title: Small RNA short-time

description: small RNA

value: seedlings were treated with 150 mM solution of NaCl for 4 hours


title: qsp1∆liv3∆ + peptide Saturated Experiment 2 RNA-Seq replicate 2

status: Public on Jun 08 2016

type: SRA

city: San Francisco

first: Christina

middle: M.

last: Homer

state: CA

department: Biochemistry & Biophysics

country: USA

institute: UCSF

library_source: transcriptomic

data_processing:
RNA-Seq data were aligned using Tophat. Indexed, sorted bam files were created and then rpkm values were calculated for pairwise comparisons between wild-type and knockout mutant samples.
Genome_build: Sequence and feature files for C. neoformans var grubii H99 were obtained from the Broad institute, Cambridge, MA as current as January 20th, 2011.
Supplementary_files_format_and_content: Peak lists and locations for ChIP-seq samples and RPKM lists and ratios for each gene for RNA-seq samples.

molecule: total RNA

organism: Cryptococcus neoformans

source_name: Yeast

growth_protocol: 50 ODs of cells from overnight YPAD cultures were washed once in water and resuspended in 20 mLs DMEM, transferred to 150mm tissue culture dishes, and incubated for 24 hours at 37ºC, 5% CO2

extract_protocol:
mRNA was isolated using trizol to isolate total RNA and oligotex mRNA mini kit to isolate mRNA. ChIP DNA was isolated from antibody incubation by SDS/proteinase K followed by purification using MN Nucleospin Gel Cleanup columns
cDNA libraries were prepared from DNase-treated mRNA using NEBNext Ultra Directional RNA Library Prep Kit. ChIP DNA libraries were prepared using End-It DNA End Repair Kit followed by A-tailing using Klenow fragment (NEB), ligation to Illumina adaptors using Rapid T4 DNA Ligase (Enzymatics), PCR amplification for 15 cycles, and size selection between 200-350bp

tag: strain

value: Kn99alpha(wild-type) with qsp1(del) liv3(del)

tag: media

value: YPAD

tag: cell density

value: Saturated


title: Small RNA CK

city: Anyang

first: Zujun

last: Yin

state: Henan

address: 38 Huanghe Dadao, Anyang 455000, Henan, China

department: Cotton Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

description: small RNA

data_processing:
Raw sequencing reads were processed into clean full-length reads by the BGI small RNA pipeline. After the raw sequence reads were obtained, adapter sequences, low quality tags, contaminants and sequences beyond 15 nt to 30 nt were filtered.
The remaining sequences were aligned to Rfam (http://www.sanger.ac.uk/resources/databases/rfam.html) and Genbank database to annotate rRNA, tRNA, snRNA, snoRNA and those containing the polyA tails.
To identify conserved miRNAs,cleandata  were align to the mature miRNAs of all plants in miRBase (http://www.mirbase.org/) allowing two mismatches and free gaps
The cleandata was further align to the above temporary miRNA database and the expression of miRNA is generated by summing the count of tags which can align to the temporary miRNA database.
The identification of novel miRNAs were analyzed by MFOLD software (http://mfold.rna.albany.edu/) on the RNA secondary structure of the miRNA::miRNA* and pre-miRNA hairpin energy.
Genome_build: miRNA Registry Database, miRBase database
Supplementary_files_format_and_content: match_mirbase.txt  This file contains small RNAs whose sequences are similar with miRNAs deposited at miRBase

organism: Gossypium hirsutum

source_name: Cotton leaves

growth_protocol: The upland cotton cultivar SN-011 was used in this study. Seeds were sterilized and germinated in vermiculite. Growth conditions were 30/22 day/night temperature, 55–70% relative humidity, and a 14 h/10 h light/dark cycle under 450 μmol m−2⋅s−1 light intensity. At the two-leaf stage, healthy seedlings were grown in pots containing aerated nutrient solution. Plants were cultured under non-saline conditions for 10 d to ensure full establishment before starting the salinity treatments. The pH was maintained close to 6.9 by adding H2SO4 or KOH as required.

extract_protocol:
Total RNA was isolated using a modified CTAB method and purified using Qiagen RNeasy columns (Qiagen, Hilden, Germany).Then,total RNA was separated by 15% denaturing polyacrylamide gel electrophoresis (PAGE) to recover the population of small RNAs.
The extracted small RNAs then was dephosphorylated using alkaline phosphatase and ligated to 5'- and 3'-RNA adaptors by T4 RNA ligase. The adaptor-ligated sRNAs were subsequently transcribed to single-stranded cDNA using SuperScript II Reverse Transcriptase. After polymerase chain reaction (PCR) amplification, PCR products were purified and subjected to SBS sequencing with a Solaxa genome analyzer II at the BGI (Beijing Genomics Institute, Shenzhen, China).

treatment_protocol: For short-term salt treatment samples, seedlings were treated with 150 mM solution of NaCl. After exposing the seedlings to salt stress for 4 h, cotton leaves of the short-term salt treatment samples were harvested. For long-term salt treatment samples, seedlings were exposed to salinity by adding NaCl to the growth medium in 50 mM increments every 12 h, until a final concentration of 150 mM was reached. After exposing the seedlings to salt stress for 5 d, leaves were harvested directly into liquid nitrogen and stored at −80 °C for subsequent use.

tag: tissue

value: leaves

tag: treatment

value: under non-saline conditions

tag: cultivar


title: qsp1∆liv3∆ + peptide Saturated Experiment 2 RNA-Seq replicate 3


title: qsp1∆liv3∆ Saturated Experiment 2 RNA-Seq replicate 1


title: qsp1∆liv3∆ + peptide Saturated Experiment 2 RNA-Seq replicate 1


title: SM_day -1_27C_sample 5

city: Sydney

first: Rachel

last: Levin

state: New South Wales

address: UNSW

country: Australia

institute: University of New South Wales

description: processed data file: day-1_SM_RSEM_genes.counts.matrix

data_processing:
Illumina Truseq (TruSeq3-SE) adapters were removed from sequence reads using Trimmomatic.
Prinseq was used to remove poly-A tails (min 6-A tail) and to filter short (min length 60 bases), low quality (min mean quality score 20, 4 base window, 1 base step), and low complexity sequences (dust method threshold 7).
RNA sequences from the 24 samples per population (four replicates, two temperature treatments, three time points) were combined for de novo assembly of the SM and MI transcriptomes using Trinity (version: 2.0.6).
transcripts shorter than 250 bp were removed from the assembeled transcriptomes
redundant transcripts (similarity > 90%) were removed from the assembled transcriptomes using cd-hit-est
Genome_build: the assembeled transcriptome
Supplementary_files_format_and_content: tab-delimited text files include expression count matrices for each sample at each time point

molecule: polyA RNA

organism: Cladocopium sp. C1

source_name: SM_day -1_27C

growth_protocol: Symbiodinium populations were cultured in filtered seawater supplemented with Daigo IMK (Wako Pure Chemical Industries, Ltd.). For temperature experiments, 5x10^7 cells (1.5x10^6 cells/ml) of each population were added to eight replicate culture flasks per population. Light was provided at an intensity of 30 µmol quanta m-2 s-1 with a 12 h light-dark cycle.

extract_protocol:
Precisely after six hours of light exposure, 2-4 x 10^6 cells per population were immediately snap frozen in liquid nitrogen within 10 s of removal from experimental incubators and stored at -80°C. Snap frozen cells were thawed at room temperature and pelleted at 4°C (3,000 x g, 5 min). Media was removed, and pellets were lysed in buffer RLT (RNeasy plant mini kit, Qiagen) containing β-mercaptoethanol by bead beating with 0.3 g of 710-1,180 µm acid-washed glass beads (Sigma) using a TissueLyser II (Qiagen) for 90 s at 30 Hz. RNA was extracted and purified using the RNeasy plant mini kit (Qiagen) with an added on-column DNase I treatment (Qiagen).
Total RNA (150-500 ng) of each sample was sent to the Australian Genome Research Facility for confirmation of high quality RNA on an Agilent 2100 bioanalyzer, polyA-purification, Illumina TruSeq stranded library preparation, and sequencing on an Illumina HiSeq2500 (single end 100 bp, ~107 reads per sample)

treatment_protocol: Two flasks per population were randomly assigned to each of four experimental incubators and acclimated at 27°C for two weeks. Two incubators were ramped on day 0 at 0.5°C/h to 32°C for the heat stress temperature treatment, while two incubators remained at 27°C.

tag: population

value: South Molle (SM)

tag: population source

value: South Molle Island, Great Barrier Reef

tag: thermal tolerance phenotype

value: sensitive

tag: sampling time point

value: day -1

tag: temperature treatment

tag: incubator

value: incubator 3

tag: sample type

value: cell culture

tag: medium

value: filtered sea water + IMK nutrient supplement

tag: coral host from which it was isolated

value: Acropora tenuis


title: qsp1∆liv3∆ Saturated Experiment 2 RNA-Seq replicate 3


title: qsp1∆ + peptide Saturated Experiment 2 RNA-Seq replicate 1

value: Kn99alpha(wild-type) with qsp1(del)


title: Kn99alpha WT Saturated Experiment 2 RNA-Seq replicate 1


title: qsp1∆ + peptide Saturated Experiment 2 RNA-Seq replicate 2


title: qsp1∆ Saturated Experiment 2 RNA-Seq replicate 2


title: qsp1∆ Saturated Experiment 2 RNA-Seq replicate 1


title: LIM_HSV1_rep1

city: New Haven

first: William

last: Khoury-Hanold

state: CT

address: The Anlyan Center, 300 Cedar St.

department: Immunobiology

institute: Yale University

data_processing:
Raw sequence reads were trimmed of sequencing adaptors and low quality regions by Btrim (Kong, Y. (2011). Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics 98, 152-153.)
The trimmed reads were mapped to mouse genome (GRCm38) by TopHat2 (Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., and Salzberg, S.L. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome biology 14, R36.) The counts of reads for each gene were based on Ensembl annotation (release 70).
For HSV-1 genes, the trimmed reads were mapped to Human herpesvirus 1 genome (NC_001806.1) by bowtie2 (Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods 9, 357-359.) The R package DESeq2 was used for read counts normalization. Reads mapped to the HSV-1 genome were normalized based on the size factors calculated by DESeq2 for mouse genes.
Genome_build: GRCm38, NC_001806.1
Supplementary_files_format_and_content: Excel spreadsheet showing normalized read counts for each sample. The first tab contains mapped Mus musculus genes; the second tab contains mapped HSV-1 genes

organism: Mus musculus

source_name: large intestinal musculara_HSV1

extract_protocol:
Six days following infection, mice were euthanized and the lumbosacral DRG and LIM were dissected and frozen on dry ice. Total RNA from the LIM was isolated using Trizol® (Ambion) and further purified using the RNeasy RNA isolation kit (Qiagen) both according to the manufacturer’s instructions. Total RNA from the lumbosacral DRG was isolated using the RNeasy RNA isolation kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 5-6 week old female mice were treated with Depo-Provera (GE Healthcare). Five to seven days later, the vaginal lumen was cleared of mucous with a Calginate swab (Fischer Scientific) and 10 μL of 10^6 PFU HSV-1 were delivered intravaginally.

value: large intestinal musculara

tag: gender

value: female

tag: viral infection status

tag: days post infection


title: Kn99alpha WT Saturated Experiment 2 RNA-Seq replicate 2

tag: strain

tag: media


title: LIM_HSV1_rep2

tag: tissue


title: Kn99alpha WT Saturated Experiment 2 RNA-Seq replicate 3

tag: cell density


title: DRG_HSV1_rep2

source_name: dorsal root ganglia_HSV1

value: dorsal root ganglia


title: LIM_mock_rep2

source_name: large intestinal musculara_mock

value: mock


title: DRG_mock_rep1

source_name: dorsal root ganglia_mock


title: LIM_mock_rep1


title: DRG_HSV1_rep1


title: qsp1∆liv3∆ Saturated Experiment 2 RNA-Seq replicate 2

value: Kn99alpha(wild-type) with qsp1(del) liv3(del)

value: YPAD


title: lacZ_10min

status: Public on Jun 07 2016

city: Cambridge

first: Xiaowei

last: Zhuang

state: MA

address: 12 Oxford St

department: Chemistry and Chemical Biology

institute: Harvard University

description: sigPep.csv

data_processing:
Sequencing reads were aligned to the mg1655 genome (NC_000913.2) or a list of the designed signal peptide fusions using bowtie 0.12.9
csv files contain 16 columns of the data, each pair corresponds to the counts from the top (odd numbers) and bottom (even numbers) strand. The first pair corresponds to counts collected at 0 minutes after rifampicin addition. Similarly, the second, third, fourth, fifth, sixth, seventh, and eigth pairs correspond to counts collected at 2, 4, 6, 8, 10, 15, and 20 minutes after rifampicin addition. The ith row in each column corresponds to the number of alignments at the ith base in NC_000913.2.
The sigPep.csv file contains the counts for each specific signal peptide fusion to each specific test gene. Entries with SP_spkA/D/G/K represent spike in control molecules used for normalization.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: sam containing aligned sequences

organism: Escherichia coli

growth_protocol: Cells were grown to an OD_600 of 0.4 in Luria Broth Lennox

extract_protocol:
Cells were collected as a function of time after rifampicin treatment at the specified times. RNA was extracted using the RNAsnap protocol.
DNA was removed with Dnase I. rRNA was removed with the gram-negative RiboZero kit. Libraries were prepared with the RNAUltra directional kit from New England Biolabs for total RNA sequencing. For signal peptide fusions, cDNA was constructed using primers that target the signal-peptide-coding/barcode region of the fusion RNAs.

treatment_protocol: Cells were treated with rifampicin before sample collection. In some cases, kasugamycin was added 15 minutes before the rifampicin addition.

tag: genotype/variaion

value: lacZ

tag: time point

value: 10 min

tag: treatment

value: rifampicin


title: WTRep1_4min

value: WT

value: 4 min


title: WTRep1_15min

value: 15 min


title: WTRep1_2min

value: 2 min


title: WTRep1_8min

value: 8 min


title: WTRep1_6min

value: 6 min


title: lacZ_6min

description: sigPep.csv


title: lacZ_8min

description: sigPep.csv


title: WTRep1_0min

value: 0 min


title: lacZ_2min

description: sigPep.csv


title: lacZ_4min

description: sigPep.csv


title: lacZ_1min

description: sigPep.csv

value: 1 min


title: lacZ_0min

description: sigPep.csv


title: phoA_15min

description: sigPep.csv

value: phoA


title: phoA_6min

description: sigPep.csv


title: phoA_2min

description: sigPep.csv


title: DRG_mock_rep2

data_processing:
Raw sequence reads were trimmed of sequencing adaptors and low quality regions by Btrim (Kong, Y. (2011). Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies. Genomics 98, 152-153.)
The trimmed reads were mapped to mouse genome (GRCm38) by TopHat2 (Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., and Salzberg, S.L. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome biology 14, R36.) The counts of reads for each gene were based on Ensembl annotation (release 70).
For HSV-1 genes, the trimmed reads were mapped to Human herpesvirus 1 genome (NC_001806.1) by bowtie2 (Langmead, B., and Salzberg, S.L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods 9, 357-359.) The R package DESeq2 was used for read counts normalization. Reads mapped to the HSV-1 genome were normalized based on the size factors calculated by DESeq2 for mouse genes.calculated by DESeq2 for mouse genes.
Genome_build: GRCm38, NC_001806.1
Supplementary_files_format_and_content: Excel spreadsheet showing normalized read counts for each sample. The first tab contains mapped Mus musculus genes; the second tab contains mapped HSV-1 genes

value: female


title: phoA_4min

description: sigPep.csv


title: WTRep1_20min

value: 20 min


title: phoA_1min

description: sigPep.csv


title: lacZ_15min

description: sigPep.csv


title: phoA_0min

description: sigPep.csv


title: PD009

city: New York

first: Peter

last: Sims

state: NEW YORK

address: 3960 Broadway blvd

institute: Columbia Medical Center

description:
Poly(A) RNA library
Sample 8

data_processing:
Basecalls were performed on-instrument
Samples were demultiplexed and the first 5 and laster 20 bases were removed with fastx_trimmer
Repeating stretches of AAAAAAA were removed with fastx_clipper
Bowtie 2 was used to map rRNA; these were filtered out.
Tophat 2 was used to map the reads to the mouse transcriptome
HTSeq in interstrict mode was used to compute read counts for reads that mapped uniquely to the  mouse transcriptome in the 5’-leader (5’-UTR) and in the CDS.
For RNA-Seq: we received fastq files containing demultiplexed, single-end 100 base reads for each sample from the Columbia Sulzberger Genome Center.
iGenomes mm10
Genome_build: mm10

source_name: Adult mouse CAMKIIa-Ribotag mouse Brain treated with AZD-8055

extract_protocol:
TruSeq V2 RNA-Seq preparation.
All tissues were homogenized using a glass dounce homogenizer. Lysates were clarified and one half used for poly(A)+ RNA extraction and the other to generate and isolate ribosome-protected RNA fragments.
For RNA-Seq libraries: Standard RNA-Seq library preparation. For ribosome profiling libraries: Ribosome footpring libraries were prepared by ligation-free methods utilizing template switching. Poly-A tailing and PCR.
RNA-Seq and Ligation-free Ribosome profiling

treatment_protocol: A single dose of AZD-8055 was administered by oral gavage (100mg/kg); animals were sacrificed 1 hour later.

value: AZD-8055 Treated

tag: origin

value: Total RNA

tag: tissue origin

value: Mouse BrainD


title: PD008

description:
Poly(A) RNA library
Sample 7

value: Mouse BrainC


title: mMaple3_15min

description: sigPep.csv


title: INPUT for RTA ChIP

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

description: DNA extracted from the sonicated chromatin

library_source: genomic

data_processing:
TRExBCBL1-Rta  cells were grown in RPMI medium with 10% FBS.
Cells were induced for lytic reactivation by Doxycycline for 24h.
Sequence were imported into CLC Henomic Workbech 7.0 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the human genome (Cellular) and KSHV genome (Viral) using CLC Workbench
Peaks were determined by taking the sequncing data of input as reference using ChIP-peak calling feature of the CLC workbench software
Genome_build: NCBI genome build of human genome, Homo sapiens (hg19) sequence, and KSHV genome sequence accession# NC_009333
Supplementary_files_format_and_content: Processed data is in CSV file format

molecule: genomic DNA

organism: Homo sapiens

source_name: TRExBCBL1-RTA cells

extract_protocol:
lytic cells were cross-linked using formaldehyde to fix the protein-DNA for ChIP assay
The libraries were constructed using Bioo scientific ChIP sequencing kit

tag: cell type

value: KSHV infected Body Cavity Based Lymphoma Cells

tag: protocol

value: RTA protein is under tet-inducible promoter

tag: fraction

value: Input DNA


title: PD007

description:
Poly(A) RNA library
Sample 6

source_name: Adult mouse CAMKIIa-Ribotag mouse Brain

value: Untreated

value: Mouse BrainB


title: phoA_10min

description: sigPep.csv

value: 10 min

value: rifampicin


title: phoA_8min

description: sigPep.csv

value: 8 min


title: mMaple3_10min

description: sigPep.csv


title: INPUT for K8 ChIP

growth_protocol: TRExBCBL1-Rta  cells were grown in RPMI medium with 10% FBS.

treatment_protocol: Cells were induced for lytic reactivation by Doxycycline for 24h.


title: mMaple3_8min

description: sigPep.csv


title: RTA-ChIP

description: ChIP DNA

tag: antibody

value: RTA

value: ChIP DNA


title: input

city: Amsterdam

first: Marjolein

last: Droog

state: Noord-Holland

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: the Netherlands Cancer Institute

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 50bp reads) and processed with the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.5.9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-7 for ChIP-seq data. DFilter was run with bs=100, ks=50 for FAIRE data and bs=50, ks=30, refine, nonzero for ChIP data.
Genome_build: hg19
Supplementary_files_format_and_content: peaks

source_name: Tamoxifen-associated endometrial tumor

extract_protocol:
Fresh Frozen tumor was crosslinked with 1% formaldehyde for 20 minutes, quenched with 2 M Glycin for 5 minutes, and washed twice with PBS. Nuclei were isolated and sonicated. ChIP was performed with ERa (sc-543; Santa Cruz), FOXA1/2 (SC-6554; Santa Cruz), RNA Pol II (ab5408; abcam) and H3K27ac (39133; Active Motif), which were coupled to Dynabeads prot A, prot G, prot G and prot A, respectively. Samples were washed with RIPA buffer and reverse crosslinked at 65 C O/N. Samples were treated with RNAse A and prot K and DNA was isolated by alcohol precipitation.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: primary tumor tissue was cryosectioned, 30x 30um sections were used

value: endometrioid adenocarcinoma

tag: chip antibody

value: input


title: WTRep1_10min

value: WT


title: K8-ChIP

description: ChIP DNA


title: PD006

description:
Poly(A) RNA library
Sample 5

value: Mouse BrainA


title: biological replicate Tumor B FOXA1

description: Chromatin IP against FOXA1

value: FOXA1/2 (SC-6554; Santa cruz)


title: biological replicate Tumor B RNA Pol II

description: Chromatin IP against RNA Pol II

value: RNA Pol II (ab5408; Abcam)


title: PD004

description:
Poly(A) RNA library
Sample 4

source_name: HA-Immunoprecipitated Adult mouse CAMKIIa-Ribotag mouse Brain

value: CAMKII_RiboTag Immunoprecipitated

value: Mouse BrainF


title: biological replicate Tumor B H3K27ac

description: Chromatin IP against H3K27ac

value: H3K27ac (39133; Active motif)


title: mMaple3_6min

description: sigPep.csv

value: 6 min


title: mMaple3_4min

description: sigPep.csv

value: 4 min


title: Tumor E H3K27ac

description: Chromatin IP against H3K27ac


title: Tumor E RNA Pol II

description: Chromatin IP against RNA Pol II


title: PD002

description:
Poly(A) RNA library
Sample 2

value: Untreated

value: Mouse BrainE


title: Tumor E FOXA1

description: Chromatin IP against FOXA1


title: PD003

description:
Poly(A) RNA library
Sample 3

value: Total RNA


title: Tumor E ERa

description: Chromatin IP against ERa

value: ERa (SC-543; Santa Cruz)


title: PD001

description:
Poly(A) RNA library
Sample 1


title: mMaple3_1min

description: sigPep.csv

value: 1 min

value: rifampicin


title: Tumor D RNA Pol II

description: Chromatin IP against RNA Pol II

value: endometrioid adenocarcinoma


title: Tumor D ERa

description: Chromatin IP against ERa


title: Tumor C RNA Pol II

description: Chromatin IP against RNA Pol II


title: Tumor C H3K27ac

description: Chromatin IP against H3K27ac


title: mMaple3_0min

description: sigPep.csv

value: 0 min


title: bla_15min

description: sigPep.csv

value: bla

value: 15 min


title: biological replicate Tumor B ERa

description: Chromatin IP against ERa


title: Tumor B H3K27ac

description: Chromatin IP against H3K27ac


title: mMaple3_2min

description: sigPep.csv

value: 2 min


title: Tumor B RNA Pol II

description: Chromatin IP against RNA Pol II

value: RNA Pol II (ab5408; Abcam)


title: Tumor C ERa

description: Chromatin IP against ERa


title: bla_8min

description: sigPep.csv

value: 8 min


title: bla_10min

description: sigPep.csv

value: 10 min


title: Tumor B FOXA1

description: Chromatin IP against FOXA1

value: FOXA1/2 (SC-6554; Santa cruz)


title: bla_6min

description: sigPep.csv

value: 6 min


title: hnRNPL KO embryo 52584-3

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

data_processing:
RNA-Seq reads were aligned to mm10 using Tophat v2.0.10
Reads were processed with Samtools.
For differential expression, countfiles were generated by mapping reads to Ensembl genes using HTSeq. Further analysis was carried out using the DESeq R package
For alternative splicing, countfiles were generated by mapping reads to Ensembl exons using Dexseq (dexseq_count.py). Further analysis carried out using the DEXSeq R package
Genome_build: mm10
Supplementary_files_format_and_content: txt files are tab-delimited text files containing counts on GRCm38 Ensembl genes or exons

source_name: Fetal Liver cells

extract_protocol:
Total RNA was extracted from day 14.5 embryos using the Ambion MagMAX Total RNA Isolation kit.
RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS.

tag: age

value: embryonic day 14.5

tag: genotype

value: hnRNPL Knock-Out

value: whole embryo


title: hnRNPL KO embryo 52585-9


title: Tumor A H3K27ac

description: Chromatin IP against H3K27ac

value: H3K27ac (39133; Active motif)


title: Tumor C FOXA1

description: Chromatin IP against FOXA1


title: hnRNPL wild-type embryo 52584-4

value: hnRNPL wild-type


title: hnRNPL wild-type embryo 53795-3


title: Tumor A FOXA1

description: Chromatin IP against FOXA1


title: Tumor A ERa

description: Chromatin IP against ERa

value: ERa (SC-543; Santa Cruz)


title: Tumor A RNA Pol II

description: Chromatin IP against RNA Pol II


title: bla_4min

description: sigPep.csv

value: 4 min

value: rifampicin


title: hnRNPL wild-type embryo 52586-1


title: C49537_D150

city: Leon

first: Juan-Jose

last: Arranz

state: Leon

address: Campus de Vegazana

department: Produccion animal

country: Spain

institute: Universidad de Leon

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to assess the quality of raw sequencing data. Reads were mapped against the ovine genome assembly v.3.1. (Oar_v3.1) using STAR aligner (v.2.3.1y)
The Cufflinks (Cufflinks v.2.1.1) option “–g” followed by the available gtf file from the Oar_v3.1 reference sequence was used to guide the assembly but not excluding new genes. Cuffmerge was used to filter genes with low or no expression from our reference gtf file.
SigCufflinks (available at http://www.sigenae.org) was used to obtain raw counts per gene
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: csv file with raw counts per gene and sample

organism: Ovis aries

source_name: Milk somatic cells

extract_protocol:
MSCs were pelleted using PBS and EDTA. RNA was harvested using Trizol (Invitrogen, Carlsbad, CA, USA). Paired-end libraries were obtained using the True-Seq RNA-Seq sample preparation Kit v2 (Illumina, San Diego, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: day of lactation

value: Day 150

tag: breed

value: Churra

value: MSC


title: CLC16

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: CCGTCC

data_processing:
The reads were mapped to the human reference genome (hg19) using Tophat
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks using default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cell line

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: HCC

tag: rna source

value: cell line


title: hnRNPL KO embryo 52585-1

tag: strain

tag: tissue


title: CLC16PDC

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: CTTGTA

source_name: PDC

value: PDC


title: C09539_D150


title: bla_1min

description: sigPep.csv

tag: genotype/variaion

value: bla

value: 1 min


title: CLC13

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: TTAGGC


title: CLC16T

description: library barcode: TGACCA

source_name: primary HCC tissue

value: primary HCC tissue


title: Tumor B ERa

description: Chromatin IP against ERa

value: endometrioid adenocarcinoma


title: CLC13PDC

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: ATGTCA


title: C04860_D150


title: A74063_D150

value: Assaf


title: A03927_D150


title: bla_0min

description: sigPep.csv

tag: time point

value: 0 min


title: neo_10min

description: sigPep.csv

value: neo

value: 10 min

tag: treatment


title: C03141_D150


title: CLC11T

description: library barcode: ACAGTG


title: CLC6


title: A03105_D150


title: CLC6PDC

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: GATCAG


title: CLC7

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: AGTCAA


title: neo_6min

description: sigPep.csv

value: 6 min


title: CLC11

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: TAGCTT


title: CLC7PDC

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: CAGATC


title: neo_8min

description: sigPep.csv

value: 8 min


title: CLC13T

description: library barcode: AGTTCC


title: bla_2min

description: sigPep.csv

value: 2 min

value: rifampicin


title: CLC5

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: GGCTAC


title: A03086_D150

value: Day 150


title: neo_15min

description: sigPep.csv

value: 15 min


title: neo_4min

description: sigPep.csv

value: 4 min


title: CLC4

value: HCC

value: cell line


title: C49537_D120

value: Day 120

value: Churra

value: MSC


title: CLC4PDC

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: GCCAAT

value: PDC


title: CLC4T

description: library barcode: TTAGGC

value: primary HCC tissue


title: CLC11PDC


title: neo_2min

description: sigPep.csv


title: neo_1min

description: sigPep.csv

value: 1 min


title: C09539_D120


title: C03141_D120


title: CLC2PDC

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: TGACCA


title: neo_0min

description: sigPep.csv

value: neo

value: 0 min


title: CLC2T

description: library barcode: CGATGT


title: CLC1


title: CLC1PDC

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: ACTTGA


title: A74063_D120

value: Assaf


title: MutRep2_20min

value: Mut

value: 20 min


title: CLC1T

description: library barcode: ATCACG


title: A03105_D120


title: CLC2


title: MutRep2_10min

value: 10 min

value: rifampicin


title: CLC5PDC

description:
Cells were grown in pirmary culture medium supplemented with FBS, growth factors and hormones. Change medium every three days and passage at a 1:5 ratio.
library barcode: ACAGTG


title: MutRep2_15min

value: 15 min


title: MutRep2_8min

value: 8 min


title: MDA-glu-RPF-rep2-readlane1

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

description:
ribosome footprinting
MDA-glu-2-RPF_isoforms.fpkm_tracking

data_processing:
FASTQ reads were quality trimmed and subjected to adapter removal (cutadapt). The trimmed sequences were then mapped against contaminating RNAs (i.e. rRNA and tRNA sequences) using Bowtie2. Unaligned reads were then combined across the technical replicates and were aligned to the human transcriptome using Tophat2.
Cufflinks and cuffdiff were used to normalize ribosome protected fragments (RPF) to total RNA (TT) prepared in parallel.
The difference between RPF to TT log fold-change for each sample was used as a measure of ribosome occupancy.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms

source_name: MDA-parental

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol:
RNA was extracted post treatment per manufacturer's instructions
Samples were prepared for sequencing per manufacturer's instructions

treatment_protocol: Cells were treated 0.1mg/ml cycloheximide

tag: cell line

value: MDA-parental

tag: rep

value: RPF


title: MDA-glu-TT-rep1-readlane2

description:
ribosome footprinting
MDA-glu-1-TT_isoforms.fpkm_tracking

value: TT


title: MDA-glu-TT-rep2-readlane2

description:
ribosome footprinting
MDA-glu-2-TT_isoforms.fpkm_tracking


title: MDA-glu-RPF-rep2-readlane2


title: MDA-glu-TT-rep1-readlane1


title: C09539_D50

value: Day 50

value: Churra

tag: cell type


title: MDA-glu-RPF-rep1-readlane2

description:
ribosome footprinting
MDA-glu-1-RPF_isoforms.fpkm_tracking


title: MDA-glu-RPF-rep1-readlane1


title: MutRep2_6min

value: 6 min


title: C49537_D50

value: MSC


title: C04860_D50


title: MutRep2_4min

value: 4 min


title: MDA-ctrl-TT-rep2-readlane2

description:
ribosome footprinting
MDA-ctrl-2-TT_isoforms.fpkm_tracking


title: A03927_D120

value: Day 120


title: MutRep2_2min

value: 2 min


title: MDA-ctrl-TT-rep2-readlane1


title: C03141_D50


title: MDA-ctrl-RPF-rep2-readlane1

description:
ribosome footprinting
MDA-ctrl-2-RPF_isoforms.fpkm_tracking


title: MDA-ctrl-RPF-rep1-readlane2

description:
ribosome footprinting
MDA-ctrl-1-RPF_isoforms.fpkm_tracking


title: MutRep2_0min

value: 0 min


title: A03927_D50

value: Assaf


title: MDA-ctrl-TT-rep1-readlane1

description:
ribosome footprinting
MDA-ctrl-1-TT_isoforms.fpkm_tracking


title: MDA-ctrl-TT-rep1-readlane2


title: MDA-ctrl-RPF-rep1-readlane1


title: MutRep1_20min

value: Mut

value: 20 min


title: A74063_D50


title: A03105_D50


title: MutRep1_15min

value: rifampicin


title: MutRep1_10min

value: 10 min


title: 200_14

description:
RNA footprint library
Sample 11

extract_protocol:
Ligation-Free Ribosome Profiling
All tissues were homogenized using a glass dounce homogenizer. Lysates were clarified and one half used for poly(A)+ RNA extraction and the other to generate and isolate ribosome-protected RNA fragments.
For RNA-Seq libraries: Standard RNA-Seq library preparation. For ribosome profiling libraries: Ribosome footpring libraries were prepared by ligation-free methods utilizing template switching. Poly-A tailing and PCR.
RNA-Seq and Ligation-free Ribosome profiling

value: AZD-8055 Treated

tag: origin

value: Total RNA

tag: tissue origin

value: Mouse BrainC


title: 204_14

description:
RNA footprint library
Sample 12

value: Mouse BrainD


title: A03086_D50

value: Day 50


title: 198_14

description:
RNA footprint library
Sample 9

value: Untreated

value: Mouse BrainA


title: C09539_D10

value: Day 10

value: Churra

value: MSC


title: 199_14

description:
RNA footprint library
Sample 10

value: Mouse BrainB


title: MutRep1_8min

value: 8 min


title: MDA-glu-TT-rep2-readlane3

value: MDA-parental

tag: fraction

value: TT


title: MDA-glu-TT-rep2-readlane1


title: MDA-glu-RPF-rep2-readlane3

value: RPF


title: MDA-glu-TT-rep1-readlane3


title: MutRep1_6min

value: Mut

value: 6 min

value: rifampicin


title: MDA-ctrl-RPF-rep2-readlane2


title: C49537_D10


title: C04860_D10


title: MDA-ctrl-TT-rep2-readlane3


title: MDA-glu-RPF-rep1-readlane3


title: MutRep1_4min

value: 4 min


title: MDA-ctrl-RPF-rep2-readlane3


title: MDA-ctrl-TT-rep1-readlane3


title: MDA-ctrl-RPF-rep1-readlane3


title: MutRep1_2min

value: 2 min


title: A74063_D10

value: Assaf


title: C03141_D10


title: MutRep1_0min

value: 0 min


title: A03927_D10


title: MDA-Arg-TT-rep1

description: ribosome footprinting

data_processing:
FASTQ reads were quality trimmed and subjected to adapter removal (cutadapt). The trimmed sequences were then mapped against contaminating RNAs (i.e. rRNA and tRNA sequences) using Bowtie2. Unaligned reads were then aligned to the human transcriptome using Tophat2.
Cufflinks and cuffdiff were used to normalize ribosome protected fragments (RPF) to total RNA (TT) prepared in parallel.
The difference between RPF to TT log fold-change for each sample was used as a measure of ribosome occupancy.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms

tag: overexpression

value: Arg


title: WTKasRep2_20min

value: WTKas

value: 20 min


title: A03105_D10

value: Day 10


title: MDA-Arg-RPF-rep2

description: ribosome footprinting


title: MDA-Arg-RPF-rep1

description: ribosome footprinting


title: MDA-ctrl-RPF-rep2

description: ribosome footprinting

value: control


title: MDA-ctrl-TT-rep1

description: ribosome footprinting


title: WTKasRep2_10min

value: 10 min


title: MDA-Arg-TT-rep2

description: ribosome footprinting


title: A03086_D10

value: MSC


title: MDA-LM2-TT-rep1

description: ribosome footprinting


title: MDA-LM2-TT-rep2

description: ribosome footprinting


title: MDA-ctrl-RPF-rep1

description: ribosome footprinting

value: MDA-parental


title: MDA-LM2-RPF-rep2

description: ribosome footprinting


title: Rab7 Control rep1

city: Munich

first: Moritz

middle: J

last: Rossner

address: Nussbaumstr. 7

department: Psychiatry

country: Germany

description: total RNA from MACS isolated cells

data_processing:
Raw reads were sorted based on barcodes and were subjected to quality analysis using FASTQC
The sequences were aligned to the genome of Mus musculus (GRCm38/Mm10) using the TMAP aligner with default parameters
The reads mapping to unique locations were quantified using RefSeq Gene Annotations(v73) into genes
Genome_build: Mus musculus (GRCm38/Mm10)
Supplementary_files_format_and_content: tab-delimited text files include normalised read counts for each Sample and Gene Symbol

source_name: Microglia

growth_protocol: Mice were housed under standard conditions

extract_protocol:
Mouse brains were triturated according to manufacturer protocols and microglial cells MACS purified (Mylteni), eluted cells were flash frozen, total RNA was extracted and frozen at -80 until usage
Total RNA was subjected to amplification using Ovation RNA-Seq System V2 (NuGEN). 1 μg of cDNA was used as input for Ion Xpress™ Plus Fragment Library Kit (ThermoFisher Scientific) to generate barcoded libraries.
RNA Seq Library Preparation using Ion Xpress Plus Fragment System using IonXpress Barcodes

treatment_protocol: Mice were untreated

value: brain

tag: age

value: 3 months


title: MDA-LM2-RPF-rep1

description: ribosome footprinting

value: RPF


title: WTKasRep2_8min

value: 8 min


title: Rab7 Control rep2

description: total RNA from MACS isolated cells


title: WTKasRep2_15min

value: 15 min

value: rifampicin


title: Rab7 deltaMG rep2

description: total RNA from MACS isolated cells


title: Rab7 deltaMG rep1

description: total RNA from MACS isolated cells


title: WTKasRep2_4min

value: 4 min


title: MDA-TT-rep1

description: ribosome footprinting

value: TT


title: MDA-RPF-rep2

description: ribosome footprinting


title: WTKasRep2_2min

value: 2 min


title: 10 weeks rep3

description: total RNA from MACS isolated cells

value: 10 weeks


title: WTKasRep2_0min

value: WTKas

value: 0 min


title: MDA-RPF-rep1

description: ribosome footprinting


title: MDA-ctrl-TT-rep2

description: ribosome footprinting


title: 10 weeks rep2

description: total RNA from MACS isolated cells


title: CN34-LM1a-TT-rep2

description: ribosome footprinting

data_processing:
Library strategy: Ribo-seq
FASTQ reads were quality trimmed and subjected to adapter removal (cutadapt). The trimmed sequences were then mapped against contaminating RNAs (i.e. rRNA and tRNA sequences) using Bowtie2. Unaligned reads were then aligned to the human transcriptome using Tophat2.
Cufflinks and cuffdiff were used to normalize ribosome protected fragments (RPF) to total RNA (TT) prepared in parallel.
The difference between RPF to TT log fold-change for each sample was used as a measure of ribosome occupancy.
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks tracking output file for transcript isoforms


title: WTKasRep1_20min

value: 20 min


title: 15 months rep3

description: total RNA from MACS isolated cells

value: 15 months


title: CN34-LM1a-TT-rep1

description: ribosome footprinting


title: WTKasRep2_6min

value: 6 min


title: WT mRNA sequencing

city: Neuherberg

first: Martin

last: Groth

address: Ingolstädter Landstr. 1

department: Institute of Functional Epigenetics

institute: Helmholtz Munich

data_processing:
RNA-seq: Reads were mapped to the TAIR10 genome with TopHat2 (Kim et al., 2013) using defaults settings, except that intron length was set to 40-5000. FPKM values and differential gene expression were analyzed with Cufflinks (Trapnell et al., 2010) using default settings, except that maximum intron length was set to 5000 and the –u option was used. The reference annotation for Cufflinks analysis was downloaded from TAIR and combined genes, including pseudogenes and transposable element genes, and TEs.
genome build: TAIR10
processed data files format and content: Cufflinks FPKM Tracking format for estimated expression values for genes.

organism: Arabidopsis thaliana

source_name: WT rosette leaves

extract_protocol:
Trizol
Unstranded libraries were generated from total RNA using Illumina's TruSeq RNA Sample Preparation Kit according to the manufacturer's high throughput protocol.

tag: ecotype

value: Col 0

tag: genotype

value: wildtype

value: rosette leaves

tag: developmental stage

value: 3 weeks after germination

tag: light cycle

value: 16 hours light, 8 hours dark


title: CN34-LM1a-RPF-rep2

description: ribosome footprinting

value: RPF


title: MDA-TT-rep2

description: ribosome footprinting

value: MDA-parental


title: mthfd1-1 b mRNA sequencing

source_name: mthfd1-1 rosette leaves


title: 15 months rep1

description: total RNA from MACS isolated cells

tag: strain

value: brain


title: WTKasRep1_8min

value: 8 min

value: rifampicin


title: WTKasRep1_6min


title: mthfd1-1 a mRNA sequencing

tag: tissue


title: CN34-TT-rep2

description: ribosome footprinting

value: TT


title: CN34-TT-rep1

description: ribosome footprinting


title: mthfd1-1  5-CH3-THF, rep. 2 bisulfite sequencing for analysis of global DNA methylation

data_processing:
Bisulfite-seq: Reads were aligned to the TAIR10 genome using BSMAP 2.87 (Xi and Li, 2009) allowing up to 2 mismatches and only retaining reads that mapped to one location. Methylation ratio are calculated by #C/(#C+#T) at CG sites.
genome build: TAIR10
processed data files format and content: : Output format: tab delimited txt file with the following columns:      1) chromosome      2) coordinate (1-based)      3) strand      4) sequence context (2nt upstream to 2nt downstream in Watson strand direction)      5) methylation ratio, calculated as #C_counts / #eff_CT_counts      6) number of effective total C+T counts on this locus (#eff_CT_counts)               CT_SNP=“no action”, #eff_CT_counts = #CT_counts              CT_SNP=“correct”, #eff_CT_counts = #CT_counts * (#rev_G_counts / #rev_GA_counts)      7) number of total C counts on this locus (#C_counts)      8) number of total C+T counts on this locuso (#CT_counts)      9) number of total G counts on this locus of reverse strand (#rev_G_counts)      10) number of total G+A counts on this locus of reverse strand (#rev_GA_counts)      11) lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion.      12) upper bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion.

source_name: mtfd1-1 seedlings

extract_protocol:
Qiagen DNeasy Plant Mini kit
Genomic DNA was fragmented with a Covaris S2 instrument, end repaired and ligated to Illumina TruSeq DNA LT adapters, bisulfite treated using Zymo EZ DNA Methylation-Lightning Kit, and amplified during 13 PCR cycles using MyTaq DNA polymerase (Bioline) and Illumina TruSeq PCR primers.

value: seedlings

value: 14 days after germination


title: 15 months rep2

description: total RNA from MACS isolated cells


title: mthfd1-1  5-CH3-THF, rep. 1 bisulfite sequencing for analysis of global DNA methylation

source_name: mthfd1-1 seedlings


title: WTKasRep1_2min

tag: genotype/variaion

value: WTKas

value: 2 min


title: WTKasRep1_4min

tag: time point

value: 4 min


title: CN34-RPF-rep2

description: ribosome footprinting


title: WT  5-CH3-THF, rep. 2 bisulfite sequencing for analysis of global DNA methylation

source_name: WT seedlings


title: WTKasRep1_15min

value: 15 min

tag: treatment


title: CN34-RPF-rep1

description: ribosome footprinting

tag: cell line


title: 10 weeks rep1

description: total RNA from MACS isolated cells

value: 10 weeks


title: WT  5-CH3-THF, rep. 1 bisulfite sequencing for analysis of global DNA methylation

value: Col 0

value: wildtype


title: mthfd1-1 SMZ bisulfite sequencing for analysis of global DNA methylation


title: WTRep2_20min

value: WT

value: 20 min


title: WTKasRep1_10min

value: 10 min


title: WTRep2_15min


title: WT SMZ bisulfite sequencing for analysis of global DNA methylation

value: 16 hours light, 8 hours dark


title: CN34-LM1a-RPF-rep1

description: ribosome footprinting

value: RPF

tag: rep


title: Midvein rep1

city: St Louis

first: Rebecca

last: Bart

state: MO

address: 975 N Warson Rd

institute: Donald Danforth Plant Science Center

data_processing:
Basecalling performed with Illumina's Real Time Analysis software version 1.18.64
RNASeq Reads were cleaned for adapter sequence and low quality reads using Trimmomatic v0.32 with parameters: PE -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
RNASeq Reads were mapped to the AM560-2 v6.1 cassava reference genome with Tophat v2.0.10 with default parameters using both the paired and unpaired reads in paired mode
Read mapping data for each replicate was used to create gene models using cufflinks v2.2.1 with parameters: --no-faux-reads -g Mesculenta_305_v6.1.gene_exons.gff3
Gene models from replicates were merged to create one common file using cuffmerge v2.2.1 with parameters: -g Mesculenta_305_v6.1.gene_exons.gff3
Fragments Per Kilobase of transcript per Millions of mapped reads (FPKM) values were calculated using cuffdiff v2.2.1 with parameters: -L Leaf,Mid_Vein,Petiole,Lateral_Bud,Stem,Storage_Root,Fibrous_Root,FEC,OES,SAM,RAM
Genome_build: Mesculenta_305_v6: AM560-2 v6.1 from Phytozome
Supplementary_files_format_and_content: Abundance measurement values were produced using cuffdiff v2.2.1. Tab deliimited files contain FPKM values, raw fragments, and scaled fragments per gene. These values come from the genes.read_group_tracking file produced by cuffdiff

organism: Manihot esculenta

source_name: Midvein

growth_protocol: Plants were grown in a greenhouse with 12 hr light; 12 hr dark photoperiod (250-500umol s-1m-2 irradiance)

extract_protocol:
tRNA from non meristem tissue type was extracted using Sigma spectrum Plant total RNA kit and for SAM and RAM tissues, Arcturus picopure RNA isolation kit was used
Libraries were prepared using NEBNext mRNA Library Master Mix Set for Illumina NEB#E6110L

treatment_protocol: Plant tissues sampled were 3 month old, FEC tissues sampled were 7 weeks old and OES were 4 weeks old. 6 meristems were dissected and pooled for the meristem tissues.

tag: cultivar

value: midvein


title: Petiole rep1

source_name: Petiole

value: petiole


title: mthfd1-1 Met, rep. 2 bisulfite sequencing for analysis of global DNA methylation


title: WTRep2_8min

value: 8 min

value: rifampicin


title: mthfd1-1 Met, rep. 1 bisulfite sequencing for analysis of global DNA methylation

value: seedlings

value: 14 days after germination


title: SAM rep3

source_name: SAM

value: sam


title: RAM rep3

source_name: RAM

value: ram


title: WTRep2_10min


title: Leaf rep1

source_name: Leaf

value: leaf


title: WT Met, rep. 2 bisulfite sequencing for analysis of global DNA methylation


title: WTRep2_4min

value: 4 min


title: WT Met., rep. 1 bisulfite sequencing for analysis of global DNA methylation

value: Col 0


title: WTKasRep1_0min

value: WTKas

value: 0 min


title: FEC rep3

source_name: FEC

value: fec


title: mthfd1-1 5-CHO-THF, rep. 2 bisulfite sequencing for analysis of global DNA methylation


title: Fibrous Root rep3

source_name: Fibrous Root


title: WTRep2_2min

value: WT

value: 2 min


title: mthfd1-1 5-CHO-THF, rep. 1 bisulfite sequencing for analysis of global DNA methylation

value: 16 hours light, 8 hours dark


title: Stem rep3

source_name: Stem

value: stem


title: 3T3-L1, CRTC2-ChIP, P6+Forskolin, Rep2

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Aligment to mm9 using STAR
Differential gene expression identified using DESeq
CRTC2 ChIP-seq binding sites identified using HOMER
Differential CRTC2 binding identified using EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

source_name: 3T3-L1 preadipocytes

growth_protocol: 3T3-L1 preadipocytes were maintained in DMEM supplemented with 10% calf serum with 2 mM L-glutamin and 100 U/ml Pen-Strep. MEFs were maintained in DMEM supplemented with 10% fetal bovine serum with  2 mM L-glutamin and 100 U/ml Pen-Strep.

extract_protocol:
Cells were harvested in Isol-RNA lysis reagent (5 PRIME) and purified according to the manufacturer's instructions.
Purified RNA was subjected to standard mRNA sample preparation for sequencing and sequenced on the Illumina platform according to the manufacturer’s instructions. ChIP-seq libraries of CRTC2 enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: Two days past confluence 3T3-L1 preadipocytes or MEFs were treated with P6 (500 nM) or vehicle (DMSO) for 15 minutes before stimulated with forskolin (10 uM) or vehicle (DMSO). RNA was harvested after 1 hour of stimulation. Chromatin was harvested in 3T3-L1 preadipocytes 15 minutes after forskolin stimulation.

tag: cell type

value: 3T3-L1 preadipocytes

tag: ChIP


title: WT 5-CHO-THF, rep. 2 bisulfite sequencing for analysis of global DNA methylation

value: wildtype


title: WT 5-CHO-THF, rep. 1 bisulfite sequencing for analysis of global DNA methylation


title: 3T3-L1, CRTC2-ChIP, Forskolin, Rep2

description: ChIP-seq libraries of CRTC2 enriched DNA were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014 Genome-Wide Profiling of Transcription Factor Binding and Epigenetic Marks in Adipocytes by ChIP-seq. Methods in Enzymology 2014, Vol. 537, pp. 261-279).

value: Forskolin


title: Lateral Bud rep3

source_name: Lateral Bud


title: Petiole rep3

value: petiole


title: mthfd1-1 mock, rep. 2 bisulfite sequencing for analysis of global DNA methylation

value: seedlings

value: 14 days after germination


title: 3T3-L1, CRTC2-ChIP, P6+Forskolin, Rep1


title: WTRep2_6min

value: 6 min

value: rifampicin


title: mthfd1-1 mock, rep. 1 bisulfite sequencing for analysis of global DNA methylation


title: 3T3-L1, P6+Forskolin, Rep2

description: Cells were harvested in Isol-RNA lysis reagent (5 PRIME) and purified according to the manufacturer's instructions.


title: OES rep3

source_name: OES

value: oes


title: 3T3-L1, CRTC2-ChIP, Forskolin, Rep1


title: RAM rep2

value: ram


title: SAM rep2

value: sam


title: mthfd1-1 whole genome bisulfite sequencing

value: Col 0

value: rosette leaves

value: 3 weeks after germination


title: Leaf rep3

value: leaf


title: WT mock, rep. 2 bisulfite sequencing for analysis of global DNA methylation

value: 16 hours light, 8 hours dark


title: 3T3-L1, Forskolin, Rep2


title: 3T3-L1, P6+Forskolin, Rep1


title: 3T3-L1, Vehicle, Rep2

value: Vehicle


title: FEC rep2

value: fec


title: 3T3-L1, Vehicle, Rep1

value: 3T3-L1 preadipocytes


title: Fibrous Root rep2


title: Storage Root rep2

source_name: Storage Root


title: WT mock, rep. 1 bisulfite sequencing for analysis of global DNA methylation

value: wildtype


title: 3T3-L1, Forskolin, Rep1

value: Forskolin


title: WTRep2_0min

value: WT

value: 0 min


title: Stem rep2

value: stem


title: p53-/-;mdm2-/- MEFs, Forskolin, Rep 1

source_name: Murine embryonic fibroblasts

tag: genotype/variation

value: Murine embryonic fibroblasts


title: Midvein rep3

value: midvein


title: Lateral Bud rep2


title: p53-/-;mdm2-/- MEFs, Vehicle, Rep 1


title: p53-/-;mdm2-/- MEFs, Forskolin, Rep 2


title: Petiole rep2

value: petiole


title: p53-/- MEFs, Forskolin, Rep 2


title: Midvein rep2


title: p53-/- MEFs, Forskolin, Rep 1


title: p53-/- MEFs, Vehicle, Rep 2


title: WT whole genome bisulfite sequencing

source_name: WT rosette leaves


title: Leaf rep2


title: OES rep2

value: oes


title: SAM rep1

value: sam


title: RAM rep1

value: ram


title: OES rep1


title: FEC rep1


title: p53-/-;mdm2-/- MEFs, Vehicle, Rep 2


title: Fibrous Root rep1


title: PDX_TX_DFBM507_rep2

status: Public on Jun 06 2016

city: Boston

first: Jean

last: Zhao

address: 450 Brookline Ave, SM936

department: Cancer Biology

institute: Dana Farber Cancer Institute

description: AmpliSeq™ Transcriptome sequencing of patient-derived HER2+ breast cancer brain metastatic xenograft

data_processing:
Data were analyzed by Torrent Suite and ampliSeqRNA analysis plugin (Thermo Fisher) to generate read counts
Bed file for target region is hg19_AmpliSeq_Transcriptome_21K_v1.bed, which was downloaded from https://ioncommunity.thermofisher.com
human genome hg19 fasta, index_version tmap-f3, was downloaded from https://ioncommunity.thermofisher.com
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited matrix table excel files, each includes raw counts of sequencing reads of 5 Samples for each repeat

source_name: HER2+ breast cancer brain metastases

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) and the RNeasy Mini Kit (Qiagen).
cDNA libraries were constructed using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher). Samples were barcoded using the Ion Xpress™ Barcode Adapter kits (Thermo Fisher)

tag: sample type

value: breast cancer brain metastases

value: patient-derived xenograft

tag: tumor type


title: PDX_TX_DFBM590_rep2


title: PDX_TX_DFBM507_rep1


title: PDX_TX_DFBM355_rep2


title: Stem rep1


title: PDX_TX_DFBM463_rep2


title: PDX_TX_DFBM355_rep1


title: PDX_TX_DFBM354_rep2


title: PDX_TX_DFBM463_rep1


title: LACZ rep3

first: Gabriela

last: Alexe

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

description:
clone id: TRCN0000072231
clone name: lacZ_1650s1c1
target sequence: CGCTAAATACTGGCAGGCGTT

data_processing:
Samples were sequenced using Illumina TruSeq strand specific library. The pool of six samples was sequenced on two lanes of an Illumina HiSeq, generating 101bp paired end reads.
Quality control tests for the unmapped reads were performed using the FASTQC software (Babraham Lab, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Read coverage per sample ranged between 44 Mbp to 48 Mbp.  Low quality sequenced reads were masked.
The sequenced reads were aligned to the whole hg19 genome (GENCODE v17 annotation) by using the RSEM v1.2.4 internal  Bowtie v1.0.0 mapper  for paired end alignment.
Transcript abundance (reads and FPKM scores) at the isoform and at the gene level was computed with the RSEM v1.2.5 software.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include the isoform level and the gene level for reads and  RPKM scores  for each sample

source_name: MOLM-14 cells transduced with lentivirus encoding shRNAs targeting LacZ

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini  kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MOLM-14 cells were transduced with lentivirus encoding shRNAs targeting MTHFD2 (shMTHFD2 hairpin TRCN0000036553, denoted M5) and control (LacZ, shControl TRCN0000072231)

tag: shRNAi

value: shControl


title: M5 rep3

description:
clone id: TRCN0000036553
clone name: NM_006636.2-772s1c1
target sequence: GCAGTTGAAGAAACATACAAT

source_name: MOLM-14 cell line transduced with lentivirus encoding shRNAs targeting MTHFD2


title: M5 rep1


title: PDX_TX_DFBM354_rep1


title: Storage Root rep1


title: LACZ rep2


title: LACZ rep1


title: p53-/- MEFs, Vehicle, Rep 1

value: Vehicle


title: PDX_TX_DFBM590_rep1


title: Lateral Bud rep1


title: ChIPSeq_WT_Vir_UTX_rep2

city: Seoul

first: Sumin

last: Oh

address: Cheongpa-ro 47-gil 100, Yongsan-gu

department: Department of Biological Science

country: South Korea

institute: Sookmyung Women's University

description: ChIP-seq

data_processing:
Basecalls performed using the CASAVA software
ChIP-seq reads were aligned to the mm9 genome assembly using the Bowtie2 program (Langmead et al., Nature method, 2012)
RNA-seq reads were aligned to the mm9 genome assembly using the STAR program (Dobin et al., Bioinformatics, 2012)
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.
Supplementary_files_format_and_content: RNA-Seq: bigWig files can be used to check RNA-seq peaks through the UCSC genome browser.

source_name: Mammary

growth_protocol: C57BL/6 mice were purchased from Charles River and used as WT controls. Kdm6af/f (Wang, 2012) and MMTV-cre transgenic mice (lineA) (Wagner,1997) were used to generate mice lacking KDM6A in mammary stem cells (KDM6A KO). All animals were handled and housed in accordance with the guidelines of the NIH and experiments were approved by the ACUC of NIDDK.

extract_protocol:
Frozen-stored mammary tissues from virgin or p13 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors). Antibodies against KDM6A (Sigma, HPA002111), NFIB (Santa Cruz, sc-5567), ERα (Santa Cruz, sc-543X), PR (Santa Cruz, sc-7208X) and H3K4me1 (Abcam, ab-8895) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

value: Mammary gland

tag: state

value: virgin

tag: genotype

value: wild type

tag: chip antibody

value: KDM6A (Sigma, HPA002111)


title: RNASeq_KO_Basal

data_processing:
Basecalls performed using the CASAVA software
ChIP-seq reads were aligned to the mm9 genome assembly using the Bowtie2 program (Langmead et al., Nature method, 2012)
RNA-seq reads were aligned to the mm9 genome assembly using the STAR program (Dobin et al., Bioinformatics, 2012)
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.
Supplementary_files_format_and_content: RNA-Seq: bedGraph files can be used to check RNA-seq peaks through the UCSC genome browser.

extract_protocol:
RNA-seq: Poly(A) RNA were purified twice with Trizol and RNeasy® Plus Mini Kit (Qiagen). cDNA was synthesized using SuperScript II (Invitrogen) and TruSeq RNA Sample Preparation Kit (Illumina). Mammary epithelial cells (MECs) were isolated from 12-week-old virgin mice using a standard protocol and non-epithelial cells were removed using the EasySepTM Mouse Mammary Stem Cell Enrichment Kit (STEMCELL TECHNOLOGY, #19757). MECs were stained with biotinylated anti-CD24-fluorescein isothiocyanate (FITC, BD Biosciences), anti-CD49f-R-phycoerythrin (R-PE, BD Biosciences) and 7-amino-actinomycin D (7AAD, BD Biosciences) and were sorted to basal (CD24+CD49fhi) and luminal (CD24hiCD49flo) cell populations after FACS analysis was performed as previously described (Yoo, 2014).
Libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: virgin epithelial cell

value: Kdm6af/f; MMTV-cre


title: RNASeq_KO_Luminal

tag: tissue


title: RNASeq_WT_Luminal


title: RNASeq_WT_Basal


title: ChIPSeq_WT_Vir_UTX

extract_protocol:
ChIP-Seq: Frozen-stored mammary tissues from virgin or p13 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors). Antibodies against KDM6A (Sigma, HPA002111), NFIB (Santa Cruz, sc-5567), ERα (Santa Cruz, sc-543X), PR (Santa Cruz, sc-7208X) and H3K4me1 (Abcam, ab-8895) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.


title: ChIPSeq_KO_Vir_UTX


title: ChIPSeq_WT_P13_ER

value: pregnancy day of 13

value: Erα (Santa Cruz, sc-543X)


title: M5 rep2


title: ChIPSeq_WT_P13_H3K4me1

value: H3K4me1 (Abcam, ab-8895)


title: ChIPSeq_WT_P13_PR

value: PR (Santa Cruz, sc-7208X)


title: ChIPSeq_WT_Vir_Input

value: no IP


title: GPS2C_Raw_ChIPseq

city: Huddinge

first: Eckardt

last: Treuter

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

data_processing:
Raw fastq files where aligned to the mm9 version of the mouse genome using bowtie2 (version 2.2.3) and default settings and saved as SAM files.
SAM files where then imported to Homer constructing tag directories and Homer was used for peak calling, annotation and to extract raw tag counts.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data are in tab delimited text format and contain the merged peaks, annotation and raw tag counts within 1 kb window of the respective peaks in the indicated samples

source_name: RAW264.7 cell line (macrophages)

growth_protocol: BMDMs were isolated from femurs and tibias, and cultured and differentiated for 7 days in DMEM medium supplemented with 10% heat-inactivated FBS, 1% P/S and 30% L929 conditioned media. RAW264.7 cells were cultured in DMEM medium supplemented with 10% heat-inactivated FBS and 1% P/S.

extract_protocol:
From the cell lysates, cell nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
The DNA samples were sent to EMBL Genomics Core Facilities (Heidelberg, Germany) for library preparation.

treatment_protocol: Cells were harvested in basal conditions. For histone marks, cells were crosslinked in 1% formaldehyde for 10 minutes. For GPS2 ChIP, cells were crosslinked with 2 mM DSG for 30 minutes and then 1% formaldehyde for 10 minutes. In all conditions the reaction was stopped adding glycine to a final concentration of 0.125M for 5 minutes.

tag: background strain

value: BALB/C

tag: month

tag: antibody

value: GPS2 C-terminal (home raised)


title: GPS2N_BMM_MKO_ChIPseq

source_name: Bone marrow derived macrophages

value: 12-16 weeks

value: GPS2 N-terminal (home raised)


title: input_BMM_WT_ChIPseq

value: WT

value: total input


title: input_Raw_ChIPseq


title: GPS2N_Raw_1_ChIPseq


title: H3K4me3_BMM_WT_2_ChIPseq

value: H3K4me3 (Abcam, ab8580)


title: GPS2N_Raw_2_ChIPseq


title: GPS2N_BMM_WT_ChIPseq


title: H3K4me3_BMM_MKO_2_ChIPseq


title: MP46_BAP1_null_rep_1_H3K27me3

city: Rotterdam

first: Eskeatnaf

last: Mulugeta

address: Wytemaweg 80

department: Cell Biology

institute: Erasmus University Medical Center Rotterdam (Erasmus MC)

data_processing:
Read Alignment to hg19 (Bowtie2)
Peak calling (HOMER & MACS2)
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

source_name: Patient derived Xenograft derived from Primary Tumor of Uveal Melanoma

extract_protocol:
ChIP was performed from 6 millions of cells originating from Patient Derived Tumour grafts; magnetic Dynabeads coupled to Protein A were used for the IP (Invitrogen). Sonication was performed to obtain fragment size of 150-300 bp.
Libraries were prepared accordingly to manufactures (TruSeq ChIP sample Prep Kit, Illumina). Sequencing was performed on a Illumina Hi-Seq 2500.

value: Tumor of Uveal Melanoma

tag: bap1 status


title: MP41_BAP1_positive_rep_2_H3K27me3

growth_protocol: ChIP was performed from 6 millions of cells originating from Patient Derived Tumour grafts

value: positive


title: MP46_BAP1_null_rep_2_H3K27me3


title: MP41_BAP1_positive_rep_1_H3K27me3


title: ChIPSeq_KO_Vir_UTX_rep2

description: ChIP-seq

value: Mammary gland

value: virgin

value: KDM6A (Sigma, HPA002111)


title: ChIPSeq_KO_P13_H3K27me3

value: Pregnancy day 13

value: Kdm6af/f; MMTV-cre

value: H3K27me3 (Millipore, 07-449)


title: H3K27ac_BMM_WT_2_ChIPseq

value: H3K27ac (Abcam, ab4729)


title: H3K27ac_BMM_MKO_2_ChIPseq


title: H3K4me3_BMM_MKO_1_ChIPseq


title: YAP/TAZ-WT-3_RNA-seq

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

data_processing:
tophat alignment (v2.0.13)
htseq counts (v0.6.1)
Genome_build: Mm10
Supplementary_files_format_and_content: htseq output file

source_name: sciatic nerve

extract_protocol:
Trizol and Rneasy
Illumina TruSeq RNA sample preparation kit

value: sciatic nerve


title: YAP/TAZ-WT-1_RNA-seq


title: YAP/TAZ-WT-2_RNA-seq


title: H3K4me3_BMM_WT_1_ChIPseq


title: YAP/TAZ-DBL-cKO-3_RNA-seq


title: A549_277_ip8_single-end

status: Public on Jun 05 2016

city: Tianjin

first: Zhenyi

last: Ma

address: 22 Qixiangtai Road

institute: Tianjin Medical University

description: Test sample

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2 v2.0.10 with parameters -a 8 -m 0 -i 50 -I 50000 -g 10 -p 24 --microexon-search --b2-N 1
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Differentially expressed genes were obtained by R package edgeR, v3.2.2, with pvalue less than 0.01 and fold change more than 2.
Genome_build: homo sapiens, UCSC, hg19
Supplementary_files_format_and_content: Sample expression file containing raw reads and normalized RPKM for each gene, by Microsoft Excel format

source_name: p8 knockdown

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Thermo RevertAid First Strand cDNA Synthesis Kit (Cat#K1622) was used with 1 ug of total mRNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard Thermo protocols

value: lung

tag: cell line

value: alveolar adenocarcinoma cells


title: YAP/TAZ-DBL-cKO-2_RNA-seq


title: H3K27ac_BMM_MKO_1_ChIPseq

value: 12-16 weeks


title: H3K27ac_BMM_WT_1_ChIPseq


title: Laublab_BglII_NA1000_Starvation_M2_90min_replicate2

city: Norwich

first: Tung

middle: Ba  Khanh

last: Le

state: Norfolk

address: Colney Lane

department: Department of Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

data_processing:
For Hi-C, Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Caulobacter CB15N (NA1000) independently by Bowtie version 0.12.7 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For RNA-seq, the same mapping procedure was used as for Hi-C but coverage was computed using BEDTools instead (Quinlan and Hall, 2010).
The two resulting SAM files were then merged together. Unaligned reads were discarded.
The Caulobacter CB15N (NA1000) genome was then divided into restriction fragments (700 BglII fragments and 2025 NcoI fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
The genome of Caulobacter CB15N was then divided into bins of either 20 kb (for BglII Hi-C) or 10 kb (for NcoI Hi-C due to higher cutting frequency of NcoI compared to BglII) and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID:    22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). Ten iterative normalization rounds were performed. Subsequent analysis and visualisation was done using Perl and R scripts.
Genome_build: NC_011916.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with _coverage_output.txt: tab-delimited text file of nucleotide-resolution coverage from RNA-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Caulobacter vibrioides CB15

source_name: Caulobacter crecentus CB15N

growth_protocol: Caulobacter crescentus were grown as described previously in Skerker et al., 2005 (PMID: 16176121). When appropriate, media were supplemented with antibiotics at the following concentrations (liquid/solid media) [ug/ml]): chloramphenicol (1/2), kanamycin (5/25), oxytetracycline (1/2), spectinomycin (25/100). Synchronizations were performed on mid-exponential phase cells using Percoll (GE Healthcare) and density gradient centrifugation as described previously in Jones et al., 2001 (PMID: 11283290). After synchronization, swarmer cells were fixed formadehyde for chromosome conformation capture and Hi-C analysis. For antibiotic treatments, swarmer cells were incubated with 50 ug/mL chloramphenicol (final concentration) for 30 minutes before fixing with formadehyde. For starvation experiment, swarmer cells were released into M2 salts for 90min before fixing with formadehyde.

extract_protocol:
Hi-C experiments were performed using either BglII or NcoI according to previous publications (Umbarger MA. 2012. Chromosome conformation capture assays in bacteria. PMID: 22776362 and Lieberman-Aiden, E. et al., 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. PMID: 19815776). RNA were extracted using Hot Trizol. Detailed protocols are listed in the Supplementary Materials
Standard library construction for Illumina Hiseq2000 sequencing platform

treatment_protocol:
Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into M2 salts for 90 min before fixation by 1% formadehyde.
None

tag: developmental stage

value: swarmer cells (0 min after synchronization, starved in M2 salts for 90min)

value: wild type

tag: restriction enzyme

value: BglII


title: Laublab_BglII_NA1000_van_PrsaA_rsaA_ter_1060bp

source_name: Caulobacter crecentus CB15

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE and fixed immediately by 1% formadehyde.

value: swarmer cells (0 min after synchronization)

value: rsaA knock-out PrsaA_rsaA at van locus ter at 1060bp from rsaA transcription start site


title: Laublab_BglII_NA1000_van_PrsaA_rsaA_ter_2060bp

value: rsaA knock-out PrsaA_rsaA at van locus ter at 2060bp from rsaA transcription start site


title: Laublab_NcoI_NA1000_pJS14ctrAD51Edel3omega_3hr_after_xylose_addition

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290), then xylose is added to 0.3% final concentration for 3hr before fixation by 1% formadehyde.

value: 3hr after xylose addition

value: NcoI


title: Laublab_BglII_NA1000_van_PrsaA_rsaA_full_length

value: rsaA knock-out PrsaA_rsaA at van locus


title: Laublab_BglII_NA1000_van_PrsaA_rsaA_ter_60bp

value: rsaA knock-out PrsaA_rsaA at van locus ter at 60bp from rsaA transcription start site


title: Laublab_BglII_NA1000_van_PrsaA_rsaA_ATGTAA_replicate2

treatment_protocol:
Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE and fixed immediately by 1% formadehyde.
None

value: rsaA knock-out PrsaA_rsaA at van locus ATG mutated to TAA


title: Laublab_RNAseq_NA1000_M2_90min

treatment_protocol: Mixed population of cells growing in PYE (OD 600=0.4) were collected and snap-frozen before RNA extraction by Hot-Trizol

value: mixed population, starved in M2 for 90min


title: Laublab_NcoI_NA1000_pJS14ctrAD51Edel3omega_2hr_after_xylose_addition

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290), then xylose is added to 0.3% final concentration for 2hr before fixation by 1% formadehyde.

value: 2hr after xylose addition


title: Laublab_BglII_NA1000_van_PrsaA_rsaA_full_length_replicate2


title: Laublab_RNAseq_NA1000_PYE

treatment_protocol: Mixed population of cells growing in PYE (OD 600=0.4) were collected, washed and incubated in M2 salts for 90 min before being snap-frozen for RNA extraction by Hot-Trizol

value: mixed population, exponential in PYE


title: Laublab_BglII_NA1000_van_PrsaA_rsaA_ter_560bp

value: rsaA knock-out PrsaA_rsaA at van locus ter at 560bp from rsaA transcription start site


title: Laublab_BglII_NA1000_van_PrsaA_rsaA_ATGTAA


title: Laublab_BglII_NA1000_van_PrsaA_antiterminator_rsaA_ATGTAA

value: rsaA knock-out PrsaA_rsaA at van locus ATG mutated to TAA with antiterminator


title: Laublab_BglII_NA1000_van_Promoterless_rsaA_rsaA

value: rsaA knock-out Promoterless_rsaA at van locus


title: Laublab_BglII_NA1000_ML2000_90min_after_IPTG_withdrawal

treatment_protocol: Cellls were washed off IPTG and allow to grow in fresh  PYE for 90 min before synchronization by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were then fixed by 1% formadehyde.

value: 90 min after IPTG withdrawal

value: Plac_dnaA hfa:Plac_lacI


title: Laublab_NcoI_NA1000_pJS14ctrAD51Edel3omega_0hr_after_xylose_addition

value: 0hr after xylose addition


title: Laublab_BglII_NA1000_ML2000_270min_after_IPTG_withdrawal

treatment_protocol: Cellls were washed off IPTG and allow to grow in fresh  PYE for 90 min before synchronization by density gradient method according to Jones et al., 2001 (PMID: 11283290). Isolated swarmer cells were allowed to grow and elongate for an addition of 180min before fixation by 1% formadehyde.

value: 270 min after IPTG withdrawal

value: BglII


title: Laublab_BglII_NA1000_ML2000_210min_after_IPTG_withdrawal

treatment_protocol: Cellls were washed off IPTG and allow to grow in fresh  PYE for 90 min before synchronization by density gradient method according to Jones et al., 2001 (PMID: 11283290). Isolated swarmer cells were allowed to grow and elongate for an addition of 120min before fixation by 1% formadehyde.

value: 210 min after IPTG withdrawal


title: A549_277_con_single-end

description: Control file

source_name: Control

value: lung

tag: cell type

value: alveolar adenocarcinoma cells


title: input DNA

value: Tumor of Uveal Melanoma


title: Laublab_BglII_NA1000_van_PrsaA_antiterminator_rsaA_ATGTAA_replicate2

value: swarmer cells (0 min after synchronization)


title: YAP/TAZ-DBL-cKO-1_RNA-seq

value: sciatic nerve


title: Laublab_BglII_NA1000_ML2000_150min_after_IPTG_withdrawal

treatment_protocol: Cellls were washed off IPTG and allow to grow in fresh  PYE for 90 min before synchronization by density gradient method according to Jones et al., 2001 (PMID: 11283290). Isolated swarmer cells were allowed to grow and elongate for an addition of 90min before fixation by 1% formadehyde.

value: 150 min after IPTG withdrawal


title: Laublab_BglII_NA1000_Chloramphenicol50_30min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into PYE + 50 µg/ml chloramphenicol for 30min, then fixed immediately by 1% formadehyde.

value: swarmer cells (0 min after synchronization, treated with chloramphenicol 50 ug/ml for 30min))

value: wild type


title: Laublab_BglII_NA1000_Starvation_M2_90min

treatment_protocol: Swarmer cells were isolated by density gradient method according to Jones et al., 2001 (PMID: 11283290). Swarmer cells were released into M2 salts for 90 min before fixation by 1% formadehyde.

value: swarmer cells (0 min after synchronization, starved in M2 salts for 90min)


title: G1-SQS_2

city: Philadelphia

first: Henry

last: Daniell

state: Pennsylvania

address: 240 South 40th street

department: Biochemistry

institute: University of Pennsylvania

description:
GS_2
normalized_counts_annotated.txt
Tobacco_GS_v_WT_DESeq_refGene.all.annotated.txt

data_processing:
Adapter sequences were removed from sequencing reads were with Cutadapt, and mapped to the Tobacco genome with Tophat2 (Martin, 2011; Kim et al., 2013).
Cufflinks was used to predict transcripts, and HTSeq and DESeq2 were used to quantify expression of each transcript and perform differential expression analysis (Love et al., 2014; Anders et al., 2015)
We used transdecoder from the Trinity package to identify open reading frames within predicted transcripts, and annotated them with BLASTP to TAIR10 proteins (Gish and States, 1993; Haas et al., 2013).
Genome_build: Ntab-K326
Supplementary_files_format_and_content: Normalized read counts (variance stabilizing transformation) for each sample with TAIR10 BlastP annotations: normalized_counts_annotated.txt
Supplementary_files_format_and_content: DESeq2 Output: differential expression analysis of RNA-seq data with TAIR10 BlastP annotations
Supplementary_files_format_and_content: Tobacco_G1_v_WT_DESeq_refGene.all.annotated.txt
Supplementary_files_format_and_content: Tobacco_GS_v_WT_DESeq_refGene.all.annotated.txt
Supplementary_files_format_and_content: Tobacco_FS_v_WT_DESeq_refGene.all.annotated.txt

organism: Nicotiana tabacum

source_name: Leaf Tissue

growth_protocol: Tissue culture with 16 h light/8 h dark

extract_protocol:
Total RNA extracted from the third youngest leaf of each plant using miRNeasy kit (Qiagen)
Poly(A)+ RNA was isolated using oligo dT beads (Life Technologies, Frederick, MD). RNA was fragmented for 7 minutes using Fragmentation Reagent (Life Technologies, Waltham, MA). mRNA-seq libraries were then generated using the Illumina mRNA-seq kit (illumina, San Diego, CA).

treatment_protocol: MS medium with 2% sucrose

value: Leaf

tag: genotype/variation

value: G1 also expressing yeast squalene synthase from the chloroplast genome


title: FPS-SQS_2

description:
FS_2
normalized_counts_annotated.txt
Tobacco_FS_v_WT_DESeq_refGene.all.annotated.txt

value: 1068 expressing avian farnesyl diphosphate synthase and yeast squalene synthase from the chloroplast genome


title: G1-SQS_1

description:
GS_1
normalized_counts_annotated.txt
Tobacco_GS_v_WT_DESeq_refGene.all.annotated.txt


title: fetal bovine

city: Yangling

first: Yang

last: Zhou

address: No.22 Xinong Road

institute: Northwest A&F University

data_processing:
Illumina Casava software used for basecalling.
using clean-fastq_v1.pl to remove adapters and low quality tags as well as contaminants
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
The clean reads were aligned to the reference annotated genes (ftp://ftp.ncbi.nih.gov/genomes/Bos_taurus/Assembled_chromosomes) using the SOAPaligner program.
Genome_build: Btau_4.6.1
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample. Additional gene descriptions are available in file Bt.seq.uniq.txt.

organism: Bos taurus

source_name: fetal bovine

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

extract_protocol:
Five bovine embryos, five adult heifers, five adult bulls, and five adult steers of Qinchuan cattle were selected for this study. The subcutaneous adipose tissues were collected immediately after the cattle were slaughtered, snap-frozen in liquid nitrogen, and stored at -80˚C until use.
Five samples were then pooled, and the total RNA was isolated from each pooled sample using the Trizol reagent.

tag: breed

value: Chinese Qinchuan

tag: tissue type

value: subcutaneous adipose tissue

value: bovine embryos of 200~250 days


title: K Mock rep2

status: Public on Jun 04 2016

city: Winston-Salem

first: Adam

last: Davidson

state: NC

address: 1834 Wake Forest Road

department: Chemistry

institute: Wake Forest University

description: Total RNA (post IP)

data_processing:
Base calling was performed using native Ion Torrent PGM software
CLCbio Genomics Workbench 8.0 was used for alignment, filtering, and normalization of abundance to RPKM
tab-delimited text files were exported to Excel (reads >50, repeatable, non-rRNA)
.xlxs files imported to GraphPad Prism for representation
Genome_build: hg19, VSV (NC_001560.1)
Supplementary_files_format_and_content: .xlsx files and GraphPad files contain RPKM and raw read counts

source_name: Mock-inefcted HeLa

growth_protocol: HeLa grown to 70-80% confluence, infected for 6 hours with rWT VSV.

extract_protocol:
cells lysed with RIPA buffer, centrifuged to remove debris. Co-IP performed. Trizol extraction of aqueous, EtOH precipitation.
Ion Total RNA-Seq Kit v2

treatment_protocol: Co-Immunoprecipitation performed using antibodies for hnRNP A1, C1/C2, K or nonspecific IgG. Protein A Sepharose used to bind ab.

value: hnRNP K


title: WT_2

description:
WT_2
normalized_counts_annotated.txt

value: Introduction 1068


title: adult heifer

source_name: adult heifer

value: 18 to 24 month adult


title: adult bull

source_name: adult bull


title: WT_1

description:
WT_1
normalized_counts_annotated.txt


title: C1C2 Mock rep2

description: Total RNA (post IP)

value: hnRNP C1/C2


title: FPS-SQS_1

description:
FS_1
normalized_counts_annotated.txt
Tobacco_FS_v_WT_DESeq_refGene.all.annotated.txt


title: A549_277_con_paired-end

description: Control file

value: lung

value: alveolar adenocarcinoma cells


title: G1_1

description:
G1_1
normalized_counts_annotated.txt
Tobacco_G1_v_WT_DESeq_refGene.all.annotated.txt

value: Introduction 1068 expressing chloroplast-targeted avian farnesyl diphosphate synthase and yeast squalene synthase


title: G1_2

description:
G1_2
normalized_counts_annotated.txt
Tobacco_G1_v_WT_DESeq_refGene.all.annotated.txt


title: K Mock rep1

description: Total RNA (post IP)


title: A1 Mock rep2

description: Total RNA (post IP)

value: hnRNP A1


title: IgG Mock rep1

description: Total RNA (post IP)

value: IgG


title: C1C2 Mock rep1

description: Total RNA (post IP)


title: A1 Mock rep1

description: Total RNA (post IP)


title: siNS rep2

city: Frederick

first: Esta

last: Sterneck

state: MD

address: 1050 Boyles Street

institute: National Cancer Institute

data_processing:
Basecalling was done with RTA 1.12.4.2 and alignment to human reference genome hg19 with Illumina Casava 1.8.2
Aligned and sorted BAM files imported onto Partek Genome Studio v6.6 and taken through the RNA-Seq Workflow
Aligned reads quantified and annotated with RefSeq 2013 using modified Expectation-Maximization algorithm
Generated normalized RPKM values in a single matrix file for all 4 samples
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited single matrix text file for all 4 samples with RPKM values for genes

source_name: MCF7 cells_control_siRNA

growth_protocol: MCF-7 cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 µg/ml streptomycin and 1 mM sodium pyruvate.

extract_protocol:
Total RNAs from MCF7 cells were purified after 48h silencing with siRNAs against CEBPD or control by using RNAeasy kit (Qiagen).
Library preparation was done by following standard protocol: IlluminaTruSeq protocol FC-122-1001

treatment_protocol: Cells were seeded 24 h before transfection at 70% confluence. The next day, 2x10^6 cells were nucleofected with 400 μM of siRNAs per 100 μl Nucleofector V solution (Amaxa Biosystems/Lonza) according to the manufacturer's instructions.

tag: time

value: 48h after transfection

tag: sirna

value: control


title: siCEBPD rep1

source_name: MCF7 cells_siCEBPD

value: CEBPD


title: siCEBPD rep2


title: siNS rep1


title: adult steer

source_name: adult steer


title: JB1_Zfp57-/-  RNA-seq

city: Naples

first: Marco

last: Cammisa

state: Naples

address: Via Castellino Pietro, 111

country: Italy

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

data_processing:
Basecalls was performed using Illumina Pipeline Casava (v1.8.2).
Adaptor trimming was performed using Cutadapt .
Reads were aligned using TopHat (v2.0.8b).
Normalized abundance measurements was obtained using quantification pipeline on SeqMonk (v0.32.1) with default parameters.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: tab-delimited text file containing log2 of normalized abundance measurements.

growth_protocol: Embryonic stem cells were cultured under standard feeder-free conditions on gelatinized tissue culture dishes with media containing DMEM (EuroClone ECM0101L) supplemented with 100 µM 2-mercaptoethanol (Sigma), 1 mM sodium pyruvate, 2 mM L-glutamine, 1 x penicillin-streptomycin, 15% foetal calf serum (HyClone) and 103 U/ml  leukemia inhibitory factor (LIF, Millipore) at 37 °C under an atmosphere of 5% CO2.

extract_protocol:
RNA was extracted from cultured ESCs by lysing the cells on the culture dish with the addition of the TRI reagent (Sigma-Aldrich) and following the protocol of the manufacturer.
Libraries was generated from 200 ng of RNA by using the Illumina TruSeq Stranded mRNA Sample Prep Kit.

value: Embryonic stem cells


title: JB1 RNA-seq

value: wild type


title: A549_277_ip8_paired-end

description: Test sample


title: E14 RNA-seq


title: E14_Zfp57-/- RNA-seq


title: E14 H3K9me3 ChIP-seq

data_processing:
Basecalls and adaptor trimming was performed using Illumina Pipeline Casava (v1.8.2).
Reads were aligned to the NCBI37/mm9 genome assembly using Bowtie (v0.12.7) with uniquely mapping options.
Genomic reads coverage was obtained using SAMtools (v0.1.18) and BEDTools suite (v2.14.3-1).
Peak-calling was performed using MACS algorithm implemented in SeqMonk software (v0.24.1).
Genome_build: (NCBI37/mm9)
Supplementary_files_format_and_content: BedGraph file reports normalized RPM (reads per Million reads) scores of genomic coverage. Bed file contain genomic coordinates of called peaks.

growth_protocol: Embryonic stem cells were cultured under standard feeder-free conditions on gelatinized tissue culture dishes with media containing DMEM (EuroClone ECM0101L) supplemented with 100 µM 2-mercaptoethanol (Sigma), 1 x non-essential amino acids (only for A3), 1 mM sodium pyruvate, 2 mM L-glutamine, 1 x penicillin-streptomycin, 10% (15% for E14) foetal calf serum (HyClone) and 103 U/ml  leukemia inhibitory factor (LIF, Millipore) at 37 °C under an atmosphere of 5% CO2.

extract_protocol:
ChIP was performed on formaldehyde cross-linked chromatin isolated from cells grown on 10 cm dishes to ~80% confluency. Briefly, the cells were detached by adding 0.05% trypsin at 37 °C for 3 min. Formaldehyde was added to the cells resuspended in PBS at a final concentration of 1% and the cells were incubated at room temperature for 15 min with shaking. The reaction was stopped by addition of glycine to a final concentration of 0.125 M. Approximately 3x107 cells were washed twice in ice-cold PBS, centrifuged and resuspended in lysis buffer 1 (50 mM HEPES pH 8, 10 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40 and 0.25% Triton X-100) for 90 min at 4 °C. Isolated nuclei were lysed in lysis buffer 2 (10 mM Tris–HCl pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) for 60 minat 4 °C. The chromatin was sheared in sonication buffer (10 mM Tris–HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% N-lauroylsarcosine) to an average size of 100–400 bp using the S220 Focused-ultrasonicators (Covaris). For each IP, 100 μg of sonicated chromatin were diluted in a final volume of 600 μl with sonication buffer and pre-cleared with 30 µl protein A/G agarose beads (SantaCruz) for 4 h at 4 °C on a rotating wheel. Anti-ZFP57 antibody (8 μg, Abcam ab45341), anti-KAP1 antibody (7 μg, Abcam ab10483) and anti-Histone H3K9me3 (7 μg, Abcam 8898) or rabbit IgG were added to the pre-cleared chromatin and incubated overnight at 4 °C on a rotating wheel. Chromatin was precipitated with 30 μl protein A/G agarose beads for 4 h at 4 °C with rotation. The beads were then washed five times with 500 μl RIPA buffer (10 mM Tris–HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 1% Triton X-100and 0.1 % SDS) and once with each of the following buffers: WASH buffer (50 mM HEPES, 0.5% sodium deoxycholate, 1% Triton X-100, 1 mM EDTA, 500 mM NaCl and 0.2% NaN3), LiCl buffer (0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris pH 8) and TE buffer (10 mM Tris pH 8, 1 mM EDTA). The bound chromatin was eluted in 100 μl TE buffer. Crosslinks were reversed by incubation O/Nat 65°C after addition of 1 μl RNAse cocktail (Ambion) and 2h at 50°C after addition of 2.5μl SDS 20% + 2.5μl 20mg/ml proteinase K (Sigma). The DNA was extracted by using the QIAquick Gel Extraction Kit (Qiagen). Immunoprecipitated or 1% input DNAswere analysed by real-time PCR using SBYRGreen PCR Master Mix (Bio-Rad) on a C1000 Thermal Cycler (Bio-Rad).
Two nanograms of DNA from immunoprecipitated and input chromatin were used for Illumina library preparation. Libraries were generated by using the NuGen Ovation Ultralow Library System Kit.


title: IgG VSV rep1

description: Total RNA (post IP)

organism:
Homo sapiens
Vesicular stomatitis virus

source_name: VSV-infected HeLa

tag: genotype

value: rWT

tag: hpi

value: igG


title: E14 RRBS

data_processing:
Basecalls and adaptor trimming was performed using Illumina Pipeline Casava (v1.8.2).
Data was filtered for low quality reads Trim Galore (v0.2.8).
Reads were aligned to the NCBI37/mm9 genome assembly using Bismark (v0.7.9).
CpG methylation calls were extracted using the Bismark methylation extractor (v0.7.9).
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: Bedgraph file report methylation level of symmetric CpGs at least 5x covered.

extract_protocol: For library preparation 100-200 ng of genomic DNA was used with the NuGEN Ovation Ultralow Methyl-Seq Library System.

tag: strain


title: K VSV rep2

description: Total RNA (post IP)


title: E14_Zfp57-/- Line2 RRBS


title: C1C2 VSV rep1

description: Total RNA (post IP)


title: C1C2 VSV rep2

description: Total RNA (post IP)


title: K VSV rep1

description: Total RNA (post IP)


title: IgG VSV rep2

description: Total RNA (post IP)


title: A3_Zfp57-/- Input ChIP-seq

tag: chip antibody


title: E14_Zfp57-/- Line1 RRBS


title: A3 Input ChIP-seq


title: A3 H3K9me3 ChIP-seq


title: A3_Zfp57-/- KAP1 ChIP-seq

value: KAP1 (Abcam, ab10483)


title: A3_Zfp57-/- ZFP57 ChIP-seq

value: ZFP57 (Abcam, ab45341)


title: A3 ZFP57 ChIP-seq


title: E14 ZFP57 ChIP-seq


title: E14 Input ChIP-seq


title: E14 KAP1 ChIP-seq


title: A3 KAP1 ChIP-seq


title: A3_Zfp57-/- RRBS


title: A3 RRBS


title: A3 BS-seq


title: A3_Zfp57-/- H3K9me3 ChIP-seq


title: A1 VSV rep2

description: Total RNA (post IP)


title: A1 VSV rep1

description: Total RNA (post IP)