title: cTEC ATAC-Seq 2

data_processing:
fastq using bcl2fastq
alignment using bowtie2  (--local,  mm9)
filter out reads that align to same place and sequence on R2 from nucleotides #1 to #15 are identical
makeTagDirectory -tbp
makeUCSCfile  -bigWig -fsize 1e20
Genome_build: mm9

source_name: Cortical TECs from WT mice

extract_protocol:
Cells were FACS sorted into MACS buffer and the open chromatin was profiled by the ATAC-seq protocol developed by (Buenrostro et al., 2013) with modifications described by (Lara-Astiaso et al., 2014).
protocol developed by (Buenrostro et al., 2013).

tag: cell type

value: Thymic EpCAM+Ly51+

tag: strain


title: thermo-neutral 5

status: Public on Dec 12 2016

type: SRA

city: Barcelona

first: Francesc

last: Villaroya

address: Avda Diagonal 643

department: Facultat de Biologia

country: Spain

institute: Universitat de Barcelona

library_source: transcriptomic

data_processing:
Sequencing reads were mapped to the Mus musculus genome (version GRCm38) using the program Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) using default options and Ensembl 73 mouse annotation. The Tophat mapper reports all mappings and split-mappings.
GTF files: Mapped reads were used to quantify mouse transcripts from the Ensembl 73 reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome_build: GRCm38
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.

molecule: polyA RNA

organism: Mus musculus

growth_protocol: eight adult male C57BL6 mice were maintained at thermoneutral temperature (29ºC). After two weeks, a subset of four mice was placed at 4ºC environment temperature for 24h

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) which favors purification of all RNA molecules longer than 200 nucleotides; further sample preparation done as described by the manufacturer (Illumina, Eindhoven, The Netherlands)
mRNA was purified from 1 µg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 39- monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bio- analyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 µl cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on an Illumina HiSeq 2000 system

tag: strain background

tag: gender

value: male

tag: age

value: adult

tag: exposed to

value: thermoneutral temperature (29C)

tag: tissue

value: Brown adipose tissue (BAT)


title: cold exposed 5

source_name: cold exposed_BAT

value: 4C environment temperature


title: cold exposed 4


title: Ribosome profiling-rep1-siYTHDF3-input

city: Chicago

first: Chuan

last: He

state: ILLINOIS

address: 929 E 57th St., GCIS E319

department: Department of Chemistry

country: USA

institute: The University of Chicago

description:
rRNA depleted and fragmented RNA
siYTHDF3_RiboProfile.xlsx

data_processing:
Library strategy: Ribo-seq
General pre-processing of reads: All samples were sequenced by illumine Hiseq2000 or Hiseq4000 with single end 50bp read length. For libraries that generated from small RNA (PAR-CLIP and ribosome profiling), the adapters were trimmed by using FASTX-Toolkit. The deep sequencing data were mapped to Human genome version hg38 by Tophat version 2.0 without any gaps and allowed for at most two mismatches. RIP and Ribosome profiling were analyzed by DESeq to generate RPKM (reads per kilobase, per million reads).
Data analysis for each experiment: (1) PAR-CLIP data were analyzed by PARalyzerv1.1 with default settings. Binding motif was analyzed by HOMER (v4.7); (2) for RIP, enrichment fold was calculated as log2(IP/input); (3) for ribosome profiling, only genes with RPKM >1 in input RNA sample and RPKM >0 in ribosome-protected fragments were used for analysis and the change fold was calculated as log2(siYTHDF3/siControl) or log2(siMETTL3/siControl);
Integrative data analysis and statistics: PAR-CLIP targets were defined as gene targets reproducible among three biological replicates (4,459). RIP targets (2,264) were genes with log2(IP/input) > 1 in both biological replicates. The overlap of PAR-CLIP and RIP targets were defined as high confident targets (1,239). For Figure 2 and Supplementary information, Figure S2, the three groups of transcripts are defined as the following: (1) YTHDF3 targets: high confident target of YTHDF3; (2) YTHDF1 unique: high confident target of YTHDF1 reported previously as “CLIP+IP” targets for YTHDF1 but not high-confident target of YTHDF3 [13]; (3) Non-target: non-target for a protein is defined as (a) complementary set of PAR-CLIP targets; (b) RIP enrichment fold <0; Non-target in the figure is defined as the intersection of YTHDF1’s non-target and YTHDF3’s non-target. For the comparison of PAR-CLIP and m6A peaks, at least 1 bp overlap was applied as the criteria of overlap peaks. Nonparametric Mann–Whitney U-test (Wilcoxon rank-sum test, two sided, significance level = 0.05) was applied in ribosome profiling data analysis as previous reported[48]. Gene Ontology (GO) term analyses were performed by DAVID[49,50]. Top terms were then selected for visualizations by the interactive graph function of REVIGO[51].
Supplementary_files_format_and_content: Excel files, see below

molecule: total RNA

organism: Homo sapiens

source_name: HeLa

growth_protocol: Human HeLa cell line used in this study was purchased from ATCC (CCL-2) and grown in DMEM (Gibco, 11995) media supplemented with 10% FBS and 1% 100 × Pen/Strep (Gibco).

extract_protocol:
Isolated according to illumina Truseq Ribo Profile kit: total RNA (>200 nt) extraction, rRNA removal, and fragmentation
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

tag: cell line

value: HeLa cells

tag: cell treatment

value: 40 nM siRNA knockdown for 48 hr, then 100 ug/ml Cycloheximide (CHX) incubation


title: Ribosome profiling-rep1-siYTHDF3-RPF

description:
small mRNA fragments protected by stalled ribosome
siYTHDF3_RiboProfile.xlsx

extract_protocol:
Isolated according to illumina Truseq Ribo Profile kit: Nuclease digestion, Microspin S-400 column separation, RNA extration, TBE gel size selection
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®


title: cold exposed 1


title: Input DNA1

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

library_source: genomic

data_processing:
ChIP-Seq reads were aligned to the mm10 mouse genome using the BWA short read aligner 58 (version 0.7.12).
The aligned reads were filtered to keep only uniquely mapping reads.
A cross-correlation analysis was performed to assess quality metrics (Phantompeakqualtools package).
Peaks of enriched Satb2 binding were called using MACS2 (version 2.1.0),  by allowing only one tag at the same location and setting the false discovery rate to 0.01 and the fold-enrichment cutoff to 2
Genome_build: mm10
Supplementary_files_format_and_content: narrow peak file (extended bed format) was generated using MACS2

molecule: genomic DNA

source_name: Input control

growth_protocol: Hippocampi were dissected from newborn C57BL/6J mice at postnatal day P0 to P1. Hippocampal tissue was trypsinized and dissociated by trituration. Neurons were plated on 100 mm tissue culture dishes , previously coated with poly-L-ornithine and laminin, at a density of 8 x 104 cells/cm2. Cells were cultured in Neurobasal medium containing B-27 supplement and antibiotics  for 11 days.

extract_protocol:
Hippocampal neurons were cross-linked with formaldehyde at 1% final concentration for 10 min at room temperature, and chromatin was prepared using the Zymo-Spin ChIP kit (Zymo Research) following manufacturer’s instructions. Sonication was performed at high power setting for 40 cycles (30 s ON, 30 s OFF) using a Bioruptor Plus (Diagenode Inc., Denville, NJ), yielding fragment size range of 200-700 bp. ChIP assays were performed in triplicates using 20 μg of chromatin and 10 μg of anti-V5 tag antibody (ab15828). IgG (12-370, Millipore) was included as a negative control. ChIP DNA was purified using ChIP DNA Clean and Concentrator (Zymo Research) and the relative abundance of a control region in V5-immunoprecipitated DNA was quantified by qPCR with sequence-specific primers.
DNA libraries (Satb2-ChIP and Input control DNA) were prepared and sequenced on a HiSeq 2000 sequencer (Illumina)

treatment_protocol: Hippocampal neurons were transduced with AAV8-hSyn-Satb2-V5 at multiplicity of infection 1.5 × 105 at DIV4 and used for ChIP-seq analysis at DIV11.

value: primary hippocampal neuron

tag: passages

tag: treatment

value: transduced with AAV8-hSyn-Satb2-V5 at DIV4

tag: chip antibody


title: ESCs biological repl1, technical repl 2

city: Milano

first: Yinxiu

last: Zhan

address: Via Adamello 16

country: Italy

institute: European Institute for Oncology

data_processing:
Single-end 51bp RNAseq reads from each sample were mapped to the mouse genomes using the QuasR software (v 1.8.4, qAlign function, default settings). Only unique alignments with a maximum of 2 mismatches were reported.
Transcriptome assembly was performed in all samples using QuasR software (v1.8.4, qCount function). Expression of each gene/transcript was measured in Reads Per Kilobase of transcript per Millions mapped reads (RPKM).
Differential expression analysis was performed using DESeq2 software (v1.10.0,). Technical replicates were pooled together.
Genome_build: mouse mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, foldchange and q-value for DE analysis from DESeq2 software

source_name: hybrid mouse ESC line F1-21.6

extract_protocol:
Total RNAs were prepared by Trizol (Invitrogen) extraction.
After ribosomal RNA depletion with Ribo-Zero (Illumina),  RNA-seq libraries were prepared using ScriptSeq v2 kit (Illumina)

tag: background strain

value: Embyonic stem cell


title: Ribosome profiling-siControl-input


title: Satb2_ChIPSeq1

value: Anti-V5 (Abcam, catalog# 15828, lot# GR195596-1)


title: cTEC ATAC-Seq 1

city: Rehovot

first: Jakub

last: Abramson

address: Herzl 234

department: Immunology

country: Israel

institute: Weizmann Institute

growth_protocol: Mice were maintained under specific-pathogen-free conditions at the Weizmann Institute’s animal facility and sacrifised at 6weeks of age by CO2

value: 6 weeks-old


title: cold exposed 2


title: mTEC Lo ATAC-Seq 1

source_name: Immature mTECs from WT mice

value: Thymic EpCAM+Ly51-MHCIIlo


title: mTEC Lo ATAC-Seq 2


title: Ribosome profiling-siControl-RPF


title: mTEC Hi ATAC-Seq 2

source_name: Mature mTECs from WT mice

value: Thymic EpCAM+Ly51-MHCIIhi


title: 15'-2

city: Waltham

first: Xiao

last: Chen

state: MA

address: 415 South St

department: Biology

institute: Brandeis University

description: Sample 22

data_processing:
cl2fastq v2.16.0.10 is used for base-calling
tophat for alignment
cufflinks for quantification
Genome_build: dm3
Supplementary_files_format_and_content: [fpkm_tracking] files generated by Cufflinks include FPKM values for each gene

organism: Drosophila melanogaster

source_name: BRAINS

growth_protocol: Drosophila were reared on standard cornmeal/agar medium supplemented with yeast under 12 hour LD cycles at 25 °C.

extract_protocol:
Brains were dissected and RNA immediately extracted with TRIzol.
Illumina mRNA library contruction protocol

treatment_protocol: Flies were reared at 18C and temperature shift to 29C for stimulation (for 0, 15, 30, 60min).

tag: temperature shift

tag: time (min)

value: young

tag: Sex

value: pooled male and female

value: BRAINS


title: Smallrnaseq Knockout Satb2 Replicate7

data_processing:
We trimmed the 3' adapters and filtered out the reads with the minimum length of 15 nucleotides using cutadapt 1.8.1 with Python 2.7.6
Read alignment done using rna-STAR version STAR_2.4.1d
parameters: readFilesCommand: zcat; outReadsUnmapped: Fastx; outSAMunmapped: Within; outFilterScoreMinOverLread: 0; outFilterMatchNmin: 16; outFilterMatchNminOverLread: 0; outFilterMismatchNoverLmax: 1; alignIntronMax: 1; alignEndsType: Local
Poor quality reads were filtered using samtools Version: 0.1.19-96b5f2294a and counts were generated by counting the mapped reads in the SAM file for each microRNA with grep -c command
Genome_build: mm10
Supplementary_files_format_and_content: htseq_counts

source_name: Knockout Satb2

extract_protocol:
Each sample was supplied with 500µl Trizol-reagent and 10 ceramic beads before homogenizing in an Omni Bead-Ruptor 24 (Omni International; Kennesaw, USA) for 10s at a relative speed of 2.6. Afterwards, the samples were incubated at RT for 5 minutes to ensure a proper lysis of the tissue. 100µl chloroform was added, samples were mixed manually for 15 seconds andincubated for another 5 minutes at RT. After centrifuging at 12,000g for 15 minutes at 4o C, the transparent upper phase was transferred to a fresh tube. 250µl isopropanol and 1µl GlycoBlue (Thermo Fisher Scientific; Waltham, USA) were added to each sample before they were incubated at -20o C over night to precipi- tatethe RNA. Then, the samples were centrifuged at 12,000g for 30 minutes at 4o C and the supernatant was discarded carefully. For washing, the RNA pellets were mixed with 300µl 75% ethanol, vortexed and centrifuged at 12,000g for 5 minutes at 4oC before removing the supernatant. This washing step was repeated once. Before redissolving the RNA, the tubes were briefly spun and freed from remaining liquid. Samples were air-dried for 2 minutes to clean the RNA from ethanol. Finally, RNA pellets were redissolved in sequencing graded water and incubated for 10 minutes at 42oC before proceeding with DNAse treatment
Standard RNAseq and smallRNAseq library preperation

tag: genotype/variation

value: Knockout Satb2

value: hippocampal CA1 region


title: Smallrnaseq Knockout Satb2 Replicate8


title: Smallrnaseq Knockout Satb2 Replicate9


title: YTHDF3-PAR-CLIP-repl.3

description:
small RNA fragments crosslinked with YTHDF3
YTHDF3_PAR-CLIP.xlsx

data_processing:
General pre-processing of reads: All samples were sequenced by illumine Hiseq2000 or Hiseq4000 with single end 50bp read length. For libraries that generated from small RNA (PAR-CLIP and ribosome profiling), the adapters were trimmed by using FASTX-Toolkit. The deep sequencing data were mapped to Human genome version hg38 by Tophat version 2.0 without any gaps and allowed for at most two mismatches. RIP and Ribosome profiling were analyzed by DESeq to generate RPKM (reads per kilobase, per million reads).
Data analysis for each experiment: (1) PAR-CLIP data were analyzed by PARalyzerv1.1 with default settings. Binding motif was analyzed by HOMER (v4.7); (2) for RIP, enrichment fold was calculated as log2(IP/input); (3) for ribosome profiling, only genes with RPKM >1 in input RNA sample and RPKM >0 in ribosome-protected fragments were used for analysis and the change fold was calculated as log2(siYTHDF3/siControl) or log2(siMETTL3/siControl);
Integrative data analysis and statistics: PAR-CLIP targets were defined as gene targets reproducible among three biological replicates (4,459). RIP targets (2,264) were genes with log2(IP/input) > 1 in both biological replicates. The overlap of PAR-CLIP and RIP targets were defined as high confident targets (1,239). For Figure 2 and Supplementary information, Figure S2, the three groups of transcripts are defined as the following: (1) YTHDF3 targets: high confident target of YTHDF3; (2) YTHDF1 unique: high confident target of YTHDF1 reported previously as “CLIP+IP” targets for YTHDF1 but not high-confident target of YTHDF3 [13]; (3) Non-target: non-target for a protein is defined as (a) complementary set of PAR-CLIP targets; (b) RIP enrichment fold <0; Non-target in the figure is defined as the intersection of YTHDF1’s non-target and YTHDF3’s non-target. For the comparison of PAR-CLIP and m6A peaks, at least 1 bp overlap was applied as the criteria of overlap peaks. Nonparametric Mann–Whitney U-test (Wilcoxon rank-sum test, two sided, significance level = 0.05) was applied in ribosome profiling data analysis as previous reported[48]. Gene Ontology (GO) term analyses were performed by DAVID[49,50]. Top terms were then selected for visualizations by the interactive graph function of REVIGO[51].
Supplementary_files_format_and_content: Excel files, see below

extract_protocol:
Fed with 200 uM 4SU, 365 nm UV crosslinked, partial digested with Rnase T1, anti-Flag beads IP, SDS-PAGE gel size selection
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

value: N terminal Flag-HA tagged YTHDF3 HeLa stable expression cell line


title: mTEC Hi ATAC-Seq 1

tag: cell type


title: Smallrnaseq Knockout Satb2 Replicate6

tag: strain


title: Smallrnaseq Knockout Satb2 Replicate5


title: YTHDF3-PAR-CLIP-repl.1


title: Smallrnaseq Knockout Satb2 Replicate4


title: YTHDF3-PAR-CLIP-repl.2


title: K562 CD24-high sorted replicate 1

city: Stanford

first: Howard

last: Chang

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford University

data_processing:
Library strategy: ATAC-seq
fastq files were aligned to the hg19 genome using Bowtie2 using the following specifications -S -X2000 -p10 -m1 --very-sensitive
Duplicates were removed and library size was estimated using PICARD tools
peaks were called using MACS2 with the --nomodel setting
Genome_build: hg19
Supplementary_files_format_and_content: bw files for UCSC upload  were generated using bedtools

extract_protocol:
Tagmentation was performed as previously described (Buenrostro et al., 2013)
Purified DNA was barcoded using a single unique adapter (i5)

value: high sorted


title: Smallrnaseq Knockout Satb2 Replicate2


title: K562 CD24-low sorted replicate 1

value: low sorted


title: K562 CD24-low sorted replicate 2


title: Smallrnaseq Knockout Satb2 Replicate1


title: Smallrnaseq Control Satb2 Replicate5

source_name: Control Satb2

value: Control Satb2


title: Smallrnaseq Control Satb2 Replicate4


title: Smallrnaseq Control Satb2 Replicate8


title: Smallrnaseq Knockout Satb2 Replicate3


title: Smallrnaseq Control Satb2 Replicate3


title: Smallrnaseq Control Satb2 Replicate9


title: Smallrnaseq Control Satb2 Replicate6


title: YTHDF3-RIP-input-ribominus

description:
rRNA depleted RNA
YTHDF3_RIP.xlsx

extract_protocol:
Extracted with Trizol, and rRNA removal with ribominus kit
Illumina TruSeq Stranded mRNA Library Prep Kit

value: HeLa cells

value: overexpress N terminal Flag tagged YTHDF3 for 24 hr (0.75 ug plasmid/ml media)


title: Smallrnaseq Control Satb2 Replicate7


title: YTHDF3-RIP-input-polyA

description:
polyA RNA
YTHDF3_RIP.xlsx

extract_protocol:
Extracted with Trizol, and poly-dT beads selection
Illumina TruSeq Stranded mRNA Library Prep Kit


title: Smallrnaseq Control Satb2 Replicate2


title: Smallrnaseq Control Satb2 Replicate1


title: YTHDF3-RIP-IP-repl.1

description:
full length RNA co-immunoprecipitated with YTHDF3
YTHDF3_RIP.xlsx

extract_protocol:
Anti-Flag beads IP
Illumina TruSeq Stranded mRNA Library Prep Kit


title: RNAseq Knockout Satb2 Replicate9


title: YTHDF3-RIP-IP-repl.2


title: RNAseq Knockout Satb2 Replicate8


title: RNAseq Knockout Satb2 Replicate6


title: RNAseq Knockout Satb2 Replicate7


title: K562 CD24-high sorted replicate 2


title: RNAseq Knockout Satb2 Replicate3


title: RNAseq Knockout Satb2 Replicate4


title: 066MDC

city: New York

first: Lisa

middle: Cole

last: Burnett

state: NY

address: 1150 St Nicholas Avenue

department: Pediatrics, Molecular Genetics

institute: Columbia University

description: Day 34 of differentiation, CD56+ iPSC-derived neuron (iPSC reprogrammed from skin fibroblast)

data_processing:
CUMC genome center uses RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming.
•CUMC genome center maps reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat software with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
•CUMC genome center estimates the relative abundance (FPKM value) of using Cufflinks software (version 2.0.2) using default settings.
•1. Sort by FPKM Status, throw out “low data” and “fail” genes (189 genes thrown out here). FPKM values of “OK” only kept. FPKM OK status determined by cufflinks to have adequate coverage.
•2. Calculate average FPKM among genotypes. Compare ratio of differential gene expression (DE) between: – PWS large del:control –PWS Micro del:control –all PWS:controlFor initial analysis, considering DE ratios >2 and <0.5. Perform 2 tailed, type 3 t-test for all genes. Set significance at P<0.05.
Genome_build: Human: NCBI/build37.2
Supplementary_files_format_and_content: csv file with FPKM values

source_name: iPSC-derived neuron

growth_protocol: See Burnett, LC, et al. Induced pluripotent stem cells (iPSC) created from skin fibroblasts of patients with Prader-Willi syndrome (PWS) retain the molecular signature of PWS. Stem Cell Research. In press. 2016.

extract_protocol:
RNA extracted with Norgen Bioteck MicroKit.
Illumina True Seq RNA prep kit

treatment_protocol: FACS sorted for CD56. Cells stored at frozen pellet (-80degC) for a <1 week prior to RNA isolation.

tag: differentiation status

value: Day 34 of differentiation CD56+ iPSC-derived neuron

value: stem cell-derived neuron

tag: genotype

value: PWS microdeletion


title: RNAseq Knockout Satb2 Replicate1


title: RNAseq Control Satb2 Replicate8


title: RNAseq Control Satb2 Replicate7


title: 066MDA


title: 031MT

value: PWS Large deletion


title: 139P


title: RNAseq Control Satb2 Replicate3


title: RNAseq Control Satb2 Replicate4


title: 1058-B7

value: unaffected control


title: RNAseq Control Satb2 Replicate2


title: 1058-6


title: RNAseq Knockout Satb2 Replicate2


title: RNAseq Control Satb2 Replicate9


title: 1043D3


title: RNAseq Control Satb2 Replicate1


title: HES42


title: RNAseq Knockout Satb2 Replicate5


title: 90'-3

description: Sample 49

treatment_protocol: Brains were dissected and incubated in 90mM KCl

value: canton-S

tag: stimulation

value: high [C] KCl

tag: age


title: 15'-3

description: Sample 46

value: young

value: pooled male and female

tag: tissue


title: 30'-3

description: Sample 47

value: BRAINS


title: 1043B1


title: 0'  cs-3

description: Sample 45

source_name: 0'  cs


title: 60'-2

description: Sample 43


title: 90'-2

description: Sample 44


title: RNAseq Control Satb2 Replicate5

value: hippocampal CA1 region


title: RNAseq Control Satb2 Replicate6


title: 30'-2

description: Sample 42


title: 0'  cs -2

description: Sample 40


title: 15'-2

description: Sample 41


title: 60'

description: Sample 38


title: 90'

description: Sample 39


title: InputDNA_T47D

city: Tampere

first: Tommi

middle: Tapani

last: Rantapero

address: Biokatu 8

department: BioMediTech

country: Finland

institute: University of Tampere

data_processing:
Read alignment to reference genome was done using Bowtie2 with default parameters
Peak calling was done using DFilter using the following parameters: The standard deviation was set to 2, bin size 100 bp and kernel size 50.
Genome_build: hg19
Supplementary_files_format_and_content: The peaks detected by DFIlter are included for each sample and treatment in separate bed-files.

growth_protocol: Cells were seeded and were grown to 80-90% confluency before treatment

extract_protocol:
The nuclei were extracted using protocol similar to Song and Crawford 2010 and the DNase I digestion was done according to Ling and Waxman 2013.
The library preparation was done according to library construction protocol of BGI

treatment_protocol: Cells were treated either with 100 ng/ml recombinant human BMP4 protein (BM4 treatment) or BMP4 dilution solution (non-treated vehicle) for 3h

tag: datatype

value: InputDNA

tag: cell line

tag: cell karyotype

value: breast cancer

tag: treatment description


title: 60'-3

description: Sample 48


title: 1013ASV


title: DnaseSeq_T47D_231_vehicle

value: DnaseSeq

tag: treatment


title: 056LB-T


title: elav-gal4 60' -3

description: Sample 34


title: s1034A3


title: 15'

description: Sample 36


title: InputDNA_MDA_MB_231

value: BMP4 (100 ng/ml)

value: 3 hours treatment with BMP4 (100 ng/ml)


title: DnaseSeq_T47D_BMP4_3h


title: elav-gal4 0' -3

description: Sample 33


title: 60' NUN

description:
Sample 57
nascent RNA

source_name: 60' NUN

treatment_protocol: Flies were on ATR-containing food for 1 day in dark. 30-second LED stimulation was applied the next day.

value: BLUE LED

value: heads


title: 0'  cs

description: Sample 35


title: 30'

description: Sample 37


title: Elav-Trp 0'-3

description: Sample 25


title: DnaseSeq_MDA_MB_231_vehicle


title: Elav-TRP 15'-3

description: Sample 26


title: Elav-TRP 30'-3

description: Sample 27


title: 30' NUN

description:
Sample 56
nascent RNA

source_name: 30' NUN


title: Elav-TRP 60'-3

description: Sample 28


title: DnaseSeq_MDA_MB_231_BMP4_3h


title: S1111B

value: Day 34 of differentiation CD56+ iPSC-derived neuron

value: stem cell-derived neuron


title: 15' NUN

description:
Sample 55
nascent RNA

source_name: 15' NUN


title: 0' NUN

description:
Sample 54
nascent RNA

source_name: 0' NUN


title: 60' Mrna

description: Sample 53

source_name: 60' Mrna


title: RNASeq_T47D_vehicle

data_processing:
Read alignment to reference genome was done using TopHat2
Raw expression estimates (raw read counts) for genes were counted using in-house tool pypette(https://github.com/annalam/pypette).
Raw expression estimates were normalized using median of ratios (similarly as implemented in DESeq2)
Genome_build: hg19
Supplementary_files_format_and_content: The median of ratios normalized expression values for each gene (Gencode Genes version 19) are provided in a single tab-separated text file (tsv).

growth_protocol: Cells were seeded and allowed to adhere for 24h before treatment

extract_protocol:
Total RNA was extracted cells using the Absolutely RNA miRNA kit (Agilent Technologies, Palo Alto, CA, USA)
The library preparation was done according to library construction protocol of BGI


title: 30' Mrna

description: Sample 52

source_name: 30' Mrna


title: RNASeq_T47D_BMP4_3h


title: RNASeq_MDA_MB_231_vehicle


title: 15' Mrna

description: Sample 51

source_name: 15' Mrna


title: RNASeq_MDA_MB_231_BMP4_3h


title: 0' Mrna

description: Sample 50

source_name: 0' Mrna


title: C155-3 60' Light

description: Sample 16


title: C155-2 60' Light

description: Sample 14


title: C155-2 0'

description: Sample 13


title: C155-1 0'

description: Sample 11


title: C155-CHR2-XXL 60'

description: Sample 10


title: Elav_CHR2-XXL_60min_2

description: Sample 8


title: MatrixB_ln1

city: Las  Cruces

first: Elba

middle: E

last: Serrano

state: NM

address: NMSU Foster Hall Biology Box 30001-3AF

institute: NMSU

data_processing:
Base-calling done by HiSeq Control Software V 1.5.15.1 and Real Time Analysis Software V 1.13.48
Sequenced reads mapped to the human genome (hg19) with TopHat Software V 2.0.8b
The countOverlaps function in the R package Genomic Ranges was used to assemble transcripts and estimate abundance
Abundance estimates were normalized to FPKM using CuffDiff V 2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: FPKM, read counts

source_name: normal human astrocytes (Lonza)

growth_protocol: The second passage of Normal Human Astrocytes was cultured for 5 days according to manufacturer's specifications

extract_protocol:
Cells were harvested by scraping, then pelleted by centrifugation. RNA was isolated using the Trizol Plus RNA Purification Kit (Ambion)
Libraries were constructed using standard Illumina TruSeq protocols.

treatment_protocol: Cells from each biological donor were cultured (1) in 3D with the peptide hydrogel Puramatrix or (2) in a monolayer on tissue culture polystyerene

tag: growth condition

value: Peptide Hydrogel Puramatrix

tag: biological donro

value: Donor B


title: MonolayerB_ln2

value: Tissue Culture Polystyrene


title: MatrixA_ln2

value: Donor A


title: C155-1 60' Light

description: Sample 12

tag: time (min)

value: young


title: Elav_CHR2-XXL_60min

description: Sample 4

tag: Sex

value: pooled male and female


title: Elav_CHR2-XXL_30min_2

description: Sample 7

value: BRAINS


title: MatrixB_ln2


title: MonolayerA_ln2


title: Elav_CHR2-XXL_30min

description: Sample 3


title: Elav_CHR2-XXL_0min_2

description: Sample 5


title: C155-CHR2-XXL 0'

description: Sample 9


title: MonolayerA_ln1


title: MatrixA_ln1


title: Elav_CHR2-XXL_0min

description: Sample 1


title: Elav_CHR2-XXL_15min

description: Sample 2


title: C155-3 0'

description: Sample 15


title: PDF-EGFP 29C-3

description: Sample 85

source_name: PDF-EGFP 29C

extract_protocol:
Brains were dissected for neuron sorting and cells were stored in lysis buffer (Ambion, Dynabead mRNA extraction kit) at -80C.
refer to Abruzzi et al., 2014

treatment_protocol: Flies were reared at 18C and temperature shift to 29C for stimulation for 60min.

tag: temperature

value: PDF+ neurons


title: PDF-EGFP 18C-3

description: Sample 84

source_name: PDF-EGFP 18C

tag: cell type


title: TH-EGFP 29C-3

description: Sample 71

source_name: TH-EGFP 29C

tag: strain

value: DA neurons


title: TH-EGFP 18C-3

description: Sample 70

source_name: TH-EGFP 18C


title: Teratoma rep1

status: Public on Dec 11 2016

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road NO.1239

country: China

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using tophat(v2.0.12) commands,expected inner distance between mate pairs is 0,inner distances between mate pairs is 20.
Differential gene expression was detemined using R package edgeR,genes with absolute value of log2 fold change less than 1.5 or p-value more than 0.05 were excluded.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM files and Counts files of gene were generated using cufflinks(v2.2.1) and htseq-count(v 0.6.0) default commands

source_name: Teratoma

extract_protocol:
During giNPC induction process, cell samples were harvested at various induction days including day1, day4, day7, day10, day14, day17 and day21. Meanwhile, samples from primary neurosphere-like cluster (pre-NPCs), established giNPC cell line at passage 6 (giNPCs P6), Brain-NPCs as well as teratoma were also collected.
Total RNA was isolated from cell pellets by Trizol reagent and RNA-Seq library were generated using KAPA Strandard mRNA-Seq Kits according to the manufacturer’s recommendations (Cat No. KK8440 box1 and KK8420 box2). Briefly, the mRNA was enriched using oligo(dT) magnetic beads and sheared to create short fragments of approximately 300 bp. cDNA was synthesized using random hexamer primers and purified using 1.8X Agencourt AMPure XP beads (Beckman). Finally, the sequencing primers linked to the cDNA fragments (approximately 300 bp) were isolated by gel electrophoresis and enriched by PCR amplification to construct the library. The sequencing was performed at the Sequencing Center in National Institute of Biology, Beijing using the HiSeq 2000 system developed by Illumina. Paired-end 100-bp sequencing was applied.

value: Teratoma


title: Teratoma rep2


title: Brain-NPCs rep2

source_name: neonatal brain derived NPCs

value: Brain-NPCs


title: giNPC P6 rep2

source_name: established giNPC cell line at passage 6

value: giNPC

tag: time

value: passage 6


title: giNPC P6 rep1


title: Elav_CHR2-XXL_15min_2

description: Sample 6

value: BLUE LED


title: MonolayerB_ln1


title: Day17 rep1

source_name: Direct conversion from MEFs to NPCs at Day17

value: MEFs during giNPC induction process

value: day 17


title: Day21 rep2

source_name: Direct conversion from MEFs to NPCs at Day21

value: day 21


title: Day21 rep1


title: Day14 rep2

source_name: Direct conversion from MEFs to NPCs at Day14

value: day 14


title: Day17 rep2


title: pre-NPCs rep1

source_name: primary neurosphere-like cluster

value: pre-NPCs


title: Day14 rep1


title: Day10 rep2

source_name: Direct conversion from MEFs to NPCs at Day10

value: day 10


title: Day7 rep2

source_name: Direct conversion from MEFs to NPCs at Day7

value: day 7


title: Day7 rep1


title: Day1 rep2

source_name: Direct conversion from MEFs to NPCs at Day1

value: day 1


title: Day1 rep1


title: Day10 rep1


title: B035 knockdown day 0

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread.
Read counts were summarized by Entrez Gene ID using featureCounts and NCBI annotation in Rsubread.
Read counts from technical replicates of the same sample were summed.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files were written from the R prompt; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: B-ALL cells

growth_protocol: Spleen cells were isolated from leukemic mice and B-ALL cells were isolated using FACS.

extract_protocol:
RNA was isolated from freshly sorted CD19+IgM- cells with RNeasyPlus Mini kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: Leukemic mice were untreated or treated with Dox for 3-10 days, resulting in shutdown of GFP-linked shRNA expression and restoration of endogenous Ikaros expression.

tag: background strain

tag: mouse model

value: BCR-ABL1(P190) transgenic

value: spleen

value: B-ALL

tag: cell markers

tag: tumor

value: Ikaros knockdown

tag: duration

value: 0 days

tag: aligner

value: Rsubread 1.14.0


title: Day4 rep1

source_name: Direct conversion from MEFs to NPCs at Day4

value: day 4


title: Day4 rep2


title: Brain-NPCs rep1

value: Brain-NPCs


title: B031 knockdown day 0 rep 1

tag: tissue


title: B031 knockdown day 3 rep 1

value: 3 days


title: B011 control day 3

value: Control


title: B011 control day 0


title: B1044 knockdown day 3

value: BCR-ABL1(P190) retroviral

value: Rsubread 1.12.6


title: pre-NPCs rep2


title: B1044 knockdown day 0


title: B1030 control day 0


title: B1030 control day 3


title: B1040 knockdown day 3


title: B891 knockdown day 0


title: B1040 knockdown day 0


title: B035 knockdown day 3


title: NPC rep2

city: La Jolla,

first: Tony

last: Hunter

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Neural progenitor cells

growth_protocol: Neuroprogenitor cells and neurons were cultured in standard N2/B27 neuronal growth medium.

extract_protocol:
Neuroprogenitor cells and neurons were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BJ fibroblast derived iPSC-1

tag: time point

value: before differentiation


title: 3weekeneuron rep2

source_name: Neuron

value: 21 days after differentiation


title: NPC rep3

value: BJ fibroblast derived iPSC-2


title: 3weekeneuron rep1


title: 3weekeneuron rep4


title: NPC rep4


title: 1weekeneuron rep4

value: 7 days after differentiation


title: 3weekeneuron rep3


title: 1weekeneuron rep3


title: 1weekeneuron rep2


title: 1weekeneuron rep1


title: Set3-6h-FK506 [33]

city: London

first: Darius

middle: P H

last: Armstrong-James

address: Faculty of Medicine

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Quality filtered Illumina paired-end reads were mapped to human reference genome (hg19) using the read alignment software TopHat2
Differential expression analyses were done with Cufflinks v2.2.1
Gene ontology enrichment, functional classification of genes and KEGG pathway enrichment analysis were carried out using  DAVID v6.7
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values all the compared data sets generated using Cufflinks

source_name: Donor1 -macrophage

growth_protocol: Monocyte-derived macrophages (MDMs) were prepared by culturing freshly isolated monocytes in RPMI 1640 medium supplemented with 10% human serum (Sigma, UK) and 5 ng/ml granulocyte macrophage colony-stimulating factor (GM-CSF) (Peprotech, UK) for 7 days at 37°C

extract_protocol:
Total RNA was extracted using TRIzol reagent (Life technologies).  RNA was further purified using an RNAeasy kit (QIAGEN) with an additional purification step by on-column DNase treatment using the RNase-free DNase Kit (QIAGEN) to ensure elimination of genomic DNA.
One microgram of total RNA was used to generate RNA-seq libraries using the mRNA seq kit v2 (Illumina, Essex, UK), according to the manufacturer’s instructions.

treatment_protocol: 5x105 MDMs were plated in 24 well plates and half of the plates pre-treated with 10 ng/ml FK506 for 1h. MDMs were then stimulated with live Aspergillus fumigatus swollen conidia (MOI=1) for 1 hour and 6 hours

value: Monocyte derived macrophage cells

tag: pre-treatments

value: 10 ng/ml FK506 for 1h

tag: stimulation


title: Set6-1h-FK506 [24]

value: Aspergillus fumigatus swollen conidia (MOI=1)


title: Set6-6h-FK506 [36]


title: Set2-6h-UT [26]


title: Set3-6h-UT [27]


title: Set4-6h-UT [28]


title: Set1-6h-FK506 [31]


title: Set2-6h-FK506 [32]


title: Set4-1h-FK506 [22]


title: Set3-1h-FK506 [21]


title: Set5-1h-FK506 [23]


title: NPC rep1


title: Set5-6h-FK506 [35]


title: Set1-6h-UT [25]


title: Set6-6h-UT [30]


title: B891 knockdown day 3

value: spleen

value: B-ALL

tag: treatment

value: Ikaros knockdown


title: Set4-6h-FK506 [34]


title: Set5-1h-UT [17]


title: Set2-1h-FK506 [20]


title: Set6-1h-UT [18]


title: Set5-0h-FK506 [11]


title: Set1-1h-UT [13]


title: Set5-6h-UT [29]


title: Set4-1h-UT [16]


title: Set4-0h-FK506 [10]


title: Set6-0h-FK506 [12]


title: Set3-0h-FK506 [9]


title: Set1-0h-FK506 [7]


title: Set2-0h-FK506 [8]


title: Set2-0h-UT [2]


title: Set1-0h-UT [1]


title: Set5-0h-UT [5]


title: NHA9-H3K4me3-ChIP

first: Scott

last: Armstrong

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

data_processing:
Low quality (< 15) bases were trimmed using cutadapt
Reads were aligned to genome assembly mm9 using Bowtie2 with default paramters
Duplicate reads were removed using Picard MarkDuplicates
The coverage data was converted to bed format using a custom script, and then to BigWig format
Genome_build: mm9
Supplementary_files_format_and_content: BigWig format

source_name: cultured NUP98-HOXA9 transformed mouse bone marrow LSK cells

growth_protocol: BM LSK cell–derived NUP98-HOXA9 transformed cells were generated by retrovirally transduction with vectors carrying C-terminally Flag-AviTagged NUP98-HOXA9 or NUP98-HOXD13, and were further transduced with a retroviral vector harboring BirA ligase. Cels were maintained in IMDM, supplemented with heat inactivated 10% fetal bovine serum, 50 U/mL penicillin/streptomycin and murine IL3 (10 ng/mL), IL6 (10 ng/mL) and SCF (20 ng/mL).

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

value: BM-derived immortalised cells

tag: passages

value: passage 5 to passage 10

tag: chip antibody


title: NHA9_Input


title: NHD_BirA_Biotin


title: NHD_Input


title: Set4-0h-UT [4]


title: Set1-1h-FK506 [19]


title: NHA9-H3K4me3-Input

value: anti-H3K4me3 (abcam, ab8580, lot GR224370-2)


title: Set6-0h-UT [6]


title: NHA9-H4K16ac-Input


title: Set2-1h-UT [14]


title: NHA9-H4K16ac-ChIP

value: anti-H4K16ac (Active Motif, 39167, lot 33311003)


title: NHA_BirA_Biotin


title: MLL1-Input


title: MLL1ff_ETOH_1

description: Mll1 non-excised, d3 post vehicle treatment

data_processing:
The reads were aligned to genome assembly mm9 using STAR
Number of reads on each transcript was counted using featurecounts
Differentially expressed genes were determined using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: Transcript read counts. 1st column is NCBI accession id, 2nd column is gene symbol, 3rd column is number of reads

source_name: Transformed bone marrow LSKs

extract_protocol:
Trizol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols, Poly-A tail selection

tag: genotype

value: ERT2-Cre; Mll1f/f

value: ETOH


title: Set3-1h-UT [15]

tag: cell type


title: MLL1ff_4OHT_1

description: Mll1 excised, d3 post 4OHT treatment

tag: strain


title: B038 knockdown day 0

value: BCR-ABL1(P190) transgenic

value: 0 days

value: Rsubread 1.16.1


title: MLL1ff_4OHT_3

description: Mll1 excised, d3 post 4OHT treatment


title: B041 control day 3

value: Control

value: 3 days


title: MLL1ff_4OHT_2

description: Mll1 excised, d3 post 4OHT treatment


title: MLL1ff_ETOH_2


title: MLL1ff_ETOH_3


title: Set3-0h-UT [3]

value: Monocyte derived macrophage cells


title: B031 knockdown day 3 rep 2


title: B035 knockdown relapse

value: Relapse


title: B038 knockdown day 3


title: B031 knockdown day 0 rep 2


title: B029 knockdown relapse


title: B027 knockdown day 7

value: 7 days


title: B027 knockdown relapse

value: spleen


title: B027 knockdown day 10

value: B-ALL

value: 10 days


title: B027 knockdown day 0

value: Ikaros knockdown


title: B014 knockdown day 0


title: B005 control day 0


title: MLL1-ChIP

value: BM-derived immortalised cells

value: passage 5 to passage 10

value: anti-MLL1 (BETHYL, A300-086A, lot 4)


title: B027 knockdown day 3


title: B005 control day 3


title: 2011-09-28

city: Umeå

first: Erik

last: Edlund

address: Bärnstensvägen 24

department: Plant physiology

country: Sweden

institute: UPSC

description: Sample 15

data_processing:
Clustered on cBot and sequenced on NN according to manufacturer's instructions. Demultiplexing and conversion using CASAVA v1.8.2. The quality scale is Sanger / phred33 / Illumina 1.8+.
quality control was perfomred with Fastqc V1.0
Sequenced reads were trimmed for adaptor sequence with Trimmomatic V 1.0 Quality required=20
Data were aligned to Populus trichocarpa  V3.0 whole genome using STAR V2.4
reads were analysed using HTSEQ
Genome_build: Populus trichocarpa  V3.0; Ptrichocarpa_210_v3.0.fa at:
http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Ptrichocarpa#
Supplementary_files_format_and_content: tab-delimited text files with raw read counts
The genes are searchable in several databases:
https://phytozome.jgi.doe.gov/pz/portal.html#!search?show=KEYWORD&method=Org_Ptrichocarpa
https://phytozome.jgi.doe.gov/jbrowse/index.html?data=genomes%2FPtrichocarpa&loc=Chr01%3A76971..158051&tracks=Transcripts%2CAlt_Transcripts%2CPASA_assembly%2CBlastx_protein%2CBlatx_Plant_protein&highlight=
There is also our public in house databases from our research center:
http://popgenie.org/start?genelist=enable

organism: Populus tremula

source_name: Leaf

extract_protocol:
Total RNA was extracted according to (Chang et al. 1993) The RNA was cleaned using a QIAGEN RNeasy Mini Kit with the standard kit protocol.
RNA libraries were prepared for sequencing using Illumina TruSeq RNA

value: Leaf

tag: collection time


title: 2011-09-22

description: Sample 13


title: B041 control day 0

tag: background strain


title: B014 knockdown day 3

tag: mouse model


title: 2011-10-01

description: Sample 16


title: 2011-09-19

description: Sample 12


title: 2011-09-26

description: Sample 14


title: 2011-09-18

description: Sample 11


title: 2011-09-13

description: Sample 9


title: 2011-09-02

description: Sample 5


title: 2011-08-31

description: Sample 4


title: 2011-09-15

description: Sample 10


title: 2011-09-09

description: Sample 7


title: 2011-09-05

description: Sample 6


title: 2011-08-19

description: Sample 3


title: 2011-07-27

description: Sample 1


title: SAL_48

status: Public on Dec 10 2016

city: Austin

first: Gizelle

middle: Marin

last: Robinson

state: TX

address: 2500 Speedway

department: Waggoner Center for Alcohol and Addiction Research

institute: University of Texas at Austin

data_processing:
Bcl2fastq version 2.15.0.4
Reads were mapped to the mouse reference genome (UCSC, mm10) using the allignment tool STAR
Raw RNA-Seq files were evaluated for quality control using FastQC and one samples was excluded from further analysis due to low sample quality
HTSeq was used for counting mapped sequencing reads.
DESeq2 was used to normalize reads and analyze differential expression
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimitated tex files including raw read counts

source_name: prefrontal cortex

extract_protocol:
The medial prefrontal cortex was dissected, minced, and resuspended in HBSS. 1% of the suspension was removed and the remaining cells were manually dissociated in Neural Tissue Dissociation Buffer (P) (Miltenyi Biotec). Myelin was removed using a 30% percoll gradient and microglia were captured using Cd11b microbeads (Miltenyi Biotec). Cells were spun at 1,000 x g and flash frozen in liquid nitrogen.
RNA was harvested using Qiagen Rneasy Micro Kit (Cat No. 74004).
Samples were Poly(A) selected using the Poly(A) Purist Kit (Thermo Fisher Scientific Inc.) and prepared using NEBNext® Ultra™ Directional RNA Library Preparation Kit (New England BioLabs, Ipswich, MA). Samples went through 15 cycles of PCR. Samples were sequenced on the NextSeq 500 (Illumina, San Diego, CA) using (75 bp; paired-end reads) to a minimum target depth of 20 million reads per sample.

treatment_protocol: mice were injected intraperitoneally with saline and sacrificed 1 week later

tag: brain region

value: prefrontal cortex

value: Saline injected

value: brain

value: microglia


title: SAL_49


title: LPS_44

treatment_protocol: mice were injected intraperitoneally with lipopolysaccharide (1.5 mg/kg) and sacrificed 1 week later

value: LPS injected


title: SAL_38


title: LPS_50


title: LPS_51


title: LPS_33


title: LPS_40


title: 2011-09-11

description: Sample 8


title: C_CD_25

treatment_protocol: Mice had access to water for 60 days

value: Control (water)


title: C_CD_24


title: C_CD_18


title: C_CD_19


title: C_CD_21


title: C_CD_15


title: E_CD_14

treatment_protocol: mice were allowed to voluntary drink 15% (v/v) ethanol every other day for 60 days. Only water was available on off days. Mice were sacrificed immediately after removal of bottles

value: Ethanol


title: C_CD_16


title: C_CD_17


title: E_CD_11


title: E_CD_7


title: E_CD_10


title: E_CD_5


title: E_CD_9


title: E_CD_3


title: 2011-08-05

description: Sample 2


title: SAL_46


title: SAL_45


title: E_CD_2


title: C_TH_26

value: mixed (total homogenate)


title: C_TH_25


title: C_TH_18

extract_protocol:
The medial prefrontal cortex was dissected, minced, and resuspended in HBSS. 1% of the suspension was taken as the total homogenate, spun at 1000 x g and flash frozen in liquid nitrogren.
RNA was harvested using Qiagen Rneasy Micro Kit (Cat No. 74004).
Samples were Poly(A) selected using the Poly(A) Purist Kit (Thermo Fisher Scientific Inc.) and prepared using NEBNext® Ultra™ Directional RNA Library Preparation Kit (New England BioLabs, Ipswich, MA). Samples went through 15 cycles of PCR. Samples were sequenced on the NextSeq 500 (Illumina, San Diego, CA) using (75 bp; paired-end reads) to a minimum target depth of 20 million reads per sample.


title: C_TH_24


title: C_TH_19


title: C_TH_17


title: C_TH_16


title: C_TH_21


title: E_TH_14


title: E_TH_13


title: E_CD_13


title: C_TH_15


title: E_TH_11


title: E_TH_10


title: E_TH_2


title: E_TH_3


title: E_TH_1


title: siCTCF_ER_ChIPseq

city: Oslo

first: Elisa

last: Fiorito

address: Forskningsparken - Gaustadalleen 21

department: Norwegian Centre for Molecular Medicine (NCMM)

country: Norway

institute: University of Oslo (UiO)

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2 with default parameters.
samtools was used to convert the SAM file into BAM and subsequently sort the BAM file.
Duplicate reads were removed with samtools and the resulting file was converted into a BED file containing the aligned unique reads.
MACS2 with default parameters was used to call the peaks over the MCF7 input DNA obtained from unChIPped material.
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain ChIP-seq peaks and were generated by using MACS2.

source_name: Luminal breast cancer cell line

growth_protocol: MCF7 cells were hormone deprived for 72 h in DMEM 5% Charcoal stripped Fetal Bovine Serum.

extract_protocol:
For each ChIP-seq, 2 plates 70-80% confluent (around total 20 millions MCF7 cells) were lysed in SDS buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.0)) and sonicated for 20 cycles 30 sec ON 30 sec OFF in Bioruptor sonicator (Diagenode). Subsequently, chromatin was diluted in dilution buffer (10 mM Tris-HCl pH 8.0, 0.5  mM EGTA pH 8.0, 1% Triton-X-100, 140 mM NaCl) and incubated over night with 10 ug of antibody coupled with magnetic beads. Afterwards, beads were washed 7 times with RIPA buffer (50mM HEPES pH7.6, 1mM EDTA pH8, 0.7% Na-deoxycholate, 1% NP-40, 0.5 M LiCl2) and reverse cross-linked at 65 degrees overnight in Elution buffer (50 mM Tris-HCl pH8, 1 mM EDTA pH8, 1% SDS). RNA was digested at 37 degrees in RNAse A (Ambion), and proteins were digested with proteinase K (Life Technologies) at 56 degrees. DNA was isolated by Phenol-chloroform extraction followed by Ethanol precipitation.
Library preparation for sequencing was done following the instructions of TruSeq DNA sample preparation kit from Illumina.

treatment_protocol: Upon hormone deprivation, MCF7 cells were treated either with 100 nM 17-beta-estradiol for 0h, 45 min or 3h.

tag: cell line

value: ER-alpha:Santa Cruz Biotechnology sc-543 (lot #F1215)

value: siCTCF


title: E_TH_7


title: E_TH_9


title: E_TH_5


title: E_CD_1


title: LaminB_E45m_ChIPseq

value: LaminB (c-20) Santa Cruz Biotechnology sc-6216 (lot #F1715)

value: estrogen

tag: time


title: siNT_ER_ChIPseq

value: siNT


title: LaminB_3hE2_ChIPseq


title: FOXA1_3hE2_ChIPseq


title: LaminB_0hE2_ChIPseq

value: control


title: FOXA1_E45m_ChIPseq


title: FOXA1_E0h_ChIPseq


title: MCF7_input_ChIPseq

value: none (input)


title: ER_E0h_ChIPseq


title: CTCF_E3h_ChIPseq


title: ER_E45m_ChIPseq


title: ER_3hE2_ChIPseq


title: CTCF_E45m_ChIPseq


title: CTCF_E0h_ChIPseq


title: siCTCF_E0h_RNAseq

data_processing:
The paired-end RNAseq data were aligned by using tophat.
The gene expression values (FPKM) were calculated by using cufflinks.
The differential expression values and plots were generated by using Cuffmerge and CummeRbund.
Genome_build: hg19
Supplementary_files_format_and_content: txt files containing fpkm values for genes

extract_protocol:
Total RNA was isolated with the total RNA isolation kit (RNeasy, Qiagen) according to the manufacturer’s protocol. RNA yield was assessed spectrophotometrically (NanoDrop 2000). Quantification and quality control for RNA-seq libraries were performed by Agilent Bioanalyzer (RNA nano 6000, Agilent).
The libraries were prepared at Norwegian Sequencing Center (NSC, Oslo). The instructions from TruSeq RNA-seq strand-specific sample protocol were followed.

treatment_protocol: In 6-well plates, MCF7 cells were transfected with siRNA targeting CTCF (ON-TARGET J-010319-05-0005, Thermo Fisher Scientific) and siControl Non-targeting (siNT) (AllStars, Qiagen) using Lipofectamine RNAiMax (Life technologies) to a final concentration of 40 nM. Upon hormone deprivation, cells were treated either with 100 nM 17-beta-estradiol for 0h or 3h.

tag: transfection

value: 0h Estrogen


title: siCTCF_E3h_RNAseq

value: 3h Estrogen


title: siNT_E3h_RNAseq


title: siNT_E0h_RNAseq


title: WT 2

city: Bethesda

first: Chuan

last: Wu

state: MD

address: 10 Center Drive, Building 10, RM 4B17

institute: National Cancer Institute

data_processing:
RNA-seq reads were aligned to the NCBI Build 37 (UCSC mm9) of the mouse genome using TopHat (Trapnell et al., 2009).
The resulting alignments were processed by Scripture (Guttman et al., 2010) to evaluate the expression of transcripts from RefSeq  (Pruitt et al., 2007).
Quantile normalization was used to further normalize the FPKM values.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: iTreg cells

growth_protocol: The naïve T cells from WT and MSC KO mice was sorted and differentiated under iTreg condtion with 1µg/ml plate anti-CD3/CD28 plus 2ng/ml TGF-beta for 3 days.

extract_protocol:
RNA was extracted from differentiated iTreg cells with Qiangen microRNA extract kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: in vitro differentiated iTreg cells

tag: genotype/variation

value: WT


title: WT 1


title: MSC KO 2

value: MSC KO


title: C_CD_26

description: sample removed after mapping therefore no processed data available for this sample.

value: prefrontal cortex

tag: tissue

value: brain

value: microglia


title: G2RY3e1

city: yangling

first: zhigui

last: he

institute: Northwest A & F University, College of Life Sciences

data_processing:
Raw Illumina fastq files were de-multiplexed, quality filtered, and analyzed using QIIME v1.7.0.
Reads containing more than three consecutive bases, receiving a quality score <20, or containing >6 nt ambiguous nucleotides (“N”) in the homopolymeric regions were discarded. Chimeric sequences were identified and removed using USEARCH.
Operational taxonomic units (OTUs) were assigned using UCLUST with a threshold level of 97% similarity.
Phylogenetic classification of the reads was determined based on the Ribosomal Database Project using a threshold of 80%.
Supplementary_files_format_and_content: dt.xlsx: envrionmental factors
Supplementary_files_format_and_content: OTU_table.txt: OTU expression data

organism: Pinellia ternata

source_name: cultivated soil_Pinellia ternata

extract_protocol:
DNA from different samples was extracted using the MicroElute Genomic DNA Kit (D3096-01, Omega, Inc., USA) according to manufacturer’s instructions. The reagent, which was designed to uncover DNA from trace amounts of sample, has been shown to be effective to prepare DNA of most bacteria. Sample blanks consisted of unused swabs processed through DNA extraction and tested to contain no 16S amplicons. The total DNA was eluted in 50 µl of elution buffer by a modification of the procedure described by manufacturer (Qiagen) and stored at −80 °C until measurement in polymerase chain reaction (PCR) by Lianchuan Biotech, Hang Zhou, P.R. China
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: soil type

value: cultivated soil

value: continuous cropping soil

tag: sample type

value: rhizosphere


title: G2RY3b1


title: G2RY3p1

source_name: cultivated soil_P.ternata-Wheats

value: rotational cropping soil


title: G2RY3r1


title: G1.2RY3c1

organism: uncultivated soil bacterium

source_name: unplanted soil

value: unplanted soil

value: bulk soil


title: G1.2RY2c1


title: G2RY2r1


title: G1.2LY3c1


title: G1.2LY2c1


title: G2RY2b1


title: G2RY2e1


title: G1.2LY1c1


title: G2RY1e1


title: G2RY1P1


title: G2RY1b1


title: G2LY3e1


title: G2LY3b1


title: G1.2RY1c1


title: G2RY1r1


title: G2LY2r1


title: GW_HS rep 3

city: LUJAN DE CUYO

first: Marcos

last: Paolinelli

state: Mendoza

address: San Martin 3853

country: Argentina

institute: CONICET-INTA

data_processing:
Illumina CASAVA v1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then used all (independent of conditions) to assemble de novo transcriptome through Trinity (r20140717 with default parameters) and then the reads for each sample independent were mapped to the transcriptome using bowtie 2 (version 2.1.0) with default parameters
Counts per Million of reads  (CPM) were calculated using edgeR package in R. The number of reads falling in the longest isoform predicted for each transcript were counted and normalized by the number of total reads for each sample.
Supplementary_files_format_and_content: tab-delimited text files with raw count values for each Sample ...

organism: Lasiodiplodia theobromae

source_name: complete mycellium

extract_protocol:
RNA extraction was done through a protocol based on Reid et al. (2006) and Vasanthaiah et al. (2008). Illumina TruSeq RNA sample Prep v2 (cat.numb. RS-122-2001) was used  with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: isolate

tag: growth protocol

value: grew on Vogel's salt with grapevine wood

tag: condition

value: Heat stressed


title: VS_HS rep 3

value: grew on Vogel's salt without grapevine wood


title: G2LY3r1


title: G2LY3p1


title: GW_HS rep 1


title: GW_HS rep 2


title: MSC KO 1


title: VS_HS rep 2


title: VS_HS rep 1


title: G2LY2e1


title: G2LY2b1


title: G2LY1r1


title: GW_noHS rep2

value: no heat stress


title: G2LY1e1


title: GW_noHS rep1


title: G2RY2p1


title: G2LY1b1


title: GW_noHS rep3


title: VS_noHS rep 2


title: VS_noHS rep 3


title: VS_noHS rep 1


title: G2LY1p1


title: G1RY3e1


title: G1RY3b1


title: 24H: 200 ug/l PCP treatment

first: Ting

last: Xu

address: No. 1239 Road Siping

data_processing:
Illumina Casava1.7 software used for basecalling.
After obtained from the raw sequencing data, clean reads were mapped into reference zebrafish genome Zv9 assembly, and also H.sapiens hg19 assembly using BLAST to increase the subsequent annotation efficiency.
Trimmed mean of M-values of library size (TMM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: zv9
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample ...

organism: Danio rerio

source_name: 24 hpf larvae

extract_protocol:
Zebrafish larvae were homogenized, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Tuebingen

value: whole larvae

tag: age

value: 24 hour post fertilization


title: 24C: DMSO vehicle


title: 10H: 200 ug/l PCP treatment

source_name: 10 hpf larvae

value: 10 hour post fertilization


title: G1RY2e1


title: G1RY3r1


title: 10C: DMSO vehicle


title: G1RY2r1


title: G2LY2p1


title: 10L: 5 ug/l PCP treatment


title: G1RY2p1


title: 24L: 5 ug/l PCP treatment


title: G1RY2b1


title: G1RY1p1


title: G1LY3e1


title: G1LY2r1


title: G1RY1b1


title: G1RY1e1


title: G1LY3b1


title: G1LY2b1


title: G1LY2p1


title: G1LY1r1


title: G1LY1e1


title: G1LY1b1


title: G1LY1p1


title: BC11_78

status: Public on Dec 09 2016

city: Seoul

first: Woosung

last: Chung

state: State...

address: Samsung Medical Center

country: South Korea

institute: Samsung Genome Institute

description: Single-cell RNA-seq

data_processing:
A modified reference was generated by merging the three array control RNA spike-ins (ThermoFisher) and the human genome reference (hg19) with the GENCODE 19 annotations.
Paired-end 100bp reads were aligned to the modified reference by 2-pass mode of STAR_2.4.0b with default parameters.
Transcripts Per Million (TPM) values were estimated using RSEM v1.2.17 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: A processed file is tab-delimited and contains the raw TPM values for 549 single cells and 14 bulk tumors.

source_name: BC11_Single-cell RNA-seq

growth_protocol: On the day of surgery, all single cells were dissociated with mechanical and enzymatical method then immediately used for assay without any in vitro culture.

extract_protocol:
Dead cells in single cell suspensions were removed by Ficoll-Paque TM PLUS (GE healthcare) separation before loading to integrated fluidic circuit (IFC) chip. Each suspension was loaded to 10-17um IFC for mRNA sequencing chip then cDNA synthesis and amplification were performed with SMARTer Ultra Low RNA Kit (Clontech) in the C1TM Single-Cell Auto Prep System (Fluidigm). RNA spike-ins 1, 4 and 7 from ArrayControl TM RNA Spikes (ThermoFisher) were added to the lysis mix for validation of array and batch effect. Bulk RNAs were extracted from ~1x10^5 cells of suspensions or tumor tissues using RNeasy Plus Micro kit (Qiagen) and 10ng of total RNAs were amplified with SMARTer kit (Clonetech) under the same conditions as single cells. All of amplified cDNAs were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies). Total 549 single cell cDNAs and 14 bulk samples were subjected to the RNA sequencing.
Starting with 0.375 ng of amplified cDNAs, sequencing libraries were constructed with the Nextera XT DNA Sample Prep Kit (Illumina). All of constructed libraries were quantified and qualified by the Qubit® 2.0 Fluorometer (Life Technologies) and 2100 Bioanalyzer (Agilent Technologies) then pooled without index overlapping. Finally pooled libraries were sequenced using the HiSeq2500 (Illumina) as 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit.

tag: patient id

tag: molecular subtype

value: triple-negative breast cancer (TNBC)

tag: cell type

value: primary breast cancer


title: BC11_88

description: Single-cell RNA-seq


title: BC11_81

description: Single-cell RNA-seq


title: G1RY1r1


title: BC11_56

description: Single-cell RNA-seq


title: BC11_70

description: Single-cell RNA-seq


title: BC11_69

description: Single-cell RNA-seq


title: BC11_01

description: Single-cell RNA-seq


title: BC11_07

description: Single-cell RNA-seq


title: G1LY3p1


title: BC11_43

description: Single-cell RNA-seq


title: G1LY2e1


title: G1LY3r1


title: BC11_04

description: Single-cell RNA-seq


title: BC10_81

description: Single-cell RNA-seq

source_name: BC10_Single-cell RNA-seq


title: BC10_80

description: Single-cell RNA-seq


title: BC10_85

description: Single-cell RNA-seq


title: BC10_95

description: Single-cell RNA-seq


title: BC10_73

description: Single-cell RNA-seq


title: BC10_69

description: Single-cell RNA-seq


title: BC10_58

description: Single-cell RNA-seq


title: BC11_28

description: Single-cell RNA-seq


title: BC10_47

description: Single-cell RNA-seq


title: BC10_54

description: Single-cell RNA-seq


title: BC10_27

description: Single-cell RNA-seq


title: BC10_67

description: Single-cell RNA-seq


title: BC10_43

description: Single-cell RNA-seq


title: BC10_16

description: Single-cell RNA-seq


title: BC10_09

description: Single-cell RNA-seq


title: G1RY3p1


title: BC09_Re_88

description: Single-cell RNA-seq (Replicate)

source_name: BC09_Re_Single-cell RNA-seq


title: BC09_Re_83

description: Single-cell RNA-seq (Replicate)


title: BC10_07

description: Single-cell RNA-seq


title: BC09_Re_95

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_68

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_60

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_94

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_74

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_62

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_59

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_46

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_61

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_72

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_32

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_39

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_37

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_41

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_66

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_44

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_57

description: Single-cell RNA-seq (Replicate)


title: BC10_20

description: Single-cell RNA-seq


title: BC09_Re_15

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_43

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_14

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_80

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_07

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_54

description: Single-cell RNA-seq (Replicate)


title: BC09_93

description: Single-cell RNA-seq

source_name: BC09_Single-cell RNA-seq


title: BC09_Re_05

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_06

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_21

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_01

description: Single-cell RNA-seq (Replicate)


title: BC09_70

description: Single-cell RNA-seq


title: BC09_37

description: Single-cell RNA-seq


title: BC09_65

description: Single-cell RNA-seq


title: BC09_45

description: Single-cell RNA-seq


title: BC09_46

description: Single-cell RNA-seq


title: BC09_34

description: Single-cell RNA-seq


title: BC09_48

description: Single-cell RNA-seq


title: BC09_33

description: Single-cell RNA-seq


title: BC09_42

description: Single-cell RNA-seq


title: BC09_83

description: Single-cell RNA-seq


title: BC09_53

description: Single-cell RNA-seq


title: BC09_92

description: Single-cell RNA-seq


title: BC09_57

description: Single-cell RNA-seq


title: BC09_86

description: Single-cell RNA-seq


title: BC09_49

description: Single-cell RNA-seq


title: BC09_Re_13

description: Single-cell RNA-seq (Replicate)


title: BC09_Re_03

description: Single-cell RNA-seq (Replicate)


title: BC09_54

description: Single-cell RNA-seq


title: BC09_50

description: Single-cell RNA-seq


title: BC09_31

description: Single-cell RNA-seq


title: BC09_44

description: Single-cell RNA-seq


title: BC09_64

description: Single-cell RNA-seq


title: BC09_29

description: Single-cell RNA-seq


title: BC09_25

description: Single-cell RNA-seq


title: BC09_21

description: Single-cell RNA-seq


title: BC09_05

description: Single-cell RNA-seq


title: BC09_13

description: Single-cell RNA-seq


title: BC09_19

description: Single-cell RNA-seq


title: BC08_88

description: Single-cell RNA-seq

source_name: BC08_Single-cell RNA-seq


title: BC08_73

description: Single-cell RNA-seq


title: BC08_56

description: Single-cell RNA-seq


title: BC08_70

description: Single-cell RNA-seq


title: BC08_36

description: Single-cell RNA-seq


title: BC08_54

description: Single-cell RNA-seq


title: BC08_95

description: Single-cell RNA-seq


title: BC08_51

description: Single-cell RNA-seq


title: BC08_94

description: Single-cell RNA-seq


title: BC08_48

description: Single-cell RNA-seq


title: BC09_27

description: Single-cell RNA-seq


title: BC08_22

description: Single-cell RNA-seq


title: BC08_83

description: Single-cell RNA-seq


title: BC08_08

description: Single-cell RNA-seq


title: BC08_12

description: Single-cell RNA-seq


title: BC08_06

description: Single-cell RNA-seq


title: BC08_04

description: Single-cell RNA-seq


title: BC08_27

description: Single-cell RNA-seq


title: BC08_59

description: Single-cell RNA-seq


title: BC08_01

description: Single-cell RNA-seq


title: BC08_24

description: Single-cell RNA-seq


title: BC07LN_90

description: Single-cell RNA-seq

source_name: BC07LN_Single-cell RNA-seq

value: metastatic breast cancer


title: BC09_02

description: Single-cell RNA-seq


title: BC07LN_30

description: Single-cell RNA-seq


title: BC07_58

description: Single-cell RNA-seq

source_name: BC07_Single-cell RNA-seq


title: BC07_55

description: Single-cell RNA-seq


title: BC07_07

description: Single-cell RNA-seq


title: BC08_33

description: Single-cell RNA-seq


title: BC08_10

description: Single-cell RNA-seq


title: BC08_31

description: Single-cell RNA-seq


title: BC06_60

description: Single-cell RNA-seq

source_name: BC06_Single-cell RNA-seq

value: human epidermal growth factor receptor 2 positive (HER2+)


title: BC06_61

description: Single-cell RNA-seq


title: BC06_62

description: Single-cell RNA-seq


title: BC06_74

description: Single-cell RNA-seq


title: BC06_58

description: Single-cell RNA-seq


title: BC06_40

description: Single-cell RNA-seq


title: BC06_39

description: Single-cell RNA-seq


title: BC06_43

description: Single-cell RNA-seq


title: BC06_28

description: Single-cell RNA-seq


title: BC06_29

description: Single-cell RNA-seq


title: BC06_57

description: Single-cell RNA-seq


title: BC06_45

description: Single-cell RNA-seq


title: BC06_26

description: Single-cell RNA-seq


title: BC06_27

description: Single-cell RNA-seq


title: BC06_49

description: Single-cell RNA-seq


title: BC06_21

description: Single-cell RNA-seq


title: BC06_10

description: Single-cell RNA-seq


title: BC06_09

description: Single-cell RNA-seq


title: BC06_07

description: Single-cell RNA-seq


title: BC06_08

description: Single-cell RNA-seq


title: BC05_96

description: Single-cell RNA-seq

source_name: BC05_Single-cell RNA-seq


title: BC06_04

description: Single-cell RNA-seq


title: BC05_94

description: Single-cell RNA-seq


title: BC05_91

description: Single-cell RNA-seq


title: BC06_25

description: Single-cell RNA-seq


title: BC06_32

description: Single-cell RNA-seq


title: BC05_92

description: Single-cell RNA-seq


title: BC05_93

description: Single-cell RNA-seq


title: BC05_90

description: Single-cell RNA-seq


title: BC05_87

description: Single-cell RNA-seq


title: BC05_88

description: Single-cell RNA-seq


title: BC06_23

description: Single-cell RNA-seq


title: BC05_79

description: Single-cell RNA-seq


title: BC05_78

description: Single-cell RNA-seq


title: BC05_84

description: Single-cell RNA-seq


title: BC05_77

description: Single-cell RNA-seq


title: BC05_85

description: Single-cell RNA-seq


title: BC05_80

description: Single-cell RNA-seq


title: BC05_81

description: Single-cell RNA-seq


title: BC05_86

description: Single-cell RNA-seq


title: BC06_22

description: Single-cell RNA-seq


title: BC05_75

description: Single-cell RNA-seq


title: BC05_83

description: Single-cell RNA-seq


title: BC05_73

description: Single-cell RNA-seq


title: BC05_72

description: Single-cell RNA-seq


title: BC05_71

description: Single-cell RNA-seq


title: BC05_69

description: Single-cell RNA-seq


title: BC05_95

description: Single-cell RNA-seq


title: BC05_74

description: Single-cell RNA-seq


title: BC05_64

description: Single-cell RNA-seq


title: BC05_68

description: Single-cell RNA-seq


title: BC05_61

description: Single-cell RNA-seq


title: BC05_59

description: Single-cell RNA-seq


title: BC05_60

description: Single-cell RNA-seq


title: BC05_57

description: Single-cell RNA-seq


title: BC05_55

description: Single-cell RNA-seq


title: BC05_49

description: Single-cell RNA-seq


title: BC05_48

description: Single-cell RNA-seq


title: BC05_47

description: Single-cell RNA-seq


title: BC05_42

description: Single-cell RNA-seq


title: BC05_40

description: Single-cell RNA-seq


title: BC05_44

description: Single-cell RNA-seq


title: BC05_46

description: Single-cell RNA-seq


title: BC05_53

description: Single-cell RNA-seq


title: BC05_39

description: Single-cell RNA-seq


title: BC05_45

description: Single-cell RNA-seq


title: BC05_35

description: Single-cell RNA-seq


title: BC05_37

description: Single-cell RNA-seq


title: BC05_36

description: Single-cell RNA-seq


title: BC05_70

description: Single-cell RNA-seq


title: BC05_34

description: Single-cell RNA-seq


title: BC05_38

description: Single-cell RNA-seq


title: BC05_41

description: Single-cell RNA-seq


title: BC05_31

description: Single-cell RNA-seq


title: BC05_62

description: Single-cell RNA-seq


title: BC05_32

description: Single-cell RNA-seq


title: BC05_29

description: Single-cell RNA-seq


title: BC05_28

description: Single-cell RNA-seq


title: BC05_30

description: Single-cell RNA-seq


title: BC05_27

description: Single-cell RNA-seq


title: BC05_52

description: Single-cell RNA-seq


title: BC05_26

description: Single-cell RNA-seq


title: BC05_43

description: Single-cell RNA-seq


title: BC05_22

description: Single-cell RNA-seq


title: BC05_23

description: Single-cell RNA-seq


title: BC05_21

description: Single-cell RNA-seq


title: BC05_20

description: Single-cell RNA-seq


title: BC05_13

description: Single-cell RNA-seq


title: BC05_17

description: Single-cell RNA-seq


title: BC05_07

description: Single-cell RNA-seq


title: BC05_33

description: Single-cell RNA-seq


title: BC04_72

description: Single-cell RNA-seq

source_name: BC04_Single-cell RNA-seq


title: BC05_16

description: Single-cell RNA-seq


title: BC05_02

description: Single-cell RNA-seq


title: BC05_09

description: Single-cell RNA-seq


title: BC05_08

description: Single-cell RNA-seq


title: BC05_12

description: Single-cell RNA-seq


title: BC05_04

description: Single-cell RNA-seq


title: BC05_01

description: Single-cell RNA-seq


title: BC04_35

description: Single-cell RNA-seq


title: BC04_30

description: Single-cell RNA-seq


title: BC04_62

description: Single-cell RNA-seq


title: BC05_25

description: Single-cell RNA-seq


title: BC04_16

description: Single-cell RNA-seq


title: BC03LN_74

description: Single-cell RNA-seq

source_name: BC03LN_Single-cell RNA-seq

value: double positive (ER+ and HER2+)


title: BC04_22

description: Single-cell RNA-seq


title: BC04_06

description: Single-cell RNA-seq


title: BC04_14

description: Single-cell RNA-seq


title: BC03_85

description: Single-cell RNA-seq

source_name: BC03_Single-cell RNA-seq


title: BC05_18

description: Single-cell RNA-seq


title: BC03_66

description: Single-cell RNA-seq


title: BC03_25

description: Single-cell RNA-seq


title: BC03_53

description: Single-cell RNA-seq


title: BC02_95

description: Single-cell RNA-seq

source_name: BC02_Single-cell RNA-seq

value: estrogen receptor positive (ER+)


title: BC02_93

description: Single-cell RNA-seq


title: BC02_96

description: Single-cell RNA-seq


title: BC02_94

description: Single-cell RNA-seq


title: BC02_89

description: Single-cell RNA-seq


title: BC02_86

description: Single-cell RNA-seq


title: BC02_88

description: Single-cell RNA-seq


title: BC02_83

description: Single-cell RNA-seq


title: BC05_63

description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


title: BC02_08

description: Single-cell RNA-seq


title: BC02_09

description: Single-cell RNA-seq


title: BC02_02

description: Single-cell RNA-seq


title: BC02_54

description: Single-cell RNA-seq


title: BC01_54

description: Single-cell RNA-seq

source_name: BC01_Single-cell RNA-seq


title: BC01_24

description: Single-cell RNA-seq


title: BC01_50

description: Single-cell RNA-seq


title: BC01_49

description: Single-cell RNA-seq


title: BC01_11

description: Single-cell RNA-seq


title: BC05_Pooled

description: Pooled RNA-seq

source_name: BC05_Pooled RNA-seq


title: MeDIP input

city: Urbana

first: Supriya

last: Prasanth

address: 601 S Goodwin Ave

department: Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

data_processing:
Raw reads were trimmed with Trimmomatic
Trimmed reads were aligned to GRCh37/hg19 using Bowtie 0.12.7
Peak calling were perfomed using MACS with default parameters
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bed

source_name: U2OS osteosarcoma cells

growth_protocol: U2OS cells were grown in Dulbecco's modified Eagle's medium cintaining high glucose and supplemented with 10% fetal bovine serum.

extract_protocol:
For ChIP, cells were fixed with 1% formaldehyde. Extracted nuclei were sonicated and subjected to pull down with respective antibodies.
The libraries were constructed with the Kapa Hyper Prep Kit from Kapa Biosystems (Kapa Biosystems, MA). Briefly, DNAs (10ng) were blunt-ended, 3’-end A-tailed and ligated to indexed adaptors with 6nt barcodes. Adaptored DNA were amplified by PCR to selectively enrich for those fragments that have adapters on both ends. Amplification was carried out for 10 cycles with the Kapa HiFi polymerase (Kapa Biosystems, Woburn, MA) to reduce the likeliness of multiple identical reads due to preferential amplification. The final libraries were run on Agilent bioanalyzer DNA high-sensitivity chip (Agilent, Santa Clara, CA) to determine the average fragment size and to confirm the presence of DNA of the expected size range. They were also quantitated by qPCR on a BioRad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA) prior to pooling and sequencing.

value: osteosarcoma cells


title: MeDIP-seq


title: BC10_Pooled

description: Pooled RNA-seq

source_name: BC10_Pooled RNA-seq


title: BC06_Pooled

description: Pooled RNA-seq

source_name: BC06_Pooled RNA-seq


title: BC09_Pooled

description: Pooled RNA-seq

source_name: BC09_Pooled RNA-seq


title: ORCA early-G1 ChIP-seq

tag: cell cycle stage


title: ORCA late-G1 input


title: ORCA late-G1 ChIP-seq


title: ORCA mid-G1 input


title: ORCA mid-G1 ChIP-seq


title: BC07LN_95

description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


title: BC07LN_89

description: Single-cell RNA-seq


title: BC08_Pooled

description: Pooled RNA-seq

source_name: BC08_Pooled RNA-seq


title: BC11_Pooled

description: Pooled RNA-seq

source_name: BC11_Pooled RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


title: BC07LN_71

description: Single-cell RNA-seq


title: BC02_Pooled

description: Pooled RNA-seq

source_name: BC02_Pooled RNA-seq


title: ORCA early G1 input


title: BC07LN_64

description: Single-cell RNA-seq

source_name: BC07LN_Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq


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description: Single-cell RNA-seq