title: miwi2HET_Liver_H3K9me3_replicate2


title: miwi2KO_GermCellsTestis_MACS_inputDNA

status: Public on Jun 13 2014

type: SRA

city: Pasadena

first: Sergei

middle: A

last: Manakov

address: 1200 E California blvd, MC 147-75

department: Biology and Biological Engeneering

country: USA

institute: California Institute of Technology

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP124

library_source: genomic

data_processing:
To assess ChIP signal distribution genome-wide and on TE bodies we consider all reads that mapped to the genome (mm10) with bowtie 0.12.7(Langmead et al. 2009) of up to 10,000 positions allowing for zero mismatches. This cut-off was used to speed- up the computation without sacrificing relevant information: It eliminates, on average, only 0.25% of distinct sequences (0.3% to 0.6% reads) of which about a third are derived from simple repeats (Table S2). For each read, we assigned the multiplicity score (NH) equal to the total number of valid alignments of that read in the genome.
Next, we divided the genome into four genomic partitions: exons, introns, and transcription start sites (TSSs) of genes and the intergenic space. Exons were defined as the region of the genome covered by any of the exons annotated by RefSeq(Pruitt et al. 2009) (RefSeq Gene table was downloaded from the UCSC genome browser(Meyer et al. 2013)); introns were defined as the regions between exonic partitions within the boundaries of a region covered by RefSeq transcripts belonging to any gene. Regions that were between exonic partitions but outside of the gene boundaries were defined as the intergenic space. The TSSs of a given gene was defined as the 1-kB region around the 5' end of the most outstanding transcript annotated to that gene (±500 bp). After the genomic partitions were defined, we counted reads that were mapped within partitions. Each read count was weighed by the multiplicity score (NH) associated with the read, thus each read i incremented the sum of reads by 1/NHi. If a read overlapped with more than one partition, then the read was assigned to the partition that contained the readʼs 5'-nucleotide. With the weighted counts, we calculated how many reads were mapped to each individual partition. Then, for each of the four partition types, counts of reads in individual partitions were totaled. Finally, for each of the four partition types, the total counts of reads were converted into reads per kilobase of sequence per million mapped reads (RPKM) values in order to account for differences in library depths and differences in lengths of partitions.
ChIP signal in TE families and classes was defined in the manner analogous to the one described above for genomic partitions. We considered regions annotated by RepeatMasker (Smit, AFA, Hubley, R. RepeatModeler Open-1.0. 2008-2010 http://www.repeatmasker.org) in the UCSC genome browser for mm10 genome(Meyer et al. 2013) as belonging to a particular family of TEs to comprise one type of genomic partition. Similarly, partition types were defined for repeat classes such as LTRs, LINEs, and satellites. We then calculated how many weighted reads were mapped to each individual partition and subsequently totaled the counts for partitions of each type. Finally, for each partition type, the counts were converted into RPKM values. ChIP enrichment was defined as the ratio of RPKMs between ChIP and input libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Description of fiellds in “gtf.tab” files: (1) Chromosome (2) start position (3) end position (4) type of genomic partition (5) RPKM (6) read count. Description of fields in “rmsk.tab” files: (1) Indexing field to speed chromosome range queries (2) Smith Waterman alignment score (3) Base mismatches in parts per thousand (4) Bases deleted in parts per thousand (5) Bases inserted in parts per thousand (6) Genomic sequence name (7) Start in genomic sequence (8) End in genomic sequence (9) -#bases after match in genomic sequence (10) Relative orientation + or - (11) Name of repeat (12) Class of repeat (13) Family of repeat (14) Start (if strand is +) or -#bases after match (if strand is -) in repeat sequence (15) End in repeat sequence (16) -#bases after match (if strand is +) or start (if strand is -) in repeat sequence (17) First digit of id field in RepeatMasker .out file. Best ignored. (18) RPKM (19) read count

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
In case of testicular cells, fixed cells were sorted using either FACS or MACS. Cells were sonicated in lysis buffer, and histone-DNA complexes were isolated from the cleared lysate using a-H3K9me3 antibody.
ChIP-seq libraries were constructed using NEBNext ChIP-seq Library Prep Master Kit (NEB, E6240) and amplified using NEBNext Multiplex Oligos for Illumina (NEB, E7335). Final libraries were purified from 1.2% agarose gel - 200-450 bp fragments were excised. RNA-seq libraries were consucted using Illumina TruSeq RNA sample prep kit (v2, 48 rxns, RS-122-2001).

tag: strain background

tag: age

value: post natal day 10

tag: genotype/variation

value: Miwi2 KO

tag: tissue/cell type

value: testicular germ cells, MACS-sorted


title: U937, D207N 0h

city: Rockville

first: Daekwan

last: Seo

state: MARYLAND

address: 1330 Piccard Dr., Ste 103

department: Bioinformatics

institute: Psomagen Inc

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor, low-quality, and artifact sequence, then mapped to hg19 with HIV genome using Tophat v.2.0.9 with parameters -p 4 --b2-very-sensitive
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using bam2rpkm v.0.06 from the University of Liverpool. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19 with HIV-1 NL4-3
Supplementary_files_format_and_content: tab-delimited text files include genes, transcripts, and RPKM values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: U937 monocytic cells infected with HIV-1-GFP

growth_protocol: U937 cells were grown in RPMI1640 supplemented with 10% fetal bovine serum, 100U/ml of penicillin, 100㎍/ml of streptomycin, and 2 mM GlutaMAX-I(Gibco). U937 cells (0.5 x 106 cells/ml) were seeded in 12-well plates and differentiated for 20 h in PMA (30 ng/ml). The cells were infected with 100 ng of viruses for 2 h and harvested at indicated time.

extract_protocol:
RNA was harvested using Trizol reagent. 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

tag: time points post-infection

tag: transduced gene

value: SAMHD1 D207N


title: miwi2HET_Liver_inputDNA_replicate2

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP84

value: Miwi2 Het

value: liver


title: miwi2HET_Liver_inputDNA_replicate3


title: miwi2KO_GermCellsTestis_MACS_H3K9me3_replicate1

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP45

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: U937, WT 3h

value: SAMHD1 Wild Type


title: KH2 control, No Dox (E13.5)

city: Cambridge

first: Yarden

last: Katz

state: MA

address: 9 Cambridge Center

department: Dept. of Biology and Whitehead Institute

institute: MIT

description:
RNA-Seq, paired end
E13.5_KH2_NoDox_A

data_processing:
Alignment to mouse genome (mm9) using Bowtie/Tophat followed by calculation of RPKM using constitutive exons of protein-coding (CDS-containing) genes.
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values for samples. Contains the gene ID (Ensembl), the read counts in the set of constitutive exons, the length of the region being considered (sum of lengths of constitutive exons), and the RPKM value.

source_name: NSCs

extract_protocol: Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for paired end RNA sequencing using Illumina paired end sequencing primers.

tag: developmental stage

tag: time point

value: 72 hours

tag: treatment

value: No Dox


title: miwi2HET_GermCellsTestis_MACS_H3

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP123

value: Histone H3, C-terminal antibody (pAb)

value: Active Motif


title: miwi2HET_SomaticCellsTestis_MACS_H3K9me3_replicate2

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP91

value: testicular somatic cells, MACS-sorted


title: U937, WT 1h


title: U937, WT 0h


title: miwi2KO_GermCellsTestis_MACS_H3K9me3_replicate3

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP101


title: miwi2HET_SomaticCellsTestis_MACS_inputDNA_replicate1

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP38


title: U937, Mock 3h

value: Mock


title: miwi2HET_GermCellsTestis_MACS_inputDNA_replicate1

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP40


title: miwi2HET_SomaticCellsTestis_MACS_H3K9me3_replicate1

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP39


title: miwi2HET_Liver_H3K9me3_replicate1


title: U937, Mock 1h


title: miwi2HET_Liver_inputDNA_replicate1


title: miwi2KO_GermCellsTestis_MACS_inputDNA_replicate3

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP100


title: miwi2KO_Testis_RNA

molecule: polyA RNA

value: total testis


title: U937, Mock 0h


title: miwi2HET_Testis_RNA


title: miwi2KO_GermCellsTestis_FACS_inputDNA

value: testicular germ cells, FACS - sorted


title: miwi2HET_GermCellsTestis_FACS_H3K9me3


title: miwi2KO_GermCellsTestis_FACS_H3K9me3


title: CAL-1-E2-2-ChIP

city: New York

first: Hiyaa

middle: Singhee

last: Ghosh

state: NY

address: 701 W 168th Street

institute: Columbia University Medical Center

description: "subpeaks" bed file is generated by splitting the peaks in the peaks_peaks.bed file

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIPSeq reads were aligned to the human hg19 genome using the short read aligner Bowtie (2.0.0)
Significantly enriched ChIP regions were identified using the Model-based analysis of ChIP-Seq (MACS) (1.4.0) using input chromatin as controls
Identified enriched regions were further split using PeakSplitter v1.0 with default settings
Genome_build: hg19
Supplementary_files_format_and_content: BED files were generated by MACS. The 5th column of MACS-generated bed files is the -10*log10pvalue of peak region.

source_name: CAL-1 cell line

growth_protocol: Cells were maintained in RPMI 1640 with 10% FBS

extract_protocol:
Chromatin was fragmented from lysated using covaris protocol in a covaris sonicator, and Mtg16 or E2-2 -DNA complexes were isolated with antibody.
Library construction and sequencing were performed at the Yale Center for Genome Analysis. Briefly, magnetic AMPure XP beads (Beckman Coulter) are used to purify the user-sheared DNA samples and remain with the sample throughout library construction.  Following each process step, DNA is selectively precipitated by weight and re-bound to the beads through the addition of a 20% polyethylene glycol, 2.5 M NaCl solution.  Following fragmentation, T4 DNA polymerase and T4 polynucleotide kinase blunt end and phosphorylate the fragments.  The large Klenow fragment then adds a single adenine residue to the 3' end of each fragment and custom adapters (IDT) are ligated using T4 DNA ligase.  The inserts are size-selected in-solution and adapter-ligated DNA fragments are then PCR amplified using custom-made primers (IDT).  During PCR, a unique 6 base index is inserted at one end of each DNA fragment. Samples were sequenced on a single-end version 3 Illumina flow cell on a HiSeq 2000

tag: cell line

tag: antibody

value: E2-2 Ab is a rabbit monoclonal Ab generated in Dr. Louis Staudt's lab


title: CAL-1-Mtg16-ChIP

value: Mtg16 is a goat polyclonal Ab from santa cruz biotech (C20)


title: mef-wt [MethylC-Seq]

city: Frederick

first: Scott

last: Durum

state: MD

address: Building 560, Room 31-71

department: CCR

institute: National Cancer Institute

data_processing:
Data were mapped to the Mus musculus reference genome (mm9).
MethylC-Seq analyses were performed as described in Lister, Mukamel et al. Global epigenomic reconfiguration during mammalian brain development. Science (2013).
Genome_build: mm9
Supplementary_files_format_and_content: Txt

source_name: WT MEFs

growth_protocol: Lsh WT and Lsh KO MEFs were maintained in DMEM supplemented with 10% (vol/vol) FBS (Gibco), 2 mM Glutamax (Invitrogen), and 1% penicillin and streptomycin (Invitrogen). WT mouse ES cells (CCE cell line) were cultured on gelatin-coated plates and maintained in Knockout DMEM supplemented with 15% (v/v) Knockout serum replacement (KOSR, Invitrogen), 0.1mM β-mercaptoethanol (BME, Sigma), 0.1mM MEM non-essential amino acid (NEAA, Invitrogen), 2mM Glutamax (Invitrogen), 1% (v/v) penicillin-streptomycin (Invitrogen) and 1,000 U/ ml of leukemia inhibitory factor (LIF, Millipore)

extract_protocol:
Genomic DNA was purified from cells using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. MethylC-Seq libraries were constructed as descibed previously [Lister R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells, Nature 471, 68-73 (2011)], except library amplification was performed with either PfuTurboCx Hotstart DNA polymerase (Agilent Technologies, Santa Clara, CA, USA) or KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA, USA).
MethylC-Seq (Bisulfite-Seq): Genomic DNA was purified from cells using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. MethylC-Seq libraries were constructed as descibed previously [Lister R. et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells, Nature 471, 68-73 (2011)], except library amplification was performed with either PfuTurboCx Hotstart DNA polymerase (Agilent Technologies, Santa Clara, CA, USA) or KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA, USA).
Genomic DNA was purified from MEFs and ES cells, sheared by sonication to 50-500 bp, ligated to methylated single-end Illumina adaptors, fragments of 140-210 bp isolated after agarose gel electrophoresis, bisulfite converted, amplified by PCR and sequenced using the Illumina HiSeq 2000 according to manufacturer's instructions

treatment_protocol: Primary  MEF cells were derived from the body of E13.5 C57Bl/6 mouse embryos and genotyping was performed to select Lsh WT and Lsh KO. WT ES cell (CCE ) is an embryonic stem cell line used in our institute's facility to generate transgenic mice.

tag: strain

tag: genotype

value: wild type

tag: tissue

value: primary MEFs


title: CAL-1 input


title: Ptf1a_ChIP_Ctrl

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

description: Ptf1a Tel Ctrl

data_processing:
Basecalls performed using CASAVA
Sequence reads were mapped to the mm9 assembly of the mouse genome with Bowtie v0.12.9 (-q -m 1 -v 2 --best)
Duplicate reads were removed, and the remaining unique reads were normalized to a 10 million read count for peak calling analysis.
Peak calling was performed by HOMER using an FDR cutoff of 0.001. Putative peaks were required to have 4-fold enrichment over the control/input sample and a cumulative Poisson p-value of <0.0001
Genome_build: mm9
Supplementary_files_format_and_content: The bedgraph files show sequence density across mm9 genome.

source_name: E12.5 Neural Tube

extract_protocol:
For Ptf1a and Rbpj E12.5 neural tube mouse embryos placed in Buffer A (15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 0.2 mM EDTA, 0.5 mM EGTA, 0.34 M sucrose) on ice. Nuclei were  liberated by Dounce homogenization and purified by centrifugation through a sucrose gradient (15 mM HEPES pH 7.6, 60 mM KCl, 15 mM NaCl, 0.1 mM EDTA, 0.25 mM EGTA, 1.25 M sucrose). Nuclei were then fixed in 1% formaldehyde for 10 minutes at 30°C, and fixation was terminated by adding glycine to a final concentration of 0.125 M. After centrifuging through another sucrose gradient, fixed nuclei were lysed in sonication buffer (1% Triton, 0.1% sodium deoxycholate, 150 mM NaCl, 50 mM Tris, 5 mM EDTA). Chromatin was sheared using a Diagenode Bioruptor for 30 minutes on high power with 30 second on:off cycles.
For Ascl1, ChIP E12.5 mouse neural tubes were dissected into PBS then fixed in 1% formaldehyde for 15 min and lysed in 1% SDS, 10 mM EDTA, and 50 mM Tris. Sonication was performed using a Bioruptor (Diagenode) at high power settings for 45 cycles (30 sec on/30 sec off).
All libraries were made according to Illumina’s ChIP-seq DNA sample prep protocol

value: ICR

value: Lab generated rabbit anti-Ptf1a


title: mef-Lshko [MethylC-Seq]

source_name: Lsh KO MEFs

value: Lsh KO


title: ES [MethylC-Seq]

source_name: CCE-ES cell line

value: cell line

value: CCE

value: blastocyte


title: miwi2KO_GermCellsTestis_MACS_inputDNA_replicate1

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP44

tag: strain background

tag: age

value: post natal day 10

value: Miwi2 KO

value: testicular germ cells, MACS-sorted


title: miwi2HET_GermCellsTestis_MACS_inputDNA

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP122

tag: genotype/variation

value: Miwi2 Het

tag: tissue/cell type


title: miwi2HET_GermCellsTestis_MACS_H3K9me3_replicate1

description:
MACS; Antibody: sc-53532, Santa Cruz, rat monoclonal, clone G8.8; Beads: anti-rat IgG Micro Beads (Miltenyi Biotec, 130-048-502)
DP41

value: Abcam


title: Rna_Ascl1_het_2

description: mRNA from FACS sorted GFP cells

data_processing:
Basecalls performed using CASAVA
Sequence reads were aligned to the mm9 build of the mouse genome using TopHat v2.0.8.
Biological replicate were specified and used to build an expression level model determined by the FPKM method of Cuffdiff v2.1.1 . Upper quartile normalization (-N option) was performed to more accurately estimate levels of low-abundance transcripts, and multiple read correction (-u option) was selected to better distribute reads mapping to multiple genomic locations. To correct any sequence-specific bias introduced during the library preparation option –b was used. All other settings were left at default values.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited .txt file showing FPKM values for each sample type

source_name: E11.5 Neural Tube

extract_protocol:
Mouse E11.5 neural tubes were dissected from Ascl1 GFP knockin or 12.4kbPtf1a::mCherry;Ptf1a Cre knockin embryos into DMEM/F12 on ice and dissociated in 0.25% trypsin for 15 minutes at 37°C. Trypsin activity was quenched with 2% fetal bovine serum, and GFP positive cells were purified from the resulting single cell suspension by fluorescence activated cell sorting. Total RNA from the sorted cells was extracted and purified with Zymo’s Mini RNA Isolation Kit.
Neural tube libraries were made according to Illumina’s mRNA-seq sample prep protocol.


title: NT_Input_Ctrl

description: NT Input control

value: none (input)


title: Rna_Ascl1_mut_2

description: mRNA from FACS sorted GFP cells


title: ChIP-seq_Rbpj_NT_1

description: Rbpj NT

value: Lab generated rabbit anti-Rbpj


title: ChIP-seq_Ptf1a_NT_2

description: Ptf1a ChIP


title: PTG KO on high-fat diet, rep1

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
Read alignment and junction mapping was accomplished using TopHat2 v2.0.4 using a 25 bp 5' segment seed for initial mapping followed by differential gene expression analysis using Cuffdiff v2.0.2 to map reads to the reference genome annotation (NCBI mouse build 37.2).
BEDTools was used to generate bedGraphs from the bam files generated from TopHat2.
Bigwig files were generated from bedGraphs using the bedGraph to bigwig command from UCSC.
Genome_build: MGSCv37
Supplementary_files_format_and_content: BigWig files for UCSC browser viewing.

source_name: liver, PTG KO, high-fat diet

growth_protocol: All mice were maintained in temperature- and humidity-controlled conditions with a 12hr light/dark cycle with free access to food and water.

extract_protocol:
Total RNA was isolated from ~30mg liver tissue using Trizol (Invitrogen) and the RNeasy mini kit with on-column DNase digestion (Qiagen) according to the manufacturers' instructions.
Standard Illumina RNA library construction with multiplexing.

treatment_protocol: Male mice between 8-10 weeks were given a high-fat diet (45% fat, D12451 Research Diets Inc.) for 12 weeks or were continued on a normal chow diet (4.5% fat, 5L0D Lab Diet) for the same duration. All of the mice were fasted 12hrs overnight and sacrificed between 8 to 10am. Liver tissues were taken out and immediately frozen in liquid nitrogen and stored at -80C.

value: PTG KO

tag: gender

value: male

value: liver

value: high-fat diet


title: PTG KO on high-fat diet, rep3

description:
PTG_KO_HFD3
Biological replicate.


title: PTG KO on high-fat diet, rep2

description:
PTG_KO_HFD2
Biological replicate.


title: WT control on high-fat diet, rep1

source_name: liver, wild type, high-fat diet

value: wild type


title: WT control on high-fat diet, rep2

description:
PTG_WT_HFD2
Biological replicate.


title: Rna_Ptf1a_mut_1

description: mRNA from FACS sorted mCherry cells

value: ICR


title: Rna_Ptf1a_mut_2

description: mRNA from FACS sorted mCherry cells


title: WT control on high-fat diet, rep3

description:
PTG_WT_HFD3
Biological replicate.


title: Rna_Ptf1a_het_1

description: mRNA from FACS sorted mCherry cells


title: PTG KO on normal chow diet, rep1

source_name: liver, PTG KO, normal chow diet

value: normal chow diet


title: miwi2HET_GermCellsTestis_FACS_inputDNA

value: testicular germ cells, FACS - sorted


title: WT control on normal chow diet, rep1

source_name: liver, wild type, normal chow diet


title: Rna_Ascl1_het_1

description: mRNA from FACS sorted GFP cells


title: WT control on normal chow diet, rep2

description:
PTG_WT_ND2
Biological replicate.


title: Population mRNA-seq_MGH31DGC

status: Public on Jun 12 2014

city: BOSTON

first: Anoop

last: Patel

address: 185 Cambridge St

department: Pathology

institute: Massachusetts General Hospital

description:
MGH31 GSC differentiated in DMEM+10% FCS for 7 days
processed data file: GBM_data_matrix.txt

data_processing:
Basecalls performed using Bcl2fastq 1.8 (Illumina)
Paired-end 25bp reads were mapped to the UCSC human transcriptome (hg19) by Bowtie  (version 1.4.1, with parameters -n 0 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 –S)
Expression levels of all genes were estimated by RSEM (version 1.2.3, using the option estimate-rspd and default parameters)  using only reads with exact matches
TPM values as defined by RSEM were added a value of 1 (to avoid zeros) and then log2-transformed. 5,948 genes with the highest composite expression either across all cells combined (average log2(TPM)>4.5) or within a single tumor (average log2(TPM)>6 in at least one tumor) were included. Cells expressing less than 2,000 of these 5,948 genes were excluded. Data was centered by subtracting the mean.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file containing normalized, centered transcripts per million (TPM) values for 5,948 genes in each single cell and population controls

source_name: Population mRNA-seq_MGH31

growth_protocol: Gliomasphere cell lines were cultured in Neurobasal Medium supplemented with 1x B27, 0.5x N2, and 10 ng/ml EGF/FGF.

extract_protocol:
Single cells were sorted into TCL buffer (Qiagen, 1031576) + 1% beta-mercaptoethanol and RNA-seq libraries generated using SMART-seq (modified from Shalek, et. al, Nature 2013) .
Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096) used for barcoding according to manufacturer's protocol

treatment_protocol: Differentiated glioma cells were generated by transitioning gliomasphere cultured cells to DMEM + 10% FCS for 7 days.

tag: cell type

value: Differentiated Glioma Cell Line


title: Rna_Ascl1_mut_1

description: mRNA from FACS sorted GFP cells


title: Boleracea_sample3

city: Warsaw

first: Anna

last: Lukasik

state: mazowieckie

address: Pawinskiego 5a

department: Department of Bioinformatics

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

data_processing:
The raw data processing included the removal of low quality reads and sequences shorter than 18 nucleotides, containing 5' primer contaminants, containing poly A tail or missing 3' primer and insert tags.
The remaining reads were combined into unique tags.
Genome build: As a reference the contigs and singletons created from Brassica oleracea EST and GSS sequences (NCBI), the Brassica rapa genome v1.2 and genome of the Arabidopsis thaliana (TAIR9) were used.
Supplementary_files_format_and_content: FASTA format files inlude reads count for each uniqe sequnce.

organism: Brassica oleracea var. capitata

source_name: mature cabbage leaves

extract_protocol:
Using the modified Trizol method as described by (Szarzynska et al. 2009), total RNA enriched with sRNA was isolated from the mature cabbage leaves (B. oleracea var. capitata, cultivar Balbro) in three independent biological replicates.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cultivar

value: Balbro

value: mature

value: leaves


title: Boleracea_sample2


title: Population mRNA-seq_MGH28GSC

description:
Cells from MGH28 cultured in gliomasphere conditions (Neurobasal medium + B27 +N2 + EGF/FGF)
processed data file: GBM_data_matrix.txt

source_name: Population mRNA-seq_MGH28

value: Gliomasphere Cell Line


title: Population mRNA-seq_MGH26DGC

description:
MGH26 GSC differentiated in DMEM+10% FCS for 7 days
processed data file: GBM_data_matrix.txt

source_name: Population mRNA-seq_MGH26


title: Population mRNA-seq_MGH26GSC

description:
Cells from MGH26 cultured in gliomasphere conditions (Neurobasal medium + B27 +N2 + EGF/FGF)
processed data file: GBM_data_matrix.txt


title: Population mRNA-seq_MGH31GSC

description:
Cells from MGH31 cultured in gliomasphere conditions (Neurobasal medium + B27 +N2 + EGF/FGF)
processed data file: GBM_data_matrix.txt


title: Boleracea_sample1

data_processing:
The raw data processing included the removal of low quality reads and sequences shorter than 18 nucleotides, containing 5' primer contaminants, containing poly A tail or missing 3' primer and insert tags.
The remaining reads were combined into unique tags.
genome build: As a reference the contigs and singletons created from Brassica oleracea EST and GSS sequences (NCBI), the Brassica rapa genome v1.2 and genome of the Arabidopsis thaliana (TAIR9) were used.
Supplementary_files_format_and_content: FASTA format files inlude reads count for each uniqe sequnce.


title: Population mRNA-seq_MGH28DGC

description:
MGH28 GSC differentiated in DMEM+10% FCS for 7 days
processed data file: GBM_data_matrix.txt


title: Population mRNA-seq_MGH30Tumor

description:
Population control for single cell sorting isolated from 1000-10000 cells
processed data file: GBM_data_matrix.txt

source_name: Population mRNA-seq_MGH30

tag: patient id

value: Glioblastoma

tag: subtype

value: Cla


title: Population mRNA-seq_MGH31Tumor


title: Population mRNA-seq_MGH29Tumor

source_name: Population mRNA-seq_MGH29

value: Mes


title: PTG KO on normal chow diet, rep2

description:
PTG_KO_ND2
Biological replicate.


title: Population mRNA-seq_MGH26Tumor

value: Pro


title: Single cell mRNA-seq_CSC8_H12

description: processed data file: GBM_data_matrix.txt

source_name: Single cell mRNA-seq_CSC8


title: Single cell mRNA-seq_CSC8_H11


title: Single cell mRNA-seq_CSC8_H10

description: Please note that this sample did not pass the quality control filtering (described in the data processing field), thus was excluded from further data processing


title: Single cell mRNA-seq_CSC8_H07


title: Single cell mRNA-seq_CSC8_H08


title: Single cell mRNA-seq_CSC8_H05


title: Single cell mRNA-seq_CSC8_H06


title: Single cell mRNA-seq_CSC8_H04


title: Single cell mRNA-seq_CSC8_H03


title: Single cell mRNA-seq_CSC8_H02


title: Single cell mRNA-seq_CSC8_H01


title: Single cell mRNA-seq_CSC8_G12


title: Single cell mRNA-seq_CSC8_G11


title: Single cell mRNA-seq_CSC8_G09


title: Single cell mRNA-seq_CSC8_G08


title: Single cell mRNA-seq_CSC8_G05


title: Single cell mRNA-seq_CSC8_G03


title: Single cell mRNA-seq_CSC8_G02


title: Single cell mRNA-seq_CSC8_G04


title: Single cell mRNA-seq_CSC8_G07


title: Single cell mRNA-seq_CSC8_G10


title: Population mRNA-seq_MGH28Tumor


title: Single cell mRNA-seq_CSC8_G06


title: Single cell mRNA-seq_CSC8_H09


title: Single cell mRNA-seq_CSC8_F10


title: Single cell mRNA-seq_CSC8_F09


title: Single cell mRNA-seq_CSC8_F08


title: Single cell mRNA-seq_CSC8_F07


title: Single cell mRNA-seq_CSC8_F11


title: Single cell mRNA-seq_CSC8_F01


title: Single cell mRNA-seq_CSC8_F02


title: Single cell mRNA-seq_CSC8_F04


title: Single cell mRNA-seq_CSC8_E12


title: Single cell mRNA-seq_CSC8_E11


title: Single cell mRNA-seq_CSC8_F03


title: Single cell mRNA-seq_CSC8_E10


title: Single cell mRNA-seq_CSC8_E09


title: Single cell mRNA-seq_CSC8_E07


title: Single cell mRNA-seq_CSC8_E06


title: Single cell mRNA-seq_CSC8_F12


title: Single cell mRNA-seq_CSC8_G01


title: Single cell mRNA-seq_CSC8_E04


title: Single cell mRNA-seq_CSC8_D11


title: Single cell mRNA-seq_CSC8_E05


title: Single cell mRNA-seq_CSC8_E03


title: Single cell mRNA-seq_CSC8_E02


title: Single cell mRNA-seq_CSC8_D12


title: Single cell mRNA-seq_CSC8_F05


title: Single cell mRNA-seq_CSC8_E01


title: Single cell mRNA-seq_CSC8_D08


title: Single cell mRNA-seq_CSC8_D07


title: Single cell mRNA-seq_CSC8_D10


title: Single cell mRNA-seq_CSC8_D09


title: Single cell mRNA-seq_CSC8_F06


title: Single cell mRNA-seq_CSC8_D06


title: Single cell mRNA-seq_CSC8_D05


title: Single cell mRNA-seq_CSC8_D02


title: Single cell mRNA-seq_CSC8_C12


title: Single cell mRNA-seq_CSC8_D03


title: Single cell mRNA-seq_CSC8_D04


title: Single cell mRNA-seq_CSC8_D01


title: Single cell mRNA-seq_CSC8_C10


title: Single cell mRNA-seq_CSC8_C09


title: Single cell mRNA-seq_CSC8_E08


title: Single cell mRNA-seq_CSC8_C11


title: Single cell mRNA-seq_CSC8_C08


title: Single cell mRNA-seq_CSC8_C07


title: Single cell mRNA-seq_CSC8_C06


title: Single cell mRNA-seq_CSC8_C05


title: Single cell mRNA-seq_CSC8_C04


title: Single cell mRNA-seq_CSC8_C03


title: Single cell mRNA-seq_CSC8_C02


title: Single cell mRNA-seq_CSC8_B12


title: Single cell mRNA-seq_CSC8_B11


title: Single cell mRNA-seq_CSC8_C01


title: Single cell mRNA-seq_CSC8_B09


title: Single cell mRNA-seq_CSC8_B10


title: Single cell mRNA-seq_CSC8_B05


title: Single cell mRNA-seq_CSC8_B04


title: Single cell mRNA-seq_CSC8_B06


title: Single cell mRNA-seq_CSC8_B03


title: Single cell mRNA-seq_CSC8_B08


title: Single cell mRNA-seq_CSC8_A11


title: Single cell mRNA-seq_CSC8_B07


title: Single cell mRNA-seq_CSC8_A12


title: Single cell mRNA-seq_CSC8_B02


title: Single cell mRNA-seq_CSC8_B01


title: Single cell mRNA-seq_CSC8_A08


title: Single cell mRNA-seq_CSC8_A06


title: Single cell mRNA-seq_CSC8_A10


title: Single cell mRNA-seq_CSC8_A07


title: Single cell mRNA-seq_CSC8_A04


title: Single cell mRNA-seq_CSC8_A02


title: Single cell mRNA-seq_CSC8_A03


title: Single cell mRNA-seq_CSC6_H12

source_name: Single cell mRNA-seq_CSC6


title: Single cell mRNA-seq_CSC6_H07


title: Single cell mRNA-seq_CSC6_H09


title: Single cell mRNA-seq_CSC6_H05


title: Single cell mRNA-seq_CSC6_H06


title: Single cell mRNA-seq_CSC6_H11


title: Single cell mRNA-seq_CSC6_H04


title: Single cell mRNA-seq_CSC6_H10


title: Single cell mRNA-seq_CSC6_H02


title: Single cell mRNA-seq_CSC6_G12


title: Single cell mRNA-seq_CSC6_G11


title: Single cell mRNA-seq_CSC6_H01


title: Single cell mRNA-seq_CSC6_G08


title: Single cell mRNA-seq_CSC6_G06


title: Single cell mRNA-seq_CSC6_G07


title: Single cell mRNA-seq_CSC8_A09


title: Single cell mRNA-seq_CSC6_G09


title: Single cell mRNA-seq_CSC6_G10


title: Single cell mRNA-seq_CSC8_A05


title: Single cell mRNA-seq_CSC6_G03


title: Single cell mRNA-seq_CSC6_G05


title: Single cell mRNA-seq_CSC6_H03


title: Single cell mRNA-seq_CSC8_A01


title: Single cell mRNA-seq_CSC6_G04


title: Single cell mRNA-seq_CSC6_G02


title: Single cell mRNA-seq_CSC6_F12


title: Single cell mRNA-seq_CSC6_G01


title: Single cell mRNA-seq_CSC6_F09


title: Single cell mRNA-seq_CSC6_F10


title: Single cell mRNA-seq_CSC6_F11


title: Single cell mRNA-seq_CSC6_F08


title: Single cell mRNA-seq_CSC6_F06


title: Single cell mRNA-seq_CSC6_F07


title: Single cell mRNA-seq_CSC6_F05


title: Single cell mRNA-seq_CSC6_F03


title: Single cell mRNA-seq_CSC6_F04


title: Single cell mRNA-seq_CSC6_H08


title: Single cell mRNA-seq_CSC6_E12


title: Single cell mRNA-seq_CSC6_F01


title: Single cell mRNA-seq_CSC6_E11


title: Single cell mRNA-seq_CSC6_E09


title: Single cell mRNA-seq_CSC6_E10


title: Single cell mRNA-seq_CSC6_F02


title: Single cell mRNA-seq_CSC6_E08


title: Single cell mRNA-seq_CSC6_E01


title: Single cell mRNA-seq_CSC6_E06


title: Single cell mRNA-seq_CSC6_E04


title: Single cell mRNA-seq_CSC6_E07


title: Single cell mRNA-seq_CSC6_D12


title: Single cell mRNA-seq_CSC6_E05


title: Single cell mRNA-seq_CSC6_E03


title: Single cell mRNA-seq_CSC6_E02


title: Single cell mRNA-seq_CSC6_D11


title: Single cell mRNA-seq_CSC6_D09


title: Single cell mRNA-seq_CSC6_D08


title: Single cell mRNA-seq_CSC6_D10


title: Single cell mRNA-seq_CSC6_D06


title: Single cell mRNA-seq_CSC6_D04


title: Single cell mRNA-seq_CSC6_D05


title: Single cell mRNA-seq_CSC6_D03


title: Single cell mRNA-seq_CSC6_C12


title: Single cell mRNA-seq_CSC6_C11


title: Single cell mRNA-seq_CSC6_C10


title: Single cell mRNA-seq_CSC6_D01


title: Single cell mRNA-seq_CSC6_C05


title: Single cell mRNA-seq_CSC6_C06


title: Single cell mRNA-seq_CSC6_C04


title: Single cell mRNA-seq_CSC6_C03


title: Single cell mRNA-seq_CSC6_C08


title: Single cell mRNA-seq_CSC6_C02


title: Single cell mRNA-seq_CSC6_B11


title: Single cell mRNA-seq_CSC6_C01


title: Single cell mRNA-seq_CSC6_D07


title: Single cell mRNA-seq_CSC6_B09


title: Single cell mRNA-seq_CSC6_B07


title: Single cell mRNA-seq_CSC6_B06


title: Single cell mRNA-seq_CSC6_B04


title: Single cell mRNA-seq_CSC6_B05


title: Single cell mRNA-seq_CSC6_A12


title: Single cell mRNA-seq_CSC6_B03


title: Single cell mRNA-seq_CSC6_B02


title: Single cell mRNA-seq_CSC6_C07


title: Single cell mRNA-seq_CSC6_B01


title: Single cell mRNA-seq_CSC6_B10


title: Single cell mRNA-seq_CSC6_A11


title: Single cell mRNA-seq_CSC6_A09


title: Single cell mRNA-seq_CSC6_A08


title: Single cell mRNA-seq_CSC6_A06


title: Single cell mRNA-seq_CSC6_A07


title: Single cell mRNA-seq_CSC6_B08


title: Single cell mRNA-seq_CSC6_A04


title: Single cell mRNA-seq_CSC6_A03


title: Single cell mRNA-seq_CSC6_A05


title: Single cell mRNA-seq_CSC6_A02


title: Single cell mRNA-seq_CSC6_A01


title: Single cell mRNA-seq_MGH30L_H12

source_name: Single cell mRNA-seq_MGH30


title: Single cell mRNA-seq_MGH30L_H11


title: Single cell mRNA-seq_MGH30L_H10


title: Single cell mRNA-seq_MGH30L_H09


title: Single cell mRNA-seq_MGH30L_H07


title: Single cell mRNA-seq_CSC6_A10


title: Single cell mRNA-seq_CSC6_D02


title: Single cell mRNA-seq_MGH30L_H03


title: Single cell mRNA-seq_MGH30L_H01


title: Single cell mRNA-seq_MGH30L_H04


title: Single cell mRNA-seq_MGH30L_H02


title: Single cell mRNA-seq_MGH30L_G12


title: Single cell mRNA-seq_MGH30L_G09


title: Single cell mRNA-seq_MGH30L_G10


title: Single cell mRNA-seq_MGH30L_G06


title: Single cell mRNA-seq_MGH30L_G08


title: Single cell mRNA-seq_MGH30L_G07


title: Single cell mRNA-seq_MGH30L_G05


title: Single cell mRNA-seq_MGH30L_G04


title: Single cell mRNA-seq_MGH30L_H08


title: Single cell mRNA-seq_MGH30L_G01


title: Single cell mRNA-seq_MGH30L_G02


title: Single cell mRNA-seq_MGH30L_F12


title: Single cell mRNA-seq_MGH30L_F11


title: Single cell mRNA-seq_MGH30L_G03


title: Single cell mRNA-seq_MGH30L_H05


title: Single cell mRNA-seq_MGH30L_H06


title: Single cell mRNA-seq_MGH30L_F08


title: Single cell mRNA-seq_MGH30L_F07


title: Single cell mRNA-seq_MGH30L_F04


title: Single cell mRNA-seq_MGH30L_F09


title: Single cell mRNA-seq_MGH30L_F06


title: Single cell mRNA-seq_MGH30L_F05


title: Single cell mRNA-seq_MGH30L_E12


title: Single cell mRNA-seq_MGH30L_F01


title: Single cell mRNA-seq_MGH30L_E11


title: Single cell mRNA-seq_MGH30L_F03


title: Single cell mRNA-seq_MGH30L_F10


title: Single cell mRNA-seq_MGH30L_G11


title: Single cell mRNA-seq_MGH30L_E04


title: Single cell mRNA-seq_MGH30L_E07


title: Single cell mRNA-seq_MGH30L_E08


title: Single cell mRNA-seq_MGH30L_E03


title: Single cell mRNA-seq_MGH30L_E01


title: Single cell mRNA-seq_MGH30L_E02


title: Single cell mRNA-seq_MGH30L_D11


title: Single cell mRNA-seq_MGH30L_D12


title: Single cell mRNA-seq_MGH30L_D08


title: Single cell mRNA-seq_MGH30L_D10


title: Single cell mRNA-seq_MGH30L_D09


title: Single cell mRNA-seq_MGH30L_F02


title: Single cell mRNA-seq_MGH30L_D04


title: Single cell mRNA-seq_MGH30L_D01


title: Single cell mRNA-seq_MGH30L_D05


title: Single cell mRNA-seq_MGH30L_D07


title: Single cell mRNA-seq_MGH30L_E09


title: Single cell mRNA-seq_MGH30L_D06


title: Single cell mRNA-seq_MGH30L_E10


title: Single cell mRNA-seq_MGH30L_C12


title: Single cell mRNA-seq_MGH30L_D03


title: Single cell mRNA-seq_MGH30L_E06


title: Single cell mRNA-seq_MGH30L_D02


title: Single cell mRNA-seq_MGH30L_C05


title: Single cell mRNA-seq_MGH30L_C07


title: Single cell mRNA-seq_MGH30L_C09


title: Single cell mRNA-seq_MGH30L_C08


title: Single cell mRNA-seq_MGH30L_C10


title: Single cell mRNA-seq_MGH30L_E05


title: Single cell mRNA-seq_MGH30L_C04


title: Single cell mRNA-seq_MGH30L_C03


title: Single cell mRNA-seq_MGH30L_B12


title: Single cell mRNA-seq_MGH30L_C01


title: Single cell mRNA-seq_MGH30L_B11


title: Single cell mRNA-seq_MGH30L_C11


title: Single cell mRNA-seq_MGH30L_B08


title: Single cell mRNA-seq_MGH30L_B05


title: Single cell mRNA-seq_MGH30L_B07


title: Single cell mRNA-seq_MGH30L_B06


title: Single cell mRNA-seq_MGH30L_B02


title: Single cell mRNA-seq_MGH30L_B03


title: Single cell mRNA-seq_MGH30L_B01


title: Single cell mRNA-seq_MGH30L_C06


title: Single cell mRNA-seq_MGH30L_A12


title: Single cell mRNA-seq_MGH30L_A09


title: Single cell mRNA-seq_MGH30L_A08


title: Single cell mRNA-seq_MGH30L_A10


title: Single cell mRNA-seq_MGH30L_A11


title: Single cell mRNA-seq_MGH30L_A06


title: Single cell mRNA-seq_MGH30L_A07


title: Single cell mRNA-seq_MGH30L_A05


title: Single cell mRNA-seq_MGH30L_A01


title: Single cell mRNA-seq_MGH31_H12

source_name: Single cell mRNA-seq_MGH31


title: Single cell mRNA-seq_MGH30L_B10


title: Single cell mRNA-seq_MGH30L_A02


title: Single cell mRNA-seq_MGH30L_C02


title: Single cell mRNA-seq_MGH31_H09


title: Single cell mRNA-seq_MGH31_H10


title: Single cell mRNA-seq_MGH31_H05


title: Single cell mRNA-seq_MGH31_H07


title: Single cell mRNA-seq_MGH31_H08


title: Single cell mRNA-seq_MGH31_H11


title: Single cell mRNA-seq_MGH31_H03


title: Single cell mRNA-seq_MGH31_H02


title: Single cell mRNA-seq_MGH31_H01


title: Single cell mRNA-seq_MGH31_G12


title: Single cell mRNA-seq_MGH30L_B09


title: Single cell mRNA-seq_MGH31_H04


title: Single cell mRNA-seq_MGH31_G11


title: Single cell mRNA-seq_MGH30L_A04


title: Single cell mRNA-seq_MGH31_G09


title: Single cell mRNA-seq_MGH31_G10


title: Single cell mRNA-seq_MGH31_G07


title: Single cell mRNA-seq_MGH31_G03


title: Single cell mRNA-seq_MGH31_G02


title: Single cell mRNA-seq_MGH31_G08


title: Single cell mRNA-seq_MGH31_G05


title: Single cell mRNA-seq_MGH31_G01


title: Single cell mRNA-seq_CSC6_C09


title: Single cell mRNA-seq_MGH31_G06


title: Single cell mRNA-seq_MGH31_F12


title: Single cell mRNA-seq_MGH30L_B04


title: Single cell mRNA-seq_MGH31_F10


title: Single cell mRNA-seq_CSC6_B12


title: Single cell mRNA-seq_MGH31_F07

value: Neu


title: Single cell mRNA-seq_MGH31_H06


title: Single cell mRNA-seq_MGH31_F08


title: Single cell mRNA-seq_MGH31_F05


title: Single cell mRNA-seq_MGH31_F09


title: Single cell mRNA-seq_MGH31_F04


title: Single cell mRNA-seq_MGH31_E12


title: Single cell mRNA-seq_MGH31_F01


title: Single cell mRNA-seq_MGH31_F03


title: Single cell mRNA-seq_MGH31_E11


title: Single cell mRNA-seq_MGH31_E09


title: Single cell mRNA-seq_MGH31_E07


title: Single cell mRNA-seq_MGH31_G04


title: Single cell mRNA-seq_MGH31_E05


title: Single cell mRNA-seq_MGH31_E04


title: Single cell mRNA-seq_MGH31_E03


title: Single cell mRNA-seq_MGH31_E02


title: Single cell mRNA-seq_MGH31_E01


title: Single cell mRNA-seq_MGH30L_A03


title: Single cell mRNA-seq_MGH31_D11


title: Single cell mRNA-seq_MGH31_F06


title: Single cell mRNA-seq_MGH31_D12


title: Single cell mRNA-seq_MGH31_F11


title: Single cell mRNA-seq_MGH31_E10


title: Single cell mRNA-seq_MGH31_F02


title: Single cell mRNA-seq_MGH31_D04


title: Single cell mRNA-seq_MGH31_D05


title: Single cell mRNA-seq_MGH31_D08


title: Single cell mRNA-seq_MGH31_D07


title: Single cell mRNA-seq_MGH31_D09


title: Single cell mRNA-seq_MGH31_D02


title: Single cell mRNA-seq_MGH31_D06


title: Single cell mRNA-seq_MGH31_C12


title: Single cell mRNA-seq_MGH31_C07


title: Single cell mRNA-seq_MGH31_E08


title: Single cell mRNA-seq_MGH31_C06


title: Single cell mRNA-seq_MGH31_C04


title: Single cell mRNA-seq_MGH31_C11


title: Single cell mRNA-seq_MGH31_C10


title: Single cell mRNA-seq_MGH31_C01


title: Single cell mRNA-seq_MGH31_C09


title: Single cell mRNA-seq_MGH31_C02


title: Single cell mRNA-seq_MGH31_E06


title: Single cell mRNA-seq_MGH31_B10


title: Single cell mRNA-seq_MGH31_B08


title: Single cell mRNA-seq_MGH31_C05


title: Single cell mRNA-seq_MGH31_D10


title: Single cell mRNA-seq_MGH31_B09


title: Single cell mRNA-seq_MGH31_B12


title: Single cell mRNA-seq_MGH31_B06


title: Single cell mRNA-seq_MGH31_D01


title: Single cell mRNA-seq_MGH31_B11


title: Single cell mRNA-seq_MGH31_B01


title: Single cell mRNA-seq_MGH31_B05


title: Single cell mRNA-seq_MGH31_C03


title: Single cell mRNA-seq_MGH31_B03


title: Single cell mRNA-seq_MGH31_B02


title: Single cell mRNA-seq_MGH31_B07


title: Single cell mRNA-seq_MGH31_D03


title: Single cell mRNA-seq_MGH31_C08


title: Single cell mRNA-seq_MGH31_A11


title: Single cell mRNA-seq_MGH31_A10


title: Single cell mRNA-seq_MGH31_A08


title: Single cell mRNA-seq_MGH31_A09


title: Single cell mRNA-seq_MGH31_A07


title: Single cell mRNA-seq_MGH31_A06


title: Single cell mRNA-seq_MGH31_A04


title: Single cell mRNA-seq_MGH31_A05


title: Single cell mRNA-seq_MGH31_B04


title: Single cell mRNA-seq_MGH31_A01


title: Single cell mRNA-seq_MGH31_A02


title: Single cell mRNA-seq_MGH31_A03


title: Single cell mRNA-seq_MGH31_A12


title: Single cell mRNA-seq_MGH30_H12


title: Single cell mRNA-seq_MGH30_H07


title: Single cell mRNA-seq_MGH30_H06


title: Single cell mRNA-seq_MGH30_H08


title: Single cell mRNA-seq_MGH30_H02


title: Single cell mRNA-seq_MGH30_H10


title: Single cell mRNA-seq_MGH30_H09


title: Single cell mRNA-seq_MGH30_H04


title: Single cell mRNA-seq_MGH30_H11


title: Single cell mRNA-seq_MGH30_G12


title: Single cell mRNA-seq_MGH30_H05


title: Single cell mRNA-seq_MGH30_G10


title: Single cell mRNA-seq_MGH30_G08


title: Single cell mRNA-seq_MGH30_H01


title: Single cell mRNA-seq_MGH30_H03


title: Single cell mRNA-seq_MGH30_G05

value: Pro+Cla


title: Single cell mRNA-seq_MGH30_G06


title: Single cell mRNA-seq_MGH30_G09


title: Single cell mRNA-seq_MGH30_G11


title: Single cell mRNA-seq_MGH30_G07


title: Single cell mRNA-seq_MGH30_G02


title: Single cell mRNA-seq_MGH30_G04


title: Single cell mRNA-seq_MGH30_G03


title: Single cell mRNA-seq_MGH30_F11


title: Single cell mRNA-seq_MGH30_F12


title: Single cell mRNA-seq_MGH30_F10


title: Single cell mRNA-seq_MGH30_F05


title: Single cell mRNA-seq_MGH30_F08

value: Cla+Mes


title: Single cell mRNA-seq_MGH30_F04


title: Single cell mRNA-seq_MGH30_G01


title: Single cell mRNA-seq_MGH30_F02


title: Single cell mRNA-seq_MGH30_E12


title: Single cell mRNA-seq_MGH30_F07


title: Single cell mRNA-seq_MGH30_F03


title: Single cell mRNA-seq_MGH30_E09


title: Single cell mRNA-seq_MGH30_E08


title: Single cell mRNA-seq_MGH30_E06


title: Single cell mRNA-seq_MGH30_E05


title: Single cell mRNA-seq_MGH30_E10


title: Single cell mRNA-seq_MGH30_E02


title: Single cell mRNA-seq_MGH30_E04


title: Single cell mRNA-seq_MGH30_E11


title: Single cell mRNA-seq_MGH30_E03


title: Single cell mRNA-seq_MGH30_E01


title: Single cell mRNA-seq_MGH30_D11


title: Single cell mRNA-seq_MGH30_D12


title: Single cell mRNA-seq_MGH30_F09


title: Single cell mRNA-seq_MGH30_F01


title: Single cell mRNA-seq_MGH30_D10


title: Single cell mRNA-seq_MGH30_D03


title: Single cell mRNA-seq_MGH30_D09


title: Single cell mRNA-seq_MGH30_D06


title: Single cell mRNA-seq_MGH30_C12


title: Single cell mRNA-seq_MGH30_E07


title: Single cell mRNA-seq_MGH30_D07


title: Single cell mRNA-seq_MGH30_D08


title: Single cell mRNA-seq_MGH30_C10


title: Single cell mRNA-seq_MGH30_D02


title: Single cell mRNA-seq_MGH30_D04


title: Single cell mRNA-seq_MGH30_C11


title: Single cell mRNA-seq_MGH30_C09

value: Pro+Neu


title: Single cell mRNA-seq_MGH30_D01


title: Single cell mRNA-seq_MGH30_C07


title: Single cell mRNA-seq_MGH30_C08


title: Single cell mRNA-seq_MGH30_D05


title: Single cell mRNA-seq_MGH30_C04


title: Single cell mRNA-seq_MGH30_C03


title: Single cell mRNA-seq_MGH30_C06


title: Single cell mRNA-seq_MGH30_C05


title: Single cell mRNA-seq_MGH30_C01


title: Single cell mRNA-seq_MGH30_B12


title: Single cell mRNA-seq_MGH30_B09


title: Single cell mRNA-seq_MGH30_C02


title: Single cell mRNA-seq_MGH30_B11


title: Single cell mRNA-seq_MGH30_B10


title: Single cell mRNA-seq_MGH30_B08


title: Single cell mRNA-seq_MGH30_F06


title: Single cell mRNA-seq_MGH30_B07


title: Single cell mRNA-seq_MGH30_B06


title: Single cell mRNA-seq_MGH30_B05


title: Single cell mRNA-seq_MGH30_B04


title: Single cell mRNA-seq_MGH30_B01


title: Single cell mRNA-seq_MGH30_A10


title: Single cell mRNA-seq_MGH30_A08


title: Single cell mRNA-seq_MGH30_A11


title: Single cell mRNA-seq_MGH30_B03

value: Neu+Cla


title: Single cell mRNA-seq_MGH30_A06


title: Single cell mRNA-seq_MGH30_A12


title: Single cell mRNA-seq_MGH30_A09


title: Single cell mRNA-seq_MGH30_A07


title: Single cell mRNA-seq_MGH30_A05


title: Single cell mRNA-seq_MGH30_A02


title: Single cell mRNA-seq_MGH30_A01


title: Single cell mRNA-seq_MGH29_H11

source_name: Single cell mRNA-seq_MGH29


title: Single cell mRNA-seq_MGH30_A03


title: Single cell mRNA-seq_MGH29_H08


title: Single cell mRNA-seq_MGH29_H12


title: Single cell mRNA-seq_MGH29_H06


title: Single cell mRNA-seq_MGH29_H09


title: Single cell mRNA-seq_MGH29_H10


title: Single cell mRNA-seq_MGH29_H07


title: Single cell mRNA-seq_MGH29_H05


title: Single cell mRNA-seq_MGH29_H04


title: Single cell mRNA-seq_MGH29_H02


title: Single cell mRNA-seq_MGH29_H03

value: Neu+Mes


title: Single cell mRNA-seq_MGH30_B02


title: Single cell mRNA-seq_MGH29_H01


title: Single cell mRNA-seq_MGH29_G11


title: Single cell mRNA-seq_MGH29_G12


title: Single cell mRNA-seq_MGH29_G08


title: Single cell mRNA-seq_MGH29_G09


title: Single cell mRNA-seq_MGH29_G10


title: Single cell mRNA-seq_MGH30_A04


title: Single cell mRNA-seq_MGH29_G06


title: Single cell mRNA-seq_MGH29_G07


title: Single cell mRNA-seq_MGH29_G04


title: Single cell mRNA-seq_MGH29_G03


title: Single cell mRNA-seq_MGH29_G01


title: Single cell mRNA-seq_MGH29_G02


title: Single cell mRNA-seq_MGH29_F11


title: Single cell mRNA-seq_MGH29_F12


title: Single cell mRNA-seq_MGH29_F04


title: Single cell mRNA-seq_MGH29_F08


title: Single cell mRNA-seq_MGH29_F06


title: Single cell mRNA-seq_MGH29_F10


title: Single cell mRNA-seq_MGH29_F01


title: Single cell mRNA-seq_MGH29_F07


title: Single cell mRNA-seq_MGH29_F05


title: Single cell mRNA-seq_MGH29_F09


title: Single cell mRNA-seq_MGH29_E12


title: Single cell mRNA-seq_MGH29_E10


title: Single cell mRNA-seq_MGH29_E09


title: Single cell mRNA-seq_MGH29_E08


title: Single cell mRNA-seq_MGH29_G05


title: Single cell mRNA-seq_MGH29_E06


title: Single cell mRNA-seq_MGH29_E04


title: Single cell mRNA-seq_MGH29_E07


title: Single cell mRNA-seq_MGH29_E05


title: Single cell mRNA-seq_MGH29_E02


title: Single cell mRNA-seq_MGH29_D12


title: Single cell mRNA-seq_MGH29_E03


title: Single cell mRNA-seq_MGH29_D11


title: Single cell mRNA-seq_MGH29_F03


title: Single cell mRNA-seq_MGH29_D09


title: Single cell mRNA-seq_MGH29_D10


title: Single cell mRNA-seq_MGH29_E11


title: Single cell mRNA-seq_MGH29_F02


title: Single cell mRNA-seq_MGH29_D07


title: Single cell mRNA-seq_MGH29_D05


title: Single cell mRNA-seq_MGH29_D03


title: Single cell mRNA-seq_MGH29_D06


title: Single cell mRNA-seq_MGH29_C10


title: Single cell mRNA-seq_MGH29_D02


title: Single cell mRNA-seq_MGH29_D01


title: Single cell mRNA-seq_MGH29_C12


title: Single cell mRNA-seq_MGH29_C07


title: Single cell mRNA-seq_MGH29_C06


title: Single cell mRNA-seq_MGH29_C08


title: Single cell mRNA-seq_MGH29_C05


title: Single cell mRNA-seq_MGH29_C04


title: Single cell mRNA-seq_MGH29_E01


title: Single cell mRNA-seq_MGH29_C01


title: Single cell mRNA-seq_MGH29_B12


title: Single cell mRNA-seq_MGH29_D08


title: Single cell mRNA-seq_MGH29_B11


title: Single cell mRNA-seq_MGH29_C03


title: Single cell mRNA-seq_MGH29_B10


title: Single cell mRNA-seq_MGH29_B09


title: Single cell mRNA-seq_MGH29_B08


title: Single cell mRNA-seq_MGH29_B07


title: Single cell mRNA-seq_MGH29_D04


title: Single cell mRNA-seq_MGH29_B06


title: Single cell mRNA-seq_MGH29_C09


title: Single cell mRNA-seq_MGH29_B03


title: Single cell mRNA-seq_MGH29_C11


title: Single cell mRNA-seq_MGH29_B01


title: Single cell mRNA-seq_MGH29_B02


title: Single cell mRNA-seq_MGH29_A12


title: Single cell mRNA-seq_MGH29_B05


title: Single cell mRNA-seq_MGH29_B04


title: Single cell mRNA-seq_MGH29_A10


title: Single cell mRNA-seq_MGH29_A09


title: Single cell mRNA-seq_MGH29_A11


title: Single cell mRNA-seq_MGH29_A07


title: Single cell mRNA-seq_MGH29_C02


title: Single cell mRNA-seq_MGH29_A05


title: Single cell mRNA-seq_MGH29_A06


title: Single cell mRNA-seq_MGH29_A02


title: Single cell mRNA-seq_MGH29_A04


title: Single cell mRNA-seq_MGH28_H12

source_name: Single cell mRNA-seq_MGH28


title: Single cell mRNA-seq_MGH28_H11


title: Single cell mRNA-seq_MGH28_H09


title: Single cell mRNA-seq_MGH29_A01


title: Single cell mRNA-seq_MGH28_H08


title: Single cell mRNA-seq_MGH28_H06


title: Single cell mRNA-seq_MGH28_H04


title: Single cell mRNA-seq_MGH28_H05


title: Single cell mRNA-seq_MGH28_H02


title: Single cell mRNA-seq_MGH28_H01


title: Single cell mRNA-seq_MGH28_G11


title: Single cell mRNA-seq_MGH29_A08


title: Single cell mRNA-seq_MGH28_G12


title: Single cell mRNA-seq_MGH28_G05


title: Single cell mRNA-seq_MGH28_G10


title: Single cell mRNA-seq_MGH28_G08


title: Single cell mRNA-seq_MGH28_G09


title: Single cell mRNA-seq_MGH28_G06


title: Single cell mRNA-seq_MGH28_G07


title: Single cell mRNA-seq_MGH28_G03


title: Single cell mRNA-seq_MGH28_G04


title: Single cell mRNA-seq_MGH29_A03


title: Single cell mRNA-seq_MGH28_G01


title: Single cell mRNA-seq_MGH28_H10


title: Single cell mRNA-seq_MGH28_G02


title: Single cell mRNA-seq_MGH28_H07


title: Single cell mRNA-seq_MGH28_F12


title: Single cell mRNA-seq_MGH28_H03


title: Single cell mRNA-seq_MGH28_F06


title: Single cell mRNA-seq_MGH28_F09


title: Single cell mRNA-seq_MGH28_F10


title: Single cell mRNA-seq_MGH28_F11


title: Single cell mRNA-seq_MGH28_F07


title: Single cell mRNA-seq_MGH28_F08


title: Single cell mRNA-seq_MGH28_F04


title: Single cell mRNA-seq_MGH28_F02


title: Single cell mRNA-seq_MGH28_F03


title: Single cell mRNA-seq_MGH28_F01


title: Single cell mRNA-seq_MGH28_F05


title: Single cell mRNA-seq_MGH28_E12


title: Single cell mRNA-seq_MGH28_E09


title: Single cell mRNA-seq_MGH28_E07


title: Single cell mRNA-seq_MGH28_E06


title: Single cell mRNA-seq_MGH28_E08


title: Single cell mRNA-seq_MGH28_E03


title: Single cell mRNA-seq_MGH28_D12


title: Single cell mRNA-seq_MGH28_E01


title: Single cell mRNA-seq_MGH28_D11


title: Single cell mRNA-seq_MGH28_E02


title: Single cell mRNA-seq_MGH28_D10


title: Single cell mRNA-seq_MGH28_D09


title: Single cell mRNA-seq_MGH28_D08


title: Single cell mRNA-seq_MGH28_D07


title: Single cell mRNA-seq_MGH28_C12


title: Single cell mRNA-seq_MGH28_D01


title: Single cell mRNA-seq_MGH28_D04


title: Single cell mRNA-seq_MGH28_D05


title: Single cell mRNA-seq_MGH28_D03


title: Single cell mRNA-seq_MGH28_D02


title: Single cell mRNA-seq_MGH28_D06


title: Single cell mRNA-seq_MGH28_C11


title: Single cell mRNA-seq_MGH28_E11


title: Single cell mRNA-seq_MGH28_C07


title: Single cell mRNA-seq_MGH28_C09


title: Single cell mRNA-seq_MGH28_E04


title: Single cell mRNA-seq_MGH28_E05


title: Single cell mRNA-seq_MGH28_C08


title: Single cell mRNA-seq_MGH28_C10


title: Single cell mRNA-seq_MGH28_C06


title: Single cell mRNA-seq_MGH28_C01


title: Single cell mRNA-seq_MGH28_C05


title: Single cell mRNA-seq_MGH28_C02


title: Single cell mRNA-seq_MGH28_C03


title: Single cell mRNA-seq_MGH28_B09


title: Single cell mRNA-seq_MGH28_B11


title: Single cell mRNA-seq_MGH28_B12


title: Single cell mRNA-seq_MGH28_B07


title: Single cell mRNA-seq_MGH28_B06


title: Single cell mRNA-seq_MGH28_B10


title: Single cell mRNA-seq_MGH28_B05


title: Single cell mRNA-seq_MGH28_B08


title: Single cell mRNA-seq_MGH28_B04


title: Single cell mRNA-seq_MGH28_A12


title: Single cell mRNA-seq_MGH28_B01


title: Single cell mRNA-seq_MGH28_A10


title: Single cell mRNA-seq_MGH28_A11


title: Single cell mRNA-seq_MGH28_B02


title: Single cell mRNA-seq_MGH28_B03


title: Single cell mRNA-seq_MGH28_A08


title: Single cell mRNA-seq_MGH28_E10


title: Single cell mRNA-seq_MGH28_A09


title: Single cell mRNA-seq_MGH28_A05


title: Single cell mRNA-seq_MGH28_C04


title: Single cell mRNA-seq_MGH28_A06


title: Single cell mRNA-seq_MGH28_A04


title: Single cell mRNA-seq_MGH28_A03


title: Single cell mRNA-seq_MGH26-2_H12

source_name: Single cell mRNA-seq_MGH26


title: Single cell mRNA-seq_MGH26-2_H09


title: Single cell mRNA-seq_MGH26-2_H11


title: Single cell mRNA-seq_MGH26-2_H08


title: Single cell mRNA-seq_MGH26-2_H06


title: Single cell mRNA-seq_MGH26-2_H04


title: Single cell mRNA-seq_MGH26-2_H05


title: Single cell mRNA-seq_MGH26-2_H03


title: Single cell mRNA-seq_MGH26-2_H02


title: Single cell mRNA-seq_MGH26-2_G12


title: Single cell mRNA-seq_MGH26-2_H01


title: Single cell mRNA-seq_MGH28_A07


title: Single cell mRNA-seq_MGH26-2_G11


title: Single cell mRNA-seq_MGH28_A01


title: Single cell mRNA-seq_MGH26-2_G03


title: Single cell mRNA-seq_MGH28_A02


title: Single cell mRNA-seq_MGH26-2_G05


title: Single cell mRNA-seq_MGH26-2_G07


title: Single cell mRNA-seq_MGH26-2_H10


title: Single cell mRNA-seq_MGH26-2_F11


title: Single cell mRNA-seq_MGH26-2_G09


title: Single cell mRNA-seq_MGH26-2_G06


title: Single cell mRNA-seq_MGH26-2_F10


title: Single cell mRNA-seq_MGH26-2_G02


title: Single cell mRNA-seq_MGH26-2_G04


title: Single cell mRNA-seq_MGH26-2_F09


title: Single cell mRNA-seq_MGH26-2_G01


title: Single cell mRNA-seq_MGH26-2_F12


title: Single cell mRNA-seq_MGH26-2_G08


title: Single cell mRNA-seq_MGH26-2_F07


title: Single cell mRNA-seq_MGH26-2_F04


title: Single cell mRNA-seq_MGH26-2_F06


title: Single cell mRNA-seq_MGH26-2_F08


title: Single cell mRNA-seq_MGH26-2_F05


title: Single cell mRNA-seq_MGH26-2_F02


title: Single cell mRNA-seq_MGH26-2_G10


title: Single cell mRNA-seq_MGH26-2_E12


title: Single cell mRNA-seq_MGH26-2_F01


title: Single cell mRNA-seq_MGH26-2_E10


title: Single cell mRNA-seq_MGH26-2_E07


title: Single cell mRNA-seq_MGH26-2_E08


title: Single cell mRNA-seq_MGH26-2_E05


title: Single cell mRNA-seq_MGH26-2_E06


title: Single cell mRNA-seq_MGH26-2_E03


title: Single cell mRNA-seq_MGH26-2_F03


title: Single cell mRNA-seq_MGH26-2_D09


title: Single cell mRNA-seq_MGH26-2_E01


title: Single cell mRNA-seq_MGH26-2_D10


title: Single cell mRNA-seq_MGH26-2_H07


title: Single cell mRNA-seq_MGH26-2_E04


title: Single cell mRNA-seq_MGH26-2_D06


title: Single cell mRNA-seq_MGH26-2_D12


title: Single cell mRNA-seq_MGH26-2_D11


title: Single cell mRNA-seq_MGH26-2_E02


title: Single cell mRNA-seq_MGH26-2_E11


title: Single cell mRNA-seq_MGH26-2_D08


title: Single cell mRNA-seq_MGH26-2_D05


title: Single cell mRNA-seq_MGH26-2_D01


title: Single cell mRNA-seq_MGH26-2_D02


title: Single cell mRNA-seq_MGH26-2_D07


title: Single cell mRNA-seq_MGH26-2_C12


title: Single cell mRNA-seq_MGH26-2_D03


title: Single cell mRNA-seq_MGH26-2_C10


title: Single cell mRNA-seq_MGH26-2_C09


title: Single cell mRNA-seq_MGH26-2_D04


title: Single cell mRNA-seq_MGH26-2_E09


title: Single cell mRNA-seq_MGH26-2_C07


title: Single cell mRNA-seq_MGH26-2_C06


title: Single cell mRNA-seq_MGH26-2_C05


title: Single cell mRNA-seq_MGH26-2_C04


title: Single cell mRNA-seq_MGH26-2_C03


title: Single cell mRNA-seq_MGH26-2_C02


title: Single cell mRNA-seq_MGH26-2_B07


title: Single cell mRNA-seq_MGH26-2_B10


title: Single cell mRNA-seq_MGH26-2_B03


title: Single cell mRNA-seq_MGH26-2_B02


title: Single cell mRNA-seq_MGH26-2_A12


title: Single cell mRNA-seq_MGH26-2_A10


title: Single cell mRNA-seq_MGH26-2_B08


title: Single cell mRNA-seq_MGH26-2_B09


title: Single cell mRNA-seq_MGH26-2_A07


title: Single cell mRNA-seq_MGH26-2_C08


title: Single cell mRNA-seq_MGH26-2_B12


title: Single cell mRNA-seq_MGH26-2_C01


title: Single cell mRNA-seq_MGH26-2_B11


title: Single cell mRNA-seq_MGH26-2_B04


title: Single cell mRNA-seq_MGH26-2_B05


title: Single cell mRNA-seq_MGH26-2_A08


title: Single cell mRNA-seq_MGH26-2_A06


title: Single cell mRNA-seq_MGH26-2_C11


title: Single cell mRNA-seq_MGH26-2_A05


title: Single cell mRNA-seq_MGH26-2_B01


title: Single cell mRNA-seq_MGH26-2_A11


title: Single cell mRNA-seq_MGH26-2_A09


title: Single cell mRNA-seq_MGH26-2_A03


title: Single cell mRNA-seq_MGH26-2_A04


title: Single cell mRNA-seq_MGH26-2_A01


title: Single cell mRNA-seq_MGH26_H12


title: Single cell mRNA-seq_MGH26-2_A02


title: Single cell mRNA-seq_MGH26_H11


title: Single cell mRNA-seq_MGH26-2_B06


title: Single cell mRNA-seq_MGH26_H10


title: Single cell mRNA-seq_MGH26_H09


title: Single cell mRNA-seq_MGH26_H07


title: Single cell mRNA-seq_MGH26_H06


title: Single cell mRNA-seq_MGH26_H08


title: Single cell mRNA-seq_MGH26_H05


title: Single cell mRNA-seq_MGH26_H02


title: Single cell mRNA-seq_MGH26_H04


title: Single cell mRNA-seq_MGH26_H01


title: Single cell mRNA-seq_MGH26_H03


title: Single cell mRNA-seq_MGH26_G11


title: Single cell mRNA-seq_MGH26_G12


title: Kdm6bKD

city: Durham

first: Christopher

middle: L

last: Frank

state: NC

address: 101 Science Dr.

institute: Duke University

data_processing:
Basecalls performed using CASAVA v1.8
RNA-seq reads mapped to NCBI37/mm9 with Tophat v2.0.8b, allowing up to 2 mismatches and multireads mapping up to 4 locations
FPKM transcript abundances estimated with Cufflinks v2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: cufflinks text files contain tab-delimited gene names, chromosomal coordinates, expression estimates (FPKM), and quantification status

source_name: Cultured hippocampal neurons

growth_protocol: Dissociated hippocampal neurons from postnatal day 0 (P0) CD1 mouse pups were cultured in Neurobasal medium with B27 supplements for 11 days in vitro (DIV).

extract_protocol:
RNA was isolated by column purification with on column DNase treatment.
RNA-Seq libraries were with polyA RNA enrichment and using the Illumina TruSeq kit

treatment_protocol: On DIV4, neuronal cultures were infected with either a control lentivirus (the pLKO.1 vector) or a lentivirus expressing an shRNA targeting Kdm6b (CTGTTCTTGAGGGACAAACTC). On DIV11 neurons were either left untreated (control) or we added 50µm bicuculline and 2.5mM 4-aminopyridine (4AP) to the culture medium for 3 hr before harvesting.

tag: brain region

value: hippocampus

tag: tissue type

value: Cultured hippocampal neurons

value: Lentiviral Kdm6b shRNA infection DIV4

tag: treated with

tag: neuronal age


title: Kdm6bKD_PlusBic

value: 50µm bicuculline, 2.5mM 4-aminopyridine (4AP) for 3 hr


title: VectorControl_PlusBic

value: Lentiviral pLKO.1 infection DIV4


title: Single cell mRNA-seq_MGH26_G08


title: Single cell mRNA-seq_MGH26_G10


title: Single cell mRNA-seq_MGH26_G09


title: VectorControl


title: Single cell mRNA-seq_MGH26_G06


title: Single cell mRNA-seq_MGH26_G03


title: Single cell mRNA-seq_MGH26_G04


title: Single cell mRNA-seq_MGH26_G05


title: RA WT H3K4me3 rep1

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

department: Genetics

institute: University of North Carolina at Chapel Hill

description: processed data file: ra_wt_k4_macs_peaks.bed

data_processing:
Initial processing and basecalling was done using the Illumina Pipeline (v.1.8.2)
Alignment to the mm9 genome was performed using Bowtie
BAM files were created from bowtiefiles using samtools
Peaks were called using MACS using the input and the combined replicates for each cell/genotype/histone modification combination with default parameters and com
Reads were counted at features using custom python scripts using HTseq
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files contain read counts per feature

source_name: WT_Retinoic acid treated ES cells

growth_protocol: ES cells were cultured with LIF on feeders

extract_protocol:
Cells were trypsinized, then fixed in 0.6% Formaldehyde. Cells were sonicated, then antibody ChIP.
DNA was end repaired, A-tailed, then Illumina barcode adaptors were ligated and amplified.

treatment_protocol: ES cells were split off feeders and cultured w/wo tamoxifen (+LIF) for 3 days, allowed to recover, then split for maintenance in LIF or differentiation with retinoic acid (2 days)

value: mixed C57BL/6 CD1

value: Utx fl/fl, Jmjd3 fl/fl, CreER

value: retinoic acid (2D)

value: Retinoic acid treated ES cells

tag: passages

value: passage 9

tag: chip antibody

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #


title: RA KO H3K4me3 rep1

description: processed data file: ra_ko_k4_macs_peaks.bed

source_name: KO_Retinoic acid treated ES cells

tag: strain

value: tamoxifen (3D), retinoic acid (2D)


title: RA WT H3K27me3 rep2

description: processed data file: ra_wt_k27_macs_peaks.bed


title: RA KO H3K27me3 rep1

description: processed data file: ra_ko_k27_macs_peaks.bed


title: RA KO H3K27me3 rep2


title: RA KO H3K4me3 rep2


title: RA WT H3K4me3 rep2


title: Single cell mRNA-seq_MGH26_F12

value: Glioblastoma

value: Pro


title: Single cell mRNA-seq_MGH26_G01


title: Single cell mRNA-seq_MGH26_G02


title: RA WT Input

value: Input


title: ES KO H3k27me3 rep2

description: processed data file: es_ko_k27_macs_peaks.bed

source_name: KO_ES cells

value: tamoxifen (3D)

value: ES cells


title: ES KO H3k27me3 rep1


title: Single cell mRNA-seq_MGH26_F11


title: RA WT H3K27me3 rep1


title: ES WT Input

source_name: WT_ES cells


title: Single cell mRNA-seq_MGH26_G07


title: ES WT H3k27me3 rep1

description: processed data file: es_wt_k27_macs_peaks.bed


title: ES WT H3k27me3 rep2


title: Single cell mRNA-seq_MGH26_F07


title: Single cell mRNA-seq_MGH26_F06


title: Single cell mRNA-seq_MGH26_F05


title: Single cell mRNA-seq_MGH26_F08


title: Input

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet --solexa1.3-quals
Peak calling was done using MACS 2.0.9 with the following configurations: -q 1e-5 --llocal=10000 --bw 300 -m 5,30  --slocal=1000  -B  --keep-dup=1
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were automatically generated as an output of MACS 2.0.9;

source_name: mouse primary hepatocyte

growth_protocol: Mouse primary hepatocytes were isolated from mouse liver routinely and cultured in DMEM supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and NUCKS-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: mouse primary hepatocyte


title: Single cell mRNA-seq_MGH26_F09


title: Nucks

value: NUCKS (Rabbit polyclonal antibody is generated by i-DNA Biotechnology Pte Ltd by immunizing rabbits with bacterially expressed full-length NUCKS protein)


title: Single cell mRNA-seq_MGH26_F04


title: Single cell mRNA-seq_MGH26_F02


title: Single cell mRNA-seq_MGH26_F01


title: Single cell mRNA-seq_MGH26_E09


title: Single cell mRNA-seq_MGH26_E08


title: Single cell mRNA-seq_MGH26_E11


title: Single cell mRNA-seq_MGH26_E10


title: Single cell mRNA-seq_MGH26_E12

value: Cla


title: Single cell mRNA-seq_MGH26_E07


title: Single cell mRNA-seq_MGH26_F10

value: Pro+Cla


title: Single cell mRNA-seq_MGH26_E04


title: Single cell mRNA-seq_MGH26_E03


title: Single cell mRNA-seq_MGH26_D12


title: Single cell mRNA-seq_MGH26_E01


title: Single cell mRNA-seq_MGH26_E02


title: Single cell mRNA-seq_MGH26_D11


title: Single cell mRNA-seq_MGH26_D09


title: Single cell mRNA-seq_MGH26_D08


title: Single cell mRNA-seq_MGH26_D07


title: Single cell mRNA-seq_MGH26_D10


title: Single cell mRNA-seq_MGH26_D02


title: Single cell mRNA-seq_MGH26_D04


title: Single cell mRNA-seq_MGH26_F03


title: Single cell mRNA-seq_MGH26_D03


title: Single cell mRNA-seq_MGH26_D01


title: Single cell mRNA-seq_MGH26_C12


title: Single cell mRNA-seq_MGH26_D06

value: Neu


title: Single cell mRNA-seq_MGH26_C10


title: Single cell mRNA-seq_MGH26_C11


title: Single cell mRNA-seq_MGH26_E05


title: Single cell mRNA-seq_MGH26_C06


title: Single cell mRNA-seq_MGH26_C09


title: Single cell mRNA-seq_MGH26_C08


title: Single cell mRNA-seq_MGH26_C07


title: Single cell mRNA-seq_MGH26_C03


title: Single cell mRNA-seq_MGH26_E06


title: Single cell mRNA-seq_MGH26_C02


title: Single cell mRNA-seq_MGH26_B12


title: Single cell mRNA-seq_MGH26_B11


title: Single cell mRNA-seq_MGH26_B09


title: Single cell mRNA-seq_MGH26_B10


title: Single cell mRNA-seq_MGH26_C04


title: Single cell mRNA-seq_MGH26_B07


title: Single cell mRNA-seq_MGH26_B08


title: Single cell mRNA-seq_MGH26_D05


title: Single cell mRNA-seq_MGH26_B05


title: Single cell mRNA-seq_MGH26_A11


title: Single cell mRNA-seq_MGH26_A12


title: Single cell mRNA-seq_MGH26_B01


title: Single cell mRNA-seq_MGH26_A10


title: Single cell mRNA-seq_MGH26_B02


title: Single cell mRNA-seq_MGH26_B04


title: Single cell mRNA-seq_MGH26_B06


title: Single cell mRNA-seq_MGH26_A07


title: Single cell mRNA-seq_MGH26_C05

value: Pro+Neu


title: Single cell mRNA-seq_MGH26_A08


title: Single cell mRNA-seq_MGH26_A06


title: Single cell mRNA-seq_MGH26_A04


title: Single cell mRNA-seq_MGH26_C01

value: Neu+Cla


title: Single cell mRNA-seq_MGH26_A02


title: Single cell mRNA-seq_MGH26_A03


title: Single cell mRNA-seq_MGH26_A05


title: Single cell mRNA-seq_MGH26_A01


title: png_egg_CHX_RPF

first: Iva

last: Kronja

institute: Whitehead Institute for Biomedical Research

description:
GCCAAT
Overlap_samples_43_54.txt

data_processing:
Samples 1-42: RNA-seq reads were checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low quality reads and adapter sequences were removed with FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) when necessary. mRNAs associated with six different fractions of polysomal gradient (RNPs, 40S, 60S+80S, low polysomes, medium polysomes and heavy polysomes) were separated based on their barcodes. The Drosophila dm3 genome (from UCSC Genome Bioinformatics) and the S.cerevisiae genome (from Ensembl assembly EF2 release 62) were merged, and a new gene annotation file was created by combining fly .gtf with yeast .gtf downloaded from the same sources. Then, RNA-seq reads were mapped to the merged genome using TopHat v1.3.2 (PMID:19289445) with option --segment-length 20, and guided with the merged annotation file. Next, htseq-count (http://wwwhuber.embl.de/users/anders/HTSeq/doc/overview.html) was used for counting the reads in fly and yeast genes. Any reads mapped to rRNAs were removed from further analysis. We represented fly and yeast gene express levels with rpkm (reads per kilobase per million of mapped reads): rpkm = 109 (read count in gene exons/gene length) / (total fly reads +total yeast reads). If a gene has multiple isoforms, the length of its longest transcript was used as gene length. To quantitatively compare the levels of every mRNA across the polysome gradient fractions, we added into each fraction the same amount of S. cerevisiae mRNA as an exogenous spike-in. For each polysome gradient fraction, we calculated its average of the top 20 highly expressed yeast genes sorted by the highest abundance in the RNP fraction. The fly mRNA levels were normalized with the corresponding yeast scaling factor. When comparing different conditions, an mRNA had to have an rpkm greater or equal to 4 in all conditions to be considered in the analysis. For each fly gene, normalized mRNA levels of its six fractions were summed, and the percentage of the mRNA in each fraction was calculated by dividing its normalized level by this sum.
Samples 43−54: Raw read files were stipped of adapter and mapped first to the reference genome then the reference transcriptome using bowtie. Uniquely mapping reads falling within the open reading frame of annotated mRNAs (excluding the first 50 nt of each ORF) were used to calculate RPKM values for each sample, and values are reported for samples passing an mRNA-seq expression cutoff of 10 RPM.
Genome_build: dm3
Supplementary_files_format_and_content: Overlap_samples_43_54.txt: Tab-delimited text file containing the refseq gene ID and RPKM values for samples 43-54.

organism: Drosophila melanogaster

source_name: activated eggs

growth_protocol: In the case of mature oocyte samples, one day old Drosophila adult flies were fattened for additional three days in the presence of wet yeast at 25°C. The flies were four days old at the time of ovary dissection. In the case of activated eggs samples, wild type or png mutant virgin female flies were placed into collection bottles together with spermless twine (HB5) males. Activated eggs were collected for 2 hours on molasses plates in the presence of wet yeast at 23°C.

extract_protocol:
Samples 1−42: To extract RNA from the sucrose gradient fractions, 0.5% SDS was added into fractions followed by incubation with 200 μg/ml of Proteinase K (Sigma) for 30 minutes at 50°C. Next, the lysates were transferred into 15 ml Falcon phase-lock gel tubes (5 Prime), and RNA was isolated using the hot acid phenol method, followed by isopropanol precipitation. To extract RNA from the inputs, 60 μg of total RNA from unfractionated lysates of mature oocytes or activated eggs was used as a source to extract RNA by homogenizing the lysates in Trizol (Invitrogen) according to manufacturer’s instructions.
Samples 43−54: mRNA-seq: Total mRNA was used for poly(A)-selection. The RNA was randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments (25-45 nt) were used for library preparation. Ribosome profiling: Cell extracts were processed as described in Guo et al., 2010 (GSE22004)
Samples 1−42: PolyA-selected RNA from 1 μg of total RNA was used to generate a cDNA library for Illumina based mRNA-sequencing according to the manufactures protocol.
Samples 43−54: Libraries were constructed exactly as described in Guo et al., 2010 (GSE22004)

treatment_protocol:
Samples 1−42: Ovaries dissected from four days old, fattened female flies were treated with 5 mg/ml of collagenase in Grace’s Unsupplemented Insect media to individualize the egg chambers. Next, mature oocytes (stage 14) were hand selected out of dissociated egg chambers that were at different stages of oogenesis. In the case of activated eggs, 0-2h collections of laid, activated eggs  were dechorionated in 50% bleach and washed extensively with water.  Collected mature oocytes or activated eggs were lysed in a buffer containing 0.25 M KCl, 0.05 M Tris-HCl (pH 7.3), 0.05 M MgCl2, 0.2% Triton X-100, 400U/ml of extract of RNasin (Promega), 2.5 mg/ml heparin, and 0.5 mg/ml cycloheximide. The lysates were cleared by centrifugation at 10000 rpm for 5 minutes. For puromycin treatment, mature oocytes or 0-2h collections of activated eggs  were lysed in a buffer containing 0.5 M NaCl, 25 mM magnesium acetate, 50 mM Tris HCl, pH 7.5, 2 mg/ml heparin, 1 mM DTT, 50 U/ml RNasin (Promega). The lysates were cleared by centrifugation at 10000 rpm for 10 minutes. After clearing, 2 mM puromycin, was added and the samples were then incubated for 20 min on ice, followed by 20 min at 37°C. After incubation, Magnesium acetate was added to 25 mM. The lysates containing 540 μg of total RNA were applied to 11 ml of a 10-50% linear sucrose gradient prepared in 0.25 M KCl, 0.05 M Tris-HCl (pH 7.3), 0.025 M MgCl2 and 0.5 mg/ml cycloheximide. In the case of puromycin treatment, 11 ml 10-50% sucrose gradient was prepared in 0.25 M KCl, 0.05 M Tris-HCl (pH 7.3) and 0.005 M MgCl2. The gradients were centrifuged in a Beckman SW-41Ti rotor at 36000 rpm for 2 hours at 4°C. Samples were fractionated by upward displacement with 60% sucrose on a gradient fractionator (Brandel). The absorbance measurement at 254 nm was performed using an ISCO UA-5 monitor.  In the case of samples 2-7 and 23-28,  5ng of S. cerevisae mRNA were added to each of the 14 fractions collected of the gradient to allow for normalization between the fractions during the analysis of mRNA sequencing. The fractions were then pooled to generate samples of RNPs, 40S, 60S + 80S, low (2-4) polysomes, medium (5-9) polysomes and heavy (10-higher) polysomes. In the case of samples 9-14, 16-21, 30-35 and 37-42,  5ng of S. cerevisae mRNA as well as firefly luciferase mRNA (Promega) was added to the six pooled fractions: RNPs, 40S, 60S + 80S, low (2-4) polysomes, medium (5-9) polysomes and heavy (10-higher) polysomes.
Samples 43−54: Mature oocytes and activated eggs were harvested as described above and either not treated or treated with 100 μg/mL cycloheximide. Samples were added to ribosome profiling lysis buffer (10 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 100 mM KCl, 1% Triton X-100) and flash frozen in liquid nitrogen.


title: activated_egg_CHX_RPF

description:
ACAGTG
Overlap_samples_43_54.txt

value: OregonR


title: mature_oocyte_CHX_RPF

description:
TGACCA
Overlap_samples_43_54.txt

source_name: mature oocytes

tag: tissue

value: ovary


title: Single cell mRNA-seq_MGH26_B03


title: png_egg_noCHX_RPF

description:
TTAGGC
Overlap_samples_43_54.txt


title: mature_oocyte_noCHX_RPF

description:
ATCACG
Overlap_samples_43_54.txt


title: activated_egg_noCHX_RPF

description:
CGATGT
Overlap_samples_43_54.txt


title: activated_egg_CHX_RNA

description:
ACAGTG
Overlap_samples_43_54.txt


title: mature_oocyte_CHX_RNA

description:
TGACCA
Overlap_samples_43_54.txt


title: activated_egg_noCHX_RNA

description:
CGATGT
Overlap_samples_43_54.txt


title: Single cell mRNA-seq_MGH26_A09


title: png_egg_noCHX_RNA

description:
TTAGGC
Overlap_samples_43_54.txt


title: mature_oocyte_noCHX_RNA

description:
ATCACG
Overlap_samples_43_54.txt


title: heavy_polysomes_fraction_activated_eggs_replicate_puromycin_treatment

description:
ACACCT
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: medium_polysomes_fraction_activated_eggs_replicate_puromycin_treatment

description:
GAGAAC
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: input_(unfractionated lysate)_activated_eggs_puromycin_treatment

description:
GAGAGA
Unlike for below mentioned samples, 60 μg of total RNA from unfractionated lysates was used as a source to extract RNA by homogenizing the lysates in Trizol (Invitrogen) according to manufacturer’s instructions.


title: 40S_fraction_activated_eggs_replicate_puromycin_treatment

description:
ACACAC
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: 60S+80S_fraction_activated_eggs_replicate_puromycin_treatment

description:
CTCTCT
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: heavy_polysomes_fraction_activated_eggs_replicate_2

description:
ACACCT,ACNCCT
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: medium_polysomes_fraction_activated_eggs_replicate_2

description:
GAGAAC,GANAAC
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: MR1 MM TEX(-)

city: Berkeley

first: Wenjun

last: Shao

address: 2151 Berkeley Way

department: Molecular and Cell Biology

institute: University of California

description:
dRNA-Seq
Indexed and sequenced twice on Illumina MiSeq; raw file was from a single index and a combination of two runs.

data_processing:
Sequenced reads were trimmed for adaptor sequence.
Trimmed reads were mapped to the MR-1 whole genome using bowtie v0.12.7 with parameters -t -q -v 2 -m 1.
Some reads were matched perfectly to the genome sequence except for a couple bases at the 5' end. For those reads, 1-2 nt at the beginning that are mismatched were trimmed off.
Peaks were called by counting the total number of reads whose starts mapped to the genome location.
Genome_build: NC_004347.2, NC_004349.1
Supplementary_files_format_and_content: wig file per sample per scaffold per strand.

organism: Shewanella oneidensis MR-1

source_name: S. oneidensis MR-1 grown in D,L-lactate medium till mid-log-phase, minus TEX

growth_protocol:
Aerobic growth to mid-log phase at 30C with shaking at 200 rpm.
Lactate medium: 20 mM D,L-lactate, 30 mM PIPES, salts (1.5 g/L NH4Cl, 0.1 g/L KCl, 1.75 g/L NaCl, 0.61 g/L MgCl2.6H20, 0.6 g/L NaH2PO4, Wolfe's vitamins, and Wolfe's minerals, at pH 7.

extract_protocol:
Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNase-free 50ml polypropylene tubes. Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment. RNA quality was confirmed with an Agilent Bioanalyzer.
Equal amounts of total RNA were incubated with terminator 5'-P-dependent exonuclease to degrade transcripts with monophosphate 5' ends (TEX+) or in buffer alone (TEX-). Then we used TAP phosphatase to convert 5'-PPP to 5'-P ends, blocked the 3' ends with sodium periodate and we added a sequencing adaptor onto the 5' end with Ambion T4 RNA ligase. We used random hexamer primers with a sequencing adaptor on their 5' end to obtain first-strand cDNA. We PCR amplified the library to enrich for products that contained both adaptors and to complete the 5' adaptor. A 6-mer index was incorporated into the reverse PCR primer for multiplexing. We purified the PCR products and removed unincorporated nucleotides, primers, and adaptor-only products with AMPure XP Beads (Agencourt).

treatment_protocol: Bacterial culture was mixed with RNAprotect Cell Reagent (Qiagen) prior to collection.

tag: media

value: defined lactate minimal medium

tag: growth phase

value: mid-log

tag: terminator exonuclease

value: no


title: 60S+80S_fraction_activated_eggs_replicate_2

description:
CTCTCT,CTNTCT
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: MR1 MM TEX(+)

source_name: S. oneidensis MR-1 grown in D,L-lactate medium till mid-log-phase, plus TEX

value: yes


title: low_polysomes_fraction_activated_eggs_replicate_2

description:
CTTGGA,CTNGGA
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: 40S_fraction_activated_eggs_replicate_2

description:
ACACAC,ACNCAC
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: MR1 LB TEX(-)

source_name: S. oneidensis MR-1 grown in LB till mid-log-phase, minus TEX

growth_protocol: Aerobic growth to mid-log phase at 30C with shaking at 200 rpm.

value: Luria-Bertani broth (LB)


title: MR1 LB TEX(+)

source_name: S. oneidensis MR-1 grown in LB till mid-log-phase, plus TEX


title: png_egg_CHX_RNA

description:
GCCAAT
Overlap_samples_43_54.txt


title: input_(unfractionated lysate)_activated_eggs_replicate_2

description:
TGTGTG,TGNGTG
Unlike for below mentioned samples, 60 μg of total RNA from unfractionated lysates of mature oocytes was used as a source to extract RNA by homogenizing the lysates in Trizol (Invitrogen) according to manufacturer’s instructions.


title: heavy_polysomes_fraction_activated_eggs_replicate_1


title: PAOMS.3_2

city: Braunschweig

first: Denitsa

last: Eckweiler

state: Lower Saxony

address: Spielmannstr. 7

department: Institute of Microbiology

country: Germany

institute: Technische Universität Braunschweig

data_processing:
RNA-seq reads were trimmed and mapped to the PAO1 genome using the Stampy aligner with default settings.
The Reads-per-Gene were calculated from the SAM files counting only the reads that were located within the gene boundaries
Mutations were identified using samtools version 0.1.18
Genome_build: ASM676v1
Supplementary_files_format_and_content: The processed files in TXT format include either Genes and Reads-per-gene (.rpg) or lists of called mutations (.flt.vcf)

organism: Pseudomonas aeruginosa PAO1

source_name: planktonic culture

growth_protocol: Cultures growing in LB medium at 37 °C were harvested after reaching an OD600 of 1.0

extract_protocol:
Using Rneasy kit (Qiagen) plus Qiashredder columns.
Customized protocol (Dötsch et al., PloS ONE, 2012). Bacterial rRNA was depleted using MICROBExpress kit with the Pseudomonas module (Ambion) and fragmented by sonication using Covaris Adaptive Acoustics device (Covaris). Upon ligation of barcoded adapters, reverse transcription with SuperScript II kit (Invitrogen) followed. Amplification was done by PCR using Illumina platform compatible primers. Established cDNA library was normalized by double strand specific nuclease treatment (Evrogen) according DSN Normalization Sample Preparation Guide from Illumina.

treatment_protocol: Cells from 3 pooled cultures were harvested by addition of the same volume of RNA-protect buffer (Qiagen) and centrifugation.

tag: agent


title: medium_polysomes_fraction_activated_eggs_replicate_1


title: RNPs_fraction_activated_eggs_replicate_puromycin_treatment

description:
TGTGTG
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: PAOMS_2

value: Ceftolozane-tazobactam


title: low_polysomes_fraction_activated_eggs_replicate_puromycin_treatment

description:
CTTGGA
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: low_polysomes_fraction_activated_eggs_replicate_1


title: PAOMS.2_2


title: 60S+80S_fraction_activated_eggs_replicate_1


title: RNPs_fraction_activated_eggs_replicate_1

description:
GAGAGA
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: PAO1.3_2


title: RNPs_fraction_activated_eggs_replicate_2

description:
GAGAGA,GANAGA
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: PAO1.2_2


title: PAO1.1_2


title: PAO1_2


title: PAOMS.3_1


title: input_(unfractionated lysate)_activated_eggs_replicate_1

description:
TGTGTG
Unlike for below mentioned samples, 60 μg of total RNA from unfractionated lysates of mature oocytes was used as a source to extract RNA by homogenizing the lysates in Trizol (Invitrogen) according to manufacturer’s instructions.


title: PAOMS.2_1


title: PAOMS.1_1


title: low_polysomes_fraction_mature_oocyte_replicate_puromycin_treatment


title: heavy_polysomes_fraction_mature_oocyte_replicate_puromycin_treatment

description:
ACACCT
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: medium_polysomes_fraction_mature_oocyte_replicate_puromycin_treatment

description:
GAGAAC
5 ng of in vitro transcribed Firefly luciferase (Promega) was spiked-in together with S. cerevisiae mRNA to the gradient fractions.


title: 60S+80S_fraction_mature_oocyte_replicate_puromycin_treatment


title: 40S_fraction_mature_oocyte_replicate_puromycin_treatment


title: PAOMS.1_2


title: RNPs_fraction_mature_oocyte_replicate_puromycin_treatment


title: 40S_fraction_activated_eggs_replicate_1


title: PAO1.1_1


title: input_(unfractionated lysate)_mature_oocyte_puromycin_treatment

description:
TGTGTG
Unlike for below mentioned samples, 60 μg of total RNA from unfractionated lysates  was used as a source to extract RNA by homogenizing the lysates in Trizol (Invitrogen) according to manufacturer’s instructions.


title: PAO1.2_1


title: PAO1_1


title: heavy_polysomes_fraction_mature_oocyte_replicate_2

description: ACACCT


title: medium_polysomes_fraction_mature_oocyte_replicate_2

description: GAGAAC


title: low_polysomes_fraction_mature_oocyte_replicate_2

description: CTTGGA


title: 60S+80S_fraction_mature_oocyte_replicate_2

description: CTCTCT


title: 40S_fraction_mature_oocyte_replicate_2

description: ACACAC


title: RNPs_fraction_mature_oocyte_replicate_2

description: GAGAGA


title: medium_polysomes_fraction_mature_oocyte_replicate_1

description:
GAGAAC
In the case of mature_oocyte_replicate_1 sample 5 ng of S. cerevisae mRNA were added to each of the 14 sucrose gradient fractions to allow for normalization between the fractions during the analysis of mRNA sequencing. Next, gradient fractions were fused to represent follwing six fractions: RNPs, 40S, 60S+80S, low polysomes, medium polysomes and heavy polysomes.


title: input_(unfractionated lysate)_mature_oocyte_replicate_2


title: low_polysomes_fraction_mature_oocyte_replicate_1

description:
CTTGGA
In the case of mature_oocyte_replicate_1 sample 5 ng of S. cerevisae mRNA were added to each of the 14 sucrose gradient fractions to allow for normalization between the fractions during the analysis of mRNA sequencing. Next, gradient fractions were fused to represent follwing six fractions: RNPs, 40S, 60S+80S, low polysomes, medium polysomes and heavy polysomes.


title: PAOMS_1


title: input_(unfractionated lysate)_mature_oocyte_replicate_1


title: Insulin 4 hpi rep2

city: Bad Nauheim

first: Rubén

last: Marín-Juez

address: Ludwigstrasse 43

institute: Max Planck Institute

data_processing:
Base calling was done by the Illumina HCS version 2.0.12
Data analysis was performed using Genetiles software (www.genetiles.com)
Genome_build: Zv9_toplevel
Supplementary_files_format_and_content: tab-delimited text files include read values for each Sample

organism: Danio rerio

source_name: Whole embryo

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were grown at 28,5°C in egg water (60µg/ml Instant Ocean sea salts).

extract_protocol:
Embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 1 ml of TRIZOL® Reagent (Invitrogen) and subsequently total RNA was extracted according to the manufacturer’s instructions. The RNA samples were incubated for 20 min at 37° with 10 units of DNaseI (Roche Applied Science) to remove residual genomic DNA prior to purification using the RNeasy MinElute Cleanup kit (Qiagen) according to the RNA clean up protocol. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To inject PBS and Human recombinant insulin 1 nl was injected in the caudal aorta of 4dpf zebrafish embryos using a glass capillary

tag: developmental stage

value: 4 days post fertilization

tag: treatment

value: insulin

tag: time

value: 4 hpi

value: whole embryo

tag: genetic background

value: ABTL


title: Insulin 4 hpi rep1


title: Insulin 4 hpi rep3


title: Control PBS 4 hpi rep4

value: control


title: RNPs_fraction_mature_oocyte_replicate_1

description:
GAGAGA
In the case of mature_oocyte_replicate_1 sample 5 ng of S. cerevisae mRNA were added to each of the 14 sucrose gradient fractions to allow for normalization between the fractions during the analysis of mRNA sequencing. Next, gradient fractions were fused to represent follwing six fractions: RNPs, 40S, 60S+80S, low polysomes, medium polysomes and heavy polysomes.


title: Insulin 4 hpi rep4


title: Control PBS 4 hpi rep3


title: 40S_fraction_mature_oocyte_replicate_1

description:
ACACAC
In the case of mature_oocyte_replicate_1 sample 5 ng of S. cerevisae mRNA were added to each of the 14 sucrose gradient fractions to allow for normalization between the fractions during the analysis of mRNA sequencing. Next, gradient fractions were fused to represent follwing six fractions: RNPs, 40S, 60S+80S, low polysomes, medium polysomes and heavy polysomes.


title: Sp1_KitPlus_progenitors

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: Sample 2

data_processing:
The raw sequence reads were aligned to the mm10 mouse genome build using BWA (Li and Durbin 2010).
The reads in the resulting alignment files in sam format were used to generate density maps using bedtools
Peaks were called using MACS (Zhang et al. 2008) and cisGenome (Ji et al. 2008)
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using  samtools and bedtools

source_name: Sp1 from cKitPlus progenitors

growth_protocol: ES cells were trypsinised and allowed to form embryoid bodies by plating in base methylcellulose (Stem Cell Technologies M3134) supplemented with 10% FCS, 100 units/ml Penicillin and 100 µg/ml Streptomycin, 1 mM glutamine, 0.15 mM MTG, 10 ug/ml insulin (Sigma), 5% IL-3 conditioned media, 10 ng/ml recombinant mouse M-CSF (R&D Systems), 100 units/ml IL-1 (Peprotech) at a cell concentration previously determined to give similar numbers of EB. After at least 14 days EB were counted and assessed for the number of EB.

extract_protocol:
Flk1+ve sorted cells and c-kit+ve sorted floating progenitors from Day 3 blast culture were used for ChIP-seq analysis. Cells were crosslinked for 10 min at room temperature with 1% formaldehyde (Pierce, Rockford, IL, USA) and quenched with 1/10th volume 2 M glycine. Nuclei were prepared essentially as described in Lefevre et al 2003, sonicated using a Bioruptor water bath in immunoprecipitation buffer I (25 mM Tris 1 M, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1 % TritonX-100 and 0.25 % SDS). After centrifugation the sheared 0.5-2 kb chromatin fragments (1-2 x 106 cells) were diluted with 2 volumes immunoprecipitation buffer II (25 mM Tris, pH 8.0, 150mM NaCl, 2 mM EDTA, pH 8.0, 1% TritonX-100, 7.5% glycerol) and precipitation was carried out for 2-3 hours at 4 °C using 2 µg anti-Sp1 antibody (Santa Cruz sc-17824X) coupled to 15 µl Protein-G dynabeads. Beads were washed with low salt buffer (20 mM Tris 1 M, pH 8.0, 150 mM NaCl, 2 mM EDTA, pH 8.0, 1% TritonX-100, 0.1% SDS), high salt buffer (20 mM Tris, pH 8.0, 500 mM NaCl, 2 mM EDTA, pH 8.0, 1% TritonX-100, 0.1% SDS), LiCl buffer (10 mM Tris, pH 8.0, 250 mM lithium chloride, 1 mM EDTA, pH 8.0, 0.5% NP40, 0.5 % sodium-deoxycholate) and TE pH 8.0 containing 50 mM sodium chloride. The immune complexes were eluted in 100 µl elution buffer (100 mM NaHCO3, 1 % SDS) and after adding 5 µl 5M sodium chloride and proteinase K, the crosslinks were reversed at 65°C overnight. DNA was extracted using the Ampure PCR purification kit (Beckman Coulter) according to manufacturer’s instructions and analysed by qRT-PCR. Libraries of DNA fragments from chromatin immunoprecipitation were prepared from approximately 10 ng of DNA. Firstly, overhangs were repaired by treatment of sample material with T4 DNA polymerase, T4 PNK and Klenow DNA polymerase (all enzymes obtained from New England Biolabs UK) in a reaction also containing 50 mM Tris-HCl,10 mM MgCl2, 10 mM Dithiothreitol, 0.4 mM dNTPs and 1 mM ATP. Samples were purified after each step using Ampure PCR purification kit (Beckman Coulter). ‘A’ bases were added to 3’ ends of fragments using Klenow Fragment (3´- 5´ exo-), allowing for subsequent ligation of adapter oligonucleotides (Illumina part #1000521) using Quick T4 DNA ligase. After a further Ampure clean up to remove excess adaptors, fragments were amplified in an 18-cycle PCR reaction using adapter-specific primers (5’-CAAGCAGAAGACGGCATACGAGCTCTTCCGATC*T and 5’-AATGATACGGCGACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T). The libraries were purified and adapter dimers removed by running the PCR products on 2% agarose gels and excising gel slices corresponding to fragments approximately 200-300 bp in size, which were then extracted using the Qiagen gel extraction kit. Libraries were validated using quantitative PCR for known targets, and quality assessed by running 1 µl of each sample on an Agilent Technologies 2100 Bioanalyser.  Once prepared, DNA libraries were subjected to massively parallel DNA sequencing on an Illumina Genome Analyzer IIx.
DNA from in vivo treated cells was run on an agarose gel and fragments were excised and isolated. This DNA was used to prepare the libraries, according to Illumina's sample preparation protocol

tag: cell type

value: Flk+ cKit+ progenitor


title: Insulin 0.5 hpi rep1

value: 0.5 hpi


title: Sp1_E14_Flk1Plus

description: Sample 1

source_name: Sp1 from E14 Flk1Plus

value: E14  FLK1+

value: anti-Sp1 antibody (Santa Cruz sc-17824X)


title: Insulin 0.5 hpi rep3


title: Control PBS 0.5 hpi rep4


title: Control PBS 4 hpi rep2


title: Control PBS 4 hpi rep1


title: Control PBS 0.5 hpi rep2


title: Control PBS 0.5 hpi rep1


title: Control PBS 0.5 hpi rep3


title: Insulin 0.5 hpi rep4


title: 60S+80S_fraction_mature_oocyte_replicate_1

description:
CTCTCT
In the case of mature_oocyte_replicate_1 sample 5 ng of S. cerevisae mRNA were added to each of the 14 sucrose gradient fractions to allow for normalization between the fractions during the analysis of mRNA sequencing. Next, gradient fractions were fused to represent follwing six fractions: RNPs, 40S, 60S+80S, low polysomes, medium polysomes and heavy polysomes.

value: ovary

value: OregonR