title: asc1-D109Y YPAD Ribo-Seq rep2

description:
asc1_D109Y_Fp2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz


title: Control 1

status: Public on Apr 23 2016

type: SRA

city: Nanchang

first: chenlong

last: liu

state: Jiangxi province

address: Lushanzhong street NO.888, Nanchang, China

department: Animal science and technology department

country: China

institute: Jiangxi Agricultural University

library_source: transcriptomic

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Bowtie2_build was used to build a  index file of Bos_taurus.UMD3.1.75.dna.chromosome.1-29 and X
SOAPaligner (V2.21) was used to align cleaned RNA-seq reads to reference genome to identify genes. The NOISeq method was applied to identify the differentially expressed genes and transcripts with parameters
Genome_build: Bos_taurus.UMD3.1.75.dna.chromosome 1-29 and X (unmasked reference genomic sequence) [ftp://ftp.ensembl.org/pub/release-75/fasta/bos_taurus/dna/]
Supplementary_files_format_and_content: [.rpkm] Abundances of all gene models

molecule: total RNA

organism: Bos taurus

source_name: Control

extract_protocol:
longissimus muscles were removed from  -80°C freezer , and total RNA isolated with TRIzol reagent. Illumina HiSeq 2000 was used for RNA-Seq.
RNA libraries were prepared for sequencing using standard Illumina protocols
single-end sequencing library

tag: age

value: 2 years

tag: agent

value: control

tag: tissue

value: longissimus muscle


title: TR

city: Nanjing

first: Liu

last: Yang

address: Weigang No.1

institute: Nanjing Agricultural University

data_processing:
Low-quality reads were filtered strictly. 3' adaptor sequences were trimmed and 5' adaptor contaminants were removed. Too small (<18 nt) and polyA sequences were removed.
For non-coding RNAs identification, clean reads were compared with rRNA, tRNA, snRNA, and snoRNA deposited in NCBI and Rfam database using the SOAP 2.0 program.
Then sequence tags were searched against the miRNA database, miRBase, in order to identify conserved miRNAs in cotton.
Genome_build: GenBank EST database of eggplant
Supplementary_files_format_and_content: The .fa files include small RNAs and their abundance for each sample.

organism: Solanum virginianum

source_name: the whole seedlings

growth_protocol: The eggplant seedlings were cultured in nutrient medium (quarter-strength MS solution) without sugar at 25 °C under a 16 h light: 8 h dark regime. The pathogen was respectively cultured on potato dextrose agar (PDA) plate 15 days at 25 °C to collect spores (a concentration of 5×107spores•ml-1) and in Czapeck’s liquid medium to obtain crude toxin (8 mg•ml-1) of Verticillium dahliae.

extract_protocol:
The seedlings were harvested after 12 h treatment, flash frozen on liquid nitrogen, and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seedlings were infected with a mixture of spores and crude toxin of Verticillium dahliae for 12 h. Control mock-inoculated seedlings were inoculated with water.

tag: developmental stage

value: eggplant seedlings with 3-4 main leaves

tag: treatment

value: Verticillium dahliae-inoculated


title: CK

value: water-inoculated


title: 7628

city: Seoul

first: Minseok

last: Seo

address: Kwan-ak ro 1

department: Interdisciplinary program of bioinformatics

country: South Korea

institute: Seoul National University

data_processing:
Combined left and right fastq files, respectively, in same individual
For removing adapters, we used trimmomatic with following option : PE -phred33  ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 MINLEN:75 2
Reads were mapped to the reference genome (BosTau7) using Bowtie2, included in Tophat2 with default option
The aligned result from the Tophat2 in BAM was converted to SAM format by SAMtools
After that, gene expression levels were estimated by HTseq package, implemented in python, with Bos taurus7 gene transfer format (.GTF) file
Genome_build: BosTau7
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each Sample

source_name: somatic cells in the milk

extract_protocol:
Milk samples were selected in Holstein cows and measured cell viability. Total RNA was extracted using TRIzol reagent (MRC).
Libraries were prepared using Ilumina manual and platform.

tag: strain

value: Holstein

value: Low

tag: parity


title: 3369


title: 3407


title: 7598


title: LPS 1 hr

status: Public on Apr 24 2016

city: Los Angeles

first: Alexander

last: Hoffmann

state: CA

address: 570 Boyer Hall

department: MIMG

country: USA

institute: UCLA

data_processing:
Sequencing was performed on Illumina's HiSeq 2000, according to the manufacturer’s recommendations by the University of California, San Diego Biogem facility.
Using cutadapt we removed adapters and using scythe did end trimming based on quality and  discard reads aligning to rRNA (based on sequence)
Reads were aligned to the mouse genome GRCm38  with the STAR RNA-seq aligner
filter out multimappers and reads with quality < 30 and removed rRNA based on coordinates
htseq-count (union mode) from the HTSeq Python package was used to determine raw gene read counts
Genome_build: mouse genome mm10 gencode vM4
Supplementary_files_format_and_content: .txt is text file with two columns first column contains ENSEMBEL gene IDs and read counts for corresponding gene are in second column

organism: Mus musculus

source_name: BMDM_LPS 1 hr

growth_protocol: Bone marrow derived macrophages (BMDMs) were isolated from wild type femurs. A total of 7 x 10^6 BM cells were cultured in 15 cm suspension dishes in L929-conditioned media for 7 days at 37°C with 5% CO2. BMDMs were then replated on day 7 at of 2 x 10^6 cells per 6 cm plate in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and all experiments were performed on day 8.

extract_protocol:
mRNA was extracted from 2 μg total RNA using oligo(dT) magnetic beads and fragmented at high temperature using divalent cations
cDNA library was generated using the Illumina TruSeq kits and quantitation was performed using the Roche Light Cycler 480

treatment_protocol: BMDMs were replated with 5 x 10^6 cells per 10 cm plate on day 7. On day 8, BMDMs were left unstimulated or stimulated with various stimuli.

tag: genotype

value: wild type

value: femur bone marrow

tag: cell type

value: macrophage


title: 3280

value: High


title: 3235


title: 3272


title: 3264


title: 3198


title: 3262


title: NA 1

value: Nicotinic acid


title: 3064


title: 3075


title: 3135


title: 3014


title: 3057


title: 7643


title: C_2_24hr

city: Gold Coast

first: Glen

middle: C

last: Ulett

state: QLD

address: Parklands Drive

department: School of Medical Science

country: Australia

institute: Griffith University

data_processing:
Illumina bcl2fastq version 1.8.4 software was used creating the fastq files from the bcl files.
TopHat version 2.0.11 was used to align the raw RNA-Seq fastq reads to the human reference genome version 19 from the UCSC genome browser gateway using the short read aligner Bowtie version 2.1.0. TopHat was also used to analyse the mapping results to identify splice junctions between exons. See (i). Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009; 25:1105-11 and (ii). Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009; 10:R25. and (iii). Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7:562-78
Cufflinks version 2.1.1 used the aligned reads from TopHat to assemble transcripts, estimate their abundances and test for differential expression and regulation. Cuffmerge, which is part of Cufflinks, merged the assembled transcripts to a reference annotation and tracked Cufflinks transcripts across multiple experiments. Finally, Cuffdiff was used to identify significant changes in transcript expression, splicing and promoter use. Genes that met certain criteria (i.e. fold change ≥ ±2.0 and q-value < 0.05) were further analyzed using the IPA tool. See (i) Trapnell C, Roberts A, Goff L, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7:562-78 and (ii). Trapnell C, Williams BA, Pertea G, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010; 28:511-5
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file from Cufflinks Cuffnorm that include FPKM values, normalized counts and gene symbol for each sample.

organism: Homo sapiens

source_name: RNA from OECs controls for 24h

growth_protocol: O/N LB culture of Bp at 37C was collected and concentrated into PBS by centrifugation and washes in PBS

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
Total RNA was subjected to two rounds of poly A+ selection and converted to cDNA. We used TruSeq library generation kits as per the manufacturer’s instructions (Illumina, San Diego, CA, USA). Library construction consisted of random fragmentation of the polyA mRNA, followed by cDNA production using random primers. The ends of the cDNA were repaired, A-tailed and adaptors ligated for indexing (up to twelve different barcodes per lane) during the sequencing runs. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation. Clusters were generated to yield approximately 725K-825K clusters/mm2. Cluster density and quality was determined during the run after the first base addition parameters were assessed. We ran paired end 2X50bp sequencing runs to align the cDNA sequences to the reference genome

value: Olfactory ensheathing cells (OECs)

tag: infected with

value: none (control) for 24h


title: 2920


title: C_3_24hr


title: FSL 3 hr

source_name: BMDM_FSL 3 hr


title: E5_C4_24h


title: E5_C1_24h


title: E5_C2_24h


title: E4_C2_24h


title: 2864


title: 2893


title: E5_BP08_2_24h

source_name: RNA from OECs infected with B. pseudomallei for 24h

value: B. pseudomallei for 24h


title: Bp08_2_24hr


title: 2814


title: Bp08_1_24hr


title: 3161


title: Z138 sc4 control

city: Madison

first: Xuehua

last: Zhong

state: WI

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

data_processing:
RNAseq reads were filtered for average QC score>30. Reads were mapped to hg19 genome.
RNAseq fpkm were generated by tophat and cufflink by following Trapnell et al.(2012).
Supplementary_files_format_and_content: RNA-seq (txt file: gene fpkm)

source_name: mantle cell lymphoma cell line

growth_protocol: Mantle cells were grown in RPMI1640 media plus 20%FBS,1%  penicillin, 1% streptomycin.

extract_protocol:
RNA was extracted by Rneasy plus mini kit (Qiagen) following the manufacturer’s instructions.
cDNA library was construbuted by using Illumina Truseq RNA Library Prep Kit (RS-122-2002)

value: Z138 stable cell transfected with control vectctor, and induced with Doxycyclin for 48H


title: Z138 shBTK

value: Z138 stable cell transfected with small hairpin targeting BTK, and induced with Doxycyclin for 48H


title: Mino shBTK

value: Mino stable cell transfected with small hairpin targeting BTK, and induced with Doxycyclin for 48H


title: E4_BP08_2_24h


title: E3_BP08_3_24h


title: E2_BP08_3_24h


title: Mino sc4 control

value: Mino stable cell transfected with control vectctor, and induced with Doxycyclin for 48H


title: DMPA 3, ZH8, or B32

city: Birmingham

first: Zdenek

last: Hel

state: Alabama

address: 1825 University Blvd SHEL 677

institute: University of Alabama at Birmingham

data_processing:
Illumina CASAVA version 1.8.2 demultiplexed and converted the bcl file to a compresed fastq file.
TopHat version 2.0.6 was used to align the fastq files to UCSC hg19 reference genome.
Cufflinks version 2.0.2 was used to estimate transcript abundances followed by Cuffcompare.
Finally, Cuffdiff found significant changes in transcript expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include test id,  gene id, gene name, locus, FPKM values, log2 fold change, p-value and q-value for each Sample.
Supplementary_files_format_and_content: gene_exp.diff: gene expression abundance measurements
Supplementary_files_format_and_content: isoform_exp.diff: isoform expression abundance measurements

source_name: Vaginal Epithelial Cells

extract_protocol:
Biopsies were collected on site, washed briefly with HBSS and immediately oriented in OCT compound (Sakura, Torrence, CA). Samples were frozen by immersion in pre-cooled isopentane in an acetone bath encased with dry ice. Laser capture microdissection was performed to isolate the vaginal epithelium for RNA analysis. Sections were cut at 8 um on PEN slides under RNAse free conditions. Slides were incubated for 30 seconds in EtOH, 30 sec in RNAse free dH20, and stained with cresyl violet for 45 sed. Slides were then dehydrated in progressively higher EtOH solutions and xylene. LCM was performed within 15 minutes of staining on an Arcturus Veritas 704 microdissection system with HS caps. Vaginal epithelial cells were precisely removed without an lamina propria cells. A Picopur RNA Isolation kit was used to isolate RNA from the tissue with an RNAse free DNAse Set used to remove contaminating DNA.
mRNA-sequencing was performed on the Illumina HiSeq2000, providing up to 300Gb of sequence information per flow cell. Total RNA was assessed using the Agilent 2100 Bioanalyzer followed by 2 rounds of poly A+ selection and conversion to cDNA. The cDNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation prior to cluster generation. Clusters were generated to yield approximately 725K-825K clusters/mm2. Paired end 2 x 50bp sequencing runs were performed to align the cDNA sequences to the reference genome.

value: LCM-dissected vaginal epithelium

tag: contraception

value: DMPA 3 months at least

tag: race

value: African American


title: C_2_2hr

source_name: RNA from OECs controls for 2h

value: none (control) for 2h


title: C_1_2hr


title: DMPA 1, ZH6, or B9

value: DMPA 2 years


title: DMPA 2, ZH7, or B25


title: Control 3, ZH4, or B79


title: Control 1, ZH2, or B34


title: Control 2, ZH3, or B75

value: Caucasian


title: DMPA 0, ZH5, or B4

value: DMPA 6 months-1 year


title: E5_C3_2h


title: Control 0, ZH1, or B12


title: E2_C2_2h


title: Bp08_2_2hr

source_name: RNA from OECs infected with B. pseudomallei for 2h

value: B. pseudomallei for 2h


title: E4_C4_2h


title: 72h

city: Wenjiang, Chengdu

first: Zheng

last: Aiping

state: Sichuan

address: Huimin Road 211 Hao

department: Rice Research Institute

institute: Sichuan Agricultural University

data_processing:
Illumina software for basecalling performed by BGI-Shenzhen.
Removed adaptor, low-quality sequenced reads and contaminated data that matched to rice genome sequence.
Removed rRNA,tRNA, snRNA and snoRNA reads by searching against Rfam database (version 10.1) using BLAST.
Identified candidate milRNAs using MIREAP and mirdeep2.
Aligned candidate milRNAs to R. solani AG1 IA genome using BLAST.
Genome_build: R. solani AG1 IA genome (NCBI accession: AFRT00000000.1)
Supplementary_files_format_and_content: There are two text files for milRNA sequences and statistics of reads in libraries supporting the milRNAs.

organism: Rhizoctonia solani

source_name: mycelium

growth_protocol: R. solani AG1 were germinated and mycelia cultured on potato dextrose agar.

extract_protocol:
The small RNA of these samples were extracted by using mirVana™ miRNA Isolation Kit (Ambion, USA), according to the manufacturer’s instructions.
The small RNA cDNA libraries were constructed using One Step PrimerScript miRNA cDNA Synthesis Kit (TransGen, Beijing, China), according to the manufacturer’s instructions

value: AG1 IA

tag: infection

value: 72 hours


title: 32h

value: 32 hours


title: E4_BP08_3_2h

value: Olfactory ensheathing cells (OECs)


title: 18h

value: 18 hours


title: 10h

value: 10 hours


title: Bp08_1_2hr


title: E3_C4_2h


title: E3_BP08_4_2h


title: IA

value: without infection


title: E2_BP08_2_2h


title: ChIP-Seq analysis of Input in Myc-ESCs Sample 16

status: Public on Apr 22 2016

city: Milan

first: Alessio

last: Zippo

address: Via Francesco Sforza, 35

country: Italy

institute: National Institute of Molecular Genetics

library_source: genomic

data_processing:
Sequenced reads were aligned to the mouse genome (GRCm38/mm10) by using Bowtie2 version 2.2.3 556 with default parameters; unique reads mapped to a best-matching location with no more than two mismatches were used in the subsequent analyses.
MACS version 1.4.2 657 were used to identify the regions of ChIP-seq enrichment over background, and all parameters were set to their defaults in the peak-calling analysis.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The bed files contains the genomic regions of the peaks identified after peak calling with MACS version 1.4.2 657

molecule: genomic DNA

source_name: mESCs

growth_protocol: R1 mESCs (obtained from ATCC) were cultured without feeders on plastic coated with 0.1% gelatin in DMEM supplemented with 15% FCS (Hyclone Millipore, cat. ES-009-B), 100 mM 2‐mercaptoethanol (Sigma, cat. M7522), 1 × MEM non‐essential amino acids (Invitrogen, cat. 1140‐036), 2 mM l‐glutamine, 1 mM sodium pyruvate (Invitrogen), 100 μg/ml Vitamin C (L-ascorbic acid 2-phosphatase Sigma, A8960). Where indicated 100 units/ml LIF (Millipore, cat. ESG1107) or 50 nM 4-hydroxytamoxifen (OHT) (Sigma, cat. H6278) were added to culture medium.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction was quenched by glycine at a final concentration of 0.125 M, for 5 min at room temperature. Cells were lysed in lysis buffer (50 mM Tris-HCl pH 8, 0.1 % SDS, 10 mM EDTA pH 8, 1 mM PMSF, protease inhibitor cocktail) and chromatin was sonicated to an average size of 0.1-0.5 kb, using a Branson D250 sonifier (4 cycles of 30 seconds, 20% amplitude).
Five nanograms of immunoprecipitaded and purified DNA were used to generate ChIP-seq libraries. Briefly, end repair of DNA fragments was achieved by sequential 15 min incubations at 12°C and 25°C with T4 PNK (10U/μl), T4 POL (3U/μl) and 0.1 mM dNTPs. A-base addition was performed by incubating end-repaired DNA fragments with Klenow (3’ → 5’ exo, 5U/μl) and 167 μM dATP for 30 min at 30°C. Adaptor ligation was achieved by using the NEB Quick ligation kit (M2200L) and perfoming an incubation of 15 min at 25°C. Processed DNA fragments were finally amplified with a thermal cycler for 14 cicles, by using the Agilent PfuUltra II Fusion HS DNA Pol kit (600674). All DNA purification steps between the different enzymatic reactions were performed by using Agencourt AMPure XP SPRI beads (Beckman, A63882). The obtained libraries were subjected to quality control on Agilent Bioanalyzer (Agilent Technologies, G2943CA).

treatment_protocol: LIF- and Myc-ESCs were grown in presence of either 100 units/ml LIF (Millipore, cat. ESG1107) or 50 nM 4-hydroxytamoxifen (OHT) (Sigma, cat. H6278), respectively.

tag: sample type

value: Embryonic Stem cells

tag: cell-type

value: mESCs

tag: chip antibody

value: none (genomic DNA)


title: asc1-M1X YPAD Ribo-Seq rep2

city: Cambridge

first: Wendy

middle: V

last: Gilbert

state: MA

address: 31 Ames St.

department: Biology

institute: Massachusetts Institute of Technology

description:
asc1_M1X_Fp2
Cell lysate was subjected to RNAse digestion followed by isolation of ribosomal footprints (Ribo-Seq) or used for RNA isolation, random fragmentation, and size selection (26-40 nt). Libraries were made by 3' adapter ligation or polyA-tailing, followed by reverse transcription, circularizaton of the RT product and PCR amplification. Either polyA selection or Ribo-Zero treatment was performed on total RNA samples prior to fragmentation (RNA-Seq).
yeast_mutants_rpkms.txt.gz
yeast_mutants_counts.txt.gz
yeast_mutants_scaledcounts.txt.gz
allData_FP_foldchanges.csv.gz
allData_total_foldchanges.csv.gz
allData_TE_foldchanges.csv.gz
allData_filtered_FP_foldchanges.csv.gz
allData_filtered_total_foldchanges.csv.gz
allData_filtered_TE_foldchanges.csv.gz

data_processing:
Reads were trimmed of adapter sequence: TGGAATTCTCGGGTGCCAAGG
Reads were mapped to the Sigma1278b genome using Tophat and requiring uniquely mapping reads
Mapped reads were assigned to annotated coding sequence features (excluding the first 30 codons for both Ribo-Seq and RNA-Seq) using custom scripts, counts per feature and RPKM values were calculated
Counts per feature were scaled for library size using the DESeq R package
Genome_build: Sigma1278b (SGD, downloaded 6/29/2014)
Supplementary_files_format_and_content: Counts, scaled counts, RPKM values, or log2 fold changes for all coding features

organism: Saccharomyces cerevisiae Sigma1278b

growth_protocol: Yeast were grown to mid log phase (OD 0.6-0.9) in YPAD (2% glucose) or YPAG (3% glycerol) at 30˚C.

extract_protocol:
Cells were lysed by vortexing with glass beads in lysis buffer. Lysates were clarified by centrifugation at 16k xg.
RNAse digestion of lysate and isolation of ribosomal footprints (Ribo-Seq) or random fragmentation and size selection (26-40 nt) of polyA-selected total RNA (RNA-Seq) was followed by 3' adapter ligation, reverse transcription, circularization of the RT product and PCR amplification.

treatment_protocol: Cells were treated with 0.1 mg/ml cycloheximide at 30˚C for 2 minutes. Cells were then cooled and harvested by centrifugation. Cells were resuspended in cold lysis buffer + cycloheximide.

tag: library type

value: Ribo-Seq

tag: media

value: YPAD (2% glucose w/v)

tag: total rna selection method

tag: 3' capture method

value: adapter ligation

tag: rt enzyme

value: Superscript III

tag: harvest method

value: pour over ice, freeze cell pellet in liquid nitrogen, thaw and lyse


title: CK (without copper)

first: Yingchun

last: Xu

state: Jiangsu

address: College of Horticulture, Nanjing Agricultural University

department: College of Horticulture

description: small RNA

data_processing:
Low-quality reads were filtered strictly. 3' adaptor sequences were trimmed and 5' adaptor contaminants were removed. Too small (<18 nt) and polyA sequences were removed.
For non-coding RNAs identification, clean reads were compared with rRNA, tRNA, snRNA, and snoRNA deposited in NCBI and Rfam database using the SOAP 2.0 program.
Then sequence tags were searched against the miRNA database, miRBase 20, in order to identify conserved miRNAs in Paeonia ostii
Genome_build: miRBase 20
Supplementary_files_format_and_content: The .fa files include small RNA sequences and their abundance for each sample.

organism: Paeonia ostii

source_name: control-treated Roots, stems and leaves

growth_protocol: Paeonia ostii (Paoenia ostii ‘Feng Dan’) was used in this study. Paeonia ostii seedlings were cultured in nutrient medium (quarter-strength MS solution) at 20/15 °C (day/night), with a light intensity of 200 μmol m–2s–1 and 12 h photoperiod.

extract_protocol:
For small RNA sequencing, the roots, stems and leaves of seedlings were separately harvested after 1, 6, 12 and 24 h of treatment and immediately frozen in liquid nitrogen for analysis.Total RNA was extracted from frozen roots, stems and leaves of Paeonia ostii with Trizol (Invitrogen, Carlsbad, CA, USA).
Two sets of total RNA were prepared, with one derived from the original RNA pool prepared form Cu-treated tissues (roots, stems and leaves) (+Cu) at 1, 6, 12 and 24 h time points and the other form the RNA pool derived from Cu-free tissues (-Cu) at the same time points. The samples were then subjected to 15% denaturing polyacrylamide gel electrophoresis, after which the sRNA fragments of 18-28 nt were isolated from the gel and purified. Next, the sRNA molecules were ligated to a 5’ adaptor and a 3’ adaptor sequentially and then converted to DNA by RT-PCR. Finally, approximately 20 μg product of RT-PCR was sequenced directly using standard Illumina protocols.

treatment_protocol: After growing in quarter-strength MS solution  for 1 week, uniform seedlings were incubated in solution containing 0 and 100 μM CuSO4 for different times.

tag: tissue

value: Roots, stems and leaves

tag: age

value: 30 days

tag: cultivar

value: Feng Dan

tag: treatment

value: quarter-strength MS solution


title: Copper

description: small RNA

source_name: copper-treated Roots, stems and leaves

value: quarter-strength MS solution containing 100 μM CuSO4


title: 24h

tag: strain

value: AG1 IA

value: 24 hours


title: Cd

data_processing:
Low-quality reads were filtered strictly. 3' adaptor sequences were trimmed and 5' adaptor contaminants were removed. Too small (<18 nt) and polyA sequences were removed.
For non-coding RNAs identification, clean reads were compared with rRNA, tRNA, snRNA, and snoRNA deposited in NCBI and Rfam database using the SOAP 2.0 program.
Then sequence tags were searched against the miRNA database, miRBase 21, in order to identify conserved miRNAs in Typha angustifolia
Genome_build: Typha angustifolia  transcriptome sequencing data
Supplementary_files_format_and_content: The .fa files include small RNAs and their abundance for each sample.

organism: Typha angustifolia

source_name: T. angustifolia_with cadmium-treatment

growth_protocol: Typha angustifolia seedlings were cultured in nutrient medium (quarter-strength MS solution) at 20/15 °C (day/night), with a light intensity of 200 μmol m–2s–1 and 12 h photoperiod.

extract_protocol:
For small RNA sequencing, the roots, stems and leaves of seedlings were separately harvested after 1, 6, 12 and 24 h of treatment and immediately frozen in liquid nitrogen for analysis.
Two sets of total RNA were prepared, with one derived from the original RNA pool prepared form Cd-treated tissues (roots, stems and leaves) (+Cd) at 1, 6, 12 and 24 h time points and the other form the RNA pool derived from Cd-free tissues (-Cd) at the same time points. The samples were then subjected to 15% denaturing polyacrylamide gel electrophoresis, after which the sRNA fragments of 18-28 nt were isolated from the gel and purified. Next, the sRNA molecules were ligated to a 5’ adaptor and a 3’ adaptor sequentially and then converted to DNA by RT-PCR. Finally, approximately 20 μg product of RT-PCR was sequenced directly using standard Illumina protocols.

treatment_protocol: After growing for 1 week, uniform seedlings were incubated in a solution containing 0 and 100 μM CdCl2 for different times.

value: T. angustifolia 'wild type'

value: quarter-strength MS solution containing 100 μM CdCl2

value: roots, stems and leaves


title: ChIP-Seq analysis of H3K4me3 in Myc-ESCs Sample 15

value: Embryonic Stem cells

value: mESCs

value: H3K4me3 (anti-trimethyl histone H3 Lys4 07-473 Millipore)


title: E1_BP08_2_2h

tag: cell type

value: Olfactory ensheathing cells (OECs)

tag: infected with

value: B. pseudomallei for 2h


title: 48h

tag: infection

value: 48 hours


title: CK (without cadmium)


title: ChIP-Seq analysis of SUZ12 in Myc-ESCs Sample 13

tag: sample type

value: Suz12 (anti-Suz12 D39F6 Cell Signalling)


title: ChIP-Seq analysis of Input in LIF-ESCs Sample 12

tag: cell-type

value: none (chromatin processed without incubation with the antibody)


title: ChIP-Seq analysis of Input in Myc-ESCs Sample 8

tag: chip antibody

value: none (genomic DNA)


title: ChIP-Seq analysis of H3K27me3 in LIF-ESCs Sample 10

value: H3K27me3 (anti-trimethyl histone H3 Lys27 07-449 Millipore)


title: ChIP-Seq analysis of H3K4me3 in Myc-ESCs Sample 7


title: ChIP-Seq analysis of H3K4me3 in LIF-ESCs Sample 11


title: ChIP-Seq analysis of H3K27me3 in Myc-ESCs Sample 6


title: ChIP-Seq analysis of Input in LIF-ESCs Sample 4


title: ChIP-Seq analysis of H3K27me3 in LIF-ESCs Sample 2


title: ChIP-Seq analysis of SUZ12 in LIF-ESCs Sample 9


title: ChIP-Seq analysis of H3K4me3 in LIF-ESCs Sample 3


title: ChIP-Seq analysis of SUZ12 in Myc-ESCs Sample 5


title: ChIP-Seq analysis of SUZ12 in LIF-ESCs Sample 1


title: IP_ERRa

city: Basel

first: Christoph

last: Handschin

address: Spitalstrasse 41

country: Switzerland

institute: Biozentrum, University of Basel

description: antibody: ERRα Rabbit Monoclonal Antibody, Clone ID: EPR46Y, Epitomics

data_processing:
The sequenced reads were filtered based on the quality score of each read and its alignments. Reads were retained when Phred score >= 20, read length >= 25 bps and number of wrongly called nucleotides (Ns) <= 2.
Those reads that passed the filter were aligned to the mouse genome, UCSC mm9 assembly, using Bowtie version 0.12.7 (Langmead et al., 2009) using parameters --best --strata -a --m 100.
We used a peak calling algorithm as described in more detail in the manuscript. To identify regions that were significantly enriched in the ChIP, we passed a 200 bps long sliding window along the genome, sliding by 25 bps between consecutive windows, and estimated the fraction of all ChIP reads fIP that fall within the window, as well as the fraction fWCE of reads from the WCE that fall in the same window (which we estimate from a 2000 bps long window centered on the same genomic location). All regions with a Z-statistic larger than 4.5 as significantly enriched were defined as "peaks" and used for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated .bed format: chromosome, start, end.

source_name: C2C12 myotubes, IP ERRalpha

growth_protocol: C2C12 cells were grown to 90% confluence in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 Units/ml penicilin and 100ug/ml steptomycin. The differentiation to myotubes was induced by changing DMEM supplementet with 2% horse serum (HS) for 72h.

extract_protocol:
The chromatin immunoprecipitation (ChIP) was performed according to the Agilent Mammalian ChIP-on-ChIP protocol version 10.0 with around 1x10^8 C2C12 cells. Magnetic beads (Dynabeads® Protein G, Invitrogen) couted with the monoclonal anit-ERRa antibody (ERRa Rabbit Monoclonal Antibody, Clone ID: EPR46Y, Epitomocs).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Differentiated myotubes were infected with flag-tag PGC-1a adenovirusfor 48h.

value: C2C12 myotubes


title: WCE

description: antibody: none

source_name: C2C12 myotubes, WCE


title: PECAM1plusPDGFRaplusExp2

city: Palermo

first: Antonio

last: Lo Nigro

address: Via tricomi 5

institute: Ismett

data_processing:
Illumina Casava1.8 software used for basecalling.
Low quality ends of sequence reads were trimmed using FastX 0.0.13. Adapters were trimmed with cutadapt 1.2.1. Low quality sequence reads were filtered using FastX 0.0.13 and ShortRead1.20.0. Contaminants were removed using bowtie 2.1.0.
Reads were mapped to the reference genome of Mus musculus (Mus musculus GRCm38.73) using Tophat v2.0.8b with parameters: --library-type fr-firststrand --min-intron-length  50 --max-intron-length 500000 --no-coverage-search  --no-mixed --read-realign-edit-dist 3.
The number of reads in the alignments that overlap with the gene features was counted by htseq-count 0.5.4p3 with parameters: -m union --stranded=no -a 0 -t exon -i geneid. Genes for which all samples have less than 1 counts-per-million (absent genes) were filtered.
RPKM  (Reads per kilobase of gene sequence and per Million reads of library size) was calculated as following: Counts for each gene were divided by the total number of counts (in million) and by the gene length (in kbp).
Genome_build: Mus musculus GRCm38.73
Supplementary_files_format_and_content: tab-delimited text files of matrix tables of raw counts and RPKM values for all samples

source_name: Embryonic stem cells

growth_protocol: ESC were maintained feeder-free on gelatin (EmbryoMax® 0.1% Gelatin Solution, ES-006-B; Millipore) coated plates, in Knockout DMEM (10829–018; Gibco), 20% Knockout Serum Replacement (KSR, 10828-028; Gibco), 2 mM L-glutamine (25030-024; Gibco), 1X minimal essential medium nonessential amino acids (11140-035; Gibco), penicillin (100 U/ml)/streptomycin(100 μg/ml) (15140-122; Gibco), 100 μM β-Mercaptoethanol (31350; Gibco) and 1,000 U/ml recombinant mouse leukemia inhibitory factor (ESGRO, ESG1107; Chemicon International).

extract_protocol:
RNA from 100000 sorted events for each subpopulation was extracted by using the Mirneasy RNA micro kit (QIAGEN). RNA was amplified by using the Ovation® RNA Amplification System V2 (NUGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Single-cell suspensions of ESCs were obtained by dissociating with 0cell dissociation buffer (Invitrogen) at 37°C. Cells were incubated with the primary antibodies in PBS for 30 min on ice and sorted using a FACSariaIII

value: undifferentiated ESC culture

tag: passages

tag: cell subpopulation


title: PECAM1plusPDGFRaplusExp1


title: PECAM1plusPDGFRaminExp2


title: ChIP-Seq analysis of H3K27me3 in Myc-ESCs Sample 14


title: PECAM1plusPDGFRaminExp1


title: PECAM1minPDGFRaplusExp2


title: PECAM1minPDGFRaplusExp1


title: C12-d100-2

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

data_processing:
Basecalls performed using CASAVA version 1.4
Image processing and sequence extraction were done using the standard Illumina Pipeline. RNA-seq reads were aligned using tophat v2.0.13 (Trapnell et al., 2012) and differential RPKM expression values were extracted using cuffdiff v2.2.1 (Trapnell et al., 2012). Statistical significance were determined by cuffdiff in duplicated samples per condition. Gene Ontology analyses were on biological process (BP) performed by The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 (Huang da et al., 2009).
Supplementary_files_format_and_content: Organoid.gene_exp.txt reports RPKMs.

growth_protocol: Human iPSC lines used in the current study were previously fully characterized (Wen et al., 2014; Yoon et al., 2014). They were cultured in stem cell medium consisting of DMEM:F12 (Invitrogen) supplemented with 20% Knockout Serum Replacer (Gibco), 1X Non-essential Amino Acids (Invitrogen), 1X Penicillin/Streptomycin, 1X 2-Mercaptoenthanol (Millipore), 1X Glutamax (Invitrogen), and 10 ng/ml FGF-2 as previously described (Yoon et al., 2014). Culture medium was changed every day. Human iPSCs were passaged every week onto a new plate pre-seeded with irradiated CF1 mouse embryonic fibroblasts (Charles River). iPSCs were detached from the plate by treatment of 1 mg/ml Collagenase Type IV (Invitrogen) for 1 hr. iPSC colonies were further dissociated into smaller pieces by manual pipetting. All studies were performed with approved protocols of Johns Hopkins University School of Medicine.

extract_protocol:
Total RNA was extracted from cerebral organoids by RNeasy (Qiagen), and 1 μg total RNA was primed with Oligo(dT)20 primers (Invitrogen) for cDNA synthesis.
RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol. An Agilent 2100 BioAnalyzer was used to quantify amplified cDNA and qPCR was applied to accurately quantify library concentration. 20 pM diluted libraries were used for sequencing. 50-cycle pair-end sequencings were performed using Illumina MISeq or HISeq 2000.

treatment_protocol: To generate forebrain-specific organoids (Figure 1B), human iPSC colonies were detached with Collagenase Type IV 7 days after passage, washed with fresh stem cell medium and cultured in a 15 ml conical tube. On day 1, detached and washed iPSC colonies were transferred to an Ultra-Low attachment 6-well plate (Corning Costar), containing 3 ml of stem cell medium (without FGF-2), plus 2 µM Dorsomorphine (Sigma) and 2  µM A83-01 (Tocris). On days 5-6, half of the medium was replaced with induction medium consisting of DMEM:F12, 1X N2 Supplement (Invitrogen), 10  µg/ml Heparin (Sigma), 1X Penicillin/Streptomycin, 1X Non-essential Amino Acids, 1X Glutamax, 4 ng/ml WNT-3A (R&D Systems), 1 µM CHIR99021 (Cellagentech), and 1  µM SB-431542 (Cellangentech). On day 7, organoids were embedded in Matrigel (BD Biosciences) and continued to grow in induction medium for 6 more days. On day 14, embedded organoids were mechanically dissociated from Matrigel by pipetting up and down onto the plate with a 5 ml pipette tip. Typically, 10 - 20 organoids were transferred to each well of a 12-well spinning bioreactor (SpinΩ) containing differentiation medium consisting of DMEM:F12, 1X N2 and B27 Supplements (Invitrogen), 1X Penicillin/Streptomycin, 1X 2-Mercaptoenthanol, 1X Non-essential Amino Acids, 2.5  µg/ml Insulin (Sigma). At day 71, differentiation medium was exchanged with maturation medium consisting of Neurobasal (Gibco), 1X B27 Supplement, 1X Penicillin/Streptomycin, 1X 2-Mercaptoenthanol, 0.2 mM Ascorbic Acid, 20 ng/ml BDNF (Peprotech), 20 ng/ml GDNF (Peprotech), 1 ng/ml TFGbeta (Peprotech), and 0.5 mM cAMP (Sigma). The organoids could grow beyond 110 days in maturation medium. All media were changed every other day. For the stationary culture, day 14 organoids were generated following the same protocol and then maintained in ultra-low attachment 6 well plate (Corning Costar) with differentiation media. The “intrinsic protocol” for spontaneous differentiation of human iPSCs into cerebral organoids followed the published protocol (Lancaster et al., 2013).

tag: organoid culture

value: cerebral organoids

tag: time

value: 100 days from the beginning of organoid culture


title: ALB_sugarmaple_fed_3

city: Lincoln

first: Erin

middle: D

last: Scully

state: NE

address: 137 Keim Hall, UNL East Campus

institute: USDA-ARS Grain, Forage, and Bioenergy Research Unit

data_processing:
Reads were quality filtered using ea-utils.  Reads with more than 50% of the bases containing Phred quality scores <30 were discarded.  Residual adapter sequence and low quality bases (Phred quality score < 30) were trimmed from read ends.  Reads < 75 bp after quality trimming were discarded.
Filtered forward reads were mapped to the Anoplophora glabripennis genome assembly (version_0.5.3) available from the i5k workspace (ftp://ftp.hgsc.bcm.edu/I5K-pilot/Asian_long-horned_beetle).
Differential expression analysis was performed using edgeR.  Reads were normalized and tagwise dispersions were used to estimate biological variation.  Differential expression analysis was performed using the Fisher's exact test with an FDR cutoff of 0.05.
Genome_build: version_0.5.3
Supplementary_files_format_and_content: Tab delimited files include raw numbers of mapped reads for each locus (raw abundance )

organism: Anoplophora glabripennis

source_name: Midgut

extract_protocol:
Total RNA was extracted from midguts collected from diet-fed and sugar maple-fed larval ALBs using the Powermicrobiome RNA Isolation Kit (MoBio).  rRNAs were depleted from the sample using Ribominus Eukaryotic Kit for RNA-Seq (Life Technologies).  Removal of rRNA was confirmed by the RNA Nano Assay (Agilent), which was performed on an Agilent Biolanalyzer.
RNA Seq libraries were prepared using Illumina TruSeq adapters following the manufacturer's protocol.  However, the polyA enrichment step was omitted because rRNA had previously been depleted from the sample.

value: 3rd instar

tag: developmental stage

value: larvae

value: midgut


title: ALB_dietfed_1


title: ALB_sugarmaple_fed_1


title: C12-d100-1


title: ALB_sugarmaple_fed_2


title: ALB_sugarmaple_fed_4


title: C12-d54-3.1

value: 54 days from the beginning of organoid culture


title: ALB_dietfed_2


title: ALB_dietfed_4


title: ALB_dietfed_3


title: C12-d40-3.1

value: 40 days from the beginning of organoid culture


title: C12-d54-2.2


title: C12-d40-2.2


title: C12-d54-2.1


title: C12-d54-1.1


title: C12-d40-3.2


title: C12-d40-2.1


title: C12-d40-1.2


title: C12-d26-3.1

value: 26 days from the beginning of organoid culture


title: C12-d26-3.2


title: C12-d26-1.1


title: C12-d26-2.2


title: C12-d26-1.2


title: C6

city: London

first: Paul

last: Kelly

state: UK

address: Turner Street

department: Immunobiology

country: United Kingdom

institute: Blizard Institute Barts & The London School of Medicine

data_processing:
TopHat (Bowtie2) alignments to human GRCh37-lite reference.
Htseq to characterize read counts (abundance) using GTF gene annotation.
DESeq for variance stablizing normalization and calculation of differential expression.
Ingenuity iReport analysis of differentially expressed genes (fold change).
Genome_build: GRCh37-lite
Supplementary_files_format_and_content: expression_broad.txt: abundance measurements (DESeq)
Supplementary_files_format_and_content: case_vs_control_foldgenes_broad.txt: Ingenuity iReport: The fold changes and p-values for all genes, sorted by magnitude of fold change.
Supplementary_files_format_and_content: treated_vs_control_foldgenes_broad.txt: Ingenuity iReport: The fold changes and p-values for all genes, sorted by magnitude of fold change.
Supplementary_files_format_and_content: untreated_vs_control_foldgenes_broad.txt: Ingenuity iReport: The fold changes and p-values for all genes, sorted by magnitude of fold change.
Supplementary_files_format_and_content: 106942997-all_sequences.gtf: GTF gene annotation

source_name: coronary artery

growth_protocol: not applicable; autopsy or transplant formalin-fixed, paraffin-embedded tissues

extract_protocol:
Rneasy FFPE kit (Qiagen, Valencia, CA),  RiboMinus (LifeTechnologies, Grand Island, NY) or RiboZero (Epicentre,Madison,WI), RNA Clean and Concentrate 5 (ZymoResearch, Irvine, CA)
Illumina TruSeq RNA kit, no fragmentation step performed

treatment_protocol: not applicable

value: coronary artery

tag: disease

value: Control


title: C7

tag: tissue


title: C12-d54-3.2


title: C12-d54-1.2


title: C5


title: KD3 - untreated

value: untreated Kawasaki Disease


title: KD8 - treated

value: treated Kawasaki Disease


title: C1


title: KD7 - treated


title: C3


title: C4


title: C2


title: KD2 - untreated


title: KD1 - untreated


title: KD6 - treated


title: KD5 - treated


title: Infected + SEA 2

first: Shabaana

last: Khader

state: MO

address: 660 South Euclid Avenue

department: Department of Molecular Microbiology

institute: Washington University in St.Louis

data_processing:
alignment w/ bwa 0.75
reads were counted with Samtools 0.1.19
Genome_build: mm9
Supplementary_files_format_and_content: mapped reads counts

source_name: Lung CD4+ T cells

growth_protocol: Single cell suspensions from DNAse/collagenase-treated lung tissue or spleen were prepared from the lungs of naïve or Mtb-infected mice. CD4+ T cells were isolated using magnetic CD4+ beads (GK1.5, MiltenyiBiotech).

extract_protocol:
Cell pellets were processed for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For Schistosoma egg antigen (SEA) treatment, cells were incubated in the presence of irradiated splenocytes, 5μg/ml ESAT-6 peptide, 10U/mL IL-2 with 50μg/ml SEA. T cells were incubated for six days at 37°C and 5% CO2 and supplemented with an equivalent volume of media containing IL-2 (10U/ml) on day 3. Control cells were incubated using the same peptide and cytokine concentrations in the absence of SEA. After 6 days, T cells were restimulated with irradiated splenocytes and 5µg/mL ESAT-6 peptide for 48h.

value: CD4+ T cells

tag: mouse strain

tag: bacterial strain

value: Mycobacterium tuberculosis H37Rv


title: KD4 - untreated


title: Infected + SEA 1


title: C12-d40-1.1


title: Infected 2


title: PC3 control rep2

city: San Francisco

first: Maurizio

last: Pellegrino

address: 953 Indiana Street

institute: Mission Bio

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole human genome using TopHat v2.0.13 and Bowtie 2.2.4.0
Aligned reads were processed using HTSEQ to count the number of reads mapped to genes in the hg19 genome.
HTSEQ counts were used as inputs for the R package edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene raw count values for each sample

source_name: PC3 control

growth_protocol: DMEM supplemented with 10%FBS and Penicillin/Streptomycin

extract_protocol:
Cells were lysed and cell material was extracted using Zymo Quick-RNA MicroPrep (R1050, see manuscript for details).
RNA libraries were processed using the Clontech SMARTer Stranded RNA-Seq kit.

tag: tissue source

value: prostate

tag: cell line


title: Infected + SEA 3

tag: cell type


title: RAJI control rep2

source_name: RAJI control

value: Lymphoblast-like

value: RAJI


title: Infected 1


title: PC3 control rep1


title: Infected 3


title: C12-d26-2.1

value: cerebral organoids


title: RAJI+PC3 control rep1

source_name: RAJI+PC3 control

value: Lymphoblast-like+prostate


title: RAJI+PC3 control rep2


title: VIM+-sorted rep2

source_name: VIM+-sorted


title: VIM+-sorted rep1


title: ca1v_2 (Hipposeq)

city: Vancouver

first: Mark

middle: Steven

last: Cembrowski

state: BC

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

country: Canada

institute: University of British Columbia

data_processing:
Reads for each library were mapped using TopHat v2.0.6 9.  The following options were used: “--num-threads 8 --GTF mouseGtf.gtf” , where mouseGtf.gtf reflects the concatenated Ensembl NCBIM37 transcript annotation file and the annotated ERCC spike-in controls
For FPKM-based quantification and differential expression, the annotated mouseGtf.gtf was used in Cuffdiff v2.1.1 using the accepted_hits.bam files for all replicates.  The following options were used: “--frag-bias-correct mouseFa.fa --mask-file mouseMask.gtf --max-bundle-frags 10000000 --num-threads 8 --multi-read-correct --no-effective-length-correction”, where mouseFa.fa is the Ensembl NCBIM37 reference FASTA and mouseMask.gtf is a mask file that ignores all alignments corresponding to genes annotated in mouseGtf.gtf annotated as tRNA, rRNA, or snRNA; in addition, Nat8l, Psd2, Xist, Gm15459, and Gm10335 were masked.
For count-based quantification and differential expression, aligned reads were processed by HTSeq using the mouseGtf.gtf and the following options: "--format=bam --stranded=no".
Processed data were analyzed in the R environment using a combination of cummeRbund v3.0 (http://compbio.mit.edu/cummeRbund/), DESeq2, and custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited files containing FPKM values and pairwise DE calls, as well as count values

source_name: Ventral CA1 pyramidal cells

extract_protocol:
Manual sorting to purify for fluorescent neurons from microdissected slices was performed according to previous methods (Hempel et al., 2007).
Total RNA was isolated from each sample using PicoPure RNA Isolation kit (Life Technologies, Frederick, MD) including the on-column RNAseq-free DNAseI treatment (Qiagen, Hilden, Germany) following the manufacturers’ recommendations.  Eluted RNA (11 ul) was dried in a speed vac to approximately 2-4 ul.  ERCC control RNAs (Life Technologies) were added using 1 ul of 1:100,000 dilution for every 50 cells.  cDNA was amplified from this input material using Ovation RNA-seq v2 kit (NuGEN, San Carlos, CA).  Approximately half of the resulting cDNA was used to make the sequencing libraries using the Ovation Rapid DR Multiplexing kit (NuGEN).

value: CA1 pyramidal cell

tag: location

value: hippocampus


title: ca1v_1 (Hipposeq)


title: ca1d_2 (Hipposeq)

source_name: Dorsal CA1 pyramidal cells


title: RAJI control rep1


title: ca2_1 (Hipposeq)

source_name: Dorsal CA2 pyramidal cells

value: CA2 pyramidal cell


title: ca3v_1 (Hipposeq)

source_name: Ventral CA3 pyramidal cells

value: CA3 pyramidal cell


title: ca2_2 (Hipposeq)


title: ca1d_0 (Hipposeq)


title: ca3d_0 (Hipposeq)

source_name: Dorsal CA3 pyramidal cells


title: ca3d_1 (Hipposeq)


title: dgd_2 (Hipposeq)

source_name: Dorsal DG granule cells

value: DG granule cell

value: DG


title: ca1d_1 (Hipposeq)


title: ca2_0 (Hipposeq)


title: ca3d_2 (Hipposeq)


title: dgd_0 (Hipposeq)


title: ca3v_0 (Hipposeq)


title: dgd_1 (Hipposeq)


title: ca3v_2 (Hipposeq)


title: ca4_0 (Hipposeq)

source_name: Dorsal DG mossy cells

value: DG mossy cell


title: ca4_2 (Hipposeq)


title: dgv_1 (Hipposeq)

source_name: Ventral DG granule cells


title: dgv_2 (Hipposeq)


title: cKO_Cre_neg_LSK_1331 ERRBS

city: New York

first: Barbara

last: Spitzer

state: NY

address: 411 E 67th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and then mapped to mm10 using a whole genome using the bismark alignment software with a maximum of 2 mismatches in a directional manner. Only uniquely aligning reads were retained
methylation score were determined for cytosines with at least 20 phred quality score and 10× coverage
Percentage of bisulfite converted Cytosines (Cs; representing unmethylated Cs) and non-converted Cs (representing methylated Cs) were recorded for each C position in a CpG context
Percent methylation values for CpG dinucleotides are calculated by dividing the number of methylated Cs by total coverage on that base.
Genome_build: mm10, ENSEMBL Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: tab-delimited text files include the number of methylated Cs and Ts per position (base) covered

source_name: bone marrow

extract_protocol:
Bone marrow was extracted from femurs, tibiae and iliac crests. After red blood cell lysis and magnetic lineage depletion cells were FACS-sorted to isolate Lin- Sca1+ cKit+ (LSK) and Lin- Sca1- cKit+ CD34+ FcgR+ (GMP) cells. Total RNA was extracted using AllPrep Kit (Qiagen)
Genomic DNA was purified from murine cells, digested with MspI restriction enzyme, subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors. Fragments of 150-400 bp were isolated by size selection and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers.  Libraries were sequenced using an Illumina HiSeq2500 per manufacturer’s recommended protocol for 50bp single end read reads

treatment_protocol: Mx1-driven Cre-mediated recombination was induced by 5 IP injections of poly(I:C)

value: LSK

tag: strain

tag: genotype


title: cKO_Mx_pos_LSK_1334 ERRBS


title: cKO_Mx_pos_LSK_1333 ERRBS


title: cKO_Cre_neg_LSK_1330 ERRBS


title: dgv_0 (Hipposeq)


title: cKO_Mx_pos_LSK_1327 ERRBS


title: cKO_Cre_neg_LSK_1326 ERRBS


title: cKO_Cre_neg_GMP_349 ERRBS

value: GMP


title: cKO_Mx_pos_GMP_179 ERRBS


title: cKO_Mx_pos_GMP_352 ERRBS


title: ca4_1 (Hipposeq)


title: cKO_Mx_pos_GMP_178 ERRBS


title: cKO_Cre_neg_LSK_1330 RNA-Seq

description:
Dnmt3a_KO_LSK_counts_raw.csv
Dnmt3a_KO_LSK_counts_norm.csv

data_processing:
Raw reads for all samples were aligned to the mm10 genome using STAR RNA-seq aligner (v.2.3.0e) with default parameters
For all samples, counts per gene were computed using HTSeq count v0.5.3p3 using the "intersection-nonempty" parameter. One sequenced sample was excluded from the LSK RNA-seq analysis due to poor mapability.
Differential expression analysis for GMPs was performed with the R Bioconductor DESeq v.1.18.0 package using default parameters
Differential expression analysis for LSKs was performed with the R Bioconductor DESeq2 v.1.4.5 package using default parameters
Genome_build: mm10, ENSEMBL Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: Raw and normalized count tables as computed by DESeq or DESeq2

extract_protocol:
Bone marrow was extracted from femurs, tibiae and iliac crests. After red blood cell lysis and magnetic lineage depletion cells were FACS-sorted to isolate Lin- Sca1+ cKit+ (LSK) and Lin- Sca1- cKit+ CD34+ FcgR+ (GMP) cells. Total RNA was extracted using AllPrep Kit (Qiagen)
Libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold from Illumina


title: cKO_Mx_pos_LSK_1333 RNA-Seq


title: cKO_Mx_pos_LSK_1327 RNA-Seq


title: cKO_Cre_neg_GMP_346 ERRBS


title: cKO_Mx_pos_LSK_1334 RNA-Seq


title: cKO_Mx_pos_GMP_178 RNA-Seq

description:
Dnmt3a_KI_counts_raw.csv
Dnmt3a_KI_counts_norm.csv


title: skin208 36m 3.75nM rotenone 8w rep6

status: Public on Apr 21 2016

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing: FASTQ files were extracted using Illumina Casava software v1.8.2.

organism: Danio rerio

source_name: total RNA extracted from skin

growth_protocol: Zebrafish (Danio rerio) were raised under standard conditions.

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of around 2.5 ug of total RNA per sample was processed using Illumina's TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer's instruction.

treatment_protocol: Tanks with male zebrafish were supplemented with 3.75 nM rotenone or DMSO (control) for 3 weeks and  8 weeks, respectively. 50% tank water was changed twice a week and fresh Rotenone and DMSO was added to the tanks.

value: skin

tag: age

value: 36 months

tag: treatment

value: 3.75nM rotenone

tag: duration

value: 8 weeks


title: cKO_Mx_pos_GMP_179 RNA-Seq


title: skin207 36m 3.75nM rotenone 8w rep5


title: cKO_Cre_neg_LSK_1326 RNA-Seq


title: skin206 36m 3.75nM rotenone 8w rep4


title: cKO_Mx_pos_GMP_352 RNA-Seq

description:
Dnmt3a_KO_LSK_counts_raw.csv
Dnmt3a_KI_LSK_counts_norm.csv


title: AS1_Input

city: Smithville

first: Sharon

middle: Roth

last: Dent

state: Texas

address: 1808 Park Road 1C

institute: Univ Texas M.D. Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
Sequenced DNA reads were mapped to yeast genome sacCer3 using Illumina analysis pipeline CASAVA (version 1.8.2) and only the reads that were mapped to unique position were retained. To avoid PCR bias, for multiple reads that were mapped to the same genomic position, only one copy was retained for further analysis.
Peaks of H3K4me2/H3K4me3 were detected by MACS (version 1.4.2) using total input DNA as control. The window size was set as 200 bp and the p-value cutoff was 1e-5.
Genome_build: sacCer3
Supplementary_files_format_and_content: [peakinfo.txt] Columns include PeakID (peak ID); Chr (chromosome of the peak); Start (start position of the peak); End (end position of the peak); Summit (summit position of the peak); PVALUE (p-value of the peak); NumTags (number of tags within the peak); Fold (fold change of the peak comparing to total input)

organism: Saccharomyces cerevisiae

source_name: AS1, Input

growth_protocol: Yeast cells were grown to mid-log phase and fixed with formaldehyde for 20 minutes prior to ChIP experiment

extract_protocol:
Chromatin was digested from nuclei with MNase and histone H3K4 methyl-DNA complexes were isolated with antibodies specific for either H3K4me2 or H3K4me3
Libraries were prepared for sequencing using standard Illumina protocols

tag: growth conditions

value: YEPD Mid-log phase

tag: chip antibody


title: cKO_Cre_neg_GMP_350 RNA-Seq


title: AS1_H3K4me3

source_name: AS1, H3K4me3

value: H3K4me3 (Active Motif, catalog# 39159, lot# 12613005)


title: skin205 36m 3.75nM rotenone 8w rep3


title: skin203 36m 3.75nM rotenone 8w rep1


title: skin168 36m 3.75nM rotenone 3w rep1

value: 3 weeks


title: skin172 36m 3.75nM rotenone 3w rep5


title: skin169 36m 3.75nM rotenone 3w rep2


title: cKO_Cre_neg_GMP_346 RNA-Seq


title: skin188 36m control 8w rep4


title: skin186 36m control 8w rep2


title: AS1_H3K4me2

source_name: AS1, H3K4me2

value: H3K4me2 (Active Motif, catalog# 39141, lot# 01008001)


title: skin161 36m control 3w rep2


title: skin185 36m control 8w rep1


title: skin162 36m control 3w rep3


title: skin187 36m control 8w rep3


title: liver207 36m 3.75nM rotenone 8w rep5

source_name: total RNA extracted from liver

value: liver


title: skin204 36m 3.75nM rotenone 8w rep2


title: liver208 36m 3.75nM rotenone 8w rep6


title: skin184 12m control 8w rep3

value: 12 months


title: skin158 12m control 3w rep2


title: skin160 36m control 3w rep1


title: skin159 12m control 3w rep3


title: skin171 36m 3.75nM rotenone 3w rep4


title: skin157 12m control 3w rep1


title: skin182 12m control 8w rep1


title: liver203 36m 3.75nM rotenone 8w rep1


title: liver205 36m 3.75nM rotenone 8w rep3


title: liver172 36m 3.75nM rotenone 3w rep4


title: skin170 36m 3.75nM rotenone 3w rep3


title: liver170 36m 3.75nM rotenone 3w rep2


title: liver171 36m 3.75nM rotenone 3w rep3


title: liver188 36m control 8w rep3


title: ca1v_0 (Hipposeq)

value: CA1 pyramidal cell

value: hippocampus


title: skin183 12m control 8w rep2


title: liver186 36m control 8w rep2


title: liver159 12m control 3w rep2


title: liver161 36m control 3w rep1


title: liver162 36m control 3w rep2


title: liver206 36m 3.75nM rotenone 8w rep4


title: liver204 36m 3.75nM rotenone 8w rep2


title: liver184 12m control 8w rep3


title: liver182 12m control 8w rep1


title: liver183 12m control 8w rep2


title: liver157 12m control 3w rep1


title: brain206 36m 3.75nM rotenone 8w rep4

source_name: total RNA extracted from brain

value: brain


title: brain172 36m 3.75nM rotenone 3w rep5


title: brain205 36m 3.75nM rotenone 8w rep3


title: brain171 36m 3.75nM rotenone 3w rep4


title: brain203 36m 3.75nM rotenone 8w rep1


title: brain188 36m control 8w rep4


title: brain170 36m 3.75nM rotenone 3w rep3


title: brain208 36m 3.75nM rotenone 8w rep6


title: brain168 36m 3.75nM rotenone 3w rep1


title: liver168 36m 3.75nM rotenone 3w rep1


title: brain187 36m control 8w rep3


title: brain185 36m control 8w rep1


title: liver185 36m control 8w rep1


title: brain161 36m control 3w rep2


title: brain162 36m control 3w rep3


title: brain160 36m control 3w rep1


title: brain184 12m control 8w rep3


title: brain182 12m control 8w rep1


title: brain183 12m control 8w rep2


title: brain159 12m control 3w rep3


title: brain157 12m control 3w rep1


title: brain204 36m 3.75nM rotenone 8w rep2


title: brain158 12m control 3w rep2


title: brain169 36m 3.75nM rotenone 3w rep2


title: brain207 36m 3.75nM rotenone 8w rep5


title: brain186 36m control 8w rep2


title: ΔL51MD1

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

data_processing:
using bowtie, searching for end-to-end hits with at most three mismatches. Alignment results were recorded in BAM format for further downstream analysis.
Read counts per gene were calculated for each transcriptome library using a shell script and were collapsed into a table in the statistical software R.
Only genes with at least three reads per million were considered for differential expression analyses, this was done using the edgeR package.
Normalization of the data was performed using the Cox-Reid prole-adjusted likelihood (CR) method. A dispersión of 0.0348 was calculated for the whole experiment.
For determining differential expression between the different comparison we use the generalized linear model (GLM) likelihood ratio test.
False discovery rates (FDR) were calculated using the Benjamini & Hochberg procedure. Genes with a FDR<0.05 were considered differentially expressed and was not established a limit for fold-change.
Supplementary_files_format_and_content: tab-delimited text files output of edgeR

organism: Phycomyces blakesleeanus

source_name: ΔL51 strain Mycelium dark replicate 1

growth_protocol: Grown on PDA

extract_protocol:
RNA extraction by Trizol protocol
Message Amp-II kit (Ambion)

treatment_protocol: growth in light and in darkness

tag: structure

value: Mycelium

value: photoreceptors mutant


title: ΔL51ML3

source_name: ΔL51 strain Mycelium light replicate 3


title: ΔL51SL1

source_name: ΔL51 strain Sporangiophore light replicate 1

value: Sporangiophore


title: ΔL51MD2

source_name: ΔL51 strain Mycelium dark replicate 2


title: WTSL3

source_name: WT strain Sporangiophore light replicate 3

value: wild type


title: ΔL51MD3

source_name: ΔL51 strain Mycelium dark replicate 3


title: ΔL51SD2

source_name: ΔL51 strain Sporangiophore dark replicate 2


title: ΔL51SD3

source_name: ΔL51 strain Sporangiophore dark replicate 3


title: ΔL51SD1

source_name: ΔL51 strain Sporangiophore dark replicate 1


title: ΔL51SL3

source_name: ΔL51 strain Sporangiophore light replicate 3


title: ΔL51ML1

source_name: ΔL51 strain Mycelium light replicate 1


title: WTSL2

source_name: WT strain Sporangiophore light replicate 2


title: WTSL1

source_name: WT strain Sporangiophore light replicate 1


title: WTSD3

source_name: WT strain Sporangiophore dark replicate 3


title: WTSD2

source_name: WT strain Sporangiophore dark replicate 2


title: WTSD1

source_name: WT strain Sporangiophore dark replicate 1


title: WTML3

source_name: WT strain Mycelium light replicate 3


title: ΔL51SL2

source_name: ΔL51 strain Sporangiophore light replicate 2


title: MEF_K4me3

first: Ying

last: Liu

address: 1300 York Ave

department: Medicine

institute: Weill Cornell Medical College

description: MEFs isolated from E13.5 embryos from H3.3B-HA mice

data_processing:
Illumina Casava1.8.2 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using BWA (version 0.5.9) with default parameters
Duplicates were removed using Picard (version 1.69).
The software ChIPseeqer 2.0 was applied to the ChIP-seq data with sequencing data from input DNA as control to identify genomic enrichment (peak) of specific histone modifications (FDR<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: bed files include all unique reads that mapped to a single best-matching location.

source_name: mouse embryonic fibroblast (MEF)

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle medium (DMEM) with high glucose (4500 mg/liter), 10% fetal bovine serum, and penicillin (100 U/ml)/streptomycin (100 μg/ml)/amphotericin (0.2 μg/ml).

extract_protocol:
Chromatin immunoprecipitation was performed with 1x10^7 cells per experiment. The cells were collected and cross-linked for 15min in 1% paraformaldehyde, washed and lysed. Chromatin was sheared using a Bioruptor to create fragments of approximately 150 base pairs, incubated with about 2–5 μg antibody bound to 75 μl Dynabeads M-280 (Invitrogen) and rotated overnight at 4 °C, then washed and eluted. The eluted chromatin was reverse-cross-linked and column purified.
ChIP samples were prepared for sequencing using Illumina TruSeq DNA Sample Preparation Kit according to the standard preparation protocol.

value: H3K4me3 (Abcam ab8580)

value: mouse embryonic fibroblast (MEF)


title: MEF_K27me3

value: H3K27me3 (Abcam ab6002)


title: MAC_K27me3

source_name: macrophage

value: macrophage


title: WTML1

source_name: WT strain Mycelium light replicate 1


title: MEF_input


title: MAC_K4me3


title: HSC_K27me3_2

description: Lin- HSC cultured on E4ORF1-HUVECs feeders

source_name: haematopoietic stem and progenitor cell (HSC)

growth_protocol: Whole bone marrow cells from C57BL/6J mice were isolated and Lin- cells were enriched by mouse Lineage Cell Depletion Kit (Miltenyi Biotec). Purified cells were plated with E4ORF1-HUVECs in X-Vivo serum-free media (Lonza) supplemented with 10 ng/ml of soluble Kit Ligand (sKitL) (Biosource). Total expanded cells were collected, enriched for Lin- cells, and plated with new E4ORF1-HUVECs feeders every 7 days. Total hematopoietic cell expansion was enriched for Lin- cells by mouse Lineage Cell Depletion Kit before collection.


title: ΔL51ML2

source_name: ΔL51 strain Mycelium light replicate 2


title: WTMD3

source_name: WT strain Mycelium dark replicate 3


title: MAC_input


title: WTML2

source_name: WT strain Mycelium light replicate 2


title: HSC_K27me3_1

value: haematopoietic stem and progenitor cell (HSC)


title: HSC_input


title: iPS_K27me3_1

description: Generated from 2 μg/ml doxycycline induced reprogramming of E13.5 tetO-4F2A x H3.3B-HA MEFs. Colonies with typical undifferentiatied ESC morphology were identified by phase microscopy and mechanically separated from the plate using Pasteur pipettes.

source_name: induced pluripotent stem (iPS) cell

growth_protocol: Cells were maintained using standard ESC culture procedures. In brief, cells were cultured with MEFs in standard ESC medium containing KnockOut DMEM (Gibco) and supplements as follows: KnockOut Serum Replacement, 10% (Gibco); penicillin (100 U/ml)/streptomycin (100 μg/ml)/amphotericin (0.2 μg/ml) (Media-tech); L-glutamine, 2 mM (Media-tech); MEM nonessential amino acids, 1× (Gibco); β-mercaptoethanol, 50 μM (Gibco); ESGRO Leukemia Inhibitory Factor (LIF), 1000 U/ml (Millipore). All the cells applied to further experiments were serially passaged and collected within 20 passages.

value: induced pluripotent stem (iPS) cell


title: iPS_K4me3_2


title: iPS_K27me3_2


title: WTMD2

source_name: WT strain Mycelium dark replicate 2


title: SSC_K27me3_2

source_name: Spermatogonial stem and progenitor cell (SSC)

growth_protocol: Mouse SSCs were cultured on MEFs in SSC medium containing StemPro-34 (Invitrogen) and supplements as follows: D(+) glucose, 6 mg/ml; BSA, 0.50%; insulin, 25 μg/ml (Sigma-Aldrich); MEM nonessential amino acids, 1× (Gibco); MEM vitamin solution, 1× (Gibco); penicillin (100 U/ml)/streptomycin (100 μg/ml)/amphotericin (0.2 μg/ml) (Media-tech); fetal bovine serum, 1%; L-glutamine, 2 mM (Media-tech); Bovine holo-transferrin, 100 μg/ml (Sigma-Aldrich); β-estradiol, 30 ng/ml (Calbiochem); progesterone, 60 ng/ml (Calbiochem); putrescine, 60 μM (Research Organics); sodium selenite, 30 nM (Sigma-Aldrich); pyruvic acid, 30 μg/ml (Sigma-Aldrich); d(L)-lactic acid, 1 μg/ml (Baker); β-mercaptoethanol, 50 μM (Gibco); ascorbic acid, 100 μM (EMD); D-biotin, 10 μg/ml (Calbiochem); human GDNF, 10 ng/ml (R&D Systems); human bFGF, 10 ng/ml (Cell Signaling); mouse EGF, 20 ng/ml (R&D Systems). To remove residual feeder cells in the collection, cells were plated in gelatin-coated plates in fresh SSC medium for 2 hours. All the floating cells were then gently collected, washed once in PBS, and subjected to experiments.


title: SSC_K27me3_3

value: Spermatogonial stem and progenitor cell (SSC)


title: NorflIP IP ParC-flag 2

city: Paris

first: Olivier

last: Espeli

address: 11 place Marcelin Berthelot

department: CIRB

country: France

institute: College de France

description: Imunoprecipitation with M2-Flag antibody coupled to agarose beads

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the E. coli NC_000913 genome using BWA 0.6.2
Genome_build: NC_000913
Supplementary_files_format_and_content: Enrichement (IP/input) wig files were generated using homemade matlab code

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli MG1655 parC::flag

growth_protocol: E. coli were grown in LB or minimal medium supplemented with casaminoacids (0,1%) and succinate (0,1%) until OD 0,2-0,4

extract_protocol:
Bacteria were lyzed with lyzozyme and sonicated to shear DNA. TopoIV-DNA complexes were isolated with antibody .
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (FC-104-5001). 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: For ChIP-seq experiments E. coli culture were fixed with formaldehyde (1% final concentration); for NorfliP experiments TopoIV was crosslinked with Norfloxacin (2µM)

value: LB growth OD 0,3

value: antiFlag M2


title: SSC_K27ac

value: H3K27ac (Abcam ab4729)


title: NorflIP Input ParE-flag 1

description: input DNA

source_name: E. coli MG1655 parE::flag


title: NorflIP Input ParC-flag 2

description: input DNA


title: NorflIP IP ParE-flag 1


title: SSC_K4me3_2


title: SSC_K4me3_1


title: SSC_input_2


title: SSC_K27me3_1


title: SSC_input_1


title: SSC_K4me3_3


title: MASC_K27me3_3

description: Generated from SSC conversion after long-term in vitro expansion. Colonies with typical undifferentiatied ESC morphology were identified by phase microscopy and mechanically separated from the plate using Pasteur pipettes.

source_name: multipotent adult spermatogonial-derived stem cell (MASC)


title: MASC_K27ac

value: multipotent adult spermatogonial-derived stem cell (MASC)


title: NorflIP IP ParC-flag 1


title: iPS_K4me3_1


title: WTMD1

source_name: WT strain Mycelium dark replicate 1


title: NorflIP Input ParC-flag 1

description: input DNA


title: HSC_K4me3_1


title: HSC_K4me3_2


title: IP ParE-flag G2

value: Minimal Medium A  supplemented with casaminoacids (0,1%) and succinate (0,2%),  OD 0,2 at 40°C


title: MASC_K27me3_2


title: Input ParE-flag G2

description: input DNA


title: SSC_input_3


title: Input ParE-flag S40min

description: input DNA


title: MASC_K4me3_3


title: MASC_K4me3_2


title: MASC_K4me3_1


title: IP ParE-flag S40min


title: Input ParE-flag S20min

description: input DNA


title: RNAseq_MEF

data_processing:
Illumina Casava1.8.2 software used for basecalling.
RNA-seq reads were aligned to the mm9 genome assembly using TopHat (version 2.0.11) with default parameters
Fragments Per Kilobase Million (FPKM) were calculated with CuffLinks.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each RNA-seq Sample.

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy Kit.
4 ug of Dnase I treated RNA was used for sequence library preparation. RNA libraries were prepared using Illumina Tru-seq protocol.


title: IP ParE-flag S20min


title: RNAseq_HSC_2


title: Input ParE-flag G1

description: input DNA


title: IP ParE-flag G1


title: RNAseq_SSC_4


title: RNAseq_SSC_3


title: RNAseq_iPS_1


title: RNAseq_iPS_2


title: Input ParE-flag 2

description: input DNA

value: LB growth OD 0,5


title: RNAseq_SSC_2


title: IP ParE-flag 2


title: Input ParE-flag 1

description: input DNA


title: MASC_K27me3_1


title: RNAseq_MASC_6


title: RNAseq_SSC_1


title: IP ParE-flag 1


title: RNAseq_MASC_4


title: RNAseq_MASC_1


title: RNAseq_MASC_5


title: RNAseq_MASC_3


title: Input ParC-flag 1

description: input DNA


title: RNAseq_MASC_2


title: RNAseq_HSC_1


title: RNAseq_ESC_1

source_name: embryonic stem cell (ESC)

value: embryonic stem cell (ESC)


title: IP ParC-flag 1


title: RNAseq_ESC_2


title: MASC_input


title: Anterior_ovariole_Day4_Replicate2

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
We performed single-end 75 bp sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego, CA) according to the manufacturer.  De-multiplexed reads (Chastity > 0.6) FASTQ output was from Illumina CASAVA v.1.8.2. Reads were mapped to FlyBase release 6 version 07 (FlyBase file: dmel-all-chromosome-r6.07.fasta) of the Drosophila melanogaster genome appended with the ERCC sequences (ERCC-00009, ERCC-00014, ERCC-00057, ERCC-00059, ERCC-00099, ERCC-00108, ERCC-00116 were strand-corrected from ERCC_reference.fa, and ERCC-00085 was re-identified as Subpool C; Jiang et al., Genome Research, 2011, PMID 21816910).  We appended the ERCC annotation to the Drosophila melanogaster annotation (dmel-all-r6.07.ERCC.gtf ). Reads were also mapped to the transposable elements dataset from BDGP (BDGP file: FASTA.FORMAT.v.9.4.1) (Kaminker et al; Genome Biol, 2002, PMID 12537573). We used HiSAT (2.0.1-beta) (Kim et al., 2014, Nature methods, PMID 25751142) with parameters (-x indexed_genome_with_ERCC --dta –U) for the mapping, and mapped reads at the gene-level were counted by HTSeq (v0.6.1p1) (--stranded=reverse with dmel_ERCC.gtf) (Anders et al., Bioinformatics, 2015, PMID 25260700). We used SAMtools (v0.1.2) (Li et al., Bioinformatics, 2009, PMID 19505943) to index chromosomes and sort the alignments.
Genome_build: Drosophila melanogaster Release 6
Supplementary_files_format_and_content: There are two supplemental files. The tab-delimited merged.hisat2_htseq_read_count.txt contain the gene-level output, for each library. The dmel_6.07_ERCC.gtf file contains the annotation for the alignment to release 6.07 plus the ERCC spike-ins.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: anterior ovariole

growth_protocol: Flies were raised at 25°C under constant light on Drosophila food (Labexpress, Ann Arbor, Michigan) (yeast 15 gm, cornmeal 27 gm, sucrose 43 gm, agar 8 gm, 0.4% propionic acid, 0.15% tegosept and water to 1 L). Virgins were collected based on the presence of meconium (dark spot on their abdomen) and aged at 25°C for 1 to 1.5 days, 2 to 2.5 days, 3 to 3.5 days and 4 to 4.5 days post eclosion.

extract_protocol:
Flies were collected and aged as described above and ovaries were dissected in a glass embryo dish in ice cold Phosphate Buffer Saline (PBS). Ovaries were immediately transferred to fresh ice cold PBS in a new dish. The ovarioles were teased apart using tungsten needles. Germaria and round previtellogenic egg chambers up to stage 8 were   separated from the rest of the ovary using tungsten needles and were immediately transferred to RNAlater (Life Technologies, Carlsbad, CA) on ice. Dissected samples were frozen at -80°C until RNA extraction, and each sample had 30 to 50 ovarioles. Three biological replicates were prepared for each age group. RNA was prepared after all the samples were dissected. Total RNA was isolated using the RNeasy mini kit (Qiagen, Valencia, CA) following manufacturer’s protocol with the following modification. RNAlater solution was removed from the tissue and the tissue was placed in 600 μl Buffer RLT (supplied with the kit). The tissue was then disrupted using five to ten glass beads in a mini-beadbeater (Biospec Products, Bartlesville, OK) for 2 rounds of 30 sec each. After this point we followed the manufacturers protocol exactly. RNA was quantified using Quant-iT Ribogreen RNA assay kit (Invitrogen, Carlsbad, CA) following manufacturers protocol and 200 ng of RNA was used for library preparation.
Libraries were prepared according to Lin et al. (BMC Genomics, 2016, PMID: 26732976) except we used 200 ng total RNA per sample as input.

tag: age of fly in days post eclosion

tag: Sex

value: female

tag: development stage

value: adult


title: Anterior_ovariole_Day4_Replicate1


title: input_DNA_FLAG_LPS

city: Dallas

first: Benjamin

last: Sabari

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: crosslinked chromatin

data_processing:
For ChIP-seq, data was aligned using bowtie (version 1.0.1) to the mouse mm9 genome reporting only unique reads in the best stratum, with up to 2 mismatches (bowtie -p 8 -S -q -v 2 -m 1 -k 1 --best –strata).
Samtools (version 0.1.19) was used to convert files to bam and sort
TDF files were generated by IGVtools (2.3.7) count function with processed bam files as input
Genome_build: mm9
Supplementary_files_format_and_content: TDF files contained tag density data for all ChIPseq samples

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 1% Pen/Strep and 1x Glutamax

extract_protocol:
For ChIP-seq, cells were fixed on plate with 1% formaldehyde, nuclei were isolated and then sonicated by bath ultrasonicator (Covaris). Lysates were clarified and DNA-histone complexes were isolated by either anti-AF9 (Sigman HPA001824) or anti-FLAG (Sigma F1804) immobilized by protein G dynabeads (Life).
For ChIP-seq, purified DNA was prepared for sequencing with the TruSeq ChIP sample Prep Kit (Illumina) as per manufacturer's instructions. Libraries were sequenced on either HiSeq2000 (Illumina) with 50bp single reads or NextSeq500 with 75bp single reads.

treatment_protocol: For LPS stimulation, 100ng/mL of LPS from Salmonella typhosa (Sigma L2387) was added to full media for 2hrs. For Crotonate pre-treatment, 10mM sodium crotonate (pH 7.4) was added to full media for 16 hours prior to LPS stimulation.

tag: s. typhosa lps (minutes)

tag: sodium crotonate (mm)

tag: antibody


title: input_DNA_FLAG_LPS+Crotonate

description: crosslinked chromatin

tag: cell line


title: Anterior_ovariole_Day3_Replicate3


title: Anterior_ovariole_Day3_Replicate2


title: input_DNA_FLAG_unstimulated

description: crosslinked chromatin


title: FLAG-AF9_LPS+Crotonate

description: crosslinked chromatin

value: FLAG-M2 (Sigma F1804)


title: Anterior_ovariole_Day3_Replicate1


title: Anterior_ovariole_Day2_Replicate3


title: FLAG-AF9_LPS

description: crosslinked chromatin


title: Anterior_ovariole_Day2_Replicate1


title: FLAG-AF9_unstimulated

description: crosslinked chromatin


title: Anterior_ovariole_Day2_Replicate2


title: Anterior_ovariole_Day1_Replicate2


title: input_DNA_LPS

description: crosslinked chromatin


title: WT3

first: Martin

last: Turner

address: Babraham Hall

department: Lymphocyte Signalling and Development

institute: Babraham Institute

data_processing:
Library strategy: iCLIP
Libaries were sequenced using Illumina’s HiSeq2000 (100 bp single end sequencing)
Basecalling was done using Illumina default pipeline
Sample demultiplexing was performed by identification of the 3 known bases of the 7 bases barcode introduced in the 5’ end of the read by the RCLIP primer.  The remaining four random bases were used to remove PCR duplicate reads
Reads were trimmed to remove any adaptor sequence and barcodes before mapping reads to genome mm10 using Bowtie
Identification of highly significant ZFP36L1 binding sites was performed using iCount to assign a FDR to each crosslink site
Genome_build: mm10
Supplementary_files_format_and_content: comma separated text file includes output from iCOUNT pipeline (merged results for all four biological replicates)

source_name: lymph node

growth_protocol: B cells were isolated from mouse lymph nodes by depleting CD5, CD43, CD11b and Ter119 positive cells.  The B cells were then plated at 2 million per ml in RPMI-1640 (Sigma) + 10% FCS + GlutaMAX (Gibco) + 100 U/ml Penicillin/Streptomycin (Life Technologies) + 50microM 2-mercaptoethanol (Sigma) + 1mM Na-Pyruvate (Life Technologies) + 10ug/ml LPS (Sigma) + 10ng/ml IL4 (PeproTech) + 5ng/ml IL5 (Sigma) for 48 hours at 37°C 5% CO2.

extract_protocol:
Cells were lysed and ZFP36L1-RNA complexes were pulled down with Brf1/2 antibody using protein A Dynabeads.  RNA-protein complexes were run on an SDS-PAGE gel, transfered to nitrocellulose and visualised by radiolabelling a proportion of the immunoprecipitated material.  Correctly sized complexes were cut out of the membrane and used to generate libraries.
cDNA libraries from four independent experiments were prepared using the RCLIP primers indicated and sequenced using Illumina’s HiSeq2000 (100 bp single end sequencing).  RCLIP primers used for RNA reverse transcription included a barcode at the 5’end with three known bases and four random nucleotides

treatment_protocol: Intact cells were irradiated with UV-light (300 mJ/cm2, Stratalinker 2400)

tag: cell type

value: activated B cells, lymphocyte

value: WT


title: input_DNA_unstimulated

description: crosslinked chromatin


title: WT4


title: AF9_LPS

description: crosslinked chromatin

value: AF9 (Sigma HPA001824)


title: DCKO 2

data_processing:
Libraries were sequenced by an Illumina genome analyzer II measuring 54bp single-end reads
Basecalls performed using Illumina offline basecaller version 1.8.0
Reads were trimmed to remove adapter sequences using Trim Galore
Reads were mapped using Tophat (version 1.1.4) to the NCBIm37 mouse assembly (April 2007, strain C57BL/6J)
Read counts for each gene were generated in SeqMonk: transcripts from the same gene were collapsed into a single transcript containing all exons
Differences in the abundance of transcripts between DCKO and control late pre-B cells were calculated in the R/Bioconductor program DESeq (version 1.12.1)
Genome_build: NCBIM37
Supplementary_files_format_and_content: Galloway_rawData.txt: tab-delimited text file includes raw read counts for each sample
Supplementary_files_format_and_content: Galloway_normData.txt: tab-delimited text file includes normalised read counts for each sample
Supplementary_files_format_and_content: DESeq_Output.txt: tab-delimited text file includes output from DESeq analysis

source_name: bone marrow

extract_protocol:
Cells FACS sorted from bone marrow as CD19+, IgM-, CD43-, CD25+ cells. RNA was extacted using Trizol.
0.1 µg of RNA used to make libraries using a TruSeq RNA sample preparation kit v2 modified to be strand specific using the dUTP method.

value: pre-B cell, lymphocyte

value: Zfp36l1fl/fl, Zfp36l2fl/fl, Mb1cre/+


title: AF9_unstimulated

description: crosslinked chromatin


title: Anterior_ovariole_Day1_Replicate1


title: DCKO 1


title: P0_Ctx_JB6_2 [RRBS-seq]

city: Montpellier

first: Tristan

last: Bouschet

address: 141 rue de la cardonille

department: CNRS 5203, INSERM U661

institute: Institut de Génomique Fonctionnelle

data_processing:
Image analyses and base calling were performed using the Illumina HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.17). The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
Trim Galore was used to perform adapter trimming and quality control in two subsequent steps. The 2 additional bases that contain a cytosine which was artificially introduced at the end-repair step during the library preparation (--rrbs option) were  removed.
Three genomes were prepared for Bismark using bismark_genome_preparation script: mm9 mouse reference (C57BL/6), JF1 and 129P2 references based on mm9 mouse reference; Novoutil IUPAC (option –g) was used to replace the BL/6 base with the JF1 or 129P2 base at each SNP position. Bismark software (version 0.14.3) from the Babraham Institute was used to align trimmed RRBS reads to the appropriate mouse genome.
For allele-specific methylation, two separate alignments against the C57BL/6 and JF1 genomes prepared with Bismark were performed using the Bismark option "--non_bs_mm" to also report the number of non-bisulfite mismatches per read.
Then, a script provided by Felix Krueger from the Babraham Institute (combine_Bismark_BAM_allele_specifically_SE.pl) post-processed the two resulting BAM files to decide whether the read was specific for one or the other allele or whether the read was unassignable because the number of non-BS mismatches was the same, i.e. did not cover a SNP position.
Then, bismark_methylation_extractor script extracted the methylation call for every single C analysed.
JF1 SNP positions were filtered out by a custom script (Filtre_positions_SNP-JF1_pour_CpG_report.pl) from the Montpellier GenomiX facility.
Genome_build: mm9 ; JF1 and 129P2 (based on mm9)
Supplementary_files_format_and_content: . cov files produced by Bismark : tab-delimited files with columns chromosome, start, end, methylation percentage, count methylated, count non-methylated

growth_protocol: E14atg2 ESCs were maintained on gelatin-coated dishes in DMEM (Life Technologies) supplemented with 15% ES-certified FBS (Life Technologies), 0.1mM non-essential amino acids (Life Technologies), 1mM sodium pyruvate (Life Technologies), 0.1mM beta-mercaptoethanol (Sigma), 50U/ml penicillin/streptomycin and 10³U/ml LIF (ESGRO, Millipore) as previously described (Gaspard et al., Nature. 2008 Sep 18;455(7211):351-7. doi: 10.1038/nature07287).  Hybrid ESCs were derived from blastocysts obtained by crossing a C57BL/6J female (Oct4-GFP transgenic) with a JF1 male, and reciprocally, and maintained on gelatin-coated dishes in ESGRO-complete-plus medium containing GSK3β-inhibitor, LIF and BMP4 (Millipore, SF001-500P) (Kota et al. Dev Cell. 2014;31(1):19-33).

extract_protocol:
Genomic DNA was prepared using PureLink genomic DNA kit (Life Technologies)
RRBS was performed on 200 ng of genomic DNA that was digested with MspI (Thermo Scientific) for 5 h, followed by end-repair, A-tailing (with Klenow fragment, Thermo Scientific) and ligation to methylated indexed Illumina adapters using T4 DNA ligase (Thermo Scientific) in Tango 1X buffer (Auclair et al. Genome Biol. 2014;15(12):545). Fragments were purified using AMPure XP magnetic beads (Agilent; Boyle et al. Genome Biol. 2012, 3;13(10):R92). Two rounds of bisulfite conversion were then performed using the EpiTect kit (Qiagen). Final RRBS libraries were PCR amplified with PfUTurbo Cx hotstart DNA polymerase (Agilent), purified with AMPure magnetic beads, quantified with a Qubit fluorometer (Life Technologies), and verified by Fragment analyzer (Advanced Analytical) and qPCR (Kapabiosystems).
Directional RRBS libraries were sequenced on an Illumina HiSeq 2000 as 100 bp reads using the Sequence By Synthesis technique at the Montpellier GenomiX facility.

treatment_protocol: To generate cortical cells in vitro, E14 and hybrid ESCs were plated onto gelatin-coated or matrigel (hESC qualified matrix, BD)-coated dishes, respectively. Next day, ESC media was changed for DDM as described (Gaspard et al., Nature. 2008 Sep 18;455(7211):351-7. doi: 10.1038/nature07287.), except that DDM was supplemented with B27 (without vitamin A) to improve hybrid cells survival. DDM was supplemented with cyclopamine (1 uM) from days 2 to 10 to enhance dorsalization of telencephalic progenitors (Gaspard et al., 2009). Differentiation was stopped at days 12 (d12) and 21 (d21) of culture.

value: JF1 x C57BL/6J hybrid

tag: cell/tissue type

value: neonatal cortex at P0


title: Rluc control total RNA-seq with sodium arsenite rep2

city: Stanford

first: Sekyung

last: Oh

state: CA

address: 1201 Welch Road, MSLS P224

department: Neurology and Neurological Sciences

institute: Stanford University School of Medicine

description: Total RNA depleted for ribosomal RNA

data_processing:
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg19) genome using bowtie2
gene assignment, and peak calling was performed as in ribosome profling (PMID: 19213877)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file containing unique RNAs for each replicate

growth_protocol: HEK293 cells were grown under standard serum conditions and FLAG-tagged Renilla luciferease (Rluc) control, DDX3 WT, or DDX3 R534H expression was induced by doxycycline addition.

extract_protocol:
Total RNAs were extracted using Zymo RNA Clean & Concentrator after depleting ribosomal RNAs with Ribo-Zero kit (EpiCentre).
Libraries were prepared according to the ribosome profiling protocol (PMID: 19213877) and ARTseqTM Ribosome Profiling Kit protocol (EpiCentre).

treatment_protocol: Cells were treated with or without 0.5 mM sodium arsenite for 45 minutes.

value: Embryonic kidney

tag: gender

value: sodium arsenite

tag: expressed protein

value: Rluc control


title: P0_Ctx_JB6_1 [RRBS-seq]

tag: strain


title: DDX3 R534H total RNA-seq with sodium arsenite rep2

description: Total RNA depleted for ribosomal RNA

tag: treatment

value: DDX3 R534H


title: DDX3 WT total RNA-seq with sodium arsenite rep2

description: Total RNA depleted for ribosomal RNA

value: DDX3 WT


title: P0_Ctx_BJ1_2 [RRBS-seq]

value: C57BL/6J x JF1 hybrid


title: Control 3

city: Cambridge

tag: genotype

value: Zfp36l1fl/fl, Zfp36l2fl/fl, Mb1+/+


title: P0_Ctx_BJ1_1 [RRBS-seq]


title: DDX3 WT total RNA-seq rep2

description: Total RNA depleted for ribosomal RNA

value: female

value: control


title: Control 2


title: WT2


title: e13-5_DT_JB6_2 [RRBS-seq]

value: embryonic dorsal telencephalon at E13.5


title: WT1

value: activated B cells, lymphocyte


title: Rluc control total RNA-seq rep2

description: Total RNA depleted for ribosomal RNA


title: Control 1


title: DDX3 R534H total RNA-seq with sodium arsenite rep1

description: Total RNA depleted for ribosomal RNA


title: DDX3 R534H total RNA-seq rep2

description: Total RNA depleted for ribosomal RNA


title: e13-5_DT_JB6_1 [RRBS-seq]


title: hnRNPM_k-d_+Rbfox_3

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

description:
hnRNP M RNAi, Flag-Rbfox1 expression, sample 3
barcode: AR019 GTGAAA(C)

data_processing:
illumina Casava software used for basecalling
Gene expression values, FPKM were calculated using a cufflinks program
Exon inclusion ratios were calculated using a rMATS program
Genome_build: hg19
Supplementary_files_format_and_content: Text files include exon inclusion level values for each sample.

source_name: Flp-In T-REx 293, Rbfox2 knockout cells (clone 7)

growth_protocol: Standard growth conditions according to ATCC

extract_protocol:
Trizol (Invitrogen) according to manufacturer's instructions
TruSeq stranded mRNA kit. paired-end 50nt reads, strand-specific (Illumina HiSeq2000)

treatment_protocol: The cells were grown in DMEM containing 4.6 g/L L-glucose and L-glutamine, lacking sodium pyruvate, supplemented with 10% fetal bovine serum. 9E+6 cells were transfected in suspension for three hours with 15 ug of plasmids encoding RNA hairpins and 37.5 ul of Lipofectamine 2000 (Invitrogen). The cells were grown to 40% confluent monolayer cultures in 6-well plates 2.5 days later and transfected with 4 ug of the same plasmids and 10 ul of Lipofectamine2000. The medium was supplemented with 0.5 ug/ml of Doxycycline immediately post transfections. The cultures  were expanded to 5-cm plates 24 hours later and grown for additional 24 hours in presence of doxycicline.

value: Human embryonic kidney

tag: expression of rbfox1 and hnrnp m

value: express Rbfox1 but not hnRNP M


title: DDX3 WT total RNA-seq with sodium arsenite rep1

description: Total RNA depleted for ribosomal RNA


title: Rluc control total RNA-seq with sodium arsenite rep1

description: Total RNA depleted for ribosomal RNA


title: hnRNPM_k-d_noRbfox_3

description:
hnRNP M RNAi, no Rbfox expression, sample 3
barcode: AR015 ATGTCA(G)

value: do not express hnRNP M and Rbfox1


title: hnRNPM_k-d_+Rbfox_2

description:
hnRNP M RNAi, Flag-Rbfox1 expression, sample 2
barcode: AR018 GTCCGC(A)


title: hnRNPM_k-d_+Rbfox_1

description:
hnRNP M RNAi, Flag-Rbfox1 expression, sample 1
barcode: AR016 CCGTCC(C)


title: d21_JB6_2 [RRBS-seq]

value: ESC-derived cells at d21 of corticogenesis


title: e13-5_DT_BJ1_2 [RRBS-seq]


title: DDX3 WT total RNA-seq rep1

description: Total RNA depleted for ribosomal RNA


title: DDX3 R534H total RNA-seq rep1

description: Total RNA depleted for ribosomal RNA


title: e13-5_DT_BJ1_1 [RRBS-seq]


title: Rluc control total RNA-seq rep1

description: Total RNA depleted for ribosomal RNA


title: hnRNPM_k-d_noRbfox_1

description:
hnRNP M RNAi, no Rbfox expression, sample 1
barcode: AR013 AGTCAA(C)


title: d21_JB6_1 [RRBS-seq]

value: JF1 x C57BL/6J hybrid


title: control_+Rbfox1_3

description:
contol RNAi, Flag-Rbfox1 expression, sample 3
barcode: AR012 CTTGTA(A)

value: express hnRNP M and Rbfox1


title: d21_E14_2 [RRBS-seq]


title: hnRNPM_k-d_noRbfox_2

description:
hnRNP M RNAi, no Rbfox expression, sample 2
barcode: AR014 AGTTCC(G)


title: d21_E14_1 [RRBS-seq]


title: DDX3 R534H ribosome profiling with sodium arsenite rep2

description:
Ribosome-protected mRNA fragments
Ribosome profiling

data_processing:
library strategy: Ribo-seq
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg19) genome using bowtie2
Gene assignment, and peak calling was performed as in ribosome profling (PMID: 19213877)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file containing unique ribosome-protected mRNA fragments for each replicate

extract_protocol:
Lysates were treated with RNase I, ribosomes were collected, ribosomal RNAs were depleted with Ribo-Zero kit (EpiCentre), and ribosome-protected mRNA fragments were enriched.
Libraries were prepared according to the ribosome profiling protocol (PMID: 19213877) and ARTseqTM Ribosome Profiling Kit protocol (EpiCentre).

value: Embryonic kidney


title: DDX3 WT ribosome profiling with sodium arsenite rep2

value: sodium arsenite


title: d21_BJ1_2 [RRBS-seq]


title: control_+Rbfox1_1

description:
contol RNAi, Flag-Rbfox1 expression, sample 1
barcode: AR006 GCCAAT(A)


title: d21_BJ1_1 [RRBS-seq]


title: Rluc control ribosome profiling with sodium arsenite rep2

value: Rluc control


title: d12_JB6_2 [RRBS-seq]

value: ESC-derived cells at d12 of corticogenesis


title: DDX3 R534H ribosome profiling rep2

value: DDX3 R534H


title: control_noRbfox_3

description:
contol RNAi, no Rbfox expression, sample 3
barcode: AR005 ACAGTG(A)

value: express hnRNP M but not Rbfox1


title: d12_JB6_1 [RRBS-seq]


title: DDX3 WT ribosome profiling rep2

value: DDX3 WT


title: control_noRbfox_2

description:
contol RNAi, no Rbfox expression, sample 2
barcode: AR004 TGACCA(A)


title: control_noRbfox_1

description:
contol RNAi, no Rbfox expression, sample 1
barcode: AR002 CGATGT(A)


title: Rluc control ribosome profiling rep2

value: female


title: DDX3 R534H ribosome profiling with sodium arsenite rep1


title: d12_E14_2 [RRBS-seq]


title: d12_E14_1 [RRBS-seq]


title: DDX3 WT ribosome profiling with sodium arsenite rep1


title: d12_BJ1_2 [RRBS-seq]

value: C57BL/6J x JF1 hybrid


title: Rluc control ribosome profiling with sodium arsenite rep1


title: control_+Rbfox1_2

description:
contol RNAi, Flag-Rbfox1 expression, sample 2
barcode: AR007 CAGATC(A)


title: MM27_shLuc_RNAseq_rp1

city: Milano

first: Luisa

last: Lanfrancone

address: Via Adamello, 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

data_processing:
Basecalls performed using CASAVA version 1.9
Data were filtered using the Illumina quality control flag
Reads were aligned to the homo sapiens genome build hg19 using tophat (v2.0.8), which uses Bowtie (2.1.0) and Samtools (v0.1.18) using default parameters and --transcriptome H. sapiens index, UCSC hg19 gtf.
Raw read counts were summarised using HTSeq (v0.5.3p9), then normalized for library size differences using estimateSizeFactors function from DESeq package (v1.10.1).
Differential expression of genes was calculated with the same R package, using three biological replicas for each interference condition (shLuc and shKMT2D) for each MM patient.
processed data files format and content: tab delimited text file containing differential expression fold changes (FC) for genes expressed at least in one sample (>1RPKM), between normalized baseMean intensities of shKMT2D/shLuc conditions, for each patient (3 replicas were used for each condition for each patient)
Genome_build: hg19

source_name: metastasis of cutaneous melanoma

growth_protocol: Cells isolated from secondary PDXs were infected with lentiviral vectors expressing luciferase and KMT2D shRNAs, selected in purumycin and then harvested for further analysis

extract_protocol:
total RNA was extracted with qiagen RNeasy mini kit (cat# 74106) according to manufacturer protocol
libraries were constructed using Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) starting from 1µg of total RNA

value: patient derived xenograft cells

tag: passage

tag: melanoma mutation

tag: infected shrna

value: shLuc


title: MM27_shLuc_RNAseq_rp3


title: MM27_shLuc_RNAseq_rp2


title: d12_BJ1_1 [RRBS-seq]


title: ESC_JB6_2 [RRBS-seq]

value: ESCs at d0


title: MM27_shKMT2D_RNAseq_rp2


title: DDX3 WT ribosome profiling rep1

value: control