title: C4-2B SR2211 Input chip seq

data_processing:
Sequencing tags were mapped against the Homo sapiens (Human) reference genome (hg19) using Bowtie 2
Uniquely mapped tags were used for peak calling by MACS(2.1.0) to identify regions of ChIP-Seq enrichment over background. A q value threshold of enrichment of 5 x 10^-2 was used for all data sets. Normalized genome-wide signal coverage tracks from raw read alignment files were built by  MACS2, fold-enrichment normalized wiggle files were generated by MACS by comparing ChIP treatment against input control, UCSC tools (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig/bedClip) and bedTools (http://code.google.com/p/bedtools/).
Visualization of ChIP-seq singnal at enriched genomic regions(avgprof and heatmap) was achieved by using ngs.plot (https://github.com/shenlab-sinai/ngsplot)
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files

source_name: C4-2B cells cultured in the presence of SR2211 (5 µM)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's paired-end DNA sample Prep kit.

treatment_protocol: C4-2B cells were seeded into 6 well plate and cultured in CRPC medium (RPMI 1640, 9%cds-FBS and 1% regular FBS, L-Glutamine, Pen-Strep), next day, cell were then treated with vehicle or SR2211 (5µM) for another 24 hours.

value: human prostate cancer cell line

tag: cell info.

tag: treated with

value: 5 µM SR2211 for 24hrs


title: Col-0_2

status: Public on Mar 08 2016

type: SRA

city: Frederiksberg C

first: Daniel

last: Straub

address: Thorvaldsensvej 40

department: Plant and Environmental Sciences

country: Denmark

institute: University of Copenhagen

description:
full_table_Col0-miP1b.txt
full_table_Col0-miP1a.txt
full_table_Col0-coSAIL.txt

library_source: transcriptomic

data_processing:
Basecalls performed using HiSeq Control Software v2.0.12.0
First 10 bases were clipped using Trimmomatic v0.32 (Lohse et al. 2012) with the arguments “HEADCROP:11 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50”, in each sample more than 98% of reads passed the trimming.
63-65% of clipped reads were successfully mapped to A. thaliana TAIR10 genome sequence and annotation (TAIR) using RobiNA’s v1.2.4_build656 Bowtie (Langmead et al. 2009).
normalization and statistical evaluation of differential gene expression has been performed using edgeR v2.6.12 using the Benjamini-Hochberg (1995) method for multiple testing.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include ID, LogFC, logCPM, LR, Pvalue and FDR (BH corrected) values for each Sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: leaf, 4 week old plants

growth_protocol: long-day; 16h light, 8h dark, 20°C

extract_protocol:
RNA was extracted from leaves using Roboklon total RNA purification kit
Illumina TruSeq RNA Sample Prep protocol

treatment_protocol: no treatments

tag: ecotype

tag: genotype

value: wildtype

tag: tissue

value: leaf


title: trp1-1::pGAL-H3:TRP1 Rad5+ t0 batch 1

city: Seattle

first: Sue

last: Biggins

state: WA

address: 1100 Fairview Ave N MS A2-168

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description: Sample 6

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads/bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered prior to alignment to the reference genome (UCSC hg19 assembly) using TopHat v2.1.0
Counts were generated from TopHat alignments for each gene using the Python package HTSeq v0.6.1
Genes with low counts across all samples were removed, prior to identification of differentially expressed genes using the Bioconductor package edgeR v3.12.0 A false discovery rate (FDR) method was employed to correct for multiple testing.  Differential expression was defined as |log2 (ratio) | ≥ 0.585 (± 1.5-fold) with the FDR set to 5%.
Genome_build: UCSC SacCer3
Supplementary_files_format_and_content: txt files contain edgeR results. Replicates of the corresponding genotypes in each batch were pooled for the differential expression analysis. A key to the sample names in the EdgeR output can be found on the series record in the file SampleName_to_edgeRName.xlsx.

organism: Saccharomyces cerevisiae

source_name: asynchronous cells

growth_protocol: Yeast cells were grown in YEP + Lactic Acid media to log phase at 23 degrees C. t=0 hours timepoint was taken at approx OD 0.55, galactose was added to 2%, and cells were grown for 2 hours at 23 degrees C, at which point the t=2 hour timepoint was taken.

extract_protocol:
RNA was extracted using the Acid-Phenol RNA extraction methods, followed by DNAseI treatment (Invitrogen, Amplification Grade) and phenol:chloroform extraction following by ethanol precipitation.
Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA).  RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep v2 Kit (Illumina, Inc., San Diego, CA, USA) and a Sciclone  NGSx Workstation (PerkinElmer, Waltham, MA, USA).  Library size distributions were validated using an Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, blending of pooled indexed libraries, and cluster optimization were performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).  RNA-seq libraries were pooled (18-plex) and clustered onto a flow cell lane.

tag: strain number

tag: timepoint

value: 0 hours

tag: batch

tag: medium

value: YEP + Lactic Acid


title: C4-2B ENZ

city: Sacramento

first: Junjian

last: Wang

state: california

department: Biochemistry and molecular medicine

institute: UC Davis

description: Illumina next-generation sequencing (2x100bp, paired-end)

data_processing:
sequence reads were mapped to the reference human genome assembly (Feb. 2009,GRCh37/hg19) with BWA and Bowtie software.
the Cufflinks package  was applied for transcript assembly, quantification of normalized gene and isoform expression in FPKM (Fragments per kilobase of exon per million fragments mapped), and testing for differential expression (Cuffdiff).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Gene symbol and FPKM values for each gene and were prepared from the Cufflinks output files (tracking).

organism: Homo sapiens

source_name: C4-2B cells cultured in the presence of Enzlutamide/MDV3100 (20 µM).

growth_protocol: C4-2B cells were cultured in RPMI supplemented with 10% FBS for maintenance or 9% cds-FBS and 1% regular FBS (to mimic the CRPC condition) for experiments. Cells were grown at 37℃ in 5% CO2 incubators.

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen) from C4-2B cells treated with Vehicle or SR2211  for 48 hours.
RNA-Sequencing (RNA-Seq) libraries were prepared from 1 μg total RNA using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s protocol. Briefly, poly-adenylated mRNA was purified from total RNA and rRNA removed by two rounds of binding to magnetic poly-T beads.  This was followed by RNA fragmentation by incubation in the presence of divalent cations at 94ºC for 5 minutes.  Double-stranded cDNA was generated by random-primed first-strand synthesis with SuperScript II reverse transcriptase and subsequent second strand synthesis with RNase H and DNA Polymerase I.  The cDNA was then blunt-ended with T4 and Klenow DNA polymerases to remove 3′-overhangs and fill in 5′-overhangs, phosphorylated with T4 PNK, and then 3′-A tailed by incubation with Klenow Fragment (3´→5´ exo–) and dATP.  Illumina paired-end (PE) adapters were ligated, followed by purification wit AMPure XP beads.  The library was enriched by high-fidelity PCR amplification (15 cycles) with Phusion DNA Polymerase (Finnzymes Oy) and adapter-specific primers.

treatment_protocol: C4-2B cells were seeded into 6 well plate and cultured in CRPC medium (RPMI 1640, 9%cds-FBS and 1% regular FBS, L-Glutamine, Pen-Strep), next day, cell were then treated with vehicle or ENZ (20µM)  for another 48 hours.

tag: cell line

value: C4-2B human prostate cancer cell line

tag: cell type

value: Bone metastatic LNCaP-derivative


title: htz1∆HYG Rad5+ t0 batch 1

description: Sample 5


title: Col-0_1


title: psh1∆KAN leu2-3,112::pGAL-3Flag-CSE4:LEU2 Rad5+ t0 batch 1

description: Sample 4

value: psh1_delta  pGAL-3Flag-CSE4


title: C4-2B vehicle Pol ǁ chip seq

library_source: genomic

molecule: genomic DNA

source_name: C4-2B cells cultured in medium with vehicle control

value: vehicle for 24hrs

tag: chip antibody

value: RNA Pol II (Santa cruz; sc-899)


title: psh1∆KAN Rad5+ t0 batch 1

description: Sample 2


title: C4-2B SR2211 Pol ǁ chip seq


title: C4-2B vehicle Input chip seq


title: C4-2B SR2211 H3K27ac chip seq

value: H3(acetyl K27) (Abcam; ab4729)


title: WT Rad5+ t0 batch 1

description: Sample 1

value: WT


title: RNA-seq  (S2_RNA_Rep2)

city: Montréal

first: Nicole

last: Francis

state: Quebec

address: 110, avenue des Pins Ouest

department: Département de biochimie et medécine moléculaire

country: Canada

institute: Université de Montréal

description:
S2_RNA_Rep2
ribosomal depleted total RNA

data_processing:
Basecalls performed using OLB 1.8
ChIP Sequences were aligned to the dm3 genome using bwa 0.5.9-r16, duplicates were removed
RNA Sequences were aligned uniquely to dm3 transcriptome using tophat 2.4
Genome_build: dm3
Supplementary_files_format_and_content: Chip-seq bigWig files and RNA-seq RPKM file.

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

growth_protocol: Drosphila S2 cells were grown in ESF-921 media in 10 cm dishs at 27 C

extract_protocol:
[ChIP-seq] Fixed cells were sonicated and PH-chromatin complexes were pulled down from clarified sonicated material
Sequencing libraries were generated as described previously (Bowman et al., 2013). Briefly, ends of the immunoprecipetated DNA were repaired, followed by A-tailing, ligating to universal adapters, and amplification for 10 cycles with indexed primers. Excess adapters were removed by purification with Agencourt AMPureXP beads (Beckman Coulter). Fragment size was checked by Bioanalyzer using high sensitivity DNA chip, and an average size distribution of 300-500bp was observed. Libraries we multiplexed and sequenced on using Illumina HiSeq 2000 for 50bp single end reads.
[RNA-seq] Total RNA was isolated using Qiagen RNA easy kit, ribosomal RNA was depleted by using ribozero gold kit and cDNA was prepared (and fragmented) by using Trueseq kit

treatment_protocol: Protein expression was induced by adding 0.5mM copper sulphate for 3 days

tag: genotype/variation

value: S2 cells

tag: cells derived from

value: Drosophila embryo

tag: source

value: S2 Cells obtained from Expression Systems


title: RNA-seq  (S2_RNA_Rep1)

description:
S2_RNA_Rep1
ribosomal depleted total RNA


title: C4-2B vehicle H3K27ac chip seq


title: C4-2B SR2211 H3K4me3 chip seq

value: H3K4me3 (Abcam; ab8580)


title: PH-ML input DNA  (PH-ML_Input_Rep2)

value: PH-ML

tag: pull down

value: input (no pull down)


title: PH-ML input DNA  (PH-ML_Input_Rep1)


title: co-sail_1

value: co-SAIL


title: C4-2B vehicle H3K4me3 chip seq

value: human prostate cancer cell line


title: PH-WT input DNA (PH-WT_Input_Rep1)

value: PH-WT


title: C4-2B SR2211 AR chip seq

value: 5 µM SR2211 for 24hrs

value: AR (Santa Cruz; sc-815)


title: PH-WT input DNA (PH-WT_Input_Rep2)


title: C4-2B SR2211 H3K4me2 chip seq

value: Bone metastatic LNCaP-derivative

value: H3K4me2 (Abcam ab5408)


title: 2nd time C4-2B SR2211 Input chip seq


title: PH-ML ChIP-seq  (PH-ML_Chip_Rep1)

value: Streptavidin biotin-tagged PH pull down


title: PH-WT ChIP-seq  (PH-WT_Chip_Rep1)


title: PH-ML ChIP-seq  (PH-ML_Chip_Rep2)


title: 2nd time C4-2B vehicle Input chip seq

value: vehicle for 24hrs


title: 20150127 C4-2B XY011

data_processing:
sequence reads were mapped to the reference human genome assembly (Feb. 2009,GRCh37/hg19) with BWA and Bowtie software.
the Cufflinks package  was applied for transcript assembly, quantification of normalized gene and isoform expression in RPKM (Reads per kilobase per million mapped reads) or FPKM (fragments per kilobase of exon per million fragments mapped), and testing for differential expression (Cuffdiff).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include Gene ID, symbol and FPKM or RPKM values for each gene and were prepared from the Cufflinks output files (tracking).

source_name: C4-2B cells cultured in the presence of XY011 (5 uM).

extract_protocol:
Total RNA was isolated using the TRIzol Reagent (Invitrogen) from C4-2B cells treated with Vehicle, SR2211 or XY018 for 48 hours.
RNA-Sequencing (RNA-Seq) libraries were prepared from 1 μg total RNA using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s protocol. Briefly, poly-adenylated mRNA was purified from total RNA and rRNA removed by two rounds of binding to magnetic poly-T beads.  This was followed by RNA fragmentation by incubation in the presence of divalent cations at 94ºC for 5 minutes.  Double-stranded cDNA was generated by random-primed first-strand synthesis with SuperScript II reverse transcriptase and subsequent second strand synthesis with RNase H and DNA Polymerase I.  The cDNA was then blunt-ended with T4 and Klenow DNA polymerases to remove 3′-overhangs and fill in 5′-overhangs, phosphorylated with T4 PNK, and then 3′-A tailed by incubation with Klenow Fragment (3´→5´ exo–) and dATP.  Illumina paired-end (PE) adapters were ligated, followed by purification wit AMPure XP beads.  The library was enriched by high-fidelity PCR amplification (15 cycles) with Phusion DNA Polymerase (Finnzymes Oy) and adapter-specific primers.

treatment_protocol: C4-2B cells were seeded into 6 well plate and cultured in CRPC medium (RPMI 1640, 9%cds-FBS and 1% regular FBS, L-Glutamine, Pen-Strep), next day, cell were then treated with vehicle or SR2211 (5µM) or E11/XY011  (5µM) for another 48 hours.

value: C4-2B prostate cancer cell line

tag: agent


title: 2nd time C4-2B SR2211 AR chip seq

tag: cell info.


title: 20140507 C4-2B SR2211

source_name: C4-2B cells cultured in the presence of SR2211 (5 uM).


title: 20140507 C4-2B vehicle

source_name: C4-2B cells cultured in medium with vehicle control.

value: control


title: DKONeurite2

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

institute: University of Colorado Anschutz Medical Campus

data_processing:
Alignment to mm9 with STAR
Gene expression estimates using Cuffdiff with UCSC mm9 annotation
Alternative splicing estimates with MISO
Genome_build: mm9, supplemented with alternative isoforms identified in Merkin et al (Science) 2012

molecule: polyA RNA

organism: Mus musculus

source_name: E18.5 mouse cortical neurons

growth_protocol: Double knockout mice were kept as constituitve MBNL1 knockouts and conditional (Nestin/Cre) MBNL2 knockouts

extract_protocol:
Cells were fractionated into soma / neurite fractions through the use of porous transwell inserts 48 hrs after dissection.
Nugen Low Input Library Prep

tag: compartment

value: neurite

value: Double knockout


title: 2nd time C4-2B vehicle AR chip seq

tag: treated with


title: DKONeurite1


title: DKOSoma1

value: soma


title: DKOSoma2


title: WTSoma1

value: WT


title: WTSoma2


title: Pt 392

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw output BAMs were converted back to FASTQ using PICARD Sam2Fastq. Reads were then mapped to the human genome using rnaStar. The genome used was HG19 with junctions from ENSEMBL (GRCh37.69_ENSEMBL) and a read overhang of 49. Gene level counts were computed using htseq-count and the same gene models as used in the mapping step.
HTSeq v0.5.4 is used for feature counting.
Counts were normalized and rescaled into log2 counts using the limma R package
Genome_build: hg19
Supplementary_files_format_and_content: txt files, normalized count tables from each experiment

source_name: clear cell RCC tumor

extract_protocol:
Tumors were homogenized in Trizol and processed according to instructions with reagent.
Follow Ion Torrent protocol, start with 100ng RNA using Ambion Low Input RiboMinus Eukaryote System v2 kit +  LifeTech Ion Total RNA seq kit V2

value: tumor

tag: diagnosis

value: Renal cell carcinoma


title: Pt 366

tag: tissue


title: C4-2B vehicle AR chip seq


title: C4-2B vehicle H3K4me2 chip seq


title: WTNeurite2


title: Pt 324


title: Pt 185


title: Pt 290


title: Pt 384


title: Pt 193


title: PH-WT ChIP-seq  (PH-WT_Chip_Rep2)

value: S2 cells

value: Drosophila embryo

value: S2 Cells obtained from Expression Systems


title: Pt 183


title: 20150127 C4-2B Vehicle


title: Tail 3

city: Dallas

first: James

last: Collins

state: TX

address: 6001 Forest Park

department: Pharmacology

institute: UT Southwestern

data_processing:
Mapped with STAR (v 2.5.0b)
Differential Expression Analysis with DESeq v1.22
Genome_build: v5.0
Supplementary_files_format_and_content: .xlsx file containing output from DESeq

organism: Schistosoma mansoni

source_name: Tail

growth_protocol: Schistosomes were recovered from mice 7-8 week post-infection

extract_protocol:
RNA was extracted with Trizol and subjected to Dnase Treatment
Illumina TruSeq Stranded RNA LT Kit

value: Tail

tag: gender

value: female


title: Pt 165


title: Tail 1


title: Pt 113


title: Head 3

source_name: Head

value: Head


title: psh1 pGAL-Flag-Cse4 strain input DNA

data_processing:
Illumina Real Time Analysis and CASAVA software used for base-calling
Raw reads were filtered using a custom script to include only the reads passing the Solexa quality test
Filtered reads were mapped to the S. cerevisiae reference genome version SacCer3 (SGD/UCSC) using the program BWA (Li et al, 2009).
The resulting BAM files were sorted by name using samtools sort (parameters: -n) (Li et al, 2009).
samtools fixmate was run on the name sorted BAM files to correctly label paired end reads  (Li et al, 2009).
The resulting BAM files were sorted by position using samtools sort  (Li et al, 2009).
Position sorted BAM files were filtered for proper pairs with a mapping score >30 using samtools view (parameters: -F 0x04 -f 0x02 -q 30 -b)  (Li et al, 2009).
Mononucleosomes were identified as paired end reads with insert sizes between between 50 and 240bp using custom R scripts with R Bioconductor packages GenomicRanges, rtracklayer, Rsamtools, nucleR, and the UCSC SacCer3 reference genome (Gentleman et al, 2004, Lawrence et al, 2009, Lawrence et al, 2013).
ChIP reads were compared to the input reads for each strain using the DANPOS2 (version 2.2.2) dpos function background subtraction and the background-subtracted ChIP signal was normalized to the coverage at centromeric regions for each strain and smoothed using the default DANPOS2 dpos smoothing parameters (Chen et al, 2013). (parameters: -b (strain specific input data), -m 1, -N (centromeres)).
rDNA ChIP coverage was set to 0 in WIG files using a custom R script due to uncertainty in whether the observed coverage was due to copy number variation or CENP-A(Cse4) occupancy. This region was excluded from subsequent analyses.
Peaks of CENP-A(Cse4) occupancy in each strain were called as any region where the CENP-A(Cse4) enrichment was above the threshold of the minimum average coverage at any centromere in the 3Flag-CSE4 strain using custom R scripts with R Bioconductor packages Genomic Ranges and rtracklayer SacCer3 (Gentleman et al, 2004, Lawrence et al, 2009, Lawrence et al, 2013) and the DANPOS2 dtriple function without any further normalization or smoothing (Chen et al, 2013). (danpos dtriple parameters: -n N, -u 0, -z 0, -q (threshold))
Input nucleosome peaks were also called using DANPOS2 (Chen et al, 2013).( danpos dtriple parameters: -m 1, -p 1e-10).
Genome_build: UCSC SacCer3
Supplementary_files_format_and_content: WIG files are smoothed normalized genomic coverage in 10bp bins. ChIP samples have the Input background subtracted using DANPOS 2.2.2 dpos (Chen et al, 2013), and are normalized between strains to the centromere CENP-A(Cse4 coverage). BED files are peaks of CENP-A(Cse4) ChIP enrichment greater than the minimal coverage at the centromere in the 3Flag-Cse4 strain, created using DANPOS 2.2.2 dtriple (Chen et al, 2013).

growth_protocol: Yeast cells were grown in YEP + lactic acid media to OD 0.55, and were then induced for 2 hours with 2% Galactose before harvest.

extract_protocol:
DNA was extracted using phenol:chloroform extraction and ethanol precipitation, resulting DNA was RNAse treated, and then purified using a Qiagen Reaction Cleanup kit. Antibodies used for ChIP-Seq were Monoclonal ANTI-FLAG   M2 antibody produced in mouse, Sigma-Aldrich Catalog # F3165, Lot/Batch # 080M6034.
Paired-end sequencing libraries of both input DNA from MNase-digested chromatin and 3Flag-Cse4 ChIP DNA were prepared using a modified Solexa library preparation protocol that captures DNA particles down to ~25bp (Henikoff et al, 2011 PNAS).

treatment_protocol: 3Flag-Cse4-containing nucleosomes were isolated by ChIP of 3Flag-Cse4 using monoclonal anti-Flag M2 antibodies. ChIPs were performed from Micrococcal nuclease (MNase) (Worthington Biochemical Corporation) treated chromatin as described (Henikoff et al, 2011 PNAS) with the following addition.  Before nuclei isolation, proteins were crosslinked to DNA with 1% formaldehyde for 15 minutes.  Crosslinks were then reversed before DNA extraction by the addition of 1% SDS and incubation overnight at 65 oC (Collins et al, 2005, MBC).

tag: strain number

tag: genotype

value: psh1 pGAL-3Flag-CSE4


title: pGAL-Flag-Cse4 strain Flag-Cse4 ChIP


title: pGAL-Flag-Cse4 strain input DNA


title: psh1 Flag-Cse4 strain Flag-Cse4 ChIP

value: psh1 3Flag-CSE4


title: psh1 pGAL-Flag-Cse4 strain Flag-Cse4 ChIP


title: Head 2


title: WTNeurite1


title: Flag-Cse4 strain Flag-Cse4 ChIP


title: Head 1


title: RNA-seq sample of TBP/TBP2/TLF-AS-injected embryos_1

status: Public on Mar 07 2016

city: Nijmegen

first: Gert

middle: Jan C.

last: Veenstra

address: Geert Grooteplein 28

department: Molecular Developmental Biology

country: Netherlands

institute: Faculty of Science, Radboud Institute for Molecular Life Sciences

description:
Mixture of stable antisense (AS) DNA oligonucleotides were synthesized with dimethyl-ethylene-diamine (DMED) modification (Dagle and Weeks, 2001). Sequence of TBPAS3 (7 open) Oligo 5’-T+G+C+A+T+TTCGCGCT+C+T+A+A+G-3' , TBP2-AS167 (6 open) Oligo  5’-T+C+A+T+C+GTATGGA+G+T+C+A+T-3’, TLF-AS93 (6 open) Oligo  5’-A+T+A+T+C+CAGTGCC+A+C+A+T+C-3’ (Jacobi et al., 2007; Jallow et al., 2004; Veenstra et al., 2000).
75 cyles of single-end sequencing ran on single flow of NextSeq500 (Illumina) equipment. Output data was mapped to Xenopus Genome version JGI 9.1 using STAR allowing one single mismatch. Raw data files contain 75 nucleotides long sequenses, were subjected to further analyis without additional filtering. Quality check was done by FastQ software.

data_processing:
Reads were mapped to the reference X. laevis genome assembly JGI version 9.1, downloaded from Xenbase (James-Zorn et al., 2015), using STAR (Dobin et al., 2013) and allowing one mismatch.
Differential count data for each transcripts were identified using DEseq (Anders and Huber, 2010), controlling the false discovery rate at 10% using the adjusted p-value.
Genome_build: Xenopus laevis Genome version JGI 9.1. A FASTA file with transcript sequences is available on the series page of GSE76991 or at: http://www.xenbase.org/other/static/ftpDatafiles.jsp
Supplementary_files_format_and_content: Excel file contains JGI9.1 gene IDs, transcript names, base mean of counts of samples and controls: baseMeanA for knockdown, baseMeanB for controls, fold-change ratios in log10 and log2 values, and measures of statistical significance. The interpretation of the columns of data.frame is as follows. #gene_short short name of annotated gene model #id feature identifier #name whole name of annotated gene model #baseMean mean normalised counts, averaged over all samples from both conditions #baseMeanA_TKD mean  normalised counts from TripleKD duplicates A #baseMeanB_ctrl mean normalised counts from water control duplicates #log2FoldChange_TKD_cntrl the logarithm (to basis 2) of the fold change #pval p value for the statistical significance of this change #padj p value adjusted for multiple testing with the Benjamini-Hochberg.

organism: Xenopus laevis

source_name: 10 embryos at developmental stage 10.5 (according to Nieuwkoop and Faber)

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies) and DNA-removal was done by 'DNA-free' Kit AM1906 (Ambion). Ribosomal RNA was depleted with Ribo-Zero Magnetic Gold Kit (Epicentre).
Instructions of manufacturer were followed using KAPA Hyper Prep Kit (Illumina). Sample preparation was done using Random Hexamer primers (Roche) and Hyper Prep Kit (Illumina).

treatment_protocol: Embryos were dejellied in 3% cysteine, pH=8 (in 25% MMR: 22mM NaCl, 0.5mM KCl, 0.5 mM CaCl2, 0.25mM MgCl2, 1.25mM HEPES, pH 7.4). Embryos were injected with mixure of 0.8ng of TBP/TBP2/TLF AS. Embryos were cultured in 25% MMR at 18oC. At stage 10.5 (Nieuwkoop Faber) 10 embryos were collected for RNA isolation.

tag: gene knockdown

value: TBP/TBP2/TLF triple knockdown (TKD)

tag: developmental stage at injection

value: 1-cell stage

tag: developmental stage at collection

value: stage 10.5

value: embryo


title: RNA-seq sample of TBP/TBP2/TLF-AS-injected embryos _2


title: RNA-seq sample of control water-injected embryos_1

description:
Water.
75 cyles of single-end sequencing ran on single flow of NextSeq500 (Illumina) equipment. Output data was mapped to Xenopus Genome version JGI 9.1 using STAR allowing one single mismatch. Raw data files contain 75 nucleotides long sequenses, were subjected to further analyis without additional filtering. Quality check was done by FastQ software.

value: control (Water-injected)


title: RNA-seq sample of control water-injected embryos_2


title: RNA-seq sample of water-injected control embryos _2

description:
Water
75 cyles of single-end sequencing ran on single flow of NextSeq500 (Illumina) equipment. Output data was mapped to Xenopus Genome version JGI 9.1 using STAR allowing one single mismatch. Raw data files contain 75 nucleotides long sequenses, were subjected to further analyis without additional filtering. Quality check was done by FastQ software.

data_processing:
Reads were mapped to the reference X. laevis genome assembly JGI version 9.1, downloaded from Xenbase (James-Zorn et al., 2015), using STAR (Dobin et al., 2013) and allowing one mismatch.
Differential count data for each transcripts were identified using DEseq (Anders and Huber, 2010), controlling the false discovery rate at 10% using the adjusted p-value.
Genome_build: Xenopus laevis Genome version JGI 9.1. A FASTA file of transcript sequences can be found on the GSE76991 series page and available at: http://www.xenbase.org/other/static/ftpDatafiles.jsp
Supplementary_files_format_and_content: Excel file contains JGI9.1 gene IDs, transcript names, base mean of counts of samples and controls: baseMeanA for knockdown, baseMeanB for controls, fold-change ratios in log10 and log2 values, and measures of statistical significance. The interpretation of the columns of data.frame is as follows. #gene_short short name of annotated gene model #id feature identifier #name whole name of annotated gene model #baseMean mean normalised counts, averaged over all samples from both conditions #baseMeanA_Gcn5KD mean  normalised counts from Gcn5KD duplicates A #baseMeanB_ctrl mean normalised counts from water control duplicates #log2FoldChange_Gcn5_Cntrl the logarithm (to basis 2) of the fold change #pval p value for the statistical significance of this change #padj p value adjusted for multiple testing with the Benjamini-Hochberg.

growth_protocol: Embryos were dejellied in 3% cysteine, pH=8 (in 25% MMR: 22mM NaCl, 0.5mM KCl, 0.5 mM CaCl2, 0.25mM MgCl2, 1.25mM HEPES, pH 7.4). Embryos were cultured overnight in 25% MMR at 18oC. At stage 10.5 (Nieuwkoop Faber) 10 embryos were collected for RNA isolation.

treatment_protocol: Embryos were dejellied in 3% cysteine, pH=8 (in 25% MMR: 22mM NaCl, 0.5mM KCl, 0.5 mM CaCl2, 0.25mM MgCl2, 1.25mM HEPES, pH 7.4). Embryos were injected with 0.8ng of Gcn5 AS [BJ220]. Embryos were cultured in 25% MMR at 18oC. At stage 10.5 (Nieuwkoop Faber) 10 embryos were collected for RNA isolation.


title: RNA-seq sample of Gcn5-AS-injected embryos_2

description:
Stable antisense (AS) DNA oligonucleotides were synthesized with dimethyl-ethylene-diamine (DMED) modification (Dagle and Weeks, 2001). Sequence of [BJ220] Gcn5 AS: 5’-T+C+A+A+A+CACAAGC+C+G+G+G+T+T-3’
75 cyles of single-end sequencing ran on single flow of NextSeq500 (Illumina) equipment. Output data was mapped to Xenopus Genome version JGI 9.1 using STAR allowing one single mismatch. Raw data files contain 75 nucleotides long sequenses, were subjected to further analyis without additional filtering. Quality check was done by FastQ software.


title: RNA-seq sample of water-injected control embryos_1


title: Flag-Cse4 strain input DNA


title: NSF6_i53-10-2

city: Raleigh

first: Vincent

middle: L

last: Chiang

state: NC

address: 840 Main Campus Drive

department: Forestry and Environmental Resources

institute: North Carolina State University

data_processing:
Six to twelve libraries with different index numbers were pooled by mixing equal quantities of DNA from each library and applied as one lane for Illumina GAIIx or HiSeq 2000 sequencing
68 to 100 bp average read lengths were obtained.  After removing the library sequence index sequences from each read, reads were mapped to the reference P. trichocarpa genome release V3.0 (Phytozome V10.0, http://www.phytozome.com) using the program “TOPHAT”.
Genome_build: Populus trichocarpa gene model name (version 3)
Supplementary_files_format_and_content: xlsx file with phytozome Populus trichocarpa gene model name (version 3) and the read counts

organism: Populus trichocarpa

source_name: Stem differentiating xylem

growth_protocol: P. trichocarpa Wild type and transgenic trees were grown in ½ Mircle-Gro Soil (Scotts Miracle-Gro products, Maysville, OH, USA) and ½ Metro-Mix 200 (Sun Gro, Bellevue, WA, USA) in the green house for 6 monthes (16 h light/8 h dark cycle with supplemental light of ~ 300 µE m-2 s-1) before tissue harvested for characterzation. Due to limited greenhouse space, different batch of transgenic trees with respective wild type were planted in soil and harvest at different time, there are total six batch trees were labeled with NSF1 to NSF6

extract_protocol:
Stem defferentiating xylem were scraped from the surface of the debark stem using a single-edge razor into liquid nitrogen immediately. collected tissues were ground into powder and stored in liquid nitrogen. Total RNA of SDX sample were extracted by uing Qiagen RNeasy Mini Kit (Invitrogen/Life Technologies, Grand Island, NY) with DNase I treatment option as suggested by kit manunal.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Agrobacterium mediated transformation of binary vector to knockdown or overexpression target genes driven by xylem specific promoter of 4-coumarate:CoA ligase gene[EU603323]

tag: gene perturbation type

value: knockdown of MYB002,MYB021

tag: batch of trees

value: Stem differentiating xylem


title: NSF6_WT-2

value: wild type control


title: NSF6_WT-3


title: NSF6_i53-10-3


title: NSF6_WT-1


title: NSF6_i53-10-1


title: Tail 2


title: NSF6_i53-7-3


title: NSF6_i53-5-3


title: NSF6_i53-7-2


title: NSF6_i53-5-2


title: NSF6_i53-5-1


title: NSF6_i30-4-2

value: knockdown of AldOMT2


title: NSF6_i30-15-1


title: NSF6_i30-4-3


title: NSF6_i30-15-2


title: NSF6_i30-15-3


title: NSF6_i30-4-1


title: NSF6_i30-1-3


title: NSF6_i24-12-2

value: knockdown of CCoAOMT1,CCoAOMT2


title: NSF6_i24-12-3


title: NSF6_i30-1-2


title: RNA-seq sample of Gcn5-AS-injected embryos_1

description:
Stable antisense (AS) DNA oligonucleotides were synthesized with dimethyl-ethylene-diamine (DMED) modification (Dagle and Weeks, 2001). Sequence of [BJ220] Gcn5 AS: 5’- T+C+A+A+A+CACAAGC+C+G+G+G+T+T-3’
75 cyles of single-end sequencing ran on single flow of NextSeq500 (Illumina) equipment. Output data was mapped to Xenopus Genome version JGI 9.1 using STAR allowing one single mismatch. Raw data files contain 75 nucleotides long sequenses, were subjected to further analyis without additional filtering. Quality check was done by FastQ software.


title: NSF6_i24-12-1


title: NSF6_i30-1-1


title: NSF6_i24-6-3


title: NSF6_i24-6-2


title: NSF6_i53-7-1


title: NSF6_i24-5-3


title: NSF6_i24-5-2


title: NSF6_i24-5-1


title: NSF6_i24-6-1


title: psh1 Flag-Cse4 strain input DNA


title: NSF6_i24-1-1


title: NSF6_i24-1-2


title: NSF6_i21-8-1

value: knockdown of CCoAOMT3


title: NSF6_i21-8-2


title: NSF6_i24-1-3


title: NSF6_i21-6-2


title: NSF6_i21-6-1


title: NSF6_i21-3-2


title: NSF6_i21-6-3


title: NSF6_i21-3-1


title: NSF6_i15-3-3

value: knockdown of 4CL3,4CL5


title: NSF6_i15-2-2


title: NSF6_i15-3-2


title: NSF6_i15-3-1


title: NSF6_i15-2-1


title: NSF6_a13-20-3

value: knockdown of 4CL5


title: NSF6_a13-20-2


title: NSF6_i15-1-1


title: NSF6_a13-20-1


title: NSF6_a13-6-2


title: NSF6_a13-6-1


title: NSF6_a13-4-3


title: NSF6_a13-4-2


title: NSF6_a12-10-3

value: knockdown of 4CL3


title: NSF6_a12-10-2


title: NSF6_a13-4-1


title: NSF6_a12-10-1


title: NSF6_i21-3-3


title: NSF6_a12-7-1


title: NSF5_WT-3


title: NSF6_a12-4-1


title: NSF5_i56-8-1

value: knockdown of MYB003,MYB020


title: NSF6_a12-4-3


title: NSF5_WT-2


title: NSF5_i56-3-3


title: NSF5_WT-1


title: NSF6_a12-7-3


title: NSF6_a12-7-2


title: NSF5_i56-3-2


title: NSF5_i56-8-2


title: NSF5_i56-8-3


title: NSF5_i56-10-1


title: NSF5_i56-10-2


title: NSF5_i50-8-3

value: knockdown of KNOX1


title: NSF5_i50-8-1


title: NSF5_i50-6-2


title: NSF5_i50-3-3


title: NSF5_i50-3-2


title: NSF5_i50-3-1


title: NSF5_i29-M-1

value: knockdown of CAld5H1,CAld5H2


title: NSF5_i29-L-3


title: NSF5_i29-M-3


title: NSF5_i29-M-2


title: NSF5_i29-L-2


title: NSF5_i29-L-1


title: NSF5_i50-8-2


title: NSF5_i29-H-3


title: NSF5_i19-8-3

value: knockdown of HCT1,HCT6


title: NSF5_i29-H-2


title: NSF5_i56-3-1


title: NSF5_i19-8-1


title: NSF5_i29-H-1


title: NSF5_i19-7-3


title: NSF5_i19-15-3


title: NSF5_i19-4-2


title: NSF5_i19-7-1


title: NSF5_i19-4-3


title: NSF5_i50-6-1


title: NSF5_i19-4-1


title: NSF5_i50-6-3


title: NSF5_i19-15-1


title: NSF5_a54-11-3

value: knockdown of MYB003


title: NSF5_a54-11-1


title: NSF5_a54-11-2


title: NSF5_a52-7-2

value: knockdown of MYB021


title: NSF5_a52-7-3


title: NSF5_a28-L-3

value: knockdown of CAld5H2


title: NSF5_a28-L-2


title: NSF5_a52-7-1


title: NSF5_a28-L-1


title: NSF5_a28-H-1


title: NSF5_a28-H-3


title: NSF5_i19-8-2


title: NSF5_i19-15-2


title: NSF5_i19-7-2


title: NSF5_a27-M-3

value: knockdown of CAld5H1


title: NSF5_a22-17-3

value: knockdown of CCoAOMT1


title: NSF5_a27-M-2

value: Stem differentiating xylem


title: NSF5_a22-17-1


title: NSF5_a22-17-2


title: NSF5_a22-10-2


title: NSF5_a18-9-3

value: knockdown of HCT6


title: NSF5_a22-10-3


title: NSF5_a22-10-1


title: NSF5_a18-9-2


title: NSF5_a18-9-1


title: NSF5_a18-5-2


title: NSF5_a18-4-3


title: NSF5_a18-5-1


title: NSF5_a18-4-2


title: NSF5_a18-5-3


title: NSF5_a28-H-2


title: NSF5_a18-11-2


title: NSF5_a18-11-1


title: NSF5_a17-9-3

value: knockdown of HCT1


title: NSF5_a17-9-2


title: NSF5_a18-11-3


title: NSF5_a27-M-1


title: NSF5_a17-4-2


title: NSF5_a17-9-1


title: NSF5_a17-1-1


title: NSF5_a17-10-3


title: NSF5_a17-4-1


title: NSF5_a17-10-2


title: NSF5_a17-1-2


title: NSF5_a17-10-1


title: NSF4_WT-2

value: wild type control


title: NSF4_WT-1


title: NSF4_i26-9-3

value: knockdown of CCR2


title: NSF4_WT-3


title: NSF4_i26-10-2


title: NSF4_i26-9-1


title: NSF4_i26-4-3


title: NSF4_i26-4-1


title: NSF4_i26-10-1


title: NSF4_i26-4-2


title: NSF4_a9-6-3

value: knockdown of C4H2


title: NSF4_i26-10-3


title: NSF4_a9-6-2


title: NSF4_a9-6-1


title: NSF4_a9-2-2


title: NSF4_a9-5-1


title: NSF4_a9-2-1


title: NSF4_a9-5-3


title: NSF4_a46-8-3

value: knockdown of MYB156


title: NSF4_a46-5-3


title: NSF4_i26-9-2


title: NSF4_a46-8-1


title: NSF4_a46-4-2


title: NSF4_a46-4-1


title: NSF4_a46-3-3


title: NSF4_a46-5-2


title: NSF4_a46-5-1


title: NSF4_a46-3-1


title: NSF4_a46-3-2


title: NSF4_a46-4-3


title: NSF4_a46-1-1


title: NSF4_a46-1-3


title: NSF4_a10-8-2

value: knockdown of C4H1


title: NSF4_a10-8-3


title: NSF4_a9-5-2


title: NSF4_a10-14-3


title: NSF4_a10-14-2


title: NSF4_a46-1-2


title: NSF4_a9-2-3


title: NSF4_a10-14-1


title: NSF4_a10-10-3


title: NSF4_a10-10-1


title: NSF3_WT-3


title: NSF3_WT-2


title: NSF4_a46-8-2


title: NSF3_WT-1


title: NSF3_o66-7-3

value: knockdown of CAD1 and overexpression of CAD2


title: NSF3_o66-7-2


title: NSF3_o66-7-1


title: NSF3_o66-30-2


title: NSF3_o66-30-1


title: NSF4_a46-10-3


title: NSF4_a46-10-1


title: NSF3_o66-21-2


title: NSF3_o66-21-1


title: NSF3_o66-21-3


title: NSF3_o65-7-2


title: NSF4_a10-8-1


title: NSF3_o65-7-1


title: NSF3_o65-11-2


title: NSF3_o65-16-1


title: NSF3_i69-4-3

value: knockdown of C3H3, C4H1 and C4H2


title: NSF3_o65-11-1


title: NSF3_o65-16-2


title: NSF4_a10-10-2


title: NSF3_i69-4-2


title: NSF3_i69-4-1


title: NSF3_i69-13-2


title: NSF3_i69-13-3


title: NSF3_i69-10-1


title: NSF3_i35-7-3

value: knockdown of CAD1,CAD2


title: NSF3_i35-7-2


title: NSF3_i35-7-1


title: NSF3_i69-13-1


title: NSF3_i35-15-3


title: NSF3_i35-15-2


title: NSF3_i35-15-1


title: NSF3_i35-1-2


title: NSF3_i35-1-1


title: NSF3_i34-8-1

value: knockdown of CAD2


title: NSF3_i34-8-2


title: NSF3_o65-7-3


title: NSF3_i35-1-3


title: NSF3_i34-6-2


title: NSF3_i34-2-1


title: NSF3_i33-5-3

value: knockdown of CAD1


title: NSF3_i34-2-2


title: NSF3_i33-5-2


title: NSF3_i33-5-1


title: NSF3_i34-19-1


title: NSF3_i33-2-3


title: NSF3_i34-19-2


title: NSF3_i33-2-2


title: NSF3_i33-10-3


title: NSF3_i20-5-3

value: knockdown of C3H3


title: NSF3_i33-10-2


title: NSF3_i33-2-1


title: NSF3_i20-5-2


title: NSF3_i20-5-1


title: NSF3_i20-10-3


title: NSF3_i20-2-1


title: NSF3_i20-2-3


title: NSF3_i20-10-2


title: NSF2_WT-3


title: NSF3_i34-6-1


title: NSF3_i20-10-1


title: NSF2_WT-2


title: NSF2_WT-1


title: NSF2_i8-8-2

value: knockdown of PAL1,PAL2,PAL3,PAL4,PAL5


title: NSF2_i8-8-1


title: NSF2_i8-8-3


title: NSF2_i8-1-3


title: NSF2_i8-1-1


title: NSF3_i33-10-1


title: NSF2_i8-10-1


title: NSF2_i8-10-2


title: NSF2_i6-9-1

value: knockdown of PAL1,PAL3


title: NSF2_i6-5-3


title: NSF2_i6-9-3


title: NSF2_i6-5-2


title: NSF2_i45-3-2

value: knockdown of MYB090,MYB167


title: NSF2_i6-4-3

value: Stem differentiating xylem


title: NSF2_i45-3-3


title: NSF2_i6-4-1


title: NSF2_i6-4-2


title: NSF2_i45-2-2


title: NSF2_i45-2-3


title: NSF2_i45-1-3


title: NSF2_i45-1-2


title: NSF2_i45-2-1


title: NSF2_i8-1-2


title: NSF2_i8-10-3


title: NSF2_i45-1-1


title: NSF2_i42-8-3

value: knockdown of LIM1,LIM2


title: NSF2_i42-5-3


title: NSF2_i42-12-3


title: NSF2_i42-5-1


title: NSF2_i42-5-2


title: NSF2_i42-8-1


title: NSF2_i6-5-1


title: NSF2_i42-12-2


title: NSF2_a5-6-1

value: knockdown of PAL2


title: NSF2_i45-3-1


title: NSF2_a5-2-2


title: NSF2_a5-13-1


title: NSF2_i42-8-2


title: NSF2_i6-9-2


title: NSF2_i42-12-1


title: NSF2_a47-10-2

value: knockdown of MYB221


title: NSF2_a47-5-2


title: NSF2_a47-9-2


title: NSF2_a47-9-3


title: NSF2_a47-5-1


title: NSF2_a47-5-3


title: NSF2_a4-8-1

value: knockdown of PAL5


title: NSF2_a47-9-1


title: NSF2_a47-10-3


title: NSF2_a43-17-2

value: knockdown of MYB167


title: NSF2_a47-10-1


title: NSF2_a44-9-1

value: knockdown of MYB090


title: NSF2_a44-6-3


title: NSF2_a44-9-2


title: NSF2_a44-4-3


title: NSF2_a43-17-3


title: NSF2_a44-4-2


title: NSF2_a44-9-3


title: NSF2_a44-6-2


title: NSF2_a43-12-1


title: NSF2_a44-4-1


title: NSF2_a43-12-3


title: NSF2_a43-13-1


title: NSF2_a4-6-2


title: NSF2_a44-6-1


title: NSF2_a43-17-1


title: NSF2_a43-12-2


title: NSF2_a43-13-2


title: NSF2_a43-13-3


title: NSF2_a4-3-1


title: NSF2_a41-9-3

value: knockdown of LIM2


title: NSF2_a40-1-3

value: knockdown of LIM1


title: NSF2_a41-10-1


title: NSF2_a41-9-2


title: NSF2_a41-10-3


title: NSF2_a41-10-2


title: NSF2_a40-12-2


title: NSF2_a41-7-2


title: NSF2_a40-10-2


title: NSF2_a40-1-2


title: NSF2_a41-9-1


title: NSF2_a40-10-1


title: NSF2_a3-4-1

value: knockdown of PAL4


title: NSF2_a3-11-1


title: NSF2_a40-10-3


title: NSF2_a40-12-1


title: NSF2_a41-7-3


title: NSF2_a3-3-1


title: NSF1_a2-3-2

value: knockdown of PAL3


title: NSF2_a40-1-1


title: HSPC_48

first: Betty

last: Chang

address: 1425 Madison Ave

institute: Mount Sinai School of Medicine

description: processed data file: E10_E12_HSPC_SingleCell_FPKM.txt.gz

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Sequence library reads were trimmed for adapter sequence, low quality and low complexity reads removed using FASTX-toolkit suite
Alignment to mm9 using Tophat release v2.0.12 and Bowtie2 release v2.2.3
Differential expression performed with Cufflinks release v2.2.1 and Mus musculus mm9 reference annotation
Genome_build: mm9
Supplementary_files_format_and_content: FPKM tables derived from Cufflinks cuffdiff output E10_E12_HSPC_SingleCell_FPKM.txt.gz output tab-delimited file.  See reference at http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track and Trapnell et al. Nat Biotech 2010.

extract_protocol:
Cells were sorted by FACS. Single cells isolated, RNA extracted and cDNA prepared using Fluidigm C1 System.
Single cell RNAseq libraries prepared with Nextera XT DNA Library Preparation Kit according to manufacturers instructions.

tag: strain

tag: age

value: embryonic day E12.5

tag: genotype/variation

value: wild type

value: placenta

tag: sorted cell population

value: hematopoeitic stem/progenitor cells CD45+CD34+cKit+


title: HSPC_47


title: HSPC_44


title: HSPC_45


title: HSPC_46


title: NSF1_a1-8-1

value: knockdown of PAL1


title: HSPC_42


title: HSPC_43


title: NSF2_a41-7-1


title: NSF2_a40-12-3


title: HSPC_41


title: HSPC_40


title: HSPC_38


title: HSPC_35


title: HSPC_37


title: HSPC_34


title: HSPC_29


title: HSPC_31


title: HSPC_28


title: HSPC_39


title: HSPC_36


title: HSPC_32


title: HSPC_30


title: HSPC_26


title: HSPC_23


title: HSPC_25


title: HSPC_22


title: HSPC_17


title: HSPC_18


title: HSPC_16


title: HSPC_20


title: HSPC_14


title: HSPC_19


title: HSPC_21


title: HSPC_15


title: HSPC_13


title: HSPC_27


title: HSPC_12


title: HSPC_33


title: HSPC_10


title: HSPC_11


title: HSPC_08


title: HSPC_24


title: HSPC_06


title: HSPC_07


title: HSPC_04


title: HSPC_09


title: E12_PS34CD45-_48


title: E12_PS34CD45-_47


title: HSPC_02


title: HSPC_03


title: HSPC_05


title: HSPC_01


title: E12_PS34CD45-_43


title: E12_PS34CD45-_42


title: E12_PS34CD45-_39


title: E12_PS34CD45-_40


title: E12_PS34CD45-_41


title: E12_PS34CD45-_45


title: E12_PS34CD45-_46


title: E12_PS34CD45-_37


title: E12_PS34CD45-_36


title: E12_PS34CD45-_33


title: E12_PS34CD45-_38


title: E12_PS34CD45-_35


title: E12_PS34CD45-_32


title: E12_PS34CD45-_34


title: E12_PS34CD45-_31


title: E12_PS34CD45-_44


title: E12_PS34CD45-_29


title: E12_PS34CD45-_28


title: E12_PS34CD45-_30


title: E12_PS34CD45-_27


title: E12_PS34CD45-_24


title: E12_PS34CD45-_23


title: E12_PS34CD45-_22


title: E12_PS34CD45-_18


title: E12_PS34CD45-_19


title: E12_PS34CD45-_20


title: E12_PS34CD45-_11


title: E12_PS34CD45-_15


title: E12_PS34CD45-_13


title: E12_PS34CD45-_12


title: E12_PS34CD45-_09


title: E12_PS34CD45-_10


title: E12_PS34CD45-_17


title: E12_PS34CD45-_07


title: E12_PS34CD45-_08


title: E12_PS34CD45-_14


title: E12_PS34CD45-_05


title: E12_PS34CD45-_03


title: E12_PS34CD45-_04


title: E12_PS34CD45-_26


title: E12_PS34CD45-_02


title: E10_PS34CD45-_48

value: embryonic day E10.5


title: E12_PS34CD45-_25


title: E10_PS34CD45-_47


title: E12_PS34CD45-_21


title: E10_PS34CD45-_46


title: E10_PS34CD45-_45


title: E12_PS34CD45-_16


title: E10_PS34CD45-_43


title: E10_PS34CD45-_41


title: E10_PS34CD45-_42


title: E10_PS34CD45-_40


title: E12_PS34CD45-_06


title: E10_PS34CD45-_37


title: E10_PS34CD45-_38


title: E10_PS34CD45-_33


title: E10_PS34CD45-_35


title: E10_PS34CD45-_31


title: E10_PS34CD45-_34


title: E10_PS34CD45-_29


title: E10_PS34CD45-_36


title: E10_PS34CD45-_30


title: E10_PS34CD45-_28


title: E12_PS34CD45-_01


title: E10_PS34CD45-_26


title: E10_PS34CD45-_27


title: E10_PS34CD45-_32


title: E10_PS34CD45-_44


title: E10_PS34CD45-_25


title: E10_PS34CD45-_23


title: E10_PS34CD45-_21


title: E10_PS34CD45-_22


title: E10_PS34CD45-_20


title: E10_PS34CD45-_18


title: E10_PS34CD45-_24


title: E10_PS34CD45-_19


title: E10_PS34CD45-_39


title: E10_PS34CD45-_15


title: E10_PS34CD45-_17


title: E10_PS34CD45-_16


title: E10_PS34CD45-_14


title: E10_PS34CD45-_13


title: E10_PS34CD45-_12


title: E10_PS34CD45-_10


title: E10_PS34CD45-_11


title: E10_PS34CD45-_03


title: E10_PS34CD45-_07


title: E10_PS34CD45-_06


title: E10_PS34CD45-_05


title: E10_PS34CD45-_08


title: E10_PS34CD45-_02


title: E10_PS34CD45-_01


title: KD GFP cyto Replicate A

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

country: Germany

institute: Goethe University Frankfurt

description:
PolyA+ RNAseq cyto
Cyto_Gene_FPKMs.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2
Remaining adaptor sequences were trimmed from reads using cutadapt -m 20 -q 25; For MISO all reads were trimmed to 75-bp length.
For Cufflinks and DEX-Seq RNA-seq reads were aligned to mm10 using Tophat v2.0.9 coupled with Bowtie v2.1.0. For MISO reads were mapped to mm9 using TopHat (v2.0.10) with the option -g1.
FPKMs were calculated using Cufflinks v2.1.1; Splicing changes were calculated with DEX-Seq and MISO.
Genome_build: Cufflinks: mm10; Ensembl v73. gtf-used for expression profiling was retrieved with ensembl-ids from uscc table browser. DEX-Seq: mm10; ENSEMBL v66. MISO: mm9
Supplementary_files_format_and_content: Cufflinks: Tab-delimited text files containing gene counts of all knockdown experiments separate in cytoplasmic and whole cell samples; FPKM values of all knockdown experiments separate in cytoplasmic and whole cell samples; FPKM values of separate knockdown experiments in cytoplasmic and whole cell samples. DEX-Seq:  Text files containing read counts in exon counting bins comparing KD of SR proteins to control. MISO: Text files containing changes in expression in annotated alternative last exons (ALE) and TandemUTRs including Percent Spliced In (PSI) values and confidence intervals calculated and compared between KD samples and controls.

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.

extract_protocol:
P19 Control and Knockdown cells were harvested and separated into whole cell lysates and cytoplasmic fractions. RNA was isolated using TRIzol. PolyA+ RNA was enriched with MicroPoly(A) Purist Kit (Ambion.
mRNA isolation from 1ug total RNA was done by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturers instructions. Library was prepared using TruSeq library prep kit (Illlumina).

treatment_protocol: Seven different SR proteins were knocked down using costum-made esiRNAs and Lipofectamin2000. An esiRNA against GFP was used for mock transfections. Transfections were performed for 36 hours to minimize secondary effects on gene expression.

tag: cell line

value: P19 embryonal carcinoma cell line

value: KD GFP

tag: cell fraction

value: cytoplasm


title: KD SRSF6 cyto Replicate B

description:
PolyA+ RNAseq cyto
Cyto_Gene_Counts_by_Replicate.txt

value: KD SRSF6


title: KD GFP cyto Replicate B


title: KD SRSF7 cyto Replicate A

description:
PolyA+ RNAseq cyto
SRSF7VsGFP_CytoVsWholecell_CuffDiff.txt
Cyto_Gene_FPKMs.txt

value: KD SRSF7


title: MethylC-seq_rd7_rods_rep2

city: Baltimore

first: Alisa

last: Mo

state: MD

address: 725 N. Wolfe St. PCTB805

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description:
processed data files:
MethylC-seq_DMRs_DSS_WT_cones_vs_rd7_rods_hypo_in_Cones.gz;
MethylC-seq_DMRs_DSS_WT_rods_vs_rd7_rods_hypo_in_Rods.gz;
MethylC-seq_DMRs_DSS_WT_rods_vs_rd7_rods_hypo_in_rd7.gz;
MethylC-seq_rd7_rods_UMRs_LMRs.gz;
MethylC-seq_DMRs_DSS_WT_cones_vs_rd7_rods_hypo_in_rd7.gz

data_processing:
Data was mapped to the Mus musculus reference genome (mm10).
Analysis for RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq datasets were performed as described in Mo et al., 2015 (in submission)
RNA-seq: Five base pairs were trimmed from the 5'-end of all reads to remove possible adaptor contamination (seqtk trimfq -b 5)
RNA-seq: Trimmed reads were aligned to the mm10/ERCC92 combined index using TOPHAT v1.4.0 (--GTF --no-novel-juncs) guided by protein coding gene annotation from iGenomes
RNA-seq: Gene expression levels were estimated using RSEM v1.1.20 (--fragment-length-mean 250 --fragment-length-sd 50)
RNA-seq: Visualization tracks were generated by counting genome-wide coverage of reads (BEDTOOLS v2.15.0 genomeCoverageBed -split -bg), scaling to 10M total alignments (custom perl script), and converting to bigWig format (UCSC wigToBigWig).

MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/) for alignment and mC calling
MethylC-seq: DMRs were identified using DSS [Feng H. et al. A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res. 42, e69 (2014)].
MethylC-seq: UMRs and LMRs were identified using MethylSeekR [Burger et al. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, e155 (2013)] using m (methylation) = 0.5 and 5% FDR.

ATAC-seq: Adapter sequences were trimmed from ATAC reads (cutadapt v1.3 -a CTGTCTCTTATACACATCT -q 30 --minimum-length 36 --paired-output)
ATAC-seq: Trimmed reads were aligned to the mm10 genome (BOWTIE2 v2.1.0 -t -X2000 --no-mixed --no-discordant)
ATAC-seq: Redundant reads were removed (picard MarkDuplicates).
ATAC-seq: Peaks were called with MACS2 [Zhang Y. et al. Model-based analysis of ChIP-Seq. Genome Biol. 9, R137 (2008)] (macs2 2.1.0.20140616 callpeak -p 0.00001 --call-summits --nomodel --shift -50 --extsize 100) using sub-nucleosomal (<100bp) fragments. File format is MACS2 narrowPeak.
ATAC-seq: Visualization tracks were generated by counting genome-wide coverage of all fragments (BEDTOOLS v2.15.0 genomeCoverageBed -bg), scaling to 10M total alignments (custom perl script), and converting to bigWig format (UCSC wigToBigWig).

ChIP-seq: Reads were aligned to the mm10 genome, keeping only uniquely aligning reads (BOWTIE v0.12.7 -m 1)
ChIP-seq: Visualization tracks were generated by counting genome-wide coverage of reads (BEDTOOLS v2.15.0 genomeCoverageBed -bg), scaling to 10M total alignments (custom perl script), and converting to bigWig format (UCSC wigToBigWig).
ChIP-seq: Peaks were called with SICER_V1.1 (redundancy threshold = 1; fragment size=150; W=200, G=200 for H3K27ac, H3K4me1, and H3K4me3; W=200, G=1000 for H3K27me3). Overlapping peaks from the 2 replicates were merged (BEDTOOLS merge) to generate 1 set of peaks for each histone modification.

Genome_build: mm10

Supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq, ATAC-seq, and ChIP-seq datasets
tab delimited text files of gene expression levels estimated using RSEM v1.1.20
tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
tab delimited text files of DMRs; columns in DMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - category
tab delimited text files of UMRs and LMRs; columns in UMRs/LMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 - UMR or LMR
tab delimited text files of ATAC-seq peaks; columns in peak files are: column 1 - chromosome; column 2 - start; column 3 - end
tab delimited text files of ChIP-seq peaks; columns in peak files are: column 1 - chromosome; column 2 - start; column 3 - end

source_name: Rods from rd7 mouse retina

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
The retina was rapidly dissected from 1 adult mouse on ice, and the INTACT method was used to affinity purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
MethylC-seq libraries were constructed as previously described [Mo A. et al. Epigenomic signatures of neuronal diversity in the mammalian brain. Neuron 86 1369-84 (2015)]. Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.
RNA-seq: Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA-seq: For preparation of nuclei from the whole retina, the retina was rapidly dissected from 1 adult mouse on ice, homogenized, and nuclei were pelleted by centrifugation. Pelleted nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
Bisulfite-Seq (MethylC-seq): Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
ATAC-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei.
ChIP-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
RNA-seq: RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.
Bisulfite-Seq (MethylC-seq): MethylC-seq libraries were constructed as previously described (Mo et al., 2015). Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.
OTHER: ATAC-seq: Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described (Buenrostro et al., 2013), with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
ChIP-seq: Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). ChIP-enriched and input DNA was end-repaired, linker adapted, and sequenced on an Illumina HiSeq 2500 for 50 cycles.

tag: strain background

value: 8 to 11 weeks

tag: Sex

value: male

value: retina

tag: cell type

value: rd7 rod photoreceptors


title: MethylC-seq_WT_cones_rep2

description:
processed data files:
MethylC-seq_DMRs_DSS_WT_rods_vs_WT_cones_hypo_in_Cones.gz;
MethylC-seq_DMRs_DSS_WT_cones_vs_rd7_rods_hypo_in_Cones.gz;
MethylC-seq_DMRs_DSS_WT_cones_vs_rd7_rods_hypo_in_rd7.gz;
MethylC-seq_WT_cones_UMRs_LMRs.gz;
MethylC-seq_DMRs_DSS_WT_rods_vs_WT_cones_hypo_in_Rods.gz

source_name: Cones from WT mouse retina

extract_protocol:
The retina was rapidly dissected from 2-4 adult mice on ice, and GFP+ nuclei were obtained by flow cytometry. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
MethylC-seq libraries were constructed as previously described [Mo A. et al. Epigenomic signatures of neuronal diversity in the mammalian brain. Neuron 86 1369-84 (2015)]. Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.
RNA-seq: Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
RNA-seq: For preparation of nuclei from the whole retina, the retina was rapidly dissected from 1 adult mouse on ice, homogenized, and nuclei were pelleted by centrifugation. Pelleted nuclei were resuspended in Buffer RLT for RNA purification using the RNeasy Micro kit (Qiagen 74004) with on-column DNase digestion following the standard kit protocol. RNA quality was measured by an Agilent Bioanalyzer.
Bisulfite-Seq (MethylC-seq): Mice retinas were rapidly dissected on ice, and either the INTACT method or flow cytometry was used to purify GFP+ nuclei. Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
ATAC-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei.
ChIP-seq: Mice retinas were rapidly dissected on ice, and the INTACT method was used to purify GFP+ nuclei. Nucleosomes for native ChIP-seq were prepared as previously described [Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Briefly, 1-2 million bead-bound nuclei were digested with 0.025 units/uL micrococcal nuclease (Worthington LS004798) in 500uL of 15mM HEPES pH 7, 1mM KCl, 2mM MgCl2, 2mM CaCl2, 340mM sucrose, 0.15mM spermine, 0.5mM spermidine, and 5mM sodium butyrate at 37°C for 15 minutes. The reaction was terminated by the addition of EGTA to 2mM final concentration. Nucleosomes were extracted for 30 minutes on ice with 200uL 15mM HEPES pH7, 200mM NaCl, 25mM KCl, 2mM MgCl2, 1mM EGTA, 340mM sucrose, 0.15mM spermidine, 0.15mM spermine, and 5mM sodium butyrate. A second 30 minute extraction was performed with the same buffer except the salt concentration was raised to 400mM NaCl. The extracts were combined and dialyzed overnight against 15mM HEPES pH7, 25mM KCl, 1mM β-mercaptoethanol, 1mM PMSF, and 5mM sodium butyrate using a 10K cut-off Slide-a-Lyzer dialysis device (Thermo Scientific 88401).
RNA-seq: RNA (2-50ng) was converted to cDNA and amplified using Nugen Ovation RNA-seq System V2 (Nugen 7102). All RNA samples received a 1:10,000 dilution of ERCC RNA (Life Technologies 4456740). Amplified cDNA was fragmented, end-repaired, linker adapted, and sequenced for 50 cycles on an Illumina HiSeq 2500 instrument.
Bisulfite-Seq (MethylC-seq): MethylC-seq libraries were constructed as previously described (Mo et al., 2015). Libraries were sequenced on an Illumina HiSeq 2000 up to 101 cycles.
OTHER: ATAC-seq: Approximately 50,000 bead-bound nuclei were transposed in a 50uL volume of 1X TD buffer and 2.5uL Tn5 transposase (Illumina FC-121-1030) for 30 minutes at 37°C, as previously described (Buenrostro et al., 2013), with the modification that fragmented genomic DNA was recovered using Buffer QG (Qiagen 28604). Transposed genomic DNA was amplified by five cycles of quantitative PCR. 10% of the PCR was subjected to an additional 20 cycles of SYBR green-based qPCR while the remainder of the sample was left on ice. Analysis of the qPCR data allowed a rough estimate of the number of additional cycles needed to generate product at 25% saturation. Typically, four to seven additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified on AMPure XP beads, analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 2500 for 101 cycles.
ChIP-seq: Native ChIP and library construction were combined [Garber M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810-822 (2012); Henry G.L. et al. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res. 40, 9691-9704 (2012)]. Nucleosomes prepared from 0.5-1 million nuclei were incubated with 1ug antibody and 25uL Protein G Dynabeads. The following antibodies were used: rabbit anti-H3K27me3 (Millipore 07-449), rabbit anti-H3K27ac (Abcam ab4729), rabbit anti-H3K4me3 (Abcam ab8580), and rabbit anti-H3K4me1 (Abcam ab8895). ChIP-enriched and input DNA was end-repaired, linker adapted, and sequenced on an Illumina HiSeq 2500 for 50 cycles.

value: HRGP-Cre; R26-LSL-CAG-Sun1-GFP-myc

tag: tissue

value: WT cone photoreceptors


title: MethylC-seq_WT_rods_rep2

description:
processed data files:
MethylC-seq_DMRs_DSS_WT_rods_vs_WT_cones_hypo_in_Cones.gz;
MethylC-seq_DMRs_DSS_WT_rods_vs_rd7_rods_hypo_in_Rods.gz;
MethylC-seq_DMRs_DSS_WT_rods_vs_rd7_rods_hypo_in_rd7.gz;
MethylC-seq_WT_rods_UMRs_LMRs.gz;
MethylC-seq_DMRs_DSS_WT_rods_vs_WT_cones_hypo_in_Rods.gz

source_name: Rods from WT mouse retina

value: LMOPC1-Cre; R26-LSL-CAG-Sun1-GFP-myc

value: WT rod photoreceptors


title: MethylC-seq_rd7_rods_rep1


title: MethylC-seq_WT_cones_rep1


title: E10_PS34CD45-_09

value: wild type

value: placenta


title: KD SRSF7 cyto Replicate B


title: KD SRSF6 cyto Replicate A

description:
PolyA+ RNAseq cyto
SRSF6VsGFP_CytoVsWholecell_CuffDiff.txt
Cyto_Gene_FPKMs.txt


title: KD SRSF4 cyto Replicate B

value: KD SRSF4


title: KD SRSF3 cyto Replicate B

value: KD SRSF3


title: KD SRSF4 cyto Replicate A

description:
PolyA+ RNAseq cyto
SRSF4VsGFP_CytoVsWholecell_CuffDiff.txt
Cyto_Gene_FPKMs.txt

value: P19 embryonal carcinoma cell line


title: KD SRSF5 cytol Replicate B

value: KD SRSF5


title: E10_PS34CD45-_04

value: embryonic day E10.5


title: KD SRSF2 cyto Replicate B

value: KD SRSF2

value: cytoplasm


title: KD SRSF7 whole cell Replicate B

description:
PolyA+ RNAseq whole cell
WholeCell_Gene_Counts_by_Replicate.txt

value: KD SRSF7

value: whole cell


title: KD SRSF7 whole cell Replicate A

description:
PolyA+ RNAseq whole cell
SRSF7VsGFP_CytoVsWholecell_CuffDiff.txt
WholeCell_Gene_FPKMs.txt


title: KD SRSF6 whole cell Replicate B

value: KD SRSF6


title: KD SRSF5 cyto Replicate A

description:
PolyA+ RNAseq cyto
SRSF5VsGFP_CytoVsWholecell_CuffDiff.txt
Cyto_Gene_FPKMs.txt


title: KD GFP whole cell Replicate A

description:
PolyA+ RNAseq whole cell
WholeCell_Gene_FPKMs.txt

value: KD GFP


title: MethylC-seq_WT_rods_rep1

value: 8 to 11 weeks

value: male

value: retina


title: KD SRSF1 cyto Replicate A

description:
PolyA+ RNAseq cyto
SRSF1VsGFP_CytoVsWholecell_CuffDiff.txt
Cyto_Gene_FPKMs.txt

value: KD SRSF1


title: KD SRSF4 whole cell Replicate B


title: KD SRSF3 cyto Replicate A

description:
PolyA+ RNAseq cyto
SRSF3VsGFP_CytoVsWholecell_CuffDiff.txt
Cyto_Gene_FPKMs.txt


title: KD SRSF4 whole cell Replicate A

description:
PolyA+ RNAseq whole cell
SRSF4VsGFP_CytoVsWholecell_CuffDiff.txt
WholeCell_Gene_FPKMs.txt


title: KD SRSF5 whole cell Replicate B


title: KD SRSF6 whole cell Replicate A

description:
PolyA+ RNAseq whole cell
SRSF6VsGFP_CytoVsWholecell_CuffDiff.txt
WholeCell_Gene_FPKMs.txt


title: KD SRSF5 whole cell Replicate A

description:
PolyA+ RNAseq whole cell
SRSF5VsGFP_CytoVsWholecell_CuffDiff.txt
WholeCell_Gene_FPKMs.txt


title: KD SRSF1 cyto Replicate B


title: KD SRSF1 whole cell Replicate A

description:
PolyA+ RNAseq whole cell
SRSF1VsGFP_CytoVsWholecell_CuffDiff.txt
WholeCell_Gene_FPKMs.txt


title: KD SRSF2 whole cell Replicate A

description:
PolyA+ RNAseq whole cell
SRSF2VsGFP_CytoVsWholecell_CuffDiff.txt
WholeCell_Gene_FPKMs.txt


title: KD SRSF1 whole cell Replicate B


title: KD SRSF3 whole cell Replicate A

description:
PolyA+ RNAseq whole cell
SRSF3VsGFP_CytoVsWholecell_CuffDiff.txt
WholeCell_Gene_FPKMs.txt


title: KD SRSF2 cyto Replicate A

description:
PolyA+ RNAseq cyto
SRSF2VsGFP_CytoVsWholecell_CuffDiff.txt
Cyto_Gene_FPKMs.txt


title: KD SRSF2 whole cell Replicate B


title: KD GFP whole cell Replicate B


title: Control_iCLIP_mm9_Rep3

description:
processed data file: Control_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: Control_iCLIP_all_mm9_iCLIP_clusters.bed

data_processing:
Basecalls performed using CASAVA version 1.4
For detail on data processing see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
Genome_build: mm9
Supplementary_files_format_and_content: .bed files containing the genomic coordinates for significant CLIP tags for individual replicates or combined replicates (3-6 replicates).
Supplementary_files_format_and_content: .bed files containing the genomic coordinates for significant CLIP tag clusters from combined replicates.

extract_protocol:
Cells were lysed and treated with RNase I. GFP-tagged proteins were immunoprecipitated with Gamma binding beads coupled to goat anti-EGFP antibody (D. Drechsel, MPI-CBG).
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer containing a barcode sequence. cDNA was separated into 3 size fractions by denaturing gel electrophoresis and circularized by ssDNA circligase. A specific oligonukelotide was annealed to create a restriction site for BamHI and cDNA was linearized by digest with BamHI. Linearized cDNA was PCR amplifiied with Solexa sequencing primers to create the final libraries. For more details see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

tag: fusion protein expression

value: GFP-NLS

tag: antibody

value: anti-EGFP (D. Drechsel, MPI-CBG)

tag: barcode sequence

value: CCGG


title: Control_iCLIP_mm9_Rep2

value: TTGT


title: Control_iCLIP_mm9_Rep1

value: P19 embryonal carcinoma cell line

value: GGTT


title: Control_iCLIP_mm9_Rep4

value: GGCG


title: NXF1_iCLIP_mm9_Rep1

description:
processed data file: mNXF1_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: mNXF1_iCLIP_all_mm9_iCLIP_tag_clusters.bed


title: NXF1_iCLIP_mm9_Rep2


title: KD SRSF3 whole cell Replicate B

value: KD SRSF3


title: SRSF5_iCLIP_mm9_Rep3

description:
processed data file: mSRSF5_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: mSRSF5_iCLIP_all_mm9_iCLIP_tag_clusters.bed


title: SRSF5_iCLIP_mm9_Rep4


title: SRSF6_iCLIP_mm9_Rep1

description:
processed data file: mSRSF6_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: mSRSF6_iCLIP_all_mm9_iCLIP_tag_clusters.bed

value: CAAT


title: SRSF6_iCLIP_mm9_Rep3


title: Medicago / Gigaspora replicate 3

city: Castanet-Tolosan

first: Christophe

last: Roux

address: Chemin de Borde Rouge

country: France

institute: University of Toulouse/CNRS

description:
RAW Gr Mt vs ERM
57_ATGTCA_L001

data_processing:
G. rosea raw reads trimming and filtration: Short pair-end sequencing reads generated on Illumina platforms (2x100 bp from Hiseq2000 and 2x150 bp from Miseq1000) were trimmed based on the quality scores (limit: 0.05), end ambiguity (maximum number of ambiguities: 2) and adaptor sequences using the commercial software CLC Genomic Workbench (v6.0, CLC Bio, Denmark). The reads less than 50bp after trimming were discarded. As the ERM corresponds to axenic cultures, the trimmed reads from non-symbiotic samples were used for de novo assembly directly. Whereas, in the symbiotic samples (SYM+BD, SYM+MT) which were obtained from plants cultivated in pot, the reads from other organisms including the host plant and potential contaminants need to be filtered away. The plant–originated reads were eliminated when they mapped on the genomes of Brachypodium distachyon (Bd21) v1.0 and Medicago truncatula (A17) v198 (ftp://ftp.jgipsf.org/pub/compgen/phytozome/v9.0/ Mtruncatula/) respectively, using CLC mapping tool. In order to eliminate the plant-originated reads sequences specifically induced in the symbiotic condition but not included in the present genome annotations, the large gap mapping (length fraction: 0.9 and similarity: 0.95) and transcript discovery (with default settings) strategies in CLC software were chosen. After removing the symbiotic reads mapped (length fraction: 0.9 and similarity: 0.9) on the plant genomes (with updated annotations based on the large-gap mapping and transcript discovery mentioned above), the remaining symbiotic reads were also further mapped onto the transcriptomes of non-mycorrhized B. distachyon and M. truncatula roots which were also generated in this study, to detect potential contaminant reads which might be introduced in the greenhouse condition. The symbiotic reads retained after all these filtrations were used for the following de novo assembly.
Gigaspora transcript assembly: in house de novo assembly using 230 084 705 cleaned reads (21 630 065 trimmed and filtered symbiotic reads plus 208 454 640 trimmed nonsymbiotic reads) was performed with CLC workbench. A total of 97 463 contigs were obtained, with an average length of 611bp. To discard possible contaminant sequence relics, we compared these 97463 contigs with NCBI nr/nt DNA database and removed 11131 sequences showing high similarity (blastn, e value cut-off at E-50) to those from other organisms than G. rosea. The remaining 86 332 contigs, constituting the first transcriptome of G. rosea (GiroV1), were considered as the nonredundant virtual transcripts (NRVTs) that will be used for the further annotation and gene expression analysis. The G. rosea transcriptome GiroV1 is approximately 55.5M in size, with an average trancript length of 643 bp and 33% of GC content. The accuracy of this refined assembly was demonstrated by the blastn result that 332 of 428 published G. rosea ESTs (downloaded from NCBI EST database using gigaspora rosea as the key word) could be found in this pool of NRVTs (e value cutoff at e-20, identity>85%). Nearly all (235 of 248) Core Eukaryotic Genes (CEGs) were found to be present in the current transcriptome (tblastn, e value cut-off at E-10), suggesting it covers most of the real transcriptome of G. rosea.
Selection of libraries: Pairwise Pearson correlations were calculated among each triplicates. Libraires with Pearson correlation lower than 0.9 were excluded: Library H4_GTCCGC (Gigaspora ERM replicate 2) and Library 55_AGTCAA (Medicago/Gigaspora replicate 1).
Read mapping: trimmed reads from all triplicates of G. rosea symbiotic samples and extraradical mycelium sample, were mapped back to the G. rosea transcriptome GiroV1 genre repertoire. To calculate gene expression, RNA-seq functionality in CLC software was used, with the settings of minimum mapped read length fraction at 0.95 and minimum similarity at 0.98. To find the NRVTs significantly upregulated during symbiosis, the RPKM of G. rosea NRVT in symbiotic samples was compared with that in their respective extraradical mycelium (ERM) using proportion-based test statistics with a False Discovery Rate (FDR) correction for multiple testing. G. rosea NRVTs were considered as significantly upregulated when meeting the requirements of RPKM fold change>5 and FDR corrected p value<0.05.

organism: Medicago truncatula

source_name: M. truncatula roots associated with R. rosea

growth_protocol: Colonized B. distachyon was achieved by directly inoculating the seedlings of 3 days with sterile spores (50-60 spores per plant), before planting into 1L pot containing sterile charred clay (1 plant per pot). After 6 weeks of growth under a long day photoperiod (16h light/8h dark at 22°C/20°C) with 40% humidity, the finer and yellowish root fragments that tend to be well mycorrhized (Hong et al., 2012) were selected for RNA extraction. A nursery system strategy was adopted to generate the highly mycorrhized M. truncatula, using 4-week of B. distachyon pre-colonized by G.rosea as the nursery plant. After 4 weeks of co-cultivation with B. distachyon under a long day photoperiod (16h light/8h dark at 22°C/20°C) with 40% humidity, only the M. truncatula roots to which there were abundant hyphae attached were enriched under stereomicroscope for RNA extraction. The Colonization level of both hosts was over 80%. Extraradical mycelium of G.rosea was directly extracted from the microbox purchased from Agronutrition S.A. (Labège, France). After dissolving the gel using citrate buffer (Doner & Bécard, 1991), mycelium pellets free of any root material were collected and rinsed in sterile water for further RNA extraction.

extract_protocol:
Biological samples were crushed with a motar and a pestle in liquid nitrogen and mRNA were extracted using RNeasy plant kit (Qiagen), according to the manufacturer instructions.
Samples were sequenced at the Genome and Transriptome platform in Toulouse, France (GeT). mRNA were isolated with polyT beads before processing, libraries were constructed according to the manufacturer's protocol.

treatment_protocol: no treatment was applied

tag: fungus strain

tag: plant species

value: Medicago truncatula A17

value: Roots

tag: growth time

value: 4 weeks


title: SRSF4_iCLIP_mm9_Rep2

description:
processed data file: mSRSF4_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: mSRSF4_iCLIP_all_mm9_iCLIP_tag_clusters.bed

value: TGGC


title: Medicago / Gigaspora replicate 2

description:
RAW Gr Mt vs ERM
56-bis_AGTTCC_L001


title: SRSF4_iCLIP_mm9_Rep1

value: CCAC


title: SRSF4_iCLIP_mm9_Rep3

value: GGTC


title: SRSF2_iCLIP_mm9_Rep5

description:
processed data file: mSRSF2_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: mSRSF2_iCLIP_all_mm9_iCLIP_tag_clusters.bed


title: SRSF5_iCLIP_mm9_Rep1


title: SRSF1_iCLIP_mm9_Rep3

description:
processed data file: mSRSF1_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: mSRSF1_iCLIP_all_mm9_iCLIP_tag_clusters.bed


title: SRSF2_iCLIP_mm9_Rep4


title: Medicago / Gigaspora replicate 1

description:
RAW Gr Mt vs ERM
55_AGTCAA_L001


title: SRSF5_iCLIP_mm9_Rep2


title: NXF1_iCLIP_mm9_Rep3


title: SRSF2_iCLIP_mm9_Rep3


title: SRSF2_iCLIP_mm9_Rep2


title: SRSF1_iCLIP_mm9_Rep4


title: SRSF1_iCLIP_mm9_Rep2


title: SRSF1_iCLIP_mm9_Rep1


title: Gigaspora ERM replicate 3

description:
present as reference in the two processed data files
H5_GTGAAA_L001

organism: Gigaspora rosea

source_name: Extra radical mycelium of Gigaspora rosea

value: hairy roots of Daucus carota DC1

value: fungus alone

value: 6 weeks


title: SRSF6_iCLIP_mm9_Rep2

value: anti-EGFP (D. Drechsel, MPI-CBG)


title: fS248A_Input

city: San Francisco

first: Barbara

last: Panning

state: CALIFORNIA

address: 600, 16TH STREET, S374 - Genentech Hall,

department: Biochemistry and Molecular biology

institute: University of California, San Francisco

description:
Sample name: fS248A_Input
fS248A-Input DNA (short).
Input DNA

data_processing:
RTA 1.13.48 software used for basecalling.
Alignment: Bowtie, discarding duplicate reads, and accepting only uniquely-mapping reads.
Filtering: Fastq-mcf to perform quality trimming (with default settings).
Peak-calling: Merged bins with input-normalized tag density threshold greater than 10.
Normalization: # ChIP tags within 75bp of each 20bp genomic bin - # input tags in same range.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Format: bigWig
Supplementary_files_format_and_content: Content: Input-normalized tag density (# tags within 75bp of each 20bp genomic bin - # input tags in same range).

source_name: fS248A-Tg mESC, input

growth_protocol: fSOX2-Tg and fS248A-Tg are the two mESCs used in this study. We generated mESC lines that express either a FLAG-tagged wild-type SOX2 (fSOX2-Tg) or a S248A (fS248A-Tg) transgene as the sole source of SOX2. SOX2 levels in fSOX2-Tg and fS248A-Tg mESCs are comparable to SOX2 levels in the parental cell line 2TS22C (accession number AES0125, Riken BioResource Center) (Masui et al., 2007). The tagged SOX2 cell lines generated were cultured in standard ESC media (KO-DMEM, 10% FBS, 2 mM glutamine, 1x non-essential amino acids, 1x penicillin/streptomycin, 0.1 mM beta-mercaptoethanol and recombinant leukemia inhibitory factor) supplemented with 1ug/mL doxycycline hyclate (Sigma).

extract_protocol:
Crosslinking and Sonication: The cells from ∼80% confluent 10 cm dishes were crosslinked with 1% formaldehyde for 10 minutes at room temperature. After quenching with 125 mM glycine for 5 min, the cells were washed twice with ice cold 1xPBS. Cell pellets were resuspended in 1ml lysis buffer 1 (50 mM HEPES-KOH (pH 7.6), 140 mM NaCl, 1 mM EDTA, 10%(v/v) Glycerol, 0.5% NP-40, 0.25% Triton X-100, 1X complete protease inhibitor cocktail (PIC) Roche, 11697498001) for 10 min at 4 oC, followed by spin at 1,350 x g for 5 min at 4oC. Discard the supernatant and resuspend the pellet in 1ml of lysis buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1X PIC) for 10 min at 4oC, followed by spin at 1,350 x g for 5 min at 4oC. Finally, resuspend the cell pellet in 700 µl of lysis buffer 3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Sodium deoxycholate, 0.5% N-Lauroylsarcosine, 1X PIC) and sonicate to desired length using Bioruptor (UCD-200; Diagenode, Delville, NJ, USA) for 30 min [10 minutes x 3 times (each cycle consists of 30s on, 30s off) at high settings]. Clarify the lysates by centrifugation at 10,000 rpm in a microcentrifuge for 10min at 4oC. Transfer the supernatant to a new tube and store at -80oC or use it immediately for ChIP. We had two sets of chromatin due to differences in fragment size distribution generated after sonication (long and short) and we used both for library preparation. Long chromatin library was generated from chromatin that still had high molecular weight fragments (1-2Kb-500bp) even after sonication. Short chromatin library was generated using sheared chromatin that had majority of fragments under small molecular weight range (500-200 bp).
Chromatin Immunoprecipitation using FLAG antibody: 50μl Protein G Magnetic beads (New England Biolabs) were washed twice with PBS with 5 mg/ml BSA and 10 μg of anti-Flag M2 antibody (Sigma, F1805) coupled in 500 μl PBS with 5 mg/ml BSA overnight at 4°C. Immunoprecipitation was performed with antibody-coupled beads and sonicated supernatants in ChIP buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) overnight at 4°C. The magnetic beads were washed twice with ChIP buffer, once with ChIP buffer including 500 mM NaCl, four times with RIPA buffer (10 mM Tris-HCl pH8.0, 0.25M LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE buffer (pH 8.0). Chromatin was eluted twice from washed beads by adding elution buffer (20 mM Tris-HCl pH8.0, 100 mM NaCl, 20 mM EDTA, 1% SDS) and incubating for 15 min at 65°C. The eluted DNA and the input samples were then reverse crosslinked at 65oC for overnight, followed by RNase A(0.2 mg/ml) digestion at 37oC for 2h and Proteinase K (0.2 µg/µl) (NEB, P8102S) digestion at 55oC for 1h. The ChIP and input DNA were recovered by phenol-chloroform extraction and ethanol precipitation.
ChIP samples were end-repaired, A-tailed and adaptor ligated using barcode adaptors. 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 (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3' end. DNA purification on Qiagen mini elute columns was performed following each enzyme reactions. The adaptor ligated material was then PCR amplified with Phusion polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 2% agarose gel. The ChIP-seq library samples were purified using Qiagen gel extraction kit, and fragment size distribution was determined on Agilent Bioanalyzer using High Sensitivity DNA chip. Library concentrations were measured using KAPA Library Quantification Kits (Kapa Biosystems, Inc., Woburn, MA) and equal amounts of indexed libraries were pooled and sequenced on the Illumina HiSeq 2000. Sequencing was performed at Center for Advanced Technology, genomics core facility at University of California, San Francisco.

tag: parental cell line

value: mouse embryonic stem cell line

tag: chromatin fragment size

value: short

tag: chip antibody

tag: sequencing lane

tag: 5' adapter barcode


title: R2b_fS248A_short

description:
Sample name: fS248A_2b
Technical replicate of BR-2.
ChIP DNA

source_name: fS248A-Tg mESC, short, ChIP

tag: cell line

value: FLAG M2 (Sigma F1805)


title: R1b_fS248A_long

description:
Sample name: fS248A_1b
Technical replicate of BR-1.
ChIP DNA

source_name: fS248A-Tg mESC, long, ChIP

value: long


title: R2a_fS248A_short

description:
Sample name: fS248A_2a
fS248ASOX2-Biological replicate-2 (BR-2) (short fragment).
ChIP DNA


title: Gigaspora ERM replicate 2


title: Gigaspora ERM replicate 1

description:
present as reference in the two processed data files
H1_ATGTCA_L001


title: Control of GR24 treatment replicate 3

description:
RAW Gr GR24 vs GR24 ctrl.txt
54_CTTGTA_L001

data_processing:
G. rosea raw reads trimming and filtration: Short pair-end sequencing reads generated on Illumina platforms (2x100 bp from Hiseq2000 and 2x150 bp from Miseq1000) were trimmed based on the quality scores (limit: 0.05), end ambiguity (maximum number of ambiguities: 2) and adaptor sequences using the commercial software CLC Genomic Workbench (v6.0, CLC Bio, Denmark). The reads less than 50bp after trimming were discarded.
Gigaspora transcript assembly: in house de novo assembly using 230 084 705 cleaned reads (21 630 065 trimmed and filtered symbiotic reads plus 208 454 640 trimmed nonsymbiotic reads) was performed with CLC workbench. A total of 97 463 contigs were obtained, with an average length of 611bp. To discard possible contaminant sequence relics, we compared these 97463 contigs with NCBI nr/nt DNA database and removed 11131 sequences showing high similarity (blastn, e value cut-off at E-50) to those from other organisms than G. rosea. The remaining 86 332 contigs, constituting the first transcriptome of G. rosea (GiroV1), were considered as the nonredundant virtual transcripts (NRVTs) that will be used for the further annotation and gene expression analysis. The G. rosea transcriptome GiroV1 is approximately 55.5M in size, with an average trancript length of 643 bp and 33% of GC content. The accuracy of this refined assembly was demonstrated by the blastn result that 332 of 428 published G. rosea ESTs (downloaded from NCBI EST database using gigaspora rosea as the key word) could be found in this pool of NRVTs (e value cutoff at e-20, identity>85%). Nearly all (235 of 248) Core Eukaryotic Genes (CEGs) were found to be present in the current transcriptome (tblastn, e value cut-off at E-10), suggesting it covers most of the real transcriptome of G. rosea.
Read mapping: trimmed reads from all triplicates of G. rosea samples, were mapped back to the G. rosea transcriptome GiroV1 genre repertoire. To calculate gene expression, RNA-seq functionality in CLC software was used, with the settings of minimum mapped read length fraction at 0.95 and minimum similarity at 0.98. To find the NRVTs significantly upregulated after stimulation with plant signals, the RPKM of G. rosea NRVT treated samples were compared to their respective control using proportion-based test statistics with a False Discovery Rate (FDR) correction for multiple testing. G. rosea NRVTs were considered as significantly upregulated when meeting the requirements of RPKM fold change>5 and FDR corrected p value<0.05.

source_name: germinating spores

growth_protocol: for the samples from 49 to 54, 500-600 spores of G.rosea were germinated in the liquid M medium supplemented with 0.02% of Phytagel for 5 days in the dark with 2% CO2 before treatment and then were maintained under the same conditions for another 2 days after treatment. for the samples from 43 to 45 young carrot (Daucus carota; DC1) hairy roots (Becard &Fortin, 1988) were transferred into fresh M medium petri-dish (14.5cm in diameter) containing 1% of sucrose (Becard &Fortin, 1988), gelled with 0.3% of Phytagel (Sigma) and then covered with sterile cellophane membrane. The covered carrot roots were cultivated in growth chamber (22-25 degrees in dark) for around 2 weeks until they spread out. Then 500-600 in vitro cultured G.rosea spores were pipetted onto the cellophane membrane and incubate in a CO2 chamber (2% of CO2, in dark) for 10 days until observed strong branching effect. Control samples from 46 to 48 were grown under the same conditions except the addition of carrot hairy roots.

extract_protocol:
Spores were crushed with a motar and a pestle in liquid nitrogen and mRNA were extracted using RNeasy plant kit (Qiagen), according to the manufacturer instructions.
Samples were sequenced at the Genome and Transriptome platform in Toulouse, France (GeT). mRNA were isolated with polyT beads before processing, libraries were constructed according to the manufacturer's protocol.

treatment_protocol: Samples 1 to 6: germinating spores were treated either with the strigolactone GR24 at a final concentration of 10-6M, or with Acetone 1/1000 and collected 2 days after growing in the same previous conditions.  Samples 43 to 45 carrot hairy root exudates were naturally produced and kept interacting with the germinating spores since the deposition of G.rosea spores to the cellophane membrane.

tag: strain

tag: treatment

value: Acetone 1/1000

tag: growth time post induction

value: 2 days


title: fSox2-Input

description:
Sample name: fSOX2_Input
fSOX2-Input DNA (long).
Input DNA

source_name: fSOX2-Tg mESC, input

tag: cell type


title: R2a_fSox2_short

description:
Sample name: fSOX2_2a
fSox2-Biological replicate-2 (BR-2) (short fragment).
ChIP DNA

source_name: fSOX2-Tg mESC, short, ChIP


title: R1a_fS248A_long

description:
Sample name: fS248A_1a
fS248ASOX2-Biological replicate-1 (BR-1) (long fragment).
ChIP DNA


title: R2b_fSox2_short

description:
Sample name: fSOX2_2b
Technical replicate of BR-2.
ChIP DNA


title: GR24 treated G.rosea replicate 3

description:
RAW Gr GR24 vs GR24 ctrl.txt
51_ACAGTG_L001


title: GR24 treated G.rosea replicate 2

description:
RAW Gr GR24 vs GR24 ctrl.txt
50_TGACCA_L001


title: R1a_fSOX2_long

description:
Sample name: fSOX2_1a
fSOX2-Biological replicate-1 (BR-1) (long fragment).
ChIP DNA

source_name: fSOX2-Tg mESC, long, ChIP


title: GR24 treated G.rosea replicate 1

description:
RAW Gr GR24 vs GR24 ctrl.txt
49-bis_CGATGT_L001


title: Control of GR24 treatment replicate 1

description:
RAW Gr GR24 vs GR24 ctrl.txt
52_GCCAAT_L001


title: Ter119_HSPC_2

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Sequence library reads were trimmed for adapter sequence, low quality and low complexity reads removed using FASTX-toolkit suite
Alignment to mm9 using Tophat release v2.0.12 and Bowtie2 release v2.2.3
Differential expression performed with Cufflinks release v2.2.1 and Mus musculus mm9 reference annotation
Genome_build: mm9
Supplementary_files_format_and_content: FPKM tables derived from Cufflinks cuffdiff output Ter119_FPKM.txt.gz output tab-delimited file, zero-values removed.  See reference at http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track and Trapnell et al. Nat Biotech 2010.

source_name: placenta

growth_protocol: cultured on OP9 stromal layers for 4 days and then in methylcellulose containing media [M3434 Stem Cell Technologies, Inc.] for 14 days

extract_protocol:
Cells were sorted by FACS and RNA was isolated using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with total RNA extracted from sorted cells for the construction of sequencing libraries Illumina protocols with the exception of the multiplexing barcodes introduction at the PCR amplification stage.

tag: developmental stage

value: embryonic day E12.5

tag: genotype

value: wildtype

value: Ter119+ derived from hematopoeitic stem/progenitor cells


title: Ter119_PS34_2

value: Ter119+ derived from hemogenic precursor cells [Prom1+Sca1+CD34+CD45-]


title: E12_HSPCs_2

data_processing:
Illumina Casava 1.8.2 software used for basecalling and demultiplexing.
Sequence library reads were trimmed for adapter sequence, low quality and low complexity reads removed using FASTX-toolkit suite
Alignment to mm9 using Tophat release 2.0.9 and Bowtie2 release2.1.0
Differential expression performed with Cufflinks release 2.1.1 and Mus musculus mm9 reference annotation
Genome_build: mm9
Supplementary_files_format_and_content: FPKM tables derived from Cufflinks cuffdiff output Placenta_FPKM_table.txt output tab-delimited file, zero-values removed.  See reference at http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track and Trapnell et al. Nat Biotech 2010.

extract_protocol:
Cells were sorted by FACS and RNA was isolated using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with up to 1 ug of total RNA for the construction of sequencing libraries Illumina protocols with the exception of the multiplexing barcodes introduction at the PCR amplification stage.

tag: embryonic day


title: E12_MBC_1


title: Ter119_PS34_1


title: SRSF2_iCLIP_mm9_Rep1

description:
processed data file: mSRSF2_iCLIP_all_mm9_iCLIP_tags.bed
processed data file: mSRSF2_iCLIP_all_mm9_iCLIP_tag_clusters.bed

value: P19 embryonal carcinoma cell line

tag: fusion protein expression

tag: antibody

tag: barcode sequence

value: GGCG


title: Control of root exudates treatment replicate 3

description:
RAW Gr RE vs RE ctr.txt
48_ATTCCT_L004

value: No treatment

value: 10 days


title: E12_cKit-_2


title: Control of root exudates treatment replicate 2

description:
RAW Gr RE vs RE ctr.txt
47_ACTGAT_L004


title: E12_cKit-_1


title: E12_HSPCs_1


title: Control of GR24 treatment replicate 2

description:
RAW Gr GR24 vs GR24 ctrl.txt
53-bis_CAGATC_L001


title: E12_cKit+_2


title: Root exudates treated G.rosea replicate 2

description:
RAW Gr RE vs RE ctr.txt
44_GTTTCG_L004

value: Root exudates


title: Root exudates treated G.rosea replicate 3

description:
RAW Gr RE vs RE ctr.txt
45_CGTACG_L004


title: E10_MBC_1

value: embryonic day E10.5


title: E12_45+_1


title: R1b_fSox2_long

description:
Sample name: fSOX2_1b
Technical replicate of BR-1.
ChIP DNA


title: Ter119_HSPC_1


title: Root exudates treated G.rosea replicate 1

description:
RAW Gr RE vs RE ctr.txt
43_GTGGCC_L004


title: E10_HSPCs_2


title: DKO_078

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
RNA-seq reads were aligned to the GRCm37/mm9 build of the Mus musculus genome using the Subread aligner. Mapping quality score was used to break the tie when more than one best location was found for a read.
Genewise counts were obtained using featureCounts. Only reads overlapping with the last 3000 exonic bases (located at 3’ end) of each gene were counted because only these bases in the genes were sequenced in this experiment. All exonic bases will be used for read counting if a gene has a total exon length of less than 3000 bases. NCBI RefSeq mouse annotation build 37.2 was used in the analysis.
Genes were filtered from downstream analysis if they failed to achieve a RPKM (reads per kilobase of exon length per million mapped reads) value of at least 0.5 in at least two libraries. Differential expression analysis was performed using Biconductor R package edgeR. A negative binomial generalized log-linear model was fitted to each gene, and likelihood ratio tests were performed to assess differential expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.1 or less and also had at least 8 RPKMs in one or both of the two cell types being compared.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including log2-RPKM values for genes in each sample

source_name: IL2ra-/-Blimp1LckCre (DKO) Bone marrow

extract_protocol:
NP366+ CD8+ T cells were purified by flow cytometric sorting from day 9 HKx31-infected PR8-primed mixed bone marrow chimeras. Total RNA was prepared using a Qiagen RNeasy Plus Mini Kit (Qiagen) according to the manufacturers instructions. RNA-seq was carried out based on a previously published single-cell protocol (Tang, F. et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nature protocols 5, 516-535, 2010). Samples were sequenced on a Solexa 1G Genome Analyzer instrument (Illumina) at the National Heart Lung and Blood Institute.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: CD8+ T cells

tag: reporter

tag: mrna extraction

value: Single-cell


title: CD25KO_GA1928

source_name: IL2ra-/-  (IL2raKO) Bone marrow


title: TbetKO_083

source_name: Tbx21-/- (T-betKO) Bone marrow


title: CD25KO_BlimpCKO_GA1926


title: E10_HSPCs_1


title: E10_cKit-_1


title: CD25KO_074

source_name: IL2ra-/- (IL2raKO) Bone marrow


title: BlimpCKO_GA1930

source_name: Blimp1LckCre (Blimp1KO) Bone marrow


title: E10_45+_2


title: Blimp1KO_076


title: E10_cKit+_1


title: WT_GA1931

source_name: Wildtype (WT) Bone marrow


title: E10_cKit+_2


title: Control of root exudates treatment replicate 1

description:
RAW Gr RE vs RE ctr.txt
46_GAGTGG_L004


title: E10_cKit-_3


title: E12_cKit+_1


title: E12_45+_2


title: WT_GA1929


title: E10_cKit-_2


title: TbetKO_081


title: Brachypodium / Gigaspora replicate 3

description:
RAW Gr Bd vs ERM
42_GGCTAC_L004

organism: Brachypodium distachyon

source_name: B. distachyon roots associated with R. rosea

tag: fungus strain

tag: plant species

value: Brachypodium distachyon Bd21

tag: tissue

value: Roots

tag: growth time

value: 6 weeks


title: WT_079


title: WT_082


title: WT_075


title: Brachypodium / Gigaspora replicate 2

description:
RAW Gr Bd vs ERM
41_TAGCTT_L004


title: WT_080


title: E10_45+_1


title: WT_GA1927


title: Brachypodium / Gigaspora replicate 1

description:
RAW Gr Bd vs ERM
40_GATCAG_L004


title: NSF1_WT-3

source_name: Stem differentiating xylem

tag: gene perturbation type

value: wild type control

tag: batch of trees

value: Stem differentiating xylem


title: NSF1_WT-2


title: NSF1_WT-1