title: Mouse VZ5

status: Public on Jul 03 2012

city: Leipzig

first: Martin

last: Kircher

address: Deutscher Platz 6

country: Germany

institute: Max Planck Society

description:
Sample 39
VZ5

data_processing:
The φX174 control reads were aligned to the corresponding reference sequence to obtain a training data set for the base caller IBIS, which was then used to recall bases and quality scores.
Sequencing reads were separated by index, allowing up to one substitution in the index sequence but requiring that all quality scores in the index read were ≥10 (PHRED-scale). Reads of the same sample on different sequencing lanes were combined and represent the submitted raw data.
Raw reads were subjected to adapter trimming, and reads shorter than 60 nucleotides or with more than five bases below a quality score of 15 (PHRED-scale) were removed.
The processed reads were aligned to the human reference genome (hg19/GRCh37, release date Feb. 2009, excluding additional haplotypes) and mouse reference genome (mm9/NCBI37, release date Jul. 2007) using TopHat v1.2.0.
Gene models (Ensembl) were quantified using cufflinks from the alignments of each species. A combined table as created using the 1:1 ortholog assignment from Ensembl.
Genome_build: Fetal human neocortex: h19, Embryonic mouse neocortex: mm9
Supplementary_files_format_and_content: text files with FPKM values, quantified gene models (Ensembl) using cufflinks from the alignments of each species , and combined mouse/human orthologs.

source_name: Embryonic mouse neocortex

extract_protocol: Total RNA was extracted from microdissected germinal zones (VZ, SVZ) and the CP of fetal human and embryonic mouse neocortex using the Qiagen RNeasy Micro Kit. For each zone and human fetus/mouse embryo, a cDNA library was generated from 25 ng of the total RNA using the Illumina TruSeq RNA sample preparation kits. cDNA libraries (10 nM each) were pooled and sequenced on an Illumina Genome Analyzer IIx according to the manufacturer's instructions for Multiplex Single Read sequencing and using 76 + 7 cycles, except that an indexed φX174 control library was added, yielding about 1% of sequencing reads in each lane.

tag: age

value: Neocortex

tag: germinal zone

value: ventricular zone (VZ)


title: Mouse VZ3

type: SRA

description:
Sample 37
VZ3

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: strain

tag: tissue


title: Mouse VZ2

description:
Sample 36
VZ2


title: Myf5-GM

status: Public on Jul 05 2012

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: Pulldown of FLAG and TAP tagged Myf5. Instrument model: Illumina GA-IIx

library_source: genomic

data_processing: Solexa read alignment and peak calling. Solexa reads (36 bp) were aligned to mouse genome (NCBI37) by Eland (Illumina) with up to two mismatches.

molecule: genomic DNA

source_name: cycling myoblasts with TAP tagged Myf5

growth_protocol: HAMS's F10 + 20% FBS + bFGF(4ng/ml)

extract_protocol: Cycling cells or differentiated myotubes stably expressing a c-terminus TAP tagged fusion proteins were cross linked with with 1% formaldehyde in 1x PBS for 10 minutes. A solution containing 0.125 M glycine in 1x PBS was used for quenching for 5 minutes at room temperature. Cells were harvested and the pellet dissolved in ChIP lysis buffer (40 mM Tris-HCl, pH8.0; 1% Triton-X100; 4 mM EDTA; 300 mM NaCl) containing protease inhibitors. Chromatin was fragmented by sonication in a water bath sonicator at 4 ºC to an average length of 200 base pairs. The lysate was spun at 14K for 15 minutes and the supernatant was diluted 1:1 in ChIP dilution buffer containing 40 mM Tris-HCl, pH 8.0; 4 mM EDTA plus protease inhibitors. FLAG immunoprecipitation was done on 15 milligram of cell lysate using M2 conjugated agarose beads (Sigma Aldrich) for 2 hours at 4 ºC following manufacture’s recommendation. Beads were washed 3 times with 10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 0.1% Triton-X100 plus protease inhibitors. Protein complex was eluted from M2-conjugated agarose beads using proteolytic cleavage with Tobacco Etch Virus (TEV) protease (Invitrogen) together with 3xFLAG peptide (Sigma Aldrich) competition over night at 4 ºC using 1x TEV buffer (Invitrogen). Two additional rounds of elution with 3xFLAG peptides were done using 200 µg/ml of 3xFLAG peptide in TBS (50 mM Tris-HCl, pH 7.4; 150 mM NaCl). 6xHis immunoprecipitation and purification was done using His-Select nickel beads (Sigma-Aldrich) for three hours at 4 ºC following manufacture’s recommendations. Beads were washed three times with wash buffer (20 mM Tris-HCl, pH 7.4; 150 mM NaCl; 5 mM Imidazole plus protease inhibitors). Final DNA/protein complex was eluted by 400 mM imidazole at room temperature. Reverse cross linking and phenol/chloroform extraction of chromatin were performed. The ChIP DNA library was prepared according to the Illumina protocol (www.illumina.com)

value: Balb/c

tag: genotype/variation

value: wild type

tag: tissue of origin

value: skeletal muscle

tag: cell type

value: myoblasts

tag: transcription factor

tag: sample type

value: ChIP

tag: flag immunoprecipitation

value: anti-FLAG M2 agarose resin

tag: 6xhis immunoprecipitation

value: His-Select nickel beads


title: Mouse VZ1

description:
Sample 35
VZ1


title: Mouse SVZ5

description:
Sample 34
SVZ5

value: subventricular zone (SVZ)


title: Mouse CP5

description:
Sample 29
CP5

value: cortical plate (CP)


title: Mouse SVZ1

description:
Sample 30
SVZ1


title: Mouse SVZ4

description:
Sample 33
SVZ4


title: Mouse CP2

description:
Sample 26
CP2


title: Mouse SVZ3

description:
Sample 32
SVZ3


title: Mouse SVZ2

description:
Sample 31
SVZ2


title: Mouse CP3

description:
Sample 27
CP3


title: Human VZ5

description:
Sample 23
w16_1_VZ

organism: Homo sapiens

source_name: Fetal human neocortex


title: Mouse CP4

description:
Sample 28
CP4


title: Human VZ3

description:
Sample 21
w14_2_VZ


title: Human VZ4

description:
Sample 22
w15_1_VZ


title: Mouse CP1

description:
Sample 25
CP1


title: Human VZ2

description:
Sample 20
w14_1_VZ


title: Mouse VZ4

description:
Sample 38
VZ4


title: Human OSVZ6

description:
Sample 18
w16_2_OSVZ

value: outer subventricular zone (OSVZ)


title: Human VZ1

description:
Sample 19
w13_VZ


title: histone.D1_IP

status: Public on Jul 07 2012

city: Beijing

first: Zhi-Xiong

last: Zhou

address: No.7, ZGC Life Science Park

country: China

institute: National Institute of Biological Sciences, Beijing

data_processing:
Basecalling by Illumina Casava software
Sequencing reads were trimmed for index sequence, and mapped to S. pombe reference genome using SOAP2 software, allowing only perfectly and uniquely-matched reads
Genome_build: S. pombe 972 strain
Supplementary_files_format_and_content: bed file. The values indicate the number of sequencing reads mapped to certain location.

organism: Schizosaccharomyces pombe

source_name: Haploid cells

growth_protocol: Cells used for ChIP assay were cultured in EMM (Edinburgh Minimal Medium) with necessary supplements at 30°C unless otherwise noted.

extract_protocol: ChIP DNA or input DNA was pre-denatured at 95°C and quenched on ice. The DNA was mixed with two pre-annealed adaptors added at final concentrations of 1.5 uM each. Adaptor 1 was composed of oligo A (5'-GCTCTTCCGATCXXXXCNNNNNN-3') and oligo B (5'-p-GXXXXGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-NH2-3'). XXXX in the oligo sequence denotes 4-nucleotide multiplex indexes. Adaptor 2 was composed of oligo C (5'-NNNNNNGTTCAGAGTTCTGCGACAGGAGAG-NH2-3') and oligo D (5'-CAAGCAGAAGACGGCATACGACCTCTCCTGTCGCAGAACTCTGAAC-3'). The ligation reaction was conducted using the Quick Ligation Kit (New England Biolabs) at 16°C overnight. The ligation product was then separated on a Low Range Ultra agarose gel (Bio-Rad). DNA in the 250-500-bp range was retrieved with the GFX PCR DNA and Gel Band Purification Kit (GE Healthcare). The gel-purified DNA was amplified by PCR using primers P1 (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA-3') and P2 (5'-CAAGCAGAAGACGGCATACGA-3') for 25 cycles. The PCR product was processed by gel-based size selection, again retaining DNA in the 250-500-bp range. Equal amounts of DNA tagged with different multiplex indexes were mixed together and sequenced on an Illumina GA-II instrument using the sequence primer 5'-ACACTCTTTCCCTACACGACGCTCTTCCGATC-3'.

tag: genotype

value: h- ura4-D18 leu1-32 his3-D1 arg3-D4 (hht1-hhf1)D::arg3 hhf2::ura4 Otr1:ade6 rad22-CFP-TAP-natMX

tag: chip antibody

value: IgG Sepharose 6 Fast Flow

tag: antibody vendor/catalog#

value: GE Healthcare, 17-0969-02


title: Human OSVZ2

description:
Sample 14
w14_1_OSVZ


title: Human OSVZ5

description:
Sample 17
w16_1_OSVZ


title: Human OSVZ1

description:
Sample 13
w13_OSVZ


title: Human OSVZ3

description:
Sample 15
w14_2_OSVZ


title: Human OSVZ4

description:
Sample 16
w15_OSVZ


title: Human ISVZ6

description:
Sample 12
w16_2_ISVZ

value: inner subventricular zone (ISVZ)


title: Human ISVZ5

description:
Sample 11
w16_1_ISVZ


title: Human ISVZ3

description:
Sample 9
w14_2_ISVZ


title: Human VZ6

description:
Sample 24
w16_2_VZ


title: Human ISVZ2

description:
Sample 8
w14_1_ISVZ


title: Human CP5

description:
Sample 5
w16_1_CP


title: Human CP4

description:
Sample 4
w15_CP


title: Human CP6

description:
Sample 6
w16_2_CP


title: Human ISVZ1

description:
Sample 7
w13_ISVZ


title: Human CP1

description:
Sample 1
w13_CP


title: Human CP2

description:
Sample 2
w14_1_CP


title: Endogenous small RNAs from peach root

city: Kearneysville

first: HONG

last: ZHU

state: WV

address: 2217 Wiltshire Rd.

country: USA

institute: USDA-AFRS

description: collected from young seedling

data_processing:
Adaptors were trimmed with CLC Genomic Workbench, and counted and merged using customized perl scripts.
Genome_build: Peach Genome V1.0 scaffolds (GDR, www.rosaceae.org)

molecule: total RNA

organism: Prunus persica

source_name: peach root

growth_protocol: Peach trees are grown under normal field conditions

extract_protocol:
RNA extraction for different peach tissues was performed using Plant RNA Purification Reagent (Invitrogen, CA). Libraries for peach flower and fruit were constructed according to SOLiD total RNA-seq kit. Libraries for peach root and leaf were constructed according to the standard protocol by Beijing Genomics Institute (BGI). Degradome library was constructed using the standard protocol by BGI.
small RNA sequencing was conducted by BGI, using SOLiD System 4.0 for peach flower and fruit; Illumina HiSeq 2000 for peach root and leaf.

tag: cultivar

value: Lovell

value: peach root

tag: developmental stage

value: greenhouse seedling roots


title: Endogenous small RNAs from peach fruit

source_name: peach fruit

value: peach fruit

value: mixed stage


title: Human CP3

description:
Sample 3
w14_2_CP

value: Neocortex


title: Endogenous small RNAs from peach leaf

source_name: peach leaf

value: peach leaf

value: emerging first leaves


title: Peach degradome sequence

source_name: Mixed tissue

value: Mixed tissue


title: Endogenous small RNAs from peach flower

source_name: peach flower

value: peach flower

value: whole flower


title: RenLab-HiC-cortex_replicate one

status: Public on Jul 01 2012

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

description: equivalent to Sample GSM892304

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
cortex_HindIII_ori_HiC.nodup.hic.summary.txt.gz: mm9

source_name: Mouse cortex

growth_protocol: mESC line J1 was maintained on mitomycin C-inactivated MEF feeder layers in DME containing 15% fetal calf serum, leukemia inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino acids. All ES cells were passaged on 0.2 % gelatin twice to deplete feeder cells before harvest for experiments. H1 and IMR90 cells were grown as described in: Hawkins, R.D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-91

extract_protocol: Cortex Hi-C experiment were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).) with modifications for tissue samples. In brief, cortex from 8-week old male C57Bl/6 mice were dissected, minced and fixed with 1% formaldehyde for 20 minutes at room temperature.  After fixation, samples were homogenized and counted for cell numbers with Trypan Blue.

value: cortex

tag: restriction enzyme

value: HindIII


title: RenLab-Input-thymus

description: Input

data_processing:
fastq:  Illumina's Genome Analyzer Pipeline
bowtie files: Alignment to mm9 using Bowtie with a seed length of 32 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.

source_name: Mouse thymus

tag: antibody


title: RenLab-H3K27ac-thymus

description: H3K27ac IP

value: Active motif, 39133


title: RenLab-HiC-cortex_replicate two

description: equivalent to Sample GSM892305

data_processing:
fastq:  Illumina's HiSeq Control Software
hic.summary.txt:The paired-end Hi-C reads were mapped to mouse genome build mm9 using an in-house pipeline based on BWA using default parameter. BWA SAMPE was used to merged the pairs. Duplicated reads from the same biological library were removed.
Genome Build:
cortex_HindIII_replicate_Hic.nodup.hic.summary.txt.gz: mm9


title: RenLab-H3K4me1-thymus

description: H3K4me1 IP

value: Abcam, ab8895


title: RenLab-H3K4me3-thymus

description: H3K4me3 IP

value: Millipore, 05-745


title: RenLab-Pol2-thymus

description: RNA PolII IP

value: Canvance, MMS-126R


title: RenLab-CTCF-thymus

description: CTCF IP

value: Kim et al., 2007


title: RenLab-Input-testis

description: Input

data_processing:
fastq:  Illumina's Genome Analyzer Pipeline
bowtie files: Alignment to mm9 using Bowtie with a seed length of 32 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.
ELAND files:  Alignment to mm9 using ELAND with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.

source_name: Mouse testis


title: Human ISVZ4

description:
Sample 10
w15_ISVZ

tag: germinal zone

value: inner subventricular zone (ISVZ)

tag: age


title: RenLab-H3K27ac-testis

description: H3K27ac IP

tag: strain


title: RenLab-H3K4me3-testis

description: H3K4me3 IP


title: RenLab-Pol2-testis

description: RNA PolII IP


title: RenLab-H3K4me1-testis

description: H3K4me1 IP


title: RenLab-Input-placenta

description: Input

source_name: Mouse placenta

growth_protocol: Placenta was extracted from C57Bl/6 pregnant mice


title: RenLab-Pol2-placenta

description: RNA PolII IP


title: RenLab-H3K27ac-placenta

description: H3K27ac IP


title: RenLab-H3K4me3-placenta

description: H3K4me3 IP


title: RenLab-Input-olfactory-bulb

description: Input

source_name: Mouse olfactory bulb


title: RenLab-H3K4me3-olfactory-bulb

description: H3K4me3 IP


title: RenLab-H3K4me1-placenta

description: H3K4me1 IP


title: RenLab-H3K27ac-olfactory-bulb

description: H3K27ac IP


title: RenLab-Pol2-olfactory-bulb

description: RNA PolII IP


title: RenLab-CTCF-olfactory-bulb

description: CTCF IP


title: RenLab-CTCF-placenta

description: CTCF IP


title: RenLab-H3K27ac-intestine

description: H3K27ac IP

data_processing:
fastq:  Illumina's Genome Analyzer Pipeline
bowtie files: Alignment to mm9 using Bowtie with a seed length of 32 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.
ELAND files:  Alignment to mm9 using ELAND with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were used for further analysis.

source_name: Mouse intestine


title: RenLab-H3K4me1-olfactory-bulb

description: H3K4me1 IP


title: RenLab-Input-intestine

description: Input


title: hst4_cdc25_60min_IP

value: h- leu1-32 hst4D::kanMX cdc25-22 rad22-CFP-TAP-natMX

value: IgG Sepharose 6 Fast Flow

value: GE Healthcare, 17-0969-02


title: RenLab-H3K4me3-intestine

description: H3K4me3 IP


title: RenLab-Pol2-intestine

description: RNA PolII IP


title: RenLab-H3K4me1-intestine

description: H3K4me1 IP


title: RenLab-CTCF-intestine

description: CTCF IP


title: RenLab-H3K27ac-embryonic-liver

description: H3K27ac IP

data_processing:
fastq:  Illumina's Genome Analyzer Pipeline
bowtie files: Alignment to mm9 using Bowtie with a seed length of 32 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.
ELAND files:  Alignment to mm9 using ELAND with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were used in further analysis

source_name: Mouse E14.5 liver

growth_protocol: Cells were derived from E14.5 C57Bl/6 mouse embryos


title: RenLab-Input-embryonic-liver

description: Input


title: RenLab-Pol2-embryonic-liver

description: RNA PolII IP


title: RenLab-CTCF-testis

description: CTCF IP


title: RenLab-H3K4me3-embryonic-liver

description: H3K4me3 IP


title: RenLab-H3K4me1-embryonic-liver

description: H3K4me1 IP


title: RenLab-CTCF-embryonic-liver

description: CTCF IP


title: RenLab-Input-embryonic-limb

description: Input

data_processing:
fastq:  Illumina's Genome Analyzer Pipeline
bam files: Alignment to mm9 using Bowtie with a seed length of 32 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.

source_name: Mouse E14.5 limb


title: RenLab-Pol2-embryonic-limb

description: RNA PolII IP


title: RenLab-H3K27ac-embryonic-limb

description: H3K27ac IP


title: RenLab-H3K4me3-embryonic-limb

description: H3K4me3 IP


title: RenLab-H3K4me1-embryonic-limb

description: H3K4me1 IP


title: RenLab-H3K4me3-embryonic-heart

description: H3K4me3 IP

source_name: Mouse E14.5 heart


title: RenLab-CTCF-embryonic-heart

description: CTCF IP


title: RenLab-Pol2-embryonic-heart

description: RNA PolII IP


title: RenLab-H3K27ac-embryonic-heart

description: H3K27ac IP


title: RenLab-Input-embryonic-brain

description: Input

source_name: Mouse E14.5 brain


title: RenLab-Pol2-embryonic-brain

description: RNA PolII IP


title: RenLab-H3K4me1-embryonic-heart

description: H3K4me1 IP


title: RenLab-H3K4me1-embryonic-brain

description: H3K4me1 IP


title: RenLab-CTCF-embryonic-brain

description: CTCF IP


title: RenLab-H3K27ac-mESC

description: H3K27ac IP

source_name: Bruce4 embryonic stem cells


title: RenLab-Input-embryonic-heart

description: Input


title: RenLab-H3K4me3-embryonic-brain

description: H3K4me3 IP


title: RenLab-H3K27ac-lung

description: H3K27ac IP

source_name: Mouse lung


title: RenLab-H3K27ac-spleen

description: H3K27ac IP

source_name: Mouse spleen


title: RenLab-H3K27ac-liver

description: H3K27ac IP

source_name: Mouse liver


title: RenLab-H3K27ac-kidney

description: H3K27ac IP

source_name: Mouse kidney


title: RenLab-H3K27ac-heart

description: H3K27ac IP

source_name: Mouse heart


title: RenLab-H3K27ac-cerebellum

description: H3K27ac IP

source_name: Mouse cerebellum


title: RenLab-H3K27ac-bone-marrow

description: H3K27ac IP

source_name: Mouse bone marrow


title: RenLab-RNA-Seq-thymus

data_processing:
fastq:  Illumina's HiSeq Control Software
bam and bigWig: Alignment to mm9 using TopHat with default parameters.

source_name: mouse thymus

growth_protocol: Adult intestine, olfactory bulb, testis, and thymus were dissected from 8-week old male C57Bl/6 mice (Charles River). Placenta was extracted from C57Bl/6 pregnant mice. E14.5 brain, heart, limb and liver were derived from E14.5 C57Bl/6 mouse embryos.

extract_protocol: RNA samples from tissues and primary cells were extracted from Trizol according to protocol (Invitrogen). polyA+RNA was purified with the Dynabeads mRNA purification kit (Invitrogen). The mRNA libraries were prepared for strand-specific sequencing as described previously in Parkhomchuk, D. et al. (2009).


title: RenLab-H3K27ac-MEF

description: H3K27ac IP

source_name: Mouse embryonic fibroblast


title: RenLab-CTCF-embryonic-limb

description: CTCF IP


title: RenLab-RNA-Seq-placenta

source_name: mouse placenta


title: RenLab-RNA-Seq-olfactory

source_name: mouse olfactory


title: RenLab-RNA-Seq-E14.5-liver


title: RenLab-RNA-Seq-E14.5-limb


title: RenLab-H3K27ac-cortex

description: H3K27ac IP

source_name: Mouse cortex


title: RenLab-RNA-Seq-E14.5-heart


title: RenLab-RNA-Seq-intestine

source_name: mouse intestine


title: RenLab-RNA-Seq-E14.5-brain


title: RenLab-H3K27ac-embryonic-brain

description: H3K27ac IP


title: RenLab-RNA-Seq-testes

source_name: mouse testes


title: JYAC2_NUCseq

city: Worcester

first: Amanda

last: Hughes

state: MA

address: 364 Plantation Street

institute: University of Massachusetts Medical School

description: micrococcal nuclease digestion

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling
reads were mapped to the S288C genome and relevant foreign chromosome (from either CLIB210 or CBS767) using BLAT
the cross correlation between the reads mapping to the Watson and Crick strands was determined and the length of the reads were extended by this value to count the number of reads present at each base pair
the average read count value was calculated and the data were normalized to one
gene alignments of the normalized read counts were performed using the edge of the +1 nucleosome seen in the native species (Tsankov et al., 2010)
Genome_build: S288C (S. cerevisiae), CLIB210 (K. lactis) , CBS767 (D. hansenii)
Supplementary_files_format_and_content: tab-delimited text files of the normalized read counts showing -500 to +1000bp surrounding the edge of the endogenous +1 nucleosome

organism: Saccharomyces cerevisiae

source_name: yeast with K. lactis YAC

growth_protocol: grown in SC -Tryptophan -Uracil (0.2%), yeast extract (1.5%), peptone (1%), dextrose (2%), and adenine (0.01%)

extract_protocol: mononucleosomal DNA, which was gel purified (BioRad) and then treated with calf intestinal phosphatase (NEB), was blunt-ended, a-tailed, and ligated (Epicentre) to Illumina genomic adaptors, and the final library was amplified via PCR and size selected by gel purification (BioRad).

treatment_protocol: spheroblasting via zymolyase followed by micrococcal nuclease digestion to isolate mononucleosomes

tag: bearing

value: yeast artificial chromosomes from Kluyveromyces lactis


title: JYAC1_NUCseq

description: micrococcal nuclease digestion


title: JYAC7_NUCseq

description: micrococcal nuclease digestion

source_name: yeast with D. hansenii YAC

value: Debaryomyces hansenii artificial chromosomes


title: JYAC3_NUCseq

description: micrococcal nuclease digestion


title: RenLab-RNA-Seq-mESC

source_name: Bruce4 embryonic stem cells

growth_protocol: Adult liver, kidney, bone marrow, lung, heart, cortex, cerebellum, spleen were dissected from 8-week old male C57Bl/6 mice (Charles River). Mouse embryonic fibroblast (MEF) MEF cells were derived from E13.5 C57Bl/6 mouse embryos and genotyping was performed to select male MEF cells used for this study. mESC line Bruce4 was maintained on mitomycin C-inactivated MEF feeder layers in DME containing 15% fetal calf serum, leukemia inhibiting factor, penicillin/streptomycin, L-glutamine and non-essential amino acids. All ES cells were passaged on 0.2 % gelatin twice to deplete feeder cells before harvest for experiments.


title: JYAC6_NUCseq

description: micrococcal nuclease digestion


title: RenLab-RNA-Seq-bone-marrow


title: tj-w

city: Cold Spring Harbor

first: Benjamin

last: Czech

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description: small RNA sequencing

data_processing:
The 36nt Illumina reads were stripped of the 3’ linker, collapsed, and the resulting small RNA sequences were matched without mismatches to the Drosophila release 5 genome (dm3) using nexalign. Only reads that met these conditions were subjected to further analyses.
For annotations we used a combination of UCSC [dm3], miRBase [release 14], and Flybase [r5.26] tracks for protein coding genes, repeats/transposons, non-coding RNAs and microRNAs, as well as custom tracks (for synthetic markers, endo-siRNAs from structured loci, miR and miR* strands) with different priorities (annotation priority list available upon request). For comparison of small RNA counts between samples, libraries of dsRNA-white samples were set to one million reads. Next, all libraries were normalized based on unique mappers to the flamenco (for nos-GAL4 knockdowns) or 42AB (for tj-GAL4 knockdowns) piRNA clusters.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimted text files contain genome-matching small RNA sequences, read lengths, annotation names and read counts. Formate: SEQ = the sequence of the small RNA. LENGTH = the length of the small RNA. NAME = annotation name of the small RNA. READS = read count in respective library. All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.

organism: Drosophila melanogaster

source_name: Drosophila melanogaster ovary

growth_protocol: Flies were raised at 25°C on standard cornmeal-molasses agar medium.

extract_protocol: Total RNA from ovaries of 2-3 day old females of the indicated knockdowns was isolated using TRIzol (Invitrogen). 19- to 28-nt small RNAs were cloned as described (Brennecke et al., 2007).

treatment_protocol: Flies were fed with yeast paste.

tag: tissue

value: ovaries

tag: genotype/variaion

value: tj-GAL4 driven UAS-dsRNA knockdown of white ovaries


title: OSS_GFP_knockdown

description: mRNA seq

data_processing:
Basecalling with Illumina CASAVA version 1.3+
Sequenced reads were trimmed for adaptor sequence and iteratively mapped to the genome of Drosophila melanogaster (dm3) using Bowtie. Reads were mapped allowing 0 mismatches, and remaining reads were remapped with 1 and 2 mismatches in subsequent steps to produce a total pool of 0-, 1-, and 2- mismatch mapped reads.
Unmapped reads were mapped to annotated Drosophila melanogaster transcripts (dm3) in the refSeq database (release 48 [September 13, 2011]) using Tophat to detect reads overlapping known splice junctions using the parameters --no-novel-juncs -g 1
Bowtie and Tophat outputs were catenated and processed by Cufflinks to produce mRNAs quantified in fragments per kilobase per million reads (FPKM)
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimted text file in the standard Cufflinks FPKM Tracking Format

source_name: Ovarian Somatic Sheet (OSS) cells

growth_protocol: The OSS cells were grown in M3 media supplemented with 10% FBS, 5% Fly extract, 1X insulin and 1X glutathione and kept in a 25C incubator.

extract_protocol: Libraries were prepared using the Illumina mRNA sequencing kit. Poly-A containing mRNA was purified from 1ug of total RNA using poly-T oligo-attached magnetic beads. The mRNA is then fragmented,followed by first strand and second strand cDNA synthesis.  These cDNA fragments are then end repaired, adenylated and ligated to adaptors. These products are then PCR enriched.

treatment_protocol: OSS cells grown in a 10 cm dish were transfected with GFP dsRNA using Xfect transfection reagent.

tag: cell type

value: Ovarian Somatic Sheet cells (OSS)

tag: transfector

value: GFP dsRNA


title: tj-piwi

description: small RNA sequencing

value: tj-GAL4 driven UAS-dsRNA knockdown of piwi ovaries


title: nos-w

description: small RNA sequencing

value: nos-GAL4 driven UAS-dsRNA knockdown of white ovaries


title: RenLab-CTCF-spleen

description: CTCF IP

data_processing:
RenLab-CTCF-spleen-DM406.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
RenLab-CTCF-spleen-DM431.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.

source_name: Mouse spleen

value: CTCF

tag: chip antibody details


title: RenLab-RNA-Seq-MEF

data_processing:
fastq:  Illumina's Genome Analyzer Pipeline
bam and bigWig: Alignment to mm9 using TopHat with default parameters.


title: RenLab-RNA-Seq-kidney

source_name: Mouse kidney


title: RenLab-RNA-Seq-spleen


title: RenLab-RNA-Seq-liver

source_name: Mouse liver


title: RenLab-RNA-Seq-lung

source_name: Mouse lung


title: RenLab-RNA-Seq-heart

source_name: Mouse heart


title: tj-shu

description: small RNA sequencing

value: tj-GAL4 driven UAS-dsRNA knockdown of shu ovaries


title: RenLab-Input-spleen (Illumina HiSeq 2000)

description:
Input
The peaks and/or bigwig files are linked to the corresponding (Illumina GA IIx) Sample record.

data_processing:
RenLab-Input-spleen-DM350.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.

value: none (Input)


title: RenLab-H3K4me3-spleen (Illumina HiSeq 2000)

description:
H3K4me3 IP
The peaks and/or bigwig files are linked to the corresponding (Illumina GA IIx) Sample record.

data_processing:
RenLab-H3K4me3-spleen-DM408.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.

value: Millipore, 05-745


title: RenLab-RNA-Seq-cortex


title: RenLab-H3K4me1-spleen (Illumina HiSeq 2000)

description:
H3K4me1 IP
The peaks and/or bigwig files are linked to the corresponding (Illumina GA IIx) Sample record.

data_processing:
RenLab-H3K4me1-spleen-DM407.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.

value: Abcam, ab8895


title: RenLab-RNA-Seq-cerebellum

source_name: Mouse cerebellum


title: nos-piwi

description: small RNA sequencing

value: nos-GAL4 driven UAS-dsRNA knockdown of piwi ovaries


title: nos-shu

description: small RNA sequencing

value: nos-GAL4 driven UAS-dsRNA knockdown of shu ovaries


title: RenLab-P300-mESC

description: P300 IP

data_processing:
RenLab-P300-mESC-DM182.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
RenLab-P300-mESC-DM186.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.

value: Santa Cruz, sc585


title: Oryza sativa L. ssp. japonica zhonghua11_HT panicle sRNA

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

institute: Institute of Genetics and Developmental Biology

description: high-throughput sequencing of small RNA

data_processing: The raw data was acquired by Illumina base calling, and all the reads containing ambiguous 'N' were eliminated from raw data. Data that remained was submitted to our following bioinformatics study, including sRNA annotation, phasiRNA prediction and motif analysis etc.

organism: Oryza sativa

source_name: young panicles (4cm)

growth_protocol: The panicles were collected from plants which were grown on field.

extract_protocol: Total RNA was extracted from panicles using Trizol reagent (Invitrogen). The low molecular weight (LMW) RNA was enriched by adding equal volume of 8M LiCl, incubating on ice for 1 hour and centrifuging at 12,000 rpm for 5 min at 4°C. Approximately 150µg of low molecular weight RNA was resolved in formamide and loaded into 15% PAGE gel with 7M urea and 1×TBE buffer. The gel fragments ranging between 15-30 nt were excised from gel for further purification. The purified small RNA was then ligated with a 5’ adaptor GUUCAGAGUUCUACAGUCCGACGAUC using T4 RNA ligase (NEB) at 20℃ for 6 hours and the ligation product ranging between 40-60 nt was purified again. The purified product was further ligated to the 3’ adaptor pUCGUAUGCCGUCUUCUGCUUGidT, which has a phosphate group in the 5’ terminal and an inverted deoxythymidine in the 3’ terminal, using T4 RNA ligase. The 2nd ligation product between 60-90 nt was separated within 10% Urea-PAGE gel and the purified product was reverse transcription (RT) using primer CAAGCAGAAGACGGCATACGA. The RT product was then amplified by PCR using p5 (AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA) and p7 (CAAGCAGAAGACGGCATACGA) primers for 15 cycles. The amplified products (90-95 nt) was excised from a 6% PAGE gel without urea and purified eventually. The purified product was resolved in 1×TE buffer and submitted to SBS sequencing after quality control (QC) assay in Beijing Genomics Institution.

treatment_protocol: Collected materials were ground into a fine powder in liquid nitrogen and processed following with Trizol reagent (Invitrogen) kit to extract total RNA.

tag: background variety

tag: genotype/variation

value: wild-type

value: panicle


title: Oryza sativa L. ssp. japonica rdr701-1_LT panicle sRNA

description: high-throughput sequencing of small RNA

value: rdr701-1 mutant


title: RenLab-H3K4me3-MEF

description: H3K4me3 IP

data_processing:
fastq:  Illumina's Genome Analyzer Pipeline
bam files: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.

source_name: Mouse embryonic fibroblast

tag: chip antibody


title: RenLab-H3K4me3-mESC

description: H3K4me3 IP

data_processing:
RenLab-H3K4me3-mESC-DM159.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
RenLab-H3K4me3-mESC-DM160.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.


title: RenLab-H3K4me1-MEF

description: H3K4me1 IP


title: RenLab-H3K4me1-mESC

description: H3K4me1 IP

data_processing:
RenLab-H3K4me1-mESC-DM184.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
RenLab-H3K4me1-mESC-DM188.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.


title: RenLab-CTCF-mESC

description: CTCF IP

data_processing:
RenLab-CTCF-mESC-DM185.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
RenLab-CTCF-mESC-DM189.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.

value: Kim et al., 2007


title: RenLab-CTCF-MEF

description: CTCF IP


title: Oryza sativa L. ssp. japonica zhonghua11_LT panicle sRNA

description: high-throughput sequencing of small RNA


title: Oryza sativa L. ssp. japonica rdr701-1_HT panicle sRNA

description: high-throughput sequencing of small RNA


title: RenLab-Input-mESC

description: Input

data_processing:
RenLab-Input-mESC-DM161.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
RenLab-Input-mESC-DM162.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.


title: RenLab-Input-MEF

description: Input


title: RenLab-Pol2-liver

description: RNA PolII IP

value: Canvance, MMS-126R


title: RenLab-Input-lung

description: Input


title: RenLab-CTCF-lung

description: CTCF IP


title: RenLab-H3K4me3-lung

description: H3K4me3 IP


title: RenLab-Pol2-lung

description: RNA PolII IP


title: RenLab-H3K4me1-lung

description: H3K4me1 IP


title: RenLab-P300-lung

description: P300 IP


title: RenLab-Input-liver

description: Input


title: RenLab-P300-liver

description: P300 IP


title: RenLab-Pol2-kidney

description: RNA PolII IP


title: RenLab-P300-kidney

description: P300 IP


title: RenLab-H3K4me3-liver

description: H3K4me3 IP


title: RenLab-Input-kidney

description: Input


title: RenLab-H3K4me3-kidney

description: H3K4me3 IP


title: RenLab-H3K4me1-kidney

description: H3K4me1 IP


title: RenLab-P300-heart

description: P300 IP


title: RenLab-CTCF-kidney

description: CTCF IP


title: RenLab-Pol2-heart

description: RNA PolII IP


title: RenLab-CTCF-heart

description: CTCF IP


title: RenLab-H3K4me3-heart

description: H3K4me3 IP


title: RenLab-H3K4me1-heart

description: H3K4me1 IP


title: RenLab-Input-heart

description: Input


title: RenLab-H3K4me1-liver

description: H3K4me1 IP


title: RenLab-H3K4me3-cerebellum

description: H3K4me3 IP


title: RenLab-Input-cerebellum

description: Input


title: RenLab-CTCF-cerebellum

description: CTCF IP


title: RenLab-Pol2-mESC

description: RNA PolII IP

data_processing:
RenLab-Pol2-mESC-DM187.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
RenLab-Pol2-mESC-DM209.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.


title: RenLab-Pol2-cerebellum

description: RNA PolII IP


title: RenLab-H3K4me1-cerebellum

description: H3K4me1 IP


title: RenLab-CTCF-liver

description: CTCF IP


title: RenLab-Input-bone-marrow

description: Input

source_name: Mouse bone marrow


title: RenLab-H3K4me1-bone-marrow

description: H3K4me1 IP


title: RenLab-CTCF-bone-marrow

description: CTCF IP


title: RenLab-Pol2-MEF

description: RNA PolII IP


title: RenLab-Input-spleen (Illumina GA IIx)

description: Input

data_processing:
RenLab-Input-spleen-DM340.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.


title: hESC H9

city: MONTPELLIER

first: Emilie

last: Besnard

address: 141 rue de la Cardonille

country: France

institute: Institute of Functional Genomics

description: enrichment of short nascent strands (SNS) at replication origins with lambda exonuclease

data_processing:
The next generation sequencing of purified and sonicated SNS was realized in the Montpellier GenomiX (MGX) facility in Montpellier, France using the Illumina’s sequencing by synthesis technology.  The sequencing library was clusterized and then hybridized with sequencing primers. The sequencing of 36 bp reads by single-end pairing was performed with HiSeq 2000 of Illumina.
Image analyses were performed using HiSeq Control Software provided by Illumina.
Basecalling performed using RTA software provided by Illumina.
Sequencing reads were aligned to the hg18 genome assembly using CASAVA software (version 1.7).
Genomic position of unique sequenced reads were obtained.
To analyse the enrichment of short nascent strand with the Sole-Search tool (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi), we generated bed files from the retrieved list of sequenced reads with 6 columns.
To retrieve the maximum of replication origin positions for each cell type, we analyzed the SNS enrichment on the union set of sequencing data from two biological replicates. We compared the identified replication origins in the different cell types.
Genome_build: hg18
Supplementary_files_format_and_content: bed files with position of uniquely mapped sequenced reads, DNA sequence and strand.
Supplementary_files_format_and_content: hESC_H9.bed We analyzed the SNS enrichment on this union set of sequenced reads for further analyses
Supplementary_files_format_and_content: H9_cluster.bed We analyzed the SNS enrichment on this union set of sequenced reads for cluster analyses

source_name: embryonic pluripotent stem cells

growth_protocol: Human Embryonic Stem Cells H9 (hESC H9) were maintained on matrigel with chemically defined medium as previously described (Ludwig, T.E. et al. Feeder-independent culture of human embryonic stem cells. Nat Methods 3, 637-46 (2006)).

extract_protocol: We purified short nascent strands at replication origins in different cell types. We realized isolation of Short Nascent Strands at replication origins (SNS) of asynchronous human cells by adapting the protocol previously described (Cadoret et al. PNAS 2008). For each cell type, we purified the SNS of two biological replicates. For each sample, DNAzol was used to extract DNA of 100 millions asynchronous cells. Then DNA fragments of 1-2 kb were isolated after sucrose gradient separation. After two runs of lambda exonuclease, the quality for each purified SNS preparation was tested, as previously described (Cadoret et al. PNAS 2008).  Synthesis of second strands was realized with the kit bioprime DNA labeling system. In order to be reproducible, we realized, for each biological sample, this synthesis with the same amount of background DNA calculated on the basis of background around the replication origin at the Myc locus. In order to be able to compare the replication origins between different cells, we gave the same amount of background DNA to the sequencing platform.

treatment_protocol: No specific treatment

tag: cell line

value: hESC H9


title: RenLab-H3K4me3-spleen (Illumina GA IIx)

description: H3K4me3 IP

data_processing:
RenLab-H3K4me3-spleen-DM425.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.


title: THP1_mRNAseq

city: New York

first: Brian

last: Brown

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were filtered for low quality and mapped to the hg19 genome.
Supplementary_files_format_and_content: Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated following the protocol from Mortazavi et al, Nat Methods, 2008. Briefly, all reads falling in the exons of a given gene were counted and normalized by the length of the gene and the total reads of the run.

source_name: THP1 cells

growth_protocol: Cells were cultured in  RPMI 1640 media + 10% FBS + 2mM L-Glutamine + Pen/Strept +  0.05 mM betamercaptoethanol

extract_protocol: Total RNA was extracted from 3x106 THP1 cells following Qiazol protocol.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: human monocytic leukemia


title: HeLa

data_processing:
The next generation sequencing of purified and sonicated SNS was realized in the Montpellier GenomiX (MGX) facility in Montpellier, France using the Illumina’s sequencing by synthesis technology.  The sequencing library was clusterized and then hybridized with sequencing primers. The sequencing of 36 bp reads by single-end pairing was performed with HiSeq 2000 of Illumina. Image analyses were performed using HiSeq Control Software provided by Illumina.
Basecalling performed using RTA software provided by Illumina.
Sequencing reads were aligned to the hg18 genome assembly using CASAVA software (version 1.7).
Genomic position of unique sequenced reads were obtained.
To analyse the enrichment of short nascent strand with the Sole-Search tool (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi), we generated bed files from the retrieved list of sequenced reads with 6 columns.
To retrieve the maximum of replication origin positions for each cell type, we analyzed the SNS enrichment on the union set of sequencing data from two biological replicates. We compared the identified replication origins in the different cell types.
Genome_build: hg18
Supplementary_files_format_and_content: bed files with position of uniquely mapped sequenced reads, DNA sequence and strand.
Supplementary_files_format_and_content: HeLa.bed We analyzed the SNS enrichment on this union set of sequenced reads for further analyses
Supplementary_files_format_and_content: HeLa_cluster.bed We analyzed the SNS enrichment on this union set of sequenced reads for cluster analyses

source_name: cervical cancer cells

growth_protocol: HeLa cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen) containing 10 % heat-inactivated Fetal Bovine Serum (FBS, PAA), 1 % L-Glutamine (200 mM), 1 % penicillin and streptomycin (all from Invitrogen).

value: HeLa


title: iPSC Thomson clone 4

data_processing:
The next generation sequencing of purified and sonicated SNS was realized in the Montpellier GenomiX (MGX) facility in Montpellier, France using the Illumina’s sequencing by synthesis technology.  The sequencing library was clusterized and then hybridized with sequencing primers. The sequencing of 36 bp reads by single-end pairing was performed with HiSeq 2000 of Illumina.
Image analyses were performed using HiSeq Control Software provided by Illumina.
Basecalling performed using RTA software provided by Illumina.
Sequencing reads were aligned to the hg18 genome assembly using CASAVA software (version 1.7).
Genomic position of unique sequenced reads were obtained.
To analyse the enrichment of short nascent strand with the Sole-Search tool (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi), we generated bed files from the retrieved list of sequenced reads with 6 columns.
To retrieve the maximum of replication origin positions for each cell type, we analyzed the SNS enrichment on the union set of sequencing data from two biological replicates. We compared the identified replication origins in the different cell types.
Genome_build: hg18
Supplementary_files_format_and_content: bed files with position of uniquely mapped sequenced reads, DNA sequence and strand.
Supplementary_files_format_and_content: iPS.bed We analyzed the SNS enrichment on this union set of sequenced reads for further analyses
Supplementary_files_format_and_content: iPS_cluster.bed We analyzed the SNS enrichment on this union set of sequenced reads for cluster analyses

source_name: induced pluripotent stem cells

growth_protocol: Induced Pluripotent Stem Cells (iPSC) generated from IMR-90 cells by JA Thomson and colleagues (iPSC Th Cl-4) were maintained on matrigel with chemically defined medium as previously described (Ludwig, T.E. et al. Feeder-independent culture of human embryonic stem cells. Nat Methods 3, 637-46 (2006)).

value: iPSC Thomson clone 4


title: RenLab-Input-cortex

description: Input

source_name: Mouse cortex


title: K562 siGATA1 RNA-seq

city: Stanford

first: Xun

last: Lan

address: 318 Campus Dr. Room S240

department: Genetics

institute: Stanford University

description: Illumina TruSeq RNA Sample Prep Kit

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) (hg18) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained.
Expression: FPKM value generated with Cufflinks software were used as gene expression value.

source_name: K562 cells

growth_protocol: K562 cells were cultured in IMEM (Mediatech Inc) containing 10% FBS, 25 ïg/ml Gentamicin, 100 U/ml Penicillin, and 100 ïg/ml Streptomycin. After siRNA transfection, the cells were cultured with IMEM containing 10% FBS.

extract_protocol: The RNA libraries were prepared in accordance with the Illumina TruSeqâ¢ RNA Sample Prep Kit protocol. Briefly, mRNAs were fragmented at elevated temperature using divalent cations and transcribed into cDNA thereby generating a library of cDNA fragments. Barcoded RNA-Seq adapters provided with the Illumina kit were then ligated to the blunt ends of the cDNA fragments. The libraries of cDNA fragments were subjected to PCR amplification using universal primer sites present at the end of the ligated adapters. The libraries were then subjected to quality control steps such as verification of fragment size using the High Sensitivity DNA kit (Agilent Technologies) on an Agilent 2100 Bioanalyzer and concentration was determined by a KAPA Library Quantification Kit utilizing real-time PCR with standards suitable for Illumina sequencing libraries.

treatment_protocol: K562 cells (3 x 106) were transfected with 240 pmol of SMART pool siRNA targeting human GATA-1, GATA-2, or siGenome nontargeting siRNA pool (Dharmacon/ Fisher Scientific) with the Nucleofector II (Lonza). Cells were harvested 48 h post-transfection.

tag: knockdown


title: RenLab-Pol2-spleen

description: RNA PolII IP

data_processing:
RenLab-Pol2-spleen-DM335.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
RenLab-Pol2-spleen-DM336.bam: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.


title: K562 siGATA2 RNA-seq

description: Illumina TruSeq RNA Sample Prep Kit


title: RenLab-H3K4me1-spleen (Illumina GA IIx)

description: H3K4me1 IP

data_processing:
RenLab-H3K4me1-spleen-DM378.bam: Alignment to mm9 using Bowtie software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
fastq:  Illumina's Genome Analyzer Pipeline
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.


title: IMR-90

data_processing:
The next generation sequencing of purified and sonicated SNS was realized in the Montpellier GenomiX (MGX) facility in Montpellier, France using the Illumina’s sequencing by synthesis technology.  The sequencing library was clusterized and then hybridized with sequencing primers. The sequencing of 36 bp reads by single-end pairing was performed with HiSeq 2000 of Illumina.
Image analyses were performed using HiSeq Control Software provided by Illumina.
Basecalling performed using RTA software provided by Illumina.
Sequencing reads were aligned to the hg18 genome assembly using CASAVA software (version 1.7).
Genomic position of unique sequenced reads were obtained.
To analyse the enrichment of short nascent strand with the Sole-Search tool (http://havoc.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi), we generated bed files from the retrieved list of sequenced reads with 6 columns.
To retrieve the maximum of replication origin positions for each cell type, we analyzed the SNS enrichment on the union set of sequencing data from two biological replicates. We compared the identified replication origins in the different cell types.
Genome_build: hg18
Supplementary_files_format_and_content: bed files with position of uniquely mapped sequenced reads, DNA sequence and strand.
Supplementary_files_format_and_content: IMR-90.bed We analyzed the SNS enrichment on this union set of sequenced reads for further analyses
Supplementary_files_format_and_content: IMR-90_cluster.bed We analyzed the SNS enrichment on this union set of sequenced reads for cluster analyses

source_name: embryonic lung fibroblasts

growth_protocol: Primary human proliferative embryonic lung fibroblasts IMR-90 were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen) containing 10 % heat-inactivated Fetal Bovine Serum (FBS, PAA), 1 % L-Glutamine (200 mM), 1 % penicillin and streptomycin (all from Invitrogen).


title: RenLab-H3K4me3-bone-marrow

description: H3K4me3 IP


title: RenLab-Pol2-bone-marrow

description: RNA PolII IP


title: Endogenous small RNAs from heso1-1, replicate 2

city: shenzhen

first: Lei

last: Gao

state: guangdong

address: Nanhai Ave 3688

department: College of Life Sciences

institute: shenzhen university

data_processing: The raw sequences were filtered to remove low quality reads and the ones that passed the quality filter were trimmed to remove the adaptor sequences. Reads that matched to tRNAs and rRNAs were removed.

organism: Arabidopsis thaliana

source_name: heso1-1 rep2

growth_protocol: Plants were grown under long day (16 h light/ 8 h darkness) conditions at 22°C.

extract_protocol: Small RNAs of a desired size range (15–40 nt) were fractionated from 25ug total RNAs by 15% polyacrylamide gel electrophoresis. These small RNAs were sequentially ligated with the 3' and 5' adapters using the Small RNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions. A reverse transcription reaction followed by a low cycle PCR was performed to obtain sufficient amounts of products for deep sequencing. The wild type, heso1-1, hen1-8, and hen1-8 heso1-1 libraries were barcoded and sequenced in one channel on an Illumina Hiseq2000. Two biological replicates were performed.

tag: genetic background

tag: genotype

value: inflorescences


title: RenLab-H3K4me3-cortex

description: H3K4me3 IP

data_processing:
fastq:  Illumina's Genome Analyzer Pipeline
bam files: Alignment to mm9 using Illumina's ELAND software with a seed length of 25 bases and up to 2 mismatches.  Only sequences mapping to exactly one location were kept.  If multiple sequences aligned to the same location, all but one of the sequences were discarded.
bigWig: We divided the mouse genome into 100 base pair bins, and counted the number of reads that fell within each bin. Then we normalized the tag counts in each bin to a RPKM value (reads per kilobase per million reads). The reads for the inputs were processed in the same way and their RPKM values were subtracted from the ChIP-Seq tracks in each bin.
peaks: We identified peaks with MACS (Zhang et al., 2008) with the default parameters and the peaks filtered by a P-value of 0.00001.


title: RenLab-CTCF-cortex

description: CTCF IP

value: CTCF


title: RenLab-Pol2-cortex

description: RNA PolII IP


title: RenLab-H3K4me1-cortex

description: H3K4me1 IP


title: Endogenous small RNAs from wild-type Col, replicate 2

source_name: Col rep2

value: wt


title: Endogenous small RNAs from hen1-8 heso1-1, replicate 1

source_name: hen1-8 heso1-1 rep1

value: hen1-8 heso1-1


title: Endogenous small RNAs from heso1-1, replicate 1

source_name: heso1-1 rep1


title: Endogenous small RNAs from hen1-8, replicate 2

source_name: hen1-8 rep2


title: Endogenous small RNAs from hen1-8 heso1-1, replicate 2

source_name: hen1-8 heso1-1 rep2


title: control_RNAseq, 1

city: Portland

first: Dennis

middle: J

last: Hazelett

state: OR

address: 611 SW Campus Dr

department: Integrative Biosciences

institute: OHSU

description: RNA-Seq of polyA-selected RNA.

data_processing: Sequences were aligned to a reference Drosophila sequence (FlyBase r5.23) using Illumina's CASAVA package.

source_name: central nervous system, control

extract_protocol: RNA-Seq libraries were constructed using Illumina mRNA sequencing kits. Total RNA was subjected to two rounds of oligo-dT purification to extract the poly(A)+ component. Purified mRNA was then chemically fragmented to approximately 200 bases. Fragmented RNA was used as template for first strand cDNA synthesis using random primers and SuperScript II. The second strand was then synthesized using RNAseH and DNA Pol I. Fragment ends were repaired using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. A single 'A' was added to the 3' ends of each fragment using Klenow fragment (3' to 5' exo minus). Adaptors were ligated to the fragments and the final product was run on a 2% sizing gel. The region corresponding to 300 bp was then recovered. Templates were enriched by 15 cycles of polymerase chain reaction (PCR) using Phusion DNA polymerase. The PCR primers also included indexing sequences to "barcode" the samples. PCR was followed by a second gel to separate PCR product from unincorporated primers. Libraries were validated by examining their profiles on the Agilent Bioanalyzer.

value: central nervous system

tag: developmental stage

value: 3rd instar larva


title: LacZ_control_RNAseq, 2

description: RNA-Seq of polyA-selected RNA.

source_name: central nervous system, LacZ expression control


title: TBPH_overexpressed_RNAseq, 3

description: RNA-Seq of polyA-selected RNA.

source_name: central nervous system, TBPH overexpression


title: LacZ_control_RNAseq, 1

description: RNA-Seq of polyA-selected RNA.


title: rescue_RNAseq, 2

description: RNA-Seq of polyA-selected RNA.

source_name: central nervous system, TBPH rescue

value: G2; TBPH>TBPH


title: control_RNAseq, 2

description: RNA-Seq of polyA-selected RNA.


title: TBPH_overexpressed_RNAseq, 2

description: RNA-Seq of polyA-selected RNA.


title: TBPH_mutant_RNAseq, 2

description: RNA-Seq of polyA-selected RNA.

source_name: central nervous system, TBPH knockout


title: TBPH_mutant_RNAseq, 3

description: RNA-Seq of polyA-selected RNA.


title: control_RNAseq, 3

description: RNA-Seq of polyA-selected RNA.


title: rescue_RNAseq, 1

description: RNA-Seq of polyA-selected RNA.


title: LacZ_control_RNAseq, 3

description: RNA-Seq of polyA-selected RNA.


title: TBPH_overexpressed_RNAseq, 1

description: RNA-Seq of polyA-selected RNA.


title: polyAplus_h9_RNAseq

city: Shanghai

first: Ling-Ling

last: Chen

address: 320 Yue-Yang Road

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

description: PolyA-plus RNA.

data_processing: Alignment: Sequencing reads were obtained with Illumina Genome Analyzer Pipeline (version 1.3). All reads were uniquely aligned to the human (March, 2006; NCBI Build 36; UCSC hg18) genome by using Bowtie (version 0.10.1) with up to 2 mismatches.

source_name: hES h9 cells, poly(A)+

growth_protocol: HeLa cells were cultured under standard conditions.  hES H9 cells were maintained on plates coated with Matrigel (BD Biosciences) in either defined mTeSR medium (StemCell Technologies Inc.) or conditioned medium (CM) with irradiated mouse embryo fibroblasts supplemented with 4 ng/mL human Basic Fibroblast Growth Factor (bFGF).

extract_protocol: Total RNAs were prepared using the Trizol Reagent (Life Technologies, Inc., Grand Island, NY, USA).  After treatment with DNase I (DNA-free kit; Ambion), total RNAs were incubated with oligo(dT) magnetic beads to isolate either poly(A)+ RNAs, which were bound to the beads, or poly(A)- RNAs, which were present in the flowthrough after incubation. The poly(A)- RNA population was further processed with the RiboMinus kit (Human/Mouse Module, Invitrogen) to deplete most of the abundant ribosomal RNAs. All RNA-Seq libraries were prepared using the Illumina mRNA-Seq Sample Prep Kits (P/N 1004814) according to the manufacturer's instructions.

value: human embryonic stem cells

tag: ploidy

value: diploid

tag: passages

tag: rna polyadenylation

value: plus


title: polyAminus_h9_RNAseq

description: PolyA-minus RNA.

source_name: hES h9 cells, poly(A)-

value: minus


title: polyAminus_hela_RNAseq

description: PolyA-minus RNA.

source_name: HeLa cells, poly(A)-

value: human epithelial cervical cancer cells

value: highly polyploid


title: polyAplus_hela_RNAseq

description: PolyA-plus RNA.

source_name: HeLa cells, poly(A)+


title: Endogenous small RNAs from hen1-8, replicate 1

source_name: hen1-8 rep1


title: Endogenous small RNAs from wild-type Col, replicate 1

source_name: Col rep1


title: MM

status: Public on Jun 30 2012

city: Dalian

first: Zhiwei

last: Zhu

state: Liaoning

address: 457 Zhongshan Rd.

department: Division of Biotechnology

institute: Dalian Institute of Chemical Physics, Chinese Academy of Science

data_processing:
Image analysis, base calling were performed using the Illumina pipeline.
Raw sequences were processed with in-house Perl pipeline developed by BGI-Shenzhen. Processing included 21bp tag generation, tag alignment and count, expression level estimation, significant analysis etc.
Genome_build: genome of R. toruloides
Supplementary_files_format_and_content: tab-delimited text files include count and/or TPM (Tag per million)

organism: Rhodotorula toruloides

source_name: culture in nitrogen rich media

growth_protocol: The chemostat culture of R. toruloides was run in a 2 L continuous stirred tank reactor (Baoxing Bio-Engineering Equipment, Shanghai) equipped with Inpro 6800 O2 sensor and 405-DPAS-SC-K8S/225 pH electrodes (Mettler Toledo).The minimal medium (MM) was composed of 25 g/L glucose, 0.5 g/L MgSO4·7H2O, 3 g/L KH2PO4 and 5 g/L (NH4)2SO4, while the nitrogen limited medium (MM-N) contained the same components of MM media, but only 0.2 g/L (NH4)2SO4 as nitrogen source and 6.3 g/L K2SO4 for the supplement of equivalent sulfur element. The culture conditions were set at 30 oC and pH 5.6 adjusted with 2 M KOH and 2% H2SO4. The dissolved oxygen was above 85 % of air saturation with stirrer speed of 500 rpm and airflow of 100 L/h. The dilution rate was 0.085 h-1

extract_protocol: Total RNA was isolated with Trizol (Invitrogen) after liquid nitrogen grinding and treated with DNase I (RNase-free, NEB) to remove residual DNA. The quality was checked with Agilent 2100 bioanalyzer.The NlaIII libraries were prepared with the Illumina Tag Profiling Sample Prep kits.

treatment_protocol: Steady-state samples were harvested by centrifugation (6200g, 4 oC and 5 min), and cell pellets were frozen in liquid nitrogen and stored at -70 oC.

tag: strain

tag: culture condition

value: culture in nitrogen rich media


title: MM-N

source_name: culture in nitrogen limited media

value: culture in nitrogen limited media


title: TBPH_mutant_RNAseq, 1

description: RNA-Seq of polyA-selected RNA.

tag: tissue


title: Spi1_InVivo

city: Zurich

first: Valentina

last: Boeva

address: Universitatstrasse 6

department: Computer Science

country: Switzerland

institute: ETH Zurich

data_processing:
SOLiD ChIP-seq DNA fragment libraries were sequenced by SOLiD system 2.0 or SOLiD system 3.0 chemistries to produce DNA sequence reads of 35 and 50 nucleotides, respectively. Sequencing reads were aligned to the mm9 mouse genome using the SOLiD pipeline tools (CoronaLite, Applied Biosystems) with up to three and five mismatches per read for SOLiD system 2.0 and system 3.0, respectively. Only the reads with a unique position in the genome were kept for the following analysis. Spi-1 reads from ChIP-seq of two individual mice were pooled. To detect peaks corresponding to putative binding regions, we used FindPeaks algorithm (Fejes et al. 2008) and the MICSA pipeline (Boeva et al. 2010).
Genome Build:
Spi_inVivo_h6.5.peaks.bed: mm9
Spi-1_inVivo.wig: mm9
Spi1_inVivo_V3_50.5.bed: mm9

growth_protocol: cells were grown in a-MEM medium supplemented with 5% FBS and erythropoetin (Epo) (1U/mL)

extract_protocol: 100ng ChIP (or input) DNA was combined with 25mg of 2 microns borosilicate glass dry spheres (Duke Scientific) in round bottom borosilicate tubes. The DNA was re-sheared using the Covaris S2 Sample Prep System (Covaris) for 10 min at 4°C with maximum intensity settings to generate small DNA fragments in the 90-bp range. Sheared DNA was purified using the MinElute reaction cleanup kit (Qiagen). The End-It DNA end-repair kit (Epicentre) was used to blunt the ends of the sheared DNA fragments. The blunted DNA fragments were purified using the MinElute Reaction Cleanup Kit (Qiagen). Sheared DNA was quantified using a Qubit fluorometer (Invitrogen) and P1 and P2 adapters (Applied Biosystems) were ligated to the DNA for 10 min at room temperature using Quick ligase enzyme (NEB). Excess free adaptors were removed using the AMPure PCR purification system (Agencourt). Adapted DNA fragments were size selected by running samples through a 6% DNA retardation PAGE gel (Invitrogen). DNA fragments 150-200 bp were specifically selected using a scalpel, and the gel fragment shredded by centrifugation through a hole made with a 21G needle. ChIP fragment libraries were amplified using library PCR primers for the P1 and P2 adapters to amplify correctly adapted fragments (containing P1 and P2 on opposing ends) from a shredded gel suspension made by mixing the shredded gel with PCR SuperMix High Fidelity (Invitrogen). PCR was performed for just enough cycles (~13) to generate visible DNA on ethidium-stained agarose gels. Library DNA sample quality and size were verified using a Bioanalyzer (Agilent).

treatment_protocol: No treatment

tag: cell type

value: Spleen from Spi-1-transgenic mice with erythroleukemia in vivo


title: Input_In_Vivo

data_processing:
SOLiD ChIP-seq DNA fragment libraries were sequenced by SOLiD system 2.0 or SOLiD system 3.0 chemistries to produce DNA sequence reads of 35 and 50 nucleotides, respectively. Sequencing reads were aligned to the mm9 mouse genome using the SOLiD pipeline tools (CoronaLite, Applied Biosystems) with up to three and five mismatches per read for SOLiD system 2.0 and system 3.0, respectively. Only the reads with a unique position in the genome were kept for the following analysis. Spi-1 reads from ChIP-seq of two individual mice were pooled. To detect peaks corresponding to putative binding regions, we used FindPeaks algorithm (Fejes et al. 2008) and the MICSA pipeline (Boeva et al. 2010).
Genome Build:
Input_inVivo.wig: mm9
Input_inVivo_V3_50.5.bed: mm9


title: small RNAs (18-29nt) from shu[1]/CyO hets and shu[Def]/CyO hets. mixed

city: Vienna

first: Julius

last: Brennecke

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

data_processing:
basecalled with the instruments RTA (Run time analysis version 1.12.48.0): SCS (PN:RTA DS:Controlling software on instrument VN:1.13.48.0)
fastq files were adapter 'AGATCGGAAGAGCACACGTCT' clipped using cutadapt, version 1.0, default settings
after adapter removal, the first and last 4 bases were trimmed (both linkers contain 4 random nucleotides at their respective termini) from sequence as well using HomerTools, version 3.9
Genome_build: dmel_release 5
Supplementary_files_format_and_content: combined table of sequences matching release 5 of the genome 100%; indicating sequence, genomic mapping number and read count for each library

source_name: Ovary

growth_protocol: flies were grown at 25 degrees on standard medium

extract_protocol: small-RNAs were cloned as described in Brennecke et al. 2007.

tag: Stage

value: from 5-6 days old flies

value: ovary


title: small RNAs (18-29nt) from MTD>zuc shRNA

value: MTD>zuc shRNA


title: small RNAs (18-29nt) from MTD>armi shRNA

value: MTD>armi shRNA


title: small RNAs (18-29nt) from MTD>piwi shRNA

value: MTD>piwi shRNA


title: small RNAs from FLAG_HA_Aub Immunoprecipitation

description: IP RNA

source_name: Ovarian Somatic Cells (OSCs)

value: wt transfected with act>FLAG_HA_Aub

value: 48h after transfection

value: Ovarian Somatic Cells (OSCs)

tag: antibody

value: anti-FLAG


title: small RNAs (18-29nt) from MTD>vas shRNA

value: MTD>vas shRNA


title: small RNAs (18-29nt) from MTD>aub shRNA

value: MTD>aub shRNA


title: small RNAs (18-29nt) from MTD>vret shRNA

value: MTD>vret shRNA


title: Input

data_processing:
SOLiD ChIP-seq DNA fragment libraries were sequenced by SOLiD system 2.0 and SOLiD system 3.0 chemistries to produce DNA sequence reads of 35 and 50 nucleotides, respectively. Sequencing reads were aligned to the mm9 mouse genome using the SOLiD pipeline tools (CoronaLite, Applied Biosystems) with up to three and five mismatches per read for SOLiD system 2.0 and system 3.0, respectively. Only the reads with a unique position in the genome were kept for the following analysis. Spi-1 reads from ChIP-seq of two individual mice were pooled. To detect peaks corresponding to putative binding regions, we used FindPeaks algorithm (Fejes et al. 2008) and the MICSA pipeline (Boeva et al. 2010).
genome build: mm9

source_name: Input

value: Spleen-derived Spi-1-transgenic erythroleukemic cells


title: IgG

source_name: IgG

value: non-specific IgG


title: small RNAs (18-29nt) from UAS-Dcr-2;NGT;nanosGAL4>shu RNAi

value: UAS-Dcr-2;NGT;nanosGAL4>shu RNAi


title: small RNAs (18-29nt) from MTD>GFP shRNA

value: MTD>GFP shRNA


title: small RNAs from FLAG_HA_Piwi Immunoprecipitation

description: IP RNA

value: wt transfected with act>FLAG_HA_Piwi


title: small RNAs (18-29nt) from MTD>w-

value: MTD>w-

value: from 5-6 days old flies


title: H3k36me3_ChIPSeq


title: RNApolII_ChIPSeq

value: RNApolII


title: PBMC_differentiated and activated

city: Neuherberg

first: Brigitte

last: Waegele

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

description: normalised cDNA library

data_processing: Reads were clipped of linker sequences and assembled using the Roche Newbler software with default settings

organism: Equus caballus

source_name: blood

extract_protocol: RNA was isolated via Trizol followed by mRNA isolation via poly-A columns cDNA synthesis and amplification was done according to the Mint-Universal cDNA Synthesis Kit user manual. Amplified cDNA was used as starting material in normalization reaction using the Trimmer Kit (Evrogen, Moscow, Russia); normalized material was re-amplified. Normalized cDNA was digested with SfiI. Fragments larger than 800bp were isolated. Purified cDNA was ligated into pDNR-lib Vector.Plasmid DNA was prepared, inserts were gel-purified and ligated to high-molecular-weight DNA using a proprietary Sfi-linker. The concatenated inserts were sheared randomly by nebulization to fragments ranging in size from 400 bp to 900 bp. These fragments were end polished and the 454 A and B adaptors that are required for the emulsion PCR and sequencing were added to the ends of the fragments by ligation. The resulting fragment library was sequenced on one picotiterplate (PTP) on the GS FLX using the Roche/454 Titanium chemistry. A total of 817583 sequence reads with an average read length of 346 nucleotides were obtained.

value: blood


title: 7DPFVD3 rep5

status: Public on Jun 29 2012

city: Baltimore

first: Yuji

last: Zhang

state: MD

address: 660 W. Redwood Street

institute: University of Maryland

data_processing:
Basecalls performed using CASAVA version 1.4
mRNA-seq reads were aligned to the ZV9 assembly using Bowite 0.12.7 with the following configurations…
Gene and exon level count data were generated by HTSeq 0.5.3p3
Genome_build: ZV9
Supplementary_files_format_and_content: tab-delimited text files include raw count numbers at gene and exon level for each Sample ...

organism: Danio rerio

source_name: Zebrafish embryos/larvae

growth_protocol: Zebrafish embryos were obtained from mating of Segrest wild-type (SWT) parents under controlled barrier conditions, in the Mayo Clinic Zebrafish Core Facility, in Instant Ocean media .  Zebrafish embryos (25-30) were placed in 20 mL embryo medium (pH 7.2) containing 1-phenyl-2-thiourea (PTU) (0.003% (w/v) and were maintained at 28-30 oC.  At 24 hpf (1 day post fertilization, dpf), 10 microliters of 1a,25(OH)2D3  in ethanol was added to embryos maintained in 20 mL fresh embryo medium with PTU.  The final concentration of 1a,25(OH)2D3 was 300 pM.  Control zebrafish were treated with 10 microliters ethanol alone (vehicle controls).  The medium containing either 300 pM 1a,25(OH)2D3 or vehicle was changed every 24 h .   In experiment 1, at 2, 4, 6 and 7 dpf embryos/larvae were removed and immediately frozen at -80 0C for later RNA preparations.  25-30 embryos per set were used for preparation on RNA.  At the same times, 7-12 embryos were fixed in 4% paraformaldehyde in 0.75 X Dulbecco’s phosphate buffered saline (DPBS).  In experiment 2, 6 dpf larvae were treated with 1a,25(OH)2D3 (300 pM) or vehicle for 24 h.  RNA was prepared from three sets of larvae.

extract_protocol: RNA preparation for RNA-seq and QPCR:  RNA was prepared using RNA/protein spin columns (Clontech, Mountain View, CA).  Lysis solution was added to 25-30 frozen embryos and embryos were lysed by passage of tissue successively through 21 and 27 gauge needles.  Individual embryo lysates were applied to RNA spin columns for purification.  Preparation of libraries:  mRNA-seq libraries are prepared using the mRNA v1 sample prep kit following the manufacturer’s protocol (Illumina).  Poly-A containing mRNA is purified using poly-T oligo attached magnetic beads. The purified mRNA is fragmented using divalent cations at 95°C for 5 minutes and ethanol precipitated. The RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis is performed using DNA polymerase I and RNase H. The cDNA is purified using Qiaquick PCR columns from Qiagen. The ends are repaired and phosphorylated using Klenow, T4 polymerase, and T4 polynucleotide kinase, after which an “A” base is added to the 3’ ends of double-stranded DNA using Klenow exo- (3’ to 5’ exo minus).  Paired end DNA adaptors (Illumina) with a single “T” base overhang at the 3’ end are ligated and the resulting constructs are separated on a 2% agarose gel. DNA fragments of approximately 250-300 bp are excised from the gel using GeneCatcher tips and purified using Qiagen Gel Extraction Kits.  The adapter-modified DNA fragments are enriched by 15 cycles of PCR using primers PE 1.0 and PE 2.0 (Illumina). The concentration and size distribution of the libraries is determined on an Agilent Bioanalyzer DNA 1000 chip.  Libraries are loaded onto paired end flow cells at concentrations of 6 pM to generate cluster densities of 400,000/mm2 following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 2.  The flow cells are sequenced as 51 X 2 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS sequencing kit version 1 or version 3 and SCS version 1.1.37.0 or HCS version 1.4.8 data collection software, respectively. Base-calling is performed using Illumina’s RTA version 1.7.45.0.

value: Segrest wild type

tag: age

value: 7 days post fertilization

tag: treatment


title: 7DPFVD3 rep3

treatment_protocol: Zebrafish embryos were obtained from mating of Segrest wild-type (SWT) parents under controlled barrier conditions, in the Mayo Clinic Zebrafish Core Facility, in Instant Ocean media .  Zebrafish embryos (25-30) were placed in 20 mL embryo medium (pH 7.2) containing 1-phenyl-2-thiourea (PTU) (0.003% (w/v) and were maintained at 28-30 oC.  At 24 hpf (1 day post fertilization, dpf), 10 microliters of 1a,25(OH)2D3  in ethanol was added to embryos maintained in 20 mL fresh embryo medium with PTU.  The final concentration of 1a,25(OH)2D3 was 300 pM.  Control zebrafish were treated with 10 microliters ethanol alone (vehicle controls).  The medium containing either 300 pM 1a,25(OH)2D3 or vehicle was changed every 24 h .   In experiment 1, at 2, 4, 6 and 7 dpf embryos/larvae were removed and immediately frozen at -80 0C for later RNA preparations.  25-30 embryos per set were used for preparation on RNA.  At the same times, 7-12 embryos were fixed in 4% paraformaldehyde in 0.75 X Dulbecco’s phosphate buffered saline (DPBS).  In experiment 2, 6 dpf larvae were treated with 1a,25(OH)2D3 (300 pM) or vehicle for 24 h.  RNA was prepared from three sets of larvae.


title: 7DPFVD3 rep4


title: Spi1_ChIPSeq

tag: chip antibody


title: small RNAs (18-29nt) from shu[1]/shu[Def] mutants

value: ovary


title: 6DPFVD3 rep4

value: 6 days post fertilization


title: 4DPFVD3 rep4

value: 4 days post fertilization


title: 4DPFVD3 rep2


title: 2DPFVD3 rep4

value: 2 days post fertilization


title: 2DPFVD3 rep5


title: 2DPFVD3 rep3


title: 2DPFVD3 rep2


title: 4DPFVD3 rep5


title: 2DPFVD3 rep1


title: 7DPFVD3 rep2


title: Fcp1-RNAi replicate 2

city: Ithaca

first: Nicholas

last: Fuda

state: New York

address: 417 Biotechnology Building, Cornell University

department: Molecular Biology and Genetics

institute: Cornell University

description:
GRO-seq
Nuclear run on with 5-BromoUTP for immunopurification

data_processing:
Barcode removed and read trimmed to 26nt
Adapter removed using cutAdapt with all possible combinations of VN and a threshold of 0.2
Aligned with bowtie to dm3, allowing two mismatches and requiring unique alignment (-m1).
converted bowtie .sam file to the .bed file standard.
Genome_build: dm3
Supplementary_files_format_and_content: bed file; the reads were trimmed to 26 nucleotides, and mapped to non-repetitive regions of the Drosophila genome using Bowtie.

source_name: S2 cell line

growth_protocol: Cells were grown in M3 media (Sigma) supplemented with bacto-peptone and yeast extract + 10% FBS

extract_protocol: Ten million nuclei were allowed to run-on for 10 minutes at 30°C in a reaction containing ATP, CTP, GTP, and BrUTP. The RNA was isolated using Trizol and acid phenol extractions. The RNAs were base hydrolyzed to an average length of 100-150 nucleotides, and RNAs with incorporated BrU were purified with 2 immunoprecipitations successive using Anti-BrdUTP agarose. The RNA was treated with PNK and polyadenylated using E. coli polyA polymerase to add 50-100 As to their 3’ ends. The polyadenylated RNA was reverse transcribed used with the following bar coded oligonucleotides (INOO3: 5’-pTAGAGATCGTCGGACTGTAGAACTCT-iSp18-CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN, INOO4: 5’-pTGATGATCGTCGGACTGTAGAACTCT-iSp18-CAAGCAGAAGACGGCATACGATTTTTTTTTTTTTTTTTTTTVN). The first 4 bases have the bar-code and iSp18 indicates an 18 carbon spacer between two oligo linkers used for Illumina sequencing. The resulting DNA was gel extracted and circularized using Epicentre CircLigase, and PCR amplified for 12-15 cycles. The cDNA was then sequenced on the Illumina Genome Analyzer.

tag: cell line

tag: genotype/variation


title: Fcp1-RNAi replicate 1


title: mock infected cells

city: Munich

first: Klaus

last: Förstemann

address: Feodor-Lynen 25

department: Gene Center

institute: Ludwig-Maximilians University

description: total RNA, size-selected (17-30 nt)

data_processing:
The sequences in the fastq file were sorted according to the 5'-Barcodes and the barcode was removed. (resulting file: *_no_barcode.fastq, ad-hoc PERL script, available upon request)
The 3'-linker was removed (ad-hoc PERL script, available upon request)
The remaining small RNA sequences were filtered for length between 17 and 23 nucleotides (ad-hoc PERL script, available on request)
sample data table: Sequences were sorted and reduced to a unique set with the LINUX shell commands sort and uniq -c

growth_protocol: cells were grown in DMEM with 10 % FCS

extract_protocol: Extraction of total RNA with Trizol. Gel purification of small RNAs (17-30nt). 3'- (AMP-5’p=5’pCTGTAGGCACCATCAATdideoxyC-3’) and 5'- (5'-rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrC rUrCrUrUrCrCrGrArUrCrU-3' + 3 nt Barcode (-CUG, -GAU, -CCU)) Adapter ligation, reverse transcription + PCR to append Illumina bridge amplification sequences

treatment_protocol:
Infection with MCMV at MOI of 10, 72 hrs.
For immunoprecipitation, extracts were prepared from cells after 72 h of infection and the proteins were IP'ed with anti-Ago1 (Wako mAB 2A7, cat. no. 015-22411, lot STM2295) or anti-Ago2 (mAB 6F4, a kind gift of G. Meister, antibody published in Zhu et al. J Virol 84, p. 10266 ff), followed by RNA extraction with Trizol.

value: fibroblasts

tag: infected with

value: mock (control)

value: GAT


title: 7DPFETOH rep1

tag: genotype

value: ethanol


title: 7DPFETOH rep3


title: 7DPFETOH rep2


title: 7DPFVD3 rep1


title: MCMV infected cells

description: total RNA, size-selected (17-30 nt)

value: MCMV

value: CTG


title: 6DPFETOH rep5


title: 6DPFVD3 rep5


title: 6DPFVD3 rep3


title: 6DPFVD3 rep1


title: IP Ago1

description: total RNA after IP, size-selected (17-30 nt)

tag: ip antibody

value: anti-Ago1 mAb (2A7)

tag: ip antibody vendor

value: Wako

tag: ip antibody lot #

tag: ip antibody cat. #


title: 4DPFVD3 rep1


title: 7DPFETOH rep5


title: 6DPFVD3 rep2


title: IP Ago2

value: anti-Ago2 mAB (6F4)

tag: ip antibody provider

value: a kind gift of G. Meister, published in Zhu et al. J Virol 84, p. 10266


title: LacZ-RNAi replicate 1

value: LacZ


title: 6DPFETOH rep4

value: Segrest wild type


title: 6DPFETOH rep3


title: 6DPFETOH rep2


title: 6DPFETOH rep1


title: 4DPFETOH rep2


title: 4DPFETOH rep5


title: 2DPFETOH rep4


title: 4DPFETOH rep4


title: 4DPFETOH rep3


title: LacZ-RNAi replicate 2


title: 4DPFETOH rep1


title: 2DPFETOH rep2


title: 2DPFETOH rep3


title: CBP gd7

city: Stockholm

first: Mattias

last: Mannervik

address: Arrheniuslaboratories E3

department: Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

data_processing:
*.sgr : Smoothed ratio values in 35 bp steps, The reads were aligned against the Drosophila reference sequence (version 5.25) using the classical mapping in Applied Biosystems Bioscope software v1.2.1. The number of uniquely mapping reads was 21,667,438 (wild-type input), 17,131,635 (wild type CBP), 25,683,953 (gd7 input) and 18,325,130 (gd7 CBP). Average read-count per nucleotide was calculated for IP and input samples. For regions where the IP sample had at least the average read-count, a ratio of IP-input (in log2 scale) was calculated. If the read count in the input was below the average read-count (in the input sample) it was set to the average. All ratio values were then adjusted by reducing each value with the average read-count in IP minus the average read-count in input. This linear adjustment was to normalize for differences in sequencing depth of IP and input. Then the ratio value at an interval of 35 bp was extracted across the genome and median smoothed using a window size of 350 bp. Windows with fewer than 5 data points were discarded. The dynamic range of CBP in wild type was -2.0 – 5.1 and CBP in gd7 -1.8 – 5.1.
*.gff : High confidence peaks, To calculate peaks and bound regions, the 5% highest ratio values in both wild type and gd7 were extracted, corresponding to a cut-off of 1.9 in wild type and 1.9 in gd7. Bound regions were then defined as regions of at least 200 bp and a region was extended as long as there was a value within 200 bp of the previous value. The value of each detected region was set to the average of the highest five consecutive ratio values. The center of the peak was set to the middle position of the five highest consecutive ratio values.

source_name: gd7_CBP ChIP

growth_protocol: Embryos collected on apple juice plates with yeast at 2 hour intervals, and aged an additional 2 hours.

extract_protocol: Embryos were dechorionated in bleach, homogenised with a Dounce homogeniser to release nuclei and crosslinked in 1% formaldehyde. Nuclei were washed and sonicated using a Bioruptor (Diagenode) to generate chromatin extract. Chromatin extract was cleared by centrifugation and used in ChIP with affinity-purified anti-Drosophila CBP antibody generated in rabbit, pre-bound to a mix of Protein A and G dynabeads. CBP bound DNA was purified, and sent to Uppsala Genome Center for SOLiD (TM) ChIP-Seq Library preparation (Rev date 18 March 2010), size selection (100-150 bp + adapters 90bp ≈250 bp), and SOLiD sequencing.

value: gd7 (lacking intranuclear Dorsal)

tag: developmental stage

value: 2-4h embryo

value: rabbit anti-Drosophila CBP


title: 2DPFETOH rep5


title: input gd7 DNA


title: 2DPFETOH rep1


title: CBP w

source_name: WT_CBP ChIP

value: w1118 (wild type)


title: PHNP_shRBFOX1_biologicalreps1-5

city: Los Angeles

first: Brent

middle: L

last: Fogel

address: 710 Westwood Plaza

department: Neurology

institute: UCLA

description:
Processed data file: RBFOX1_Splicing_Events.txt
Processed data file: RBFOX1_Transcriptional_Events.txt

data_processing:
Alignment: Unique sequence reads were filtered for repetitive and ribosomal RNA sequences and then aligned to the human genome using BWA allowing a maximum of 3 mismatches to generate reads mapping to exons and exon junctions as defined by Refseq. Genome build: hg19, NCBI 37.
Junctions: To be counted as a junction, a read had to overlap two adjacent exons by a minimum of 5 nucleotides and total counts had to equal or exceed 20. Junction counts were used to define splicing events. Genome build: hg19, NCBI 37.
The annotation used for mapping potential alternatively spliced reads consisted of a previously published genome-wide alternative gene expression database source (Griffith et al. 2010 Nat Methods, 7, 843-847). Statistical comparisons for both differential splicing and differential gene expression were made using a negative binomial distribution model with the DESeq software package. A cutoff threshold of p < or = 0.05 was used for significance.
Processed results [RBFOX1_Transcriptional_Events.txt, RBFOX1_Splicing_Events.txt] represent the analysis of pooled data from the five biological replicates for each condition.

source_name: primary neural progenitors

growth_protocol: Routine

extract_protocol: RNA extracted using Qiagen miRNeasy kit; library made using Illumina protocol

treatment_protocol: Routine

tag: tissue

value: brain

value: primary neural progenitors

tag: development stage

value: 17 week

value: lentiviral-mediated knockdown of RBFOX1


title: PHNP_Non-transduced_biologicalreps1-5

tag: cell type

value: Non-transduced


title: CCTTTC

status: Public on Jun 28 2012

first: Sten

last: Linnarsson

address: Scheeles väg 2

department: MBB

institute: Karolinska Institutet

data_processing:
Base-calling was performed using CASAVA on the Genome Analyzer IIx
Raw reads were demultiplexed into 96 files (one per barcode, but 4 barcodes were unused)
Reads were aligned using Bowtie version 0.12.7 with standard parameters
Reads were then annotated using gene models obtained from UCSC on 2012-02-03.
Genome_build: hg19
Supplementary_files_format_and_content: RPM (reads per million) was calculated by considering all reads mapped onto all known exons of each gene (including spliced reads)
Supplementary_files_format_and_content: L127_RPM.tab (supplementary)  contains a matrix of RPM values for each sample and each gene, in tab-delimited text format

growth_protocol: MSCs were isolated from human subcutaneous adipose tissue, passed through a 100 µm nylon mesh and replated in 10% FBS growth medium. After 48 h   medium was replaced to remove non-adherent cells. Further cultivation was performed under standard cell culture conditions. Fibroblasts were isolated from dermal skin of the same donors   as MSCs and primary culture was established by fibroblast outgrowth from skin explants placed onto Primaria dish (BD Falcon) in 10% FBS and 1% penicillin-streptomycin DMEM-High Glucose (Gibco) growth medium.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen).  Following a phenol/chloroform extraction and isopropanol precipitation, RNA samples were treated with DNase I using DNA-free kit (Ambion). RNA-seq libraries were prepared according to the STRT protocol ("Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing" Islam et al. Nature Protocols vol. 7 no. 5, 2012)

treatment_protocol: Passage three or four cells were plated 72 hours prior to induction of differentiation. 10% FBS and 1% penicillin-streptomycin containing growth medium was supplemented with:   1µM dexamethasone, 500µM IBMX (3-isobutyl-1methylxanthine), 100µM indomethacin and 10µg/ml insulin for adipogenic induction;  100nM dexamethasone, 50µM L-ascorbic acid 2-phosphate and 10mM glycerol 2-phosphate for osteogenic induction; 50µM L-ascorbic acid 2-phosphate, 6,25µg/ml insulin and 10ng/ml TGFbeta-1   (Peprotech) for chondrogenic induction.

value: Blank

tag: day

tag: patient code name

tag: barcode

value: CCTTTC


title: CGAGTA

tag: treatment

value: CGAGTA


title: PHNP_shGFP_biologicalreps1-5

value: lentiviral-mediated knockdown of GFP (control)


title: CGCACC

value: CGCACC


title: TCACTT

value: TCACTT


title: GGGCGA

value: GGGCGA