title: SC2_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL9281_RNA-seq

status: Public on Feb 21 2015

type: SRA

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

country: USA

institute: Augusta University

description: Transcriptome analysis by RNA-seq

library_source: transcriptomic

data_processing:
TopHat 2.0.8b [1] was used for mapping sequence reads to the human genome (hg19) with the parameter for Illumina stranded sequencing (--library-type fr-firststrand).
BedTools 2.16.2 [2] and bedGraphToBigWig generated stranded binary wiggle files after in-house scripts split reads mapped to each strand.
FeatureCounts 1.4.6 was used to compute the number of reads mapped to each gene and transcript. DESeq 1.10.1 [4] for differential expression analysis.
DESeq 1.10.1 was used for differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet contains FPKM values for each transcript in all samples.

molecule: total RNA

organism: Homo sapiens

source_name: CLL primary B-cells

growth_protocol: Primary B-cells were isolated from CLL using Dynal B-cell Isolation Kit (Invitrogen, Carlsbad, CA, USA); Normal B-cell samples were purchased from ALLCells.

extract_protocol:
RNA was extracted using Qiagen AllPrep DNA/RNA/miRNA Universal Kit
RNA-seq libarary was prepared using Illumina TrueSeq mRNA library preparation kit.

tag: tissues

value: Blood

tag: cell type

value: CD19+ B-cells

tag: tissue

value: Tumor


title: CLL9193_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL9216_RNA-seq

description: Transcriptome analysis by RNA-seq


title: MBC_RNA-seq

description: Transcriptome analysis by RNA-seq

source_name: Normal Memory B-cells

value: CD19+/CD27+ memory B-cells

value: normal


title: CLL9130_RNA-seq

description: Transcriptome analysis by RNA-seq


title: NBC_RNA-seq

description: Transcriptome analysis by RNA-seq

source_name: Normal Naive B-cells

value: CD19+/ IgD+ naïve B-cells


title: CLL9128_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL9194_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL8919_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL8830_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL8845_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL8757_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL8404_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL8816_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL8545_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL8755_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL6536_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL6159_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL1104_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL1193_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL1124_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL6389_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL1031_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL5918_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL1028_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL1158_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0989_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0996_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0948_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0849_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0700_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0745_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0693_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0775_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0659_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0687_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0463_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0680_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0625_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0683_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0377_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0348_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0430_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0321_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0335_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0275_RNA-seq

description: Transcriptome analysis by RNA-seq


title: POS_RA_L122A

city: San Francisco

first: Gladstone

last: Bioinformatics

state: CA

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

data_processing:
Known Illumina adapters were trimmed using "fastq-mcf" version 1.1.2-537 (https://code.google.com/p/ea-utils/)
Aligned to mouse genome build "mm9" using the program Tophat 2.0.11. Gene annotation (GTF file) used was ENSEMBL version 65. Specific settings: --min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --mate-inner-dist=50
Per-gene counts and FPKM values provided by "DefinedRegionDifferentialSeq" version 8.6.4, part of the USeq software package (http://useq.sourceforge.net/). Gene annotation used was ENSEMBL version 65.
No additional filtering was performed.
Genome_build: mm9 (mouse)
Supplementary_files_format_and_content: FPKM and raw count data, tables in both Excel format and plain-text format.

organism: Mus musculus

growth_protocol: These transfected ES cells were routinely cultured in KO-DMEM supplemented with 15 % FCS, 1000 Units / ml LIF, and 2 µg puromycin ("Normal" culture condition).

extract_protocol:
RNA samples were extracted using RNeasy Mini PLUS Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: These transfected ES cells were cultured in "Normal",  without LIF ("-LIF"), or without LIF and with 5 µM Retinoic Acid ("+RA) conditions.

tag: cell line

value: Embryonic stem cells

tag: transfection

value: Nanog (L122A Mutant)

tag: culture condition


title: NORMAL_L122A

source_name: + L122A in "Normal"

value: "Normal"


title: POS_RA_WT

source_name: + WT in "+RA"

value: Nanog (Wild-type)


title: CLL0949_RNA-seq

description: Transcriptome analysis by RNA-seq


title: CLL0934_RNA-seq

description: Transcriptome analysis by RNA-seq


title: NEG_LIF_WT

source_name: + WT in "-LIF"

value: "-LIF"


title: NORMAL_WT

source_name: + WT in "Normal"


title: NORMAL_EGFP

source_name: + EGFP in "Normal"

value: EGFP


title: Ts65Dn MEFs Rep1

city: La Jolla

first: Long

middle: H

last: Do

address: 9500 Gilman Drive

department: Neuroscience

institute: University of California, San Diego, School of Medicine

data_processing:
Basecalling performed with CASAVA ver. 1.8.2
Reads mapped against mouse (mm10) genome using the TopHat application on Illumina BaseSpace
Differential gene analaysis performed using CuffLinks application on Illumina BaseSpace.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited textfile, contains differential gene expression analysis from CuffDiff results on normalized gene count values (FPKM)

source_name: Ts65Dn Mouse Embryonic Fibroblasts

extract_protocol:
Mouse embryos were collected, eviscerated, decapitated and then further treated with trypsin to obtain the MEFs. MEFs were cultured at least two passages in classical DMEM (Gibco) medium supplemented with antibiotics, glutamine and 10% fetal calf serum. Subconfluent MEFs were harvested in Trizol lysis buffer (Qiagen RNAeasy). Total RNA  was collected using the RNAeasy reagent (Qiagen) following the manufacturer’s instructions.
mRNA-seq libraries were prepared from 5 ug of total RNA using the Illumina mRNA-seq Sample Preparation kit following the manufacturer’s instructions.

value: Mouse embyronic fibroblasts

tag: age

tag: genotype


title: Ts65Dn MEFs Rep2


title: Ts65Dn MEFs Rep3


title: CLL0515_RNA-seq

description: Transcriptome analysis by RNA-seq


title: 2N MEFs Rep3

source_name: 2N Mouse Embryonic Fibroblasts


title: 2N MEFs Rep1


title: Basilar papilla 72 treated bs2

city: London

first: Michael

last: Lovett

state: London

address: Dovehouse St

department: NHLI

country: United Kingdom

institute: Imperial College

data_processing:
Sequences were mapped to gga3 using Tophat v1.4.0 with defaul settings
Alignment files (.bam) were inputed to Partek Genomics Suite v6.6 to caculate RPKM
Genome_build: gga3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values of individual sample

organism: Gallus gallus

source_name: Basilar papilla

extract_protocol:
Chicken basilar papilla were dissected and treated with streptomycin for 24 hours and recovered for specific time period. Total RNA was harvested with  Trizol.
RNA libraries were prepared following Illumina protocols

tag: treatment

value: streptomycin

tag: time point


title: Basilar papilla 144 control bs2


title: Basilar papilla 168 treated bs2


title: Basilar papilla 24 control bs2


title: NEG_LIF_L122A

source_name: + L122A in "-LIF"


title: Basilar papilla 24 treated bs2


title: Basilar papilla 96 treated


title: Basilar papilla 96 control


title: Basilar papilla 0 control bs2


title: POS_RA_EGFP

source_name: + EGFP in "+RA"


title: Basilar papilla 0 treated bs2


title: Basilar papilla 168 control


title: Basilar papilla 168 treated


title: Basilar papilla 168 control bs2


title: NEG_LIF_EGFP

source_name: + EGFP in "-LIF"


title: Basilar papilla 120 control


title: Basilar papilla 144 control


title: Basilar papilla 144 treated


title: Basilar papilla 48 control bs2


title: Basilar papilla 120 treated


title: Basilar papilla 144 treated bs2


title: Basilar papilla 120 treated bs2


title: Basilar papilla 24 treated


title: Basilar papilla 72 treated


title: 2N MEFs Rep2


title: Basilar papilla 72 control


title: Basilar papilla 48 control


title: Basilar papilla 0 treated


title: Basilar papilla 0 control


title: Basilar papilla 48 treated


title: Basilar papilla 48 treated bs2


title: 6544R12

city: Boston

first: Ming

last: Liu

state: MA

address: 188 Longwood Ave

department: Developmental Biology

institute: Harvard School of Dental Medicine

description: Sample 3

data_processing:
Basecalling was processed.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using DNAnexus
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Tooth germs

extract_protocol:
Tooth germs were collected and total RNA was purified using Trizol reagent and Qiagen RNAeasy mini kit.
Apollo 324™ System PrepX SPIA® RNA-Seq Library kit was used for the construction of sequencing libraries.

tag: strain background

value: FVB

tag: genotype/variation

value: YAP transgenic (Tg) control

value: embryonic day 14.5

value: tooth germ


title: 6545R12

description: Sample 4

value: YAP transgenic (Tg)


title: 6542R12

description: Sample 1

value: Yap conditional knockout (CKO) litter control


title: SingleCellNo3005

status: Public on Feb 20 2015

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA sythesis.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited table of total number of detected mRNA molecules from each gene in each cell

growth_protocol: Wild type (CD1) and transgenic mice (5HT3-EGFP on a CD1 background) between postnatal 21 and 31 days of both sexes were used. In the transgenic mouse line, EGFP is expressed under the control of the Htr3a promoter.

extract_protocol:
Mice were deeply anesthetized with ketamine/xylazine (80mg/kg; 10mg/kg). The brain was quickly dissected and transferred to ice-cold oxygenated cutting solution (87 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 75 mM sucrose, 20 mM glucose, 1 mM CaCl2, and 2 mM MgSO4) and kept in the same solution during sectioning on a vibratome (VT1200 S, Leica) in 300 µm thick slices. The area of interest was dissected from each slice, and the tissue was dissociated using the Papain dissociation system (Worthington) following the manufacturer's instructions. The cell suspension obtained was filtered with 20 µm filter (Partec) and kept in cold HBSS solution (SIGMA) with 0.2% BSA and 0.3% glucose. For FACS of EGFP cells, a BD FACSAria" III Cell Sorter B5/R3/V3 system was used. The cell suspension with 600-1000 cells/µL had C1 Suspension Reagent added (all 'C1' reagents were from Fluidigm, Inc.) in a ratio of 4 µL to every 7 µL cell suspension, and 11 µL of the cell suspension mix was immediately loaded on a C1 Single-Cell AutoPrep IFC microfluidic chip designed for 10- to 17-μm cells, and the chip was then processed on a Fluidigm C1 instrument using the 'mRNA Seq: Cell Load (1772x/1773x)' script (30 min at 4°C).
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2× BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2× BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen Qiaquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1× NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3′ fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments,  Ampure beads (Beckman Coulter) were used at 1.8× volume and eluted in 30 µL.

tag: Sex

value: male


title: 6543R12

description: Sample 2

value: Yap conditional knockout (CKO)


title: SingleCellNo2999


title: SingleCellNo2998


title: SingleCellNo3003


title: SingleCellNo3000


title: SingleCellNo2996


title: SingleCellNo3001


title: SingleCellNo3002


title: Basilar papilla 24 control


title: SingleCellNo2992


title: SingleCellNo2994


title: SingleCellNo2997


title: SingleCellNo3004


title: SingleCellNo2991


title: SingleCellNo2995


title: CLL0348_RRBS

description: DNA methylation analysis using bisulfite sequencing

library_source: genomic

data_processing:
To map the sequencing reads from RRBS, we extracted sequenceable regions from the human genome (hg18) that were within 100bp from the MspI sites at both ends. Each sequenceable region was indexed by converting all C’s and G’s to T’s and A’s, respectively, i.e., two different reference databases. Bowtie was used to map the cleaned reads to each of the two reference databases after converting all C’s to T’s.
For each read, an in-house script computed the best of all alignments for the different loci using two different reference databases based on the number of mismatches after realigning the original read and reference sequences. The script also determined the methylation status of each cytosine residue by comparing the bisulfite-converted sequence to the reference sequence.
Another in-house script piled reads for each cytosine in the reference genome and counted the numbers of reads that contained methylated and unmethylated cytosines, respectively. Finally the methylation of each CpG site was defined as the fraction of methylated reads to that of methylated and unmethylated reads combined. CpGs with < 5 reads were filtered out for further analyses.
Genome_build: hg18
Supplementary_files_format_and_content: BED format, Methylation level at each CpG sites ( a value between 0 and 1)

molecule: genomic DNA

extract_protocol:
Genomic DNA was extracted using Qiagen kit
RRBS was performed according to a previously published protocol (Gu et al. 2010; Meissner et al. 2008) with minor modifications. For each sample, 1  g genomic DNA was first digested overnight using 20 units of MspI (New England Biolabs, NEB). The digested DNA was end-repaired and adenylated in a 20  l reaction consisting of 10U of Klenow fragments (exo-, Enzymatics, MA, USA), and 2  l premixed nucleotide triphosphates (1 mM dGTP, 10 mM dATP, 1 mM methylated dCTP). The reaction was incubated at 30 C for 30 min followed by 37 C for an additional 30 min. The methylated Illumina adapters were ligated with adenylated DNA fragments in a 20  l reaction containing 1  l concentrated T4 ligase (Enzymatics) at room temperature for 15 minutes. The ligation products were gel-selected for fragments with insertion sizes of 40 to 120 bp and 120 to 220 base pairs as previously suggested (Gu et al. 2010; Meissner et al. 2008).  Bisulfite treatment of the sequencing library was conducted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) according to manufacturer's protocol. The final libraries were generated by PCR amplification of 5 ?m of bisulfite-converted template using PfuTurbo Cx Hotstart polymerase and Illumina pair-end PCR primers (PE1.0 and PE2.0).

treatment_protocol: No treatment invovled.

value: Blood

value: CD19+ B-cells

value: Tumor


title: SingleCellNo2993


title: SingleCellNo2989


title: SingleCellNo2985


title: SingleCellNo2988


title: SingleCellNo2987


title: SingleCellNo2984


title: SingleCellNo2990


title: SingleCellNo2983


title: SingleCellNo2986


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title: SingleCellNo2966


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title: SingleCellNo2952


title: SingleCellNo2951


title: SingleCellNo2980


title: SingleCellNo2950


title: SingleCellNo2957


title: SingleCellNo2947


title: SingleCellNo2946

source_name: sscortex


title: SingleCellNo2944


title: SingleCellNo2945


title: SingleCellNo2939


title: SingleCellNo2943


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title: SingleCellNo2938


title: SingleCellNo2935


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value: female


title: SingleCellNo2857


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title: Ovary

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: Ovary were collected from female F1 hybrid (BL6/spretus) carring an Xist mutation (B6.Cg-Xist<tm5Sado>) and thus having complete skewing of inactivation of the spretus X chromosome.

data_processing:
Illumina Casava1.7 software used for basecalling.
A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger Center) into the BL6 reference genome. 36bp reads were aligned to the C57BL/6J reference sequence (mm9, UCSC) and to the pseudo-spretus genome separately using TopHat/v2.0.0 with default parameters. The RefSeq mouse gene annotation was used.
RPKM values were obtained using Cufflinks/v2.0.2 with default parameters.
Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
The SNP-associated read counts were used to assess allelic expression.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include 5 columns: gene_id, locus, regular RPKM values, BL6-exon-SNP-read count, spretus-exon-SNP-read count.

organism: Mus musculus x Mus spretus

source_name: Mouse adult hybrid ovary

extract_protocol:
Mouse tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and then was subject to DNaseI digestion and purification using Qiagen RNAeasy Kit . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adult ovary

tag: strain

value: Xist+/-


title: CTCF_Patski_ChIPSeq

description: The Patski fibroblast line was originally derived from BL6/spretus hybrid embryonic kidney and has the inactive X from BL6

data_processing:
Basecalls performed using CASAVA version 1.7
A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger Center) into the BL6 reference genome. Reads from single-end or paired-end sequencing were aligned to the C57BL/6J reference sequence (mm9, UCSC) and to the pseudo-spretus genome separately using BWA (Burrows-Wheeler Aligner).
Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
Peak regions were selected using all uniquely mapped reads by both CisGenome and MACS (Model-based Analysis of ChIP-Seq) (p=1e-5 as the cutoff).
The SNP-associated read counts were used to assess average allelic occupancy.
Genome_build: mm9

source_name: Patski cells

extract_protocol:
ChIP was performed using fixed chromatin from mouse brain or cell lines. DNA from ChIP pull-down chromatin fractions were de-crosslinked and purified using QIAquick PCR purification kit. Genomic DNA was prepared from an aliquot of the same batch of nuclei from F1 brain
Sequencing libraries were prepared each from four pooled independent PolIIS5p or CTCF ChIP samples from Patski cells or from Xist mutant F1 brain, using the Illumina seq sample prep kit. Size selection of the library was done by gel excision and purification of DNA in the 300-600bp range. Control sequencing library was prepared from genomic DNA prepared from F1 brain.

value: Fibroblasts derived from hybrid embryonic kidney

tag: chip antibody

value: CTCF, MillIpore 07-730


title: SingleCellNo50


title: SingleCellNo41


title: SingleCellNo40


title: Spleen_rep1

description: One spleen was collected from female F1 hybrid (BL6/spretus) carring an Xist mutation (B6.Cg-Xist<tm5Sado>) and thus having complete skewing of inactivation of the spretus X chromosome.

source_name: Mouse adult hybrid spleen

value: Adult whole spleen