1 ml 10X DNA Ligase Buffer, 2 ml methylated adaptor(5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT), 5ml T4 DNA ligase to the system, hold overnight in 16℃ for 16 hours. Add Agencourt® AMPure® XP to purify the system with the manufature-provided manual, and get 200 ml product. Add 6 ml Loading Dye(6X), vertex and perform  2% agarose gel electrophoresis with 90V for 2 hours, select 300bp-400bp fragments for gel extraction with Qiagen Minilute Gel Purification Kit by following its protocol. Solute the product in 20 ml EB buffer. MethylCode™ Bisulfite Conversion Kit for bisulfite conversion was used by following protocol for the kit. Purify the product with EZ DNA Methylation-Gold Kit and get 10 ml product. Add 1 ml Bioo Primer, 1 ml water and 12.5 ml KAPA HiFi Hotstart Utracil+ ReadyMix (2X) to the system. PCR: 95℃ 10mins, 5 cycles: 95℃ 30s, 65℃ 30s, 72℃ 45s, 72℃ 7min, and hold in 4℃. Then purify with Agencourt® AMPure® X Beads.

treatment_protocol: treatment protocol is described in our previous study (PMCID: PMC3322377)

tag: cell line

tag: treatment/time period

value: H1 dorsomorphin induced 24h


title: h1ESC_BS-seq

value: H1 dorsomorphin induced 0h


title: Rph1- Old (S2O, Exp 8)


title: AGS5 P2 DRIP-seq

city: Davis

first: Yoong Wearn

last: Lim

address: One Shields Avenue

department: Molecular and Cellular Biology

institute: University of California, Davis

data_processing:
Library strategy: DRIP-seq
DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf and custom Perl script before mapping.
DRIP-seq: Trimmed fastq reads were mapped to hg19 using BWA 0.6.1. Peak calling was first performed by MACS 1.4.2 using input library as control. DRIP peaks were further assigned onto restriction fragments using custom Perl script. DRIP peaks from 2 AGS2 and 2 AGS4 cells were merged into one sample, respectively.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5. Count table was generated using HTSeq using the "intersection-nonempty" option.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7. Wig files containing percent methylation were generated using custom Perl script.
RRBS: Fastq files were trimmed with Trim Galore before mapping to hg19 using Bismark 0.7.7. Wig files containing percent methylation were generated using custom Perl script.
Genome_build: hg19

source_name: Primary fibroblast

extract_protocol:
Genomic DNA was extracted from primary fibroblasts and fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Monoclonal S9.6 antibody was used to enrich for RNA/DNA hybrids.
standard illumina protocol

tag: mutation


title: WT Old (S3O, Exp 8)


title: AGS1 P2 DRIP-seq


title: WT Old (S2O, Exp 8)


title: Rph1- Old (S4O, Exp 7)


title: Control 3 DRIP-seq

data_processing:
DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf and custom Perl script before mapping.
DRIP-seq: Trimmed fastq reads were mapped to hg19 using BWA 0.6.1. Peak calling was first performed by MACS 1.4.2 using input library as control. DRIP peaks were further assigned onto restriction fragments using custom Perl script. DRIP peaks from 2 AGS2 and 2 AGS4 cells were merged into one sample, respectively.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5. Count table was generated using HTSeq using the "intersection-nonempty" option.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7. Wig files containing percent methylation were generated using custom Perl script.
RRBS: Fastq files were trimmed with Trim Galore before mapping to hg19 using Bismark 0.7.7. Wig files containing percent methylation were generated using custom Perl script.
Genome_build: hg19

tag: sample type

value: Primary fibroblast


title: Rph1- Old (S3O, Exp 7)


title: Rph1- Old (S2O, Exp 7)


title: GM12697 RRBS

source_name: Lymphoblastoid cell line

extract_protocol:
Genomic DNA was extracted using phenol chloroform.
Myers lab RRBS protocol

value: Lymphoblastoid cell line


title: AGS2 LCL RRBS


title: h1ESC dorsomorphin induced 48h_BS-seq

value: H1 dorsomorphin induced 48h


title: AGS5 rep 2 RNA-seq

extract_protocol:
Total RNA was extracted using Trizol for downstream processing with the Illumina Truseq kit.
Illumina TruSeq protocol


title: WT Old (S4O, Exp 7)

value: Old


title: Rph1- Young (S2Y, Exp 7)


title: Rph1- Old (S4O, Exp 8)


title: AGS4 P2 rep 2 RNA-seq


title: WT Old (S2O, Exp 7)


title: AGS5 rep 1 RNA-seq


title: AGS4 P1 rep 2 RNA-seq


title: Rph1- Young (S1Y, Exp 8)


title: WT Young (S2Y, Exp 7)


title: WT Young (S1Y, Exp 8)


title: Rph1- Old (S4O, Exp 5)

value: Small Fragment


title: AGS4 P2 rep 1 RNA-seq


title: WT Old (S3O, Exp 7)


title: AGS2 P2 rep 2 RNA-seq


title: AGS4 P1 rep 1 RNA-seq


title: AGS2 P2 rep 1 RNA-seq


title: Rph1- Young (S2Y, Exp 5)

value: Young


title: Rph1- Old (S3O, Exp 5)


title: WT Old (S3O, Exp 5)


title: AGS2 P1 rep 1 RNA-seq


title: WT Old (S4O, Exp 8)


title: Rph1- Old (S2O, Exp 5)


title: AGS1 rep 2 RNA-seq


title: WT Old (S2O, Exp 5)


title: WT Young (S2Y, Exp 5)


title: Control 1 rep 2 RNA-seq


title: AGS1 rep 1 RNA-seq


title: Rph1- Old (S2O, Exp 4)


title: Control 1 rep 1 RNA-seq