title: Dam_Rep2_HEK293T

city: Dresden

first: Federico

last: Calegari

address: Fetscherstr. 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

institute: TU Dresden

data_processing:
library strategy: DamID-Seq
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads from each condition were merged, and then mapped to mm9 or hg19 whole genome using bowtie1 with parameters -M 1
Peaks were called using SICER1.1 with the parameters: window size 50, gap size 250 and FDR 0.01
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: Sicer peaks [chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold]

source_name: Human embryonic kidney cell line

extract_protocol:
DNA was isolated and prepared as described in Vogel et al. 2006 (Vogel, M.J., Peric-Hupkes, D., and van Steensel, B. (2007). Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat. Protoc. 2, 1467–1478.)
Sequencing libraries were prepared as described in Aprea et al. 2013
DamID-Seq - is an alternative to ChIP-Seq Sequencing for investigating DNA-Protein Interactions if no antibody is available.  DamID is based on the expression of a fusion protein consisting of a protein of interest and DNA adenine methyltransferase (Dam). This leads to methylation of adenines near sites where the protein of interest interacts with the DNA. These methylated sequences are subsequently amplified by a methylation-specific enrichment protocol and identified by NGS.  (Vogel, M.J., Peric-Hupkes, D., and van Steensel, B. (2007). Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat. Protoc. 2, 1467–1478.)

tag: triggered expression

value: DAM only


title: ToxDam_Rep1_HEK293T

status: Public on Mar 16 2015

type: SRA

country: Germany

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

value: TOX-DAM fusion protein


title: Sample_9

city: Rochester

first: B Paige

last: Lawrence

state: NY

address: 575 Elmwood Ave.

department: Environmental Medicine

country: USA

institute: University of Rochester Medical Center

library_source: transcriptomic

data_processing:
RNA-seq analysis was performed using Tuxedo programs with default parameters (45). Reads were aligned to the mouse reference genome (NCBI37, mm9) using TopHat (v1.4.1), then assembled into transcripts using Cufflinks (v.1.3.0).
Genome_build: mm9
Supplementary_files_format_and_content: BEDGRAPH

molecule: polyA RNA

organism: Mus musculus

source_name: CD8+ T cells

extract_protocol:
CD8+ T cels were enriched from tissue using negative selection magnetic beads. RNA was extracted using QIAGEN Rneasy kit, as per manufacturer's recommendations.
TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used per manufacturer’s protocols.

tag: strain

tag: tissue

value: peripheral lymph nodes

tag: developmental expsoure

value: vehicle

tag: infectious status

value: naïve

tag: replicate


title: Human_Kupffer_Cells_Control

city: New York

first: David

last: Lyden

department: Departments of Pediatrics, Cell & Developmental Biology

institute: Weill Medical College of Cornell University

description: Control

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Sequenced reads were trimmed for low-quality sequences by using fastq_quality_trimmer in the FASTX toolkit with parameters "-t 10 -l 45"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11 with default parameters.
Number of raw counts was calculated using the htseq-count script in the HTSeq package v0.6.1 with parameters "--stranded=no --mode=union --minaqual=10"; Genes with statistically significant changes in expression were selected by using the edgeR package v3.8.2.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files including gene name, RefSeq id, raw counts and normalized counts of each sample, for each gene

molecule: total RNA

source_name: Primary culture (Life technologies)

growth_protocol: RPMI + 10% exosome free FBS

extract_protocol:
RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated in 6 wells plates with 5ug/mL of exosomes every other day for 14 days

tag: cell type

value: Human Kupffer cells

tag: treatment

value: Treatment with PBS


title: Sample_11_D

data_processing:
MeDIP-seq reads were aligned to mouse reference genome (mm9) using Bowtie (version 0.12.7 parameter set -n 2 -k 1 -m 1) allowing up to 2 nucleotide mismatches to the reference genome and considering only uniquely mappable reads for downstream analyses using MEDIPS package in R and other custom perl, R scripts. Aligned reads were extended in the sequencing direction to a length of 400 nucleotides. The short read coverage of the extended reads was calculated at genome wide 50 bp bins and wiggle files were generated using MEDIPS.exportWIG function in MEDIPS R package.
Genome_build: mm9
Supplementary_files_format_and_content: WIG

extract_protocol:
CD8+ T cels were enriched from tissue using negative selection magnetic beads. DNA were extracted using QIAGEN Dneasy, as per manufacturer's recommendations. Following enzymatic digestion and sonication, immunoprecipitation was performed using anti-5meC (Eurogentek, BI-MECY-0100, lot 081103).
Methyl-seq library construction was performed with NEXTflex Methyl-seq kit (Biooscientific, Austin, TA) per manufacturer’s recommendations. Briefly, 1200 ng of genomic DNA was sheared to an average size of 200-400bp with the Covaris S2 (Covaris, Woburn, MA). Sheared DNA sizing was confirmed with a Bioanlayzer 2100 (Agilent, Santa Clara, CA) and subsequent end repair, adenylation, and adaptor ligation was performed. DNA was heated to 95°C, and incubated with anti-5methylcytosine antibody (Epigentek, Farmingdale, NY). Methylated DNA was immunoprecipitated with Dynabeads (Life Technologies, Grand Island, NY), and released from the beads using Proteinase K digestion. DNA was purified using the MinElute PCR Purification Kit (QIAGEN), followed by library PCR amplification and gel size selection.


title: yJC_rpb1-1_pA_6 (Run 1)

status: Public on Mar 17 2015

city: Cleveland

first: Jeffery

middle: Michael

last: Coller

state: OH

address: 2109 Adelbert Dr.

department: Center for RNA Molecular Biology

institute: Case Western Reserve University

description:
Sample 13
Sample name: 6544

data_processing:
Basecalling was performed using Illumina CASAVA software
Reads were aligned to the reference genome using bowtie version 0.12.7 using parameters ‘-m 1 -v 2 -p 8’
Transcripts FPKMs from aligned reads were obtained using Cufflinks 1.3.0 using GTF provided by SGD (default parameters)
Unaligned reads from bowtie were aligned to control RNA sequences to obtain relative concentration
Genome_build: SacCer2
Supplementary_files_format_and_content: Processed data files listing all FPKMs used in final analysis

organism: Saccharomyces cerevisiae

source_name: mid-log phase culture

growth_protocol: rpb1-1 mutant cells (yJC244) were grown to mid-log phase at 24C as described above. Cells were shifted to 37C, then cell aliquots were removed and total RNA was isolated. 10 time points were collected over 60 minutes, including an initial aliquot at time 0 collected before the temperature shift.

extract_protocol:
Cells were lysed by bead bashing in phenol and RNA was purified by acidic phenol-chlorofom extraction
Input RNA was spiked with control RNA and libraries were prepared using either Illumina TruSeq Stranded mRNA library prep kits or Illumina TruSeq Stranded Total RNA library prep kit as indicated above

treatment_protocol: Cells were transferred to non-permissive temperature (37C) to shut off transcription

tag: genotype/variation

value: rpb1-1 mutant

tag: mrna type

value: poly(A)+ mRNA

tag: time point (minutes)

tag: repeat


title: Sample_10_D

value: TCDD


title: Sample_14_D

value: mediastinal lymph node

value: infected with influenza virus


title: RNASeq_Sensitive1

city: Stanford

first: Jiang

last: Li

state: CA

address: 269 Campus Drive, Stanford University

department: Dermatology

institute: Stanford University

data_processing:
RNA-Seq reads were aligned to the human reference genome sequence (hg19) with TopHat. Expression in FPKM was calculated by cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: RPKM values. Each column represents an independent sample and each row represents a gene.

source_name: sensitive basal cell cancers

extract_protocol:
2ug of total RNA was extracted from tissue samples stored in RNA later using the RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. RNA integrity was confirmed with the Agilent 2001 bioanalyzer.
cDNA were prepared using the Ovation RNA- Seq System V2 (NuGen) per the manufacturer’s protocol. cDNA libraries were sheared by sonication (Covaris model S1) and purified using the Qiagen Minelute Kit. End repair was performed with T4 DNA Polymerase, T4 Polynucleotide Kinase, and Klenow DNA polymerase (New England Biolabs) at 20 ̊C for 30 min and purified using the Qiagen Minelute Kit. dA-tailing was performed with Klenow fragment 3’ to 5’ exonuclease (New England Biolabs) at 37 ̊C for 30 min and purified using the Qiagen Minelute Kit. Adapter ligation was performed with Illumina adapters and T4 DNA Ligase (New England Biolabs), purified with Qiagen Minelute Kit, and 150-400 basepair fragments were gel purified on a 3% GTG low melting point agarose gel. RNA-Seq libraries were PCR amplified 18 cycles with Phusion DNA polymerase (New England Biolabs), purified with Qiagen Minelute Kit, and size-selected on a 3% GTG low melting point agarose gel. RNA-Seq libraries were analyzed with the Agilent 2001 bioanalyzer and were sequenced paired-end at 100bp using an Illumina HiSeq 2500.

value: skin

value: basal cell carcinomas (BCCs)

tag: response to smoothened (smo) inhibitors

value: Sensitive


title: RNASeq_Sensitive4


title: CTCEXO

description: CTLexo

value: Treatment with normal pancreas exosomes


title: Sample_14


title: Sample_11


title: Sample_8_D


title: Sample_10


title: ToxDam_Rep2_HEK293T


title: RNASeq_Resistance6

source_name: resistant basal cell cancers

value: Resistance


title: RNASeq_Resistance5


title: Sample_8


title: RNASeq_Sensitive3


title: Sample_3


title: Sample_6


title: RNASeq_Sensitive2


title: RNASeq_Resistance9


title: RNASeq_Normal8

source_name: normal skin biopsies

value: Normal


title: RNASeq_Normal7


title: RNASeq_Resistance8


title: Sample_9_D


title: Wang_ctrl2_re-fed_RNASeq

city: Tianjin

first: Yajing

last: Chu

address: Nanjing Road 288

department: State Key Laboratory of Experimental Hematology

country: China

institute: Institute of Hematology, Chinese Academy of Medical Sciences

data_processing:
Illumina Casava1.6 software used for basecalling.
Raw reads were mapped to mm9 using Tophat v1.4.1 with default parameters.
Reads that have multiple hits on genome were filtered out using Samtools v1.4.1.
Cufflinks v2.0.2 was used to calculate Fragment Per Kilobase of transcripts per Million reads (FPKM) for each gene.
Cuffdiff v2.0.2 was used to copmare FPKM between Med23 KO and WT under fast or re-fed.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample. The columns are chromosome coordinates, gene symbols, and FPKM.

source_name: Liver from control mice under re-fed state (fasted 24 and then re-fed 24h)

extract_protocol:
RNA was extracted with Trizol reagent.
cDNA library was constructed using TruSeq RNA-Seq Sample Prep Kits (Illumina) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: genotype

value: control

tag: gender

value: male

tag: age

value: 8-week old

value: liver


title: RNASeq_Normal6


title: Wang_LMKO2_re-fed_RNASeq

source_name: Liver from LMKO mice under re-fed state (fasted 24 and then re-fed 24h)

value: liver-specific Med23-knockout


title: Sample_6_D


title: Wang_ctrl1_re-fed_RNASeq

value: re-fed state (fasted 24 and then re-fed 24h)


title: Dam_Rep1_HEK293T

tag: triggered expression

value: DAM only


title: RNASeq_Resistance7


title: RNASeq_Normal5


title: Sample_5

value: vehicle


title: RNASeq_Normal4


title: RNASeq_Resistance4


title: Sample_5_D


title: RNASeq_Normal3


title: RNASeq_Resistance3


title: RNASeq_Normal1


title: Sample_3_D


title: Wang_LMKO1_re-fed_RNASeq


title: RNASeq_Resistance2


title: Wang_ctrl2_fasted_RNASeq

source_name: Liver from control mice under fasted state (fasted 24h)

value: fasted state (fasted 24h)


title: DNASeq-BCC13-tumor

data_processing:
Sequencing reads were aligned to the human reference genome sequence (hg19) using Burrows-Wheeler Aligner (BWA). SAM to BAM conversion and marking of PCR duplicates were performed using Picard tools (version 1.86), followed by local realignment around indels and base quality score recalibration using the Genome Analysis Toolkit (GATK) (v2.3.9). Somatic SNVs and indels were called using GATK.
Genome_build: hg19

source_name: resistant BCCs

extract_protocol:
Fresh tissue samples of resistant BCCs and adjacent normal skin were obtained and stored in RNALater at -20 ̊C (Ambion). DNA was isolated using the DNeasy Blood & Tissue kit according to manufacturer’s protocols (Qiagen).
Capture libraries were constructed from 2 μg of DNA from BCC and normal skin using the Agilent SureSelect XT Human All Exon V4 kit according to manufacturer’s specifications. Enriched exome libraries were multiplexed and sequenced on the Illumina HiSeq 2500 platform.

tag: tissue/cell type

value: resistant


title: DNASeq-BCC12-tumor


title: RNASeq_Resistance1


title: In_Vitro_occupancy

city: Evanston

first: Liqun

last: Xi

state: IL

address: 2006 Sheridan Road

department: Statistics

institute: Northwestern University

data_processing:
Library strategy: BAC-seq
Reads were aligned to the mm9 with Bowtie-0.12.4, by allowing mismatch 0, 1, 2 and 3 gradually (with option -v 0, -v 1, -v 2, -v 3, step-by-step)
Reads were flitered to include only properly paired reads with alignments with unique matches to the genome
For each paired end read, the center of the read was calculated and a center-weighted nucleosome occupancy score was assigned to the bps +/- 73 bp away, using a gaussain distribution (see methods).
Occupancy scores for all reads across each bp were added to create final nucleosome maps across experimental regions.
Genome_build: mm9

source_name: Embryonic stem cell (ESC)

growth_protocol: Embryonic stem cells were collected via trypsinization with .05% trypsin, inactivated with serum-containing media, then combined for a total of ~5x107 cells.  Cells were resuspended in extraction buffer (10mM Tris, 0.1M EDTA, 0.5% SDS).  RNA was removed by incubating in 20mg/mL RNaseA at 37°C for 1 hour.  Protein was subsequently removed by incubating with 100mg/mL Proteinase K for 3 hours at 50°C.   The solution was phenol extracted four times, placed into a 3.5 kDa, 50mm dialysis tube, and dialyzed three times in 4L of dialysis buffer (50mM Tris, 10mM EDTA).  After dialysis, the solution was isopropanol precipitated, and the resulting genomic DNA was resuspended in 1x TE. Reconstitutions were assembled using a mass ratio of 30mg chicken erythrocyte-dervied histone octamer to 100mg genomic DNA in reconstitution buffer (2M NaCl, 5mM Tris, 1mM benzolamide, 0.5mM PMSF, 0.5mM EDTA) and placed inside 12-14kDa, 10mm diameter dialysis tubing.  Each reconstitution tube was then placed in a 6-8kDA 100mm dialysis bag filled with 100mL of reconstitution buffer.  This bag was then dialyzed 3 times in 4L of dialysis buffer (5mM Tris, 1mM benzolamide, 0.5mM PMSF, 0.5mM EDTA). Reconstitution mixture was suspended in MNase buffer (10mM Tris-Cl (pH 7.4), 15mM NaCl, 60mM KCl, 0.15mM spermine, 0.5mM spermidine, 1mM CaCl2) and digested with 5 Worthington Units of MNase per 10μg of genomic DNA present for 5 min at 37°C.  Digestion was stopped using 1/5 vol. 0.125M EDTA, and samples were purified via phenol/chloroform extraction and ethanol precipitation.  Samples were run on a 5% native acrylamide gel at 175V for 2 hours. DNA of 147bp was excised from the gel and purified using a crush and soak technique. ABI SOLiD library preparation was then performed (Invitrogen 4464411) to obtain adaptor-ligated in vitro DNA.

extract_protocol:
BAC clones of Oct4, Sox2, Nes, Pax6, Olig2 and Sox1 and surrounding regions were purified from the RPCI-23/24 library (Children’s Hospital Oakland Research Institute, Oakland, CA, USA). BACs were evenly combined into a total pool of 200ng and nicked to add biotin tags, using Roche’s nick translation kit (Roche 10976776001) and 40uM biotin-dUTP (Axxora ENZ-42811).  100ng of biotin-nicked BAC DNA was concentrated and resuspended with 10μg of Cot-1 DNA (Invitrogen 18440-016).  This mixture was denatured, suspended in 2x hybridization buffer (1.5 M NaCl, 40 mM sodium phosphate buffer (pH 7.2), 10 mM EDTA (pH 8), 10x Denhardt’s, 0.2% SDS), then incubated at 65°C for 6 hours.  1μg of  adaptor-ligated mononucleosome DNA was denatured, also suspended in 2x hybridization buffer, then combined with the BAC DNA mixture and incubated at 65°C for a further 70-80 hours.  The hybridization solution was bound to 100μL of streptavadin-coated beads (Invitrogen 11205D), suspended in 150μL of washing/binding buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA (pH 8) and 1 M NaCl) incubated for 30 minutes, then stringently washed with one wash of 1x SSC, 0.1% SDS buffer at room temperature, and three washes of 0.1x SSC, 0.1% SDS buffer at 65°C.  The DNA was eluted with 100μL of 0.1 M NaOH, neutralized with 100μL of 1M Tris-HCl (pH 7.5), then desalted and cleaned using two spin chromatography columns (Biorad 732-6223). Single-stranded enriched DNA was then amplified and isolated using a high-fidelity polymerase kit (NEB E0553S) according to recommended reaction conditions, and using ABI SOLiD library primers (Invitrogen 4464411). Test reactions of 25μL were cycle titrated to determine the appropriate number of rounds of amplification, then bulk reactions of 2x 50μL were amplified.  Theses products were loaded onto a 3.3% NuSieve agarose gel in TAE and excised and purified.
DNA libraries were prepared for sequencing using SOLiD 4 standard library preparation protocols

tag: cell line

value: Embryonic stem cell (ESC)


title: DNASeq-BCC10-tumor


title: TargetSeq-Untreated36

data_processing:
Reads were aligned to the human reference genome sequence (hg19) using the BWA aligner. Samtools mpileup was used to call variants. Only bases meeting the minimum base quality score of 20 from reads meeting the minimum mapping quality score of 20 were considered. A minimum allele frequency of 5% at a position with a read depth > 100 was required to make calls.
Identified variants were annotated using SeattleSeq138 to exclude non-pathogenic variants reported in dbSNP138 and to identify variants that had nonsynonymous consequences or affected splice sites.
Genome_build: hg19
Supplementary_files_format_and_content: excel file  containing all the variants from all the target resequencing

source_name: untreated basal cell cancers

extract_protocol:
5-8 10um sections were obtained from the FFPE tumor block and DNA was isolated using the Qiagen DNeasy Blood and Tissue kit according to manufacturer’s protocol (Qiagen). The exonic regions of PTCH1 and SMO were amplified using the Access Array platform (Fluidigm).
The samples were amplified in a multiplex format with genomic DNA (100 ng) according to the manufacturer's recommendation (Ambry Genetics). Subsequently, the multiplexed library pools were subjected to deep sequencing using the Illumina MiSeq platform.

value: N/A (Untreated)


title: Wang_LMKO2_fasted_RNASeq

source_name: Liver from LMKO mice under fasted state (fasted 24h)

tag: strain

tag: tissue


title: Wang_LMKO1_fasted_RNASeq


title: Wang_ctrl1_fasted_RNASeq


title: RNASeq_Normal2

value: skin


title: TargetSeq-Untreated34

description: The exonic regions of PTCH1 and SMO were amplified using the Access Array platform (Fluidigm)

value: basal cell carcinomas (BCCs)


title: DNASeq-BCC9-tumor


title: TargetSeq-Untreated32


title: TargetSeq-Untreated31


title: TargetSeq-Untreated30


title: DNASeq-BCC9-control

source_name: matched adjacent normal skin

value: normal skin


title: DNASeq-BCC5-tumor


title: TargetSeq-Untreated29


title: DNASeq-BCC14-tumor


title: DNASeq-BCC13-control


title: TargetSeq-Untreated28


title: DNASeq-BCC14-control


title: DNASeq-BCC11-control


title: DNASeq-BCC12-control


title: DNASeq-BCC11-tumor


title: DNASeq-BCC10-control


title: In_Vivo_occupancy

growth_protocol: Cells were permeablized while adherent to culture dishes with lysis buffer (10mM Tris-Cl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.5% NP-40, 0.15mM spermine, 0.5mM spermidine).  Chromatin was then digested with micrococcal nuclease (Sigma N3755) at a concentration of 1000 Worthington units of MNase per 100 mm culture plate in digestion buffer (10mM Tris-Cl (pH 7.4), 15mM NaCl, 60mM KCl, 0.15mM spermine, 0.5mM spermidine, 1mM CaCl2) for 30-60 minutes at room temperature.  Digestion was stopped with 1/10 volume stop solution (0.25M EDTA, 5% SDS).  DNA was isolated via phenol/chloroform extraction and ethanol precipitation. Mononucleosomal DNA was isolated by gel electrophoresis using 3.3% NuSieve (Lonza 50084) gel at 75 V for 5 hours.  DNA of 147 bp in length was excised from the gel and purified using a crush and soak technique followed by QIAquick PCR purification  (Qiagen 28104).  Finally, ABI SOLiD library preparation was performed according to manufacturer’s recommendations (Invitrogen 4464411), to obtain adaptor-ligated mononucleosomal DNA


title: TargetSeq-Untreated24


title: DNASeq-BCC3-tumor


title: DNASeq-BCC2_3-control


title: TargetSeq-Untreated33


title: DNASeq-BCC2-tumor


title: TargetSeq-Untreated20


title: TargetSeq-Untreated18


title: DNASeq-BCC1-tumor


title: DNASeq-BCC4_5-control


title: TargetSeq-Untreated17


title: TargetSeq-Untreated15


title: TargetSeq-Untreated27


title: TargetSeq-Untreated12


title: TargetSeq-Untreated4


title: TargetSeq-Untreated3


title: TargetSeq-Untreated1


title: TargetSeq-Resistance29


title: TargetSeq-Resistance26


title: TargetSeq-Untreated10


title: TargetSeq-Resistance25


title: TargetSeq-Untreated26


title: TargetSeq-Untreated25


title: DNASeq-BCC4-tumor


title: TargetSeq-Untreated35


title: TargetSeq-Untreated2


title: TargetSeq-Resistance22


title: TargetSeq-Resistance21


title: TargetSeq-Untreated23


title: TargetSeq-Untreated22


title: TargetSeq-Resistance20


title: TargetSeq-Resistance19


title: TargetSeq-Untreated21


title: TargetSeq-Untreated19


title: DNASeq-BCC1-control


title: TargetSeq-Untreated16


title: TargetSeq-Untreated14


title: TargetSeq-Untreated13


title: TargetSeq-Untreated11


title: TargetSeq-Untreated8


title: TargetSeq-Resistance11


title: TargetSeq-Untreated7


title: TargetSeq-Untreated6


title: TargetSeq-Resistance10


title: TargetSeq-Resistance9


title: TargetSeq-Untreated5


title: TargetSeq-Resistance8


title: TargetSeq-Resistance30


title: Dam_Dil2_Rep2_Neuro-2a

source_name: Mouse neuroblastoma cell line

tag: virus dilution used to infect cells with dam or tox-dam


title: TargetSeq-Resistance27


title: TargetSeq-Resistance28


title: Dam_Dil2_Rep1_Neuro-2a


title: TargetSeq-Resistance6


title: TargetSeq-Resistance24


title: TargetSeq-Resistance4


title: TargetSeq-Resistance23


title: TargetSeq-Resistance15


title: TargetSeq-Resistance17


title: TargetSeq-Resistance16


title: TargetSeq-Resistance18


title: TargetSeq-Resistance7


title: TargetSeq-Resistance14


title: shPtbp1-2

status: Public on Mar 15 2015

city: SAN FRANCISCO

first: John

last: Liu

state: California

address: 35 Medical Center Way

institute: UCSF

data_processing:
Reads were aligned to the mouse genome mm9, using Tophat v2.0.10 with --library-type fr-firststrand.
Differential expression was assessed using Cuffdiff v2.1.1 with -b genome.fa -u –library-type fr-firststrand.
A transcriptome index that includes all UCSC genes and the Pnky sequence was used for Tophat and Cufflinks.
Alternative splicing was analyzed using DEXSeq v1.8.0, using a FDR threshold of 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: genes.fpkm_table – cuffnorm output with normalized FPKM for each replicate sample
Supplementary_files_format_and_content: pnky_kd.diff – cuffdiff output for shPnky vs shCtrl
Supplementary_files_format_and_content: ptbp1_kd.diff  – cuffdiff output for shPtbp1 vs shCtrl
Supplementary_files_format_and_content: DEXSeq.pnky_FDR.01.txt – DEXSeq output for shPnky vs shCtrl
Supplementary_files_format_and_content: DEXSeq.ptbp1_FDR.01.txt  – DEXSeq output for shPtbp1 vs shCtrl

source_name: Cultured ventricular-subventricular zone cells

growth_protocol: Self-renewal medium (DMEM/F12 with Glutamax, 5% Fetal Bovine Serum, N2 supplement, 35 µg/mL bovine pituitary extract, 20 ng/mL EGF, 20 ng/mL FGF, antibiotic/antimycotic)

extract_protocol:
Total RNA was isolated by Trizol (Life Technologies), purified using the RNeasy Mini Kit (Qiagen) with on-column DNAse treatment.
Strand-specific, poly(A) selected cDNA libraries were generated using TruSeq Stranded mRNA kit (illumina).

treatment_protocol: All shRNA sequences were designed using the Dharmacon siDESIGN tool.  shRNA oligos were ordered from ELIM Biosystems, annealed, and ligated into the  PSICO-R vector (Ventura et al., 2004), which carries a GFP or mCherry marker. shRNA  targeting luciferase was used as a control. To establish pure cultures, GFP+ cells or  GFP+, mCherry+ double positive cells were sorted using a FACS Aria II.

tag: developmental stage

value: Derived from postnatal day 5-7

tag: background strain

tag: shRNA


title: TargetSeq-Resistance1

tag: cell type


title: ToxDam_Dil2_Rep1_Neuro-2a

value: TOX-DAM fusion protein


title: Basal, JMS8-5

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina Casava 1.8.0 (batch 1) and 1.8.2 (batches 2 and 3) software used for basecalling.
Sequenced reads were mapped using the align function in the Rsubread package (version 1.14.1, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.14.1) using the in-built mm10 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.6.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarise the values from replicates samples using functionality from the limma package (version 3.20.5, Smyth, 2005).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: CD24+CD29hi mammary stem cell-enriched basal cells

extract_protocol:
Cells were snap frozen and total RNA was isolated using the QIAGEN miRNeasy protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina TruSeq RNA sample preparation kit for batch 1, Illumina TruSeq RNA sample preparation kit v2 for batches 2 and 3 and TruSeq SR Cluster Kit v3-cBot-HS and TruSeq SBS Kit v3-HS chemistry for all samples).

tag: strain/background

value: FVB/N

tag: genotype/variation

value: wild type

value: 8 weeks

value: virgin female

value: mammary gland

tag: batch


title: LP, JMS9-P8c

source_name: CD24+CD29loCD61+ luminal progenitor-enriched mammary cells

value: CD24+CD29loCD61+ luminal progenitor-enriched cells


title: Dam_Dil10_Rep2_Neuro-2a

value: DAM only


title: TargetSeq-Resistance13

tag: response to smoothened (smo) inhibitors


title: ML, JMS8-3

source_name: CD24+CD29loCD61- mature luminal-enriched mammary cells

value: CD24+CD29loCD61- mature luminal-enriched cells


title: TargetSeq-Resistance12


title: Dam_Dil10_Rep1_Neuro-2a


title: TargetSeq-Resistance5


title: ToxDam_Dil10_Rep2_Neuro-2a


title: ML, 9_6_5_11


title: LP, 10_6_5_11


title: CommaDB, JMS9-CDBG

source_name: CommaD-beta-geo cells (Deugnier et al., 2006)

value: Balb/c

value: mid-pregnancy

value: CommaD-βGeo


title: TargetSeq-Resistance2

value: resistant


title: Chicken Abdominal fat, low growth (LG), 7 week of age, replicate 3, technical replicate 2

status: Public on Mar 14 2015

city: Newark

first: Larry

middle: Albert

last: Cogburn

state: DE

address: 531 South College Ave.

department: Animal and Food Sciences

institute: University of Delaware

data_processing:
Base-calling:  Illumina CASAVA vs 1.8.
Quality and adaptor trimming:  Btrim using 5 base moving average, min Q=15 followed by custom scripts to clip any adaptor sequences found and remove short (<40 base) reads.  Adaptor was identified using 11 bases at the 5' end of the adaptor sequence.  Data was re-paired to correct for any failed reads following quality and adaptor trimming
Alignment of reads to the genome was accomplished using TopHat/Bowtie to GalGal2.0 from Ensemble.  Versions: tophat/1.3.3 and bowtie/0.12.7 using default settings.
Quantitation and differential expression analysis was performed using Cuffdiff version 2.0.2.
Genome_build: Gallus Gallus version 2.0 from Ensemble

organism: Gallus gallus

source_name: Chicken Abdominal fat, low growth (LG)

growth_protocol: Standard broiler chicken growth protocol

extract_protocol:
Total RNA was extracted using a RNeasy Midi kit according to the manufacturer’s protocol (Qiagen; Valencia, CA). The RNA concentration was determined with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies; Wilmington, DE). RNA integrity was examined using a RNA 6000 Nano Assay kit and the Model 2100 Bioanalyzer (Agilent Technologies; Palo Alto, CA).
Paired-end sequencing libraries were made from 2 µg of total adipose RNA with the Illumina TruSeq® Stranded mRNA Sample Preparation Kit following standard Illumina protocols. Individual RNA samples were indexed (bar-coded) after the fragmentation step to enable multiplexing of libraries within sequencing lanes.
Bar-coded libraries were pooled and sequenced using an Illumina HiSeq 2000 Sequencing System (http://www.illumina.com/systems/hiseq_2000.ilmn, Illumina, InC., San Diego, CA) at Delaware Biotechnology Institute, University of Delaware. All 8 libraries (4 HG and 4 LG) were multiplexed together and sequenced in two replicate lanes.

treatment_protocol: Divergently selected on body weight (HG genotype).

tag: line

value: HG cockerel

value: 7 weeks

value: Abdominal adipose


title: Chicken Abdominal fat, low growth (LG), 7 week of age, replicate 1, technical replicate 2


title: TargetSeq-Resistance3

source_name: resistant basal cell cancers

value: basal cell carcinomas (BCCs)


title: ToxDam_Dil10_Rep1_Neuro-2a

value: TOX-DAM fusion protein


title: ML, JMS9-P7c

value: FVB/N

tag: gender


title: shPnky-2

value: Derived from postnatal day 5-7

value: shPnky


title: shPtbp1-1


title: Chicken Abdominal fat, high growth (HG), 7 week of age, replicate 2, technical replicate 2

source_name: Chicken Abdominal fat, high growth (HG)

tag: age


title: Chicken Abdominal fat, low growth (LG), 7 week of age, replicate 3, technical replicate 1


title: Chicken Abdominal fat, high growth (HG), 7 week of age, replicate 1, technical replicate 2


title: Basal, purep53

value: wild type

value: 8 weeks

value: virgin female

value: CD24+CD29hi mammary stem cell-enriched basal cells


title: Mammosphere, mo906111-1_m09611-2

source_name: CD24+CD29hi MaSC/Basal cell-derived mammosphere cells

value: mammary gland

value: cultured CD24+CD29hi basal cell-derived mammosphere cells


title: LP, JMS8-4

value: CD24+CD29loCD61+ luminal progenitor-enriched cells


title: Chicken Abdominal fat, high growth (HG), 7 week of age, replicate 4, technical replicate 1


title: shPnky-1


title: Chicken Abdominal fat, low growth (LG), 7 week of age, replicate 4, technical replicate 2


title: Chicken Abdominal fat, high growth (HG), 7 week of age, replicate 3, technical replicate 1


title: Basal, JMS8-2


title: Chicken Abdominal fat, high growth (HG), 7 week of age, replicate 2, technical replicate 1


title: shCtrl-2

value: shCtrl


title: shCtrl-1


title: Chicken Abdominal fat, low growth (LG), 7 week of age, replicate 2, technical replicate 1


title: Chicken Abdominal fat, low growth (LG), 7 week of age, replicate 2, technical replicate 2


title: Chicken Abdominal fat, high growth (HG), 7 week of age, replicate 4, technical replicate 2


title: R2D_100_mRNA

status: Public on Mar 13 2015

description: degraded sample

data_processing:
Instrument control: HiSeq control software v 2.2.38
Base calling and quality scoring: Real-Time Analysis v1.18.61
FASTQ file generation and de-multiplexing: CASAVA pipeline version 1.8.2
Sequenced reads were mapped using the align function in the Rsubread package (version 1.16.1, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.16.1) using the in-built hg19 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarise the values from replicates samples using functionality from the limma package (version 3.22.0, Smyth, 2005).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Human lung cancer cell lines NCI-H1975 and HCC827

extract_protocol:
Total RNA was extracted from between half a million and million cells using Total RNA Purification Kit (Norgen Biotek) with on-column DNAse treatment according to the kit instructions. RNA concentration for each pair of samples to be mixed was equalised to ~100 ng/μl using Qubit RNA BR Assay Kit (Life Technologies). Replicates were pooled in known proportions to obtain mixtures ranging from pure NCI-H1975 (100:0) to pure HCC827 (0:100) and intermediate mixtures ranging from 75:25 to 50:50 to 25:75  NCI-H1975:HCC827. All mixtured corresponding to the second replicate were split into two equal aliquots. One aliquot was left intact (we refer to this as the 'good' replicate), while the second aliquot was degraded to produce known outlier samples by incubation at 37 degrees C for 7 days in a thermal cycler with a heated lid.
10 μl from each replicated mixture (both good and degraded) were used for Next Generation Sequencing library preparation using two kits: Illumina TruSeq Total Stranded RNA with Ribozero (TotalRNA) and Illumina TruSeq RNA v2 (mRNA) according to manufacturer's instructions. Completed libraries were sequenced on HiSeq 2500 with TruSeq SBS Kit v4- HS reagents (Illumina) as 100 bp single-end reads at the Australian Genome Research Facility (AGRF), Melbourne. Approximately 30 million 100 bp single-end reads were obtained for each sample. Reads were aligned to the human reference genome hg19 and mapped to known genomic features at the gene level using the Rsubread package (version 1.16.1) (Liao et al. 2013). Single reads were then summarized into gene-level counts using FeatureCounts (Liao et al. 2014).

tag: mixture cell line nci-h1975

tag: mixture cell line hcc827

tag: replicate


title: Chicken Abdominal fat, high growth (HG), 7 week of age, replicate 3, technical replicate 2


title: R2_050_mRNA

description: good quality sample

tag: cell line

value: Human lung cancer cell lines NCI-H1975 and HCC827

tag: strain


title: R2_025_mRNA

description: good quality sample


title: Chicken Abdominal fat, low growth (LG), 7 week of age, replicate 1, technical replicate 1

value: HG cockerel

tag: tissue


title: R2_100_mRNA

description: good quality sample


title: Chicken Abdominal fat, low growth (LG), 7 week of age, replicate 4, technical replicate 1

value: 7 weeks


title: R1_100_mRNA

description: good quality sample


title: Chicken Abdominal fat, high growth (HG), 7 week of age, replicate 1, technical replicate 1

value: Abdominal adipose


title: R1_025_mRNA

description: good quality sample


title: R3_100_mRNA

description: good quality sample


title: R1_075_mRNA

description: good quality sample


title: R3_025_mRNA

description: good quality sample


title: R3_000_mRNA

description: good quality sample


title: R2D_075_mRNA

description: degraded sample


title: R2D_050_mRNA

description: degraded sample


title: R2D_025_mRNA

description: degraded sample


title: R2D_000_mRNA

description: degraded sample


title: R2_075_mRNA

description: good quality sample


title: R2_000_mRNA

description: good quality sample


title: R1_050_mRNA

description: good quality sample


title: R3_025_TotalRNA

description: good quality sample


title: R1_000_mRNA

description: good quality sample


title: R1AD1_input

city: Minneapolis

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

institute: Masonic Cancer Center, University of Minnesota

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using BWA for Illumina (version 1.2.3)
SAMtools was used to remove duplicate and non-uniquely mapped reads (MAPQ score cutoff 15)
Peaks were called with data from biological replicate 1 using MACS or CisGenome using default parameters, with a p-value cutoff 1.00E-05 and input DNA as negative control
Consensus peaks were determined by including only regions identified by both peak callers (MACS and CisGenome)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated from wig files in Galaxy.  wig files were generated from mapped read data using MACS

source_name: prostate cancer cell line

growth_protocol: R1-AD1 or R1-D567 cells were plated 5× 106 cells into a 10 cm disc in RMPI 1640 supplemented with 10% charcoal stripped FBS for 72hrs

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed for three independent biological replicate experiments exactly as described (PMID: 21602788) with the exception fo the following modifications:  R1-AD1 and R1-D567 cells (PMID 24101480) were seeded at 5x10^6 cells/plate on 10 cm plates in RMPI 1640 + 10% CSS, allowed to settle for 72h, then re-fed for 4h with RMPI 1640 + 5% CSS containing vehicle (ETH) or 1nM DHT prior to fixation.  Nuclear pellets were sonicated on ice for 8 cycles at 40% amplitude using a 450 Sonifer (Branson).  Each cycle consisted of 10 sec pulse/10 sec rests for 1 min, with 2 min rests between cycles.  Lysates were immunoprecipitated with Protein A/G Plus agarose beads (Santa Cruz Biotechnology) pre-blocked with tRNA (Sigma).  DNA was purified using a PCR purification kit (Qiagen).  For ChIP-seq, 2-10ng of DNA (ChIP-enriched or input) was used for library creation with a TruSeq ChIP Sample Preparation Kit (Illumina cat #IP-202-1012) and sequenced at the Univeristy of Minnesota Genomics Center using an Illumina HiSeq2000 at 1X50bp.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Sample Preparation Kit (Illumina cat#IP-202-1012).

treatment_protocol: R1-AD1 or R1-D567 cells were treated with Vehicle (Ethanol) or 1nM DHT for 4hrs in RMPI 1640 + 5% CSS

tag: agent

value: Ethanol (vehicle control)

tag: chip antibody

value: none (input)

tag: biological replicate number


title: R1D567_Eth_ARv567es_rep3

tag: cell type

value: AR -N20 (Santa Cruz, SC-816 lot B1012)


title: R2D_075_TotalRNA

description: degraded sample


title: R1D567_Eth_ARv567es_rep2


title: R3_100_TotalRNA

description: good quality sample


title: R3_075_mRNA

description: good quality sample


title: R2D_050_TotalRNA

description: degraded sample


title: R1AD1_DHT_AR_rep3

value: dihydrotestosterone, 1nM


title: R3_050_mRNA

description: good quality sample


title: R1AD1_DHT_AR_rep1


title: R3_075_TotalRNA

description: good quality sample


title: R2D_025_TotalRNA

description: degraded sample


title: R1D567_input


title: R1AD1_Eth_AR_rep3


title: R3_050_TotalRNA

description: good quality sample


title: R3_000_TotalRNA

description: good quality sample


title: R2_050_TotalRNA

description: good quality sample


title: R2D_100_TotalRNA

description: degraded sample


title: R2_075_TotalRNA

description: good quality sample


title: R1D567_Eth_ARv567es_rep1


title: HPC5 Input tech rep 2 bio rep 2

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

description:
technical replicate 2 of biological replicate 2
hpc5_CHIRP_con01_control_lambda.bw
library strategy: ChiRP-seq

data_processing:
Reads were mapped with Bowtie2. Uniquely mapped reads were used for peak calling by Macs2. Post-processing steps are described.
ChIRP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.0.6 with 1 mismatch in seed allowed, command=bowtie2 -p12 -k 2 -N 1. Peak calling was performed on uniquely aligned reads (lacking bowtie2 flag XS:i) with Macs2 version 2.0.10.20131216, command=macs2 callpeak -f BAMPE -g mm -m 2 50 --verbose 3 --bdg --SPMR -t treatment.bam -c control.bam , where treatment is RNA bound chromatin DNA and control is input DNA. Post-processing of peak data consisted of three steps. (1) Find concordant regions: Identify all possible regions of overlap among significant peaks called in the four LncHSC-2 and control LacZ experiments. (2) Remove non-specific regions: Exclude regions covered by LacZ peaks and regions not covered by concordant peaks in the two split-probe experiments. Require remaining regions to be covered by peaks in at least one of the two complete probe set experiments. (3) Select consensus peaks: Merge any overlapping regions, select the first intersecting peak from one of the two complete probe set experiments. Exclude the consensus peak if it has any overlap with LacZ peaks.
Genome_build: mm9
Supplementary_files_format_and_content: The narrowPeak are BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. Definition of some specific columns are: 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start. The bigWig files were created from the Macs2 bedgraph files, representing signal density of fragment pileup as signal per million reads More information may be found in the Macs2 documentation.

source_name: HPC5 cells

extract_protocol:
Cross-linked cells were lysed and sonicated to 200-500 bp fragments via bioruptor.
Chromatin fragments were incubated with the indicated biotinylated oligonucleotide probes and enriched material was selected by streptavidin magnet beads. Libraries were constructed using ThruPLEX-FD preparation kit  (Rubicon, Ann Arbor, MI)

treatment_protocol: 10 million cells were cross-linked with 1% gluteraldehyde at room temperature for 10 minutes and quenched with 0.125 M glycine for 5 minutes.

value: Bone marrow derived hematopoietic progenitor cell line

value: C57BL/6-cast (B6-cast)


title: R1AD1_DHT_AR_rep2


title: R2_000_TotalRNA

description: good quality sample


title: R2_100_TotalRNA

description: good quality sample


title: HPC5 Input tech rep 1 bio rep 2

description:
technical replicate 1 of biological replicate 2
hpc5_CHIRP_con01_control_lambda.bw
library strategy: ChiRP-seq


title: R1AD1_Eth_AR_rep2


title: R1AD1_Eth_AR_rep1


title: R1_025_TotalRNA

description: good quality sample


title: LncHSC-2 IP odd probe set tech rep 2 bio rep 1

description:
technical replicate 2 of biological replicate 1
final.consensus.narrowpeak.bed
hpc5_CHIRP_IP03_treat_pileup.bw
library strategy: ChiRP-seq

tag: 3'-biotin labeled oligo probe set


title: LncHSC-2 IP even probe set tech rep 1 bio rep 1

description:
technical replicate 1 of biological replicate 1
final.consensus.narrowpeak.bed
hpc5_CHIRP_IP04_treat_pileup.bw
library strategy: ChiRP-seq


title: LncHSC-2 IP even probe set tech rep 2 bio rep 1

description:
technical replicate 2 of biological replicate 1
final.consensus.narrowpeak.bed
hpc5_CHIRP_IP04_treat_pileup.bw
library strategy: ChiRP-seq


title: R2_025_TotalRNA

description: good quality sample


title: R1_100_TotalRNA

description: good quality sample


title: R1_075_TotalRNA

description: good quality sample


title: LacZ control probe set tech rep 2 bio rep 1

description:
technical replicate 2 of biological replicate 1
hpc5_CHIRP_con01_peaks.narrowPeak.bed
hpc5_CHIRP_con01_treat_pileup.bw
library strategy: ChiRP-seq

value: LacZ control IP (1 - 6)


title: R1_050_TotalRNA

description: good quality sample


title: R2D_000_TotalRNA

description: degraded sample


title: LncHSC-2 complete probe set IP bio rep 2

description:
technical replicate of biological replicate 2
final.consensus.narrowpeak.bed
CHIRP_IP02_run04_treat_pileup.bw
library strategy: ChiRP-seq

value: LncHSC-2 complete (1 - 12)


title: Glut2L-STZ

city: Montreal

first: Hamed

middle: S

last: Najafabadi

state: QC

address: 740 Dr. Penfield Avenue, Room 7202

department: Human Genetics

country: Canada

institute: McGill University

description: Insulin-positive Glut2-low cells from STZ-injected mice

data_processing:
Reads were mapped to the GRCm38 assembly of the mouse genome (mm10), using TopHat2, guided by gene annotations from Ensembl. Duplicate reads, which are often artifacts of PCR amplification during library preparation, were then removed using SAMtools, and gene differential expression between samples was quantified using Cuffdiff, based on Ensembl gene annotations and with fragment bias correction.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text files containing FPKM in each sample.

source_name: pancreatic islet cells

extract_protocol:
Total RNA was extracted using Norgen RNA extaction columns.
RNA libraries were prepared using TruSeq Stranded Total RNA-LT (with Ribo-Zero Gold, Illumina), according to manufacturer instructions.

treatment_protocol: STZ was dissolved in citrate buffer and injected (i.p.) to experiment group (200mg/kg). Diabetes was established 4 days later.

value: MIP-GFP C57BL/6

tag: Sex

value: male

value: 6-8 week

tag: cell population

value: Insulin-positive Glut2-low


title: LncHSC-2 IP odd probe set tech rep 1 bio rep 1

description:
technical replicate 1 of biological replicate 1
final.consensus.narrowpeak.bed
hpc5_CHIRP_IP03_treat_pileup.bw
library strategy: ChiRP-seq


title: Glut2H-Ctrl

description: Insulin-positive Glut2-high cells from vehicle-injected control mice

value: Insulin-positive Glut2-high


title: Smchd1 null replicate 2

data_processing:
Instrument control: HiSeq control software v2.0.12.0
Base calling and quality scoring: Real-Time Analysis v1.17.21.3
FASTQ file generation and de-multiplexing: CASAVA pipeline version 1.8.2
Sequenced reads were mapped using the align function in the Rsubread package (version 1.10.5, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.10.5) using the in-built mm10 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarise the values from replicates samples using functionality from the limma package (version 3.22.0, Smyth, 2005).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Lymphoma cell line

extract_protocol:
Cells were harvested, washed in 1X PBS and total RNA was isolated using the QIAGEN Rneasy Minikit as per manufacturer's instructions.
RNA libraries were prepared for sequencing from 1µg total RNA using standard Illumina protocols (TruSeq RNA Sample Preparation Kit v2, and TruSeq SR Cluster Kit v3-cBot-HS and TruSeq SBS Kit v3-HS chemistry for all samples).

value: Lymphoma cell line

value: Eµ-Myc end stage lymphoma

tag: genotype

value: Smchd1 gene trap homozygote (Smchd1 null), Eµ-Myc transgenic male

tag: batch

tag: sequencing protocol

value: paired-end


title: Wild-type replicate1

value: Smchd1 Wild-type, Eµ-Myc transgenic male

value: single-end


title: R1_000_TotalRNA

description: good quality sample

value: Human lung cancer cell lines NCI-H1975 and HCC827


title: LacZ control probe set tech rep 1 bio rep 1

description:
technical replicate 1 of biological replicate 1
hpc5_CHIRP_con01_peaks.narrowPeak.bed
hpc5_CHIRP_con01_treat_pileup.bw
library strategy: ChiRP-seq


title: T/AR-3

city: Columbus

first: Ching-Shih

last: Chen

state: Ohio

address: 500 W 12th Ave

department: Internal Medicine and Urology

institute: The Ohio State University

description:
RCSCAR6
Tumor-bearing, AR-42 treated mouse

data_processing:
Align with TopHat 2 (v2.0.7)
Assembly  and generation of FPKM values with CuffLinks 2 (c2.1.1)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab delimited table of FPKM based expression values for each sample

source_name: Gastrocnemius muscle

extract_protocol:
Total RNA was harvested using Trizol reagent and then purified using the RNAeasy Mini Kit (Qiagen).
Non-stranded RNA libraries were prepared using the Illumina TruSeq RNA sample prep kit version 2. Catalog Number: RS-122-2001

treatment_protocol: Mice were treated with either AR-42 (50 mg/kg, p.o. by gavage, every other day) or vehicle (0.5% methylcellulose and 0.1% Tween-80 in sterile water) starting 6 days after tumor cell injection.  Skeletal muscles (hind limb) were harvested at terminal sacrifice on day-15 after tumor cell injection, snap-frozen in liquid nitrogen, and stored at -80 degrees F until analysis.

value: muscle


title: Glut2H-STZ

description: Insulin-positive Glut2-high cells from STZ-injected mice

tag: age


title: cultured satellite cells PRMT5 KO Rep 2

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

data_processing:
trimming with Reaper version 13-100: -clean-length 40 -qqq-check 53/10 -trim-length 150
mapping to mm10 by STAR 2.4.0a: --outFilterMismatchNoverLmax 0.1 --chimSegmentMin 18 --chimScoreMin 12
differential expression by DESeq2 version 1.62
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tab-delimited text file produced by DESeq2 bearing differential expression analyses results

source_name: cultured satellite cells

extract_protocol:
miRNeasy micro Kit (Qiagen); DNase-Free DNase Set (Qiagen);RiboMinus Eukaryote System v2 (Life Technologies);
Ion Total RNA-Seq Kit v2 (Life Technologies)

value: Pax7CreERT2/Prmt5loxP/loxP (+TAM)

value: limb and trunk muscles

value: satellite cells

value: adult

value: PRMT5 KO

tag: background strain


title: T/AR-2

description:
RCSCAR5
Tumor-bearing, AR-42 treated mouse


title: Glut2L-Ctrl

description: Insulin-positive Glut2-low cells from vehicle-injected control mice

value: MIP-GFP C57BL/6

value: male


title: HPC5 Input bio rep 1

description:
technical replicate of biological replicate 1
CHIRP_IP01_run04_control_lambda.bw
library strategy: ChiRP-seq

value: Bone marrow derived hematopoietic progenitor cell line

value: C57BL/6-cast (B6-cast)


title: T/AR-1

description:
RCSCAR4
Tumor-bearing, AR-42 treated mouse


title: cultured satellite cells WT Rep 1

value: Pax7CreERT2/Prmt5+/loxP  (+TAM)

value: wild type


title: Wild-type replicate 3

value: Lymphoma cell line

value: Eµ-Myc end stage lymphoma


title: Smchd1 null replicate 4

value: Smchd1 gene trap homozygote (Smchd1 null), Eµ-Myc transgenic male

value: paired-end


title: T/Veh-3

description:
RCSCV06
Tumor-bearing, Vehicle treated mouse


title: Wild-type replicate 2

value: Smchd1 Wild-type, Eµ-Myc transgenic male


title: LncHSC-2 complete probe set IP bio rep 1

description:
technical replicate of biological replicate 1
final.consensus.narrowpeak.bed
CHIRP_IP01_run04_treat_pileup.bw
library strategy: ChiRP-seq

value: LncHSC-2 complete (1 - 12)


title: T/Veh-2

description:
RCSCV04
Tumor-bearing, Vehicle treated mouse

value: muscle


title: Smchd1 null replicate 1


title: cultured satellite cells PRMT5 KO Rep 1

value: Pax7CreERT2/Prmt5loxP/loxP (+TAM)

value: limb and trunk muscles


title: cultured satellite cells WT Rep 2

value: satellite cells

value: adult


title: TF/AR-2

description:
RCSCA03
Tumor-free, AR-42 treated mouse


title: T7_2h 2

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description:
new H3 at 2h
T7_2h.wig

data_processing:
Read alignment using Bowtie 2 (default parameters)
SAM files loaded into Podbat 0.6.0 (www.podbat.org) with options "first base only", "resolution"=10, "strand-specific" unchecked, MAPQ>30
Normalized to total  # reads and (for T7) additionally input amount.
Exported to wig.
Genome_build: ASM294v2
Supplementary_files_format_and_content: wig format, variable step

organism: Schizosaccharomyces pombe

source_name: new H3 at 2h

growth_protocol: Liquid cultures were grown in YES media shaking at 180 rpm at 25°C.

extract_protocol:
Immunoprecipitation was done using indicated antibody from chromatin extracts prepared from mid-logarithmic phase cells. Briefly, cells were fixed in 1% formaldehyde for 30 minutes, quenched with 125 mM glycine, and washed twice in PBS. Cells were resuspended in lysis buffer (0.1% SDS, 50 mM Hepes-KOH, 1 % Triton X-100, 0.1 % sodium deoxucholate, 1 mM EDTA and 150 mM NaCl) and lysed with glass beads in a FastPrep homogenizer. The lysate was sonicated and soluble chromatin fragments with an average size of 300 bp were collected. Chromatin was immunoprecipitated with indicated antibody and protein A magnetic beads overnight. The beads were washed.
With the immunoprecipitate still on the beads, the DNA was polished, A-tailed, and ligated to an Illumina sequencing library adaptor. Digestion lambda exonuclease (final concentration 2.5U/reaction) removed nucleotides from 5′ ends of double-stranded DNA until blocked by the formaldehyde induced protein-DNA crosslink. The crosslinks were reversed (4h at 65°C) and DNA was eluted from the beads. The single-stranded DNA was subsequently made double-stranded by primer annealing and extension. A second sequencing adaptor was ligated. Using indexing primers, the fragments were PCR amplified and gel purified (Qiagen MinElute). Samples were quantified on using Qubit (HS dsDNA).

value: H3.2-lox-HA-hygR-Lox-T7, cdc25-22 (ts)

value: T7 (EMD chemicals 69522, lot D00137263

tag: treatment

value: 36°C (5h) + estradiol (2h)


title: TF/Veh-3

description:
RCSCC04
Tumor-free, Vehicle treated mouse


title: TF/AR-3

description:
RCSCA05
Tumor-free, AR-42 treated mouse


title: HA_2h 1

description:
old H3 at 2h
HA_2h.wig

source_name: old H3 at 2h

value: HA (abcam ab9110, lot GR98618-1)


title: HA_0h 2

description:
old H3 at 0h
HA_0h.wig

source_name: old H3 at 0h


title: TF/Veh-2

description:
RCSCC03
Tumor-free, Vehicle treated mouse


title: T7_0h 2

description:
new H3 at 0h
T7_0h.wig

source_name: new H3 at 0h


title: Homozygous brain sample 3

status: Public on Mar 12 2015

first: Charis

last: Eng

address: 9500 Euclid Ave., NE-50

department: Genomic Medicine Institute

institute: Cleveland Clinic

data_processing:
Sequencing reads were aligned to the mouse mm10 reference genome using Tophat (versions 2.0.8-2.0.11)/Bowtie (versions 2.0.2-2.2.0) using the default parameters
Aligned reads were assembled into RNA transcripts using the Cufflinks package (versions 2.0.2-2.2.0) using the default parameters
Differential expression was calculated using CuffDiff 2 (within Cufflinks), using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: gene_exp.diff file from Cufflinks output, contains the FPKM values for each gene, as well as differential expression information. FPKM_values_by_replicate.csv contains the individual FPKM values for each gene for each of the 18 samples individually

source_name: Homozygous brain

extract_protocol:
Flash frozen tissues were homogenized in 1ml Trizol (Life Technologies) using 5mm stainless steel beads for 2 minutes at 25 Hz with a TissueLyserII (Qiagen). Total RNA was isolated using Trizol according to the manufacturer’s protocol. Ambion PureLink RNA Mini Kit (Life Technologies) was utilized for RNA Clean-Up and DNase. In short, 15ug total RNA mixed with lysis buffer:ethanol (1:3) was applied to the column and rinsed with Wash Buffer II (70% ethanol). DNA was digested on column for 15 minutes with PureLink DNase (Life Technologies) and RNA was rinsed twice with Wash Buffer II (70% ethanol).
Sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA with Ribo Zero kit (Illumina).
The libraries were multiplexed three to a lane, grouped in biological triplicates. 100 base pair, paired-end sequencing was performed using the Illumina HiSeq platform.

tag: strain background

value: CD-1 (outbred)

tag: genotype/variation

value: Pten m3m4/m3m4

value: 2-weeks old at sacrifice

value: Hemibrain


title: Homozygous brain sample 1


title: TF/Veh-1

description:
RCSCC02
Tumor-free, Vehicle treated mouse

tag: strain


title: HA_2h 2

description:
old H3 at 2h
HA_2h.wig


title: Heterozygous brain sample 2

source_name: Heterozygous brain

value: Pten wt/m3m4

tag: tissue


title: Heterozygous cortex sample 1

source_name: Heterozygous cortex

value: 6-weeks old at sacrifice

value: Microdissected cortex


title: Heterozygous brain sample 3


title: Wild-type brain sample 2

source_name: Wild-type brain

value: Pten wt/wt


title: Wild-type brain sample 1


title: TF/AR-1

description:
RCSCA01
Tumor-free, AR-42 treated mouse

value: muscle


title: T7_0h 1

description:
new H3 at 0h
T7_0h.wig


title: Heterozygous cortex sample 3


title: T/Veh-1

description:
RCSCV02
Tumor-bearing, Vehicle treated mouse


title: T7_2h 1

description:
new H3 at 2h
T7_2h.wig


title: INPUT_MeCP2_ChIP_Cerebellum1

city: brookline

first: Harrison

middle: Wren

last: Gabel

state: Massachusetts

address: 220 longwood avenue

department: Neurbiology

institute: Harvard Medical School

data_processing:
Base calling was performed using CASAVA software.
Illumina raw reads in .fastq files were aligned to mouse mm9 reference genome with bwa 0.6.2. Uniquely mapped reads  were extended in silico to reflect average fragment size  of the input DNA(~250bp).
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of unnormalized histograms for mapped, in silico extended reads

source_name: Cerebellum

growth_protocol: Brain tissue was taken from wild-type mice maintained under standard housing conditions.

extract_protocol:
ChIP was performed as described in Cohen et al. Neuron 2012, Ebert et al Nature 2013
Single-end short read sequencing libraires were prepared using standard protocols, following the manufacturers instructions. 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: wild type

value: 8 weeks


title: Smchd1 null replicate 3

value: Lymphoma cell line

value: Eµ-Myc end stage lymphoma

value: Smchd1 gene trap homozygote (Smchd1 null), Eµ-Myc transgenic male

value: paired-end


title: Homozygous brain sample 2


title: HA_0h 1

description:
old H3 at 0h
HA_0h.wig

value: H3.2-lox-HA-hygR-Lox-T7, cdc25-22 (ts)


title: INPUT_MeCP2_ChIP_Forebrain1

source_name: Forebrain


title: Heterozygous brain sample 1


title: INPUT_MeCP2_ChIP_Cerebellum2


title: Wild-type brain sample 3


title: Homozygous cortex sample 3

description: Animal was 6-weeks old at sacrifice

data_processing:
Sequencing reads were aligned to the mouse mm10 reference genome using Tophat (versions 2.0.8-2.0.11)/Bowtie (versions 2.0.2-2.2.0) using the default parameters
Aligned reads were assembled into RNA transcripts using the Cufflinks package (versions 2.0.2-2.2.0) using the default parameters
Differential expression was calculated using CuffDiff 2 (within Cufflinks), using default parameters
Genome_build: mm10
Supplementary_files_format_and_content: gene_exp.diff file from Cufflinks output, contains the FPKM values for each gene, as well as differential expression information.
FPKM_values_by_replicate.csv contains the individual FPKM values for each gene for each of the 18 samples individually

source_name: Ptenm3m4/m3m4 mice


title: Homozygous cortex sample 1

description: Animal was 6-weeks old at sacrifice


title: Cortex_BS-seq

description: 4 replicates

data_processing:
Reads were mapped to the mm9 genome using BS seeker, allowing up to four mismatches. Duplicate reads were removed and only uniquely mapping reads were kept.
Genome_build: mm9
Supplementary_files_format_and_content: text file containing processed data for bisulfite sequencing. One file for CG dinucleotides, one for CH dinucleotides. Each file summarizes information for the pooled data from 4 replicates for each brain regions. Each line indicates a cytosine in the genome with the following information listed for each column: Chromosome, Base on the plus strand (G or C), nucleotide position, Di or Trinucleotide context (CG, CHH or CHG), specific dinucleotide (CG, CA,CC,CT), fraction of reads non-converted base-calls at this position , number of reads non-converted bases at this position (# of C basecalls), total number of reads for the base at this position (# of C and T base-calls).

source_name: Cortex

extract_protocol:
Genomic DNA was isolated from each brain region for wild-type, dnmt3a flx/flx, or dnmt3a flx/flx Nestin-cre mice at the indicated ages. For bisulfite treatment, 25-100 ng of genomic DNA 0.25-1 ng of unmethylated lambda DNA was added and libraries were generated using the Ovation Ultralow Methyl-Seq Library System (Nugen). Bisulfite treatment was performed using the EpiTect bisulfite conversion kit (Qiagen) following manufacturer’s instructions.
Libraries were constructed using TruSeq reagents (Illumina) and sequenced on the Hiseq 2000 (Illumina).

tag: background


title: Cerebellum_BS-seq

description: 4 replicates


title: MeCP2IP_MeCP2_ChIP_Cerebellum2

tag: chip antibody

value: Total MeCP2 antibody (Chen et al. 2003)


title: Bl6_mESC_C2cells_2i_4OHT_RNA-seq_rep2

city: Boston

first: Karen

last: Adelman

state: MA

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

data_processing:
GRO-seq: GRO-seq reads were trimmed for quality and adapter sequence using cutadapt 1.2.1 , discarding pairs where either mate was trimmed shorter than 15 nt (-m 15 -q 10 --match-read-wildcards).  Read pairs originating from rRNA were filtered by aligning against an index consisting of the 45S and 5S transcripts using Bowtie 0.12.8, allowing two mismatches (-m1 -v2 -X1000 --un --max).  Unmapped pairs were subsequently aligned to the mm9 index, allowing two mismatches and retaining only uniquely aligned pairs (-m1 -v2 -X1000).  BedGraph files were generated from the combined alignments of all technical and biological replicates, reduced to their strand-specific 5’-end mapping locations (N=59,099,712 reads: individual samples had mappable read depths of 33,123,684 for Library#1, and 25,976,028 for Library #2. Agreement between replicates was strong (R2=0.96, fig. S1A), thus the data was combined for further analysis.
RNA-seq: Read pairs were filtered, requiring a mean quality score greater than or equal to 20, for both mates, then aligned to the mm9 reference genome using TopHat 2.0.4, reporting up to 10 alignments per read pair (-g 10).  Mean fragment sizes and standard deviations were determined using Picard Tools 1.86 CollectInsertSizeMetrics, based on a bowtie 0.12.8 alignment (-m1 -v2 -X10000) of a subset of one million reads to an index of RefSeq transcripts, and passed to TopHat using the --mate-inner-dist and --mate-std-dev parameters.  A total of 113,817,860 and 108,809,117 read pairs were successfully aligned for the Control and 4OHT/NELF-B KO samples, respectively. UCSC Browser tracks displaying read coverage normalized per million mappable fragments were generated from the combined replicates per condition.
Genome_build: mm9
Supplementary_files_format_and_content: GRO-seq: BedGraph files were generated from the combined alignments of all technical and biological replicates, reduced to their strand-specific 5’-end mapping locations
Supplementary_files_format_and_content: RNA-seq: bigWig tracks displaying read coverage normalized per million mappable fragments were generated from the combined replicates per condition.

source_name: embryonic stem cell

growth_protocol: All ESC culture was conducted at 37°C in 5% CO2.  NELF-BFl/Fl, CreER+/- ESCs were maintained without feeders in 2i media (knockout DMEM (KO-DMEM), 15% knockout serum replacement (KOSR, Invitrogen), 1 mM NaPyruvate (Millipore), 1% NEAA, 1% BME, 1% Pen/Strep, 1% Glutamax, 1000 U/ml ESGRO, 1 µM MEK inhibitor (PD0325901, Stemgent), and 3 µM GSK3 inhibitor (CHIR99021, Stemgent)) and passaged every 2 days.

extract_protocol:
GRO-seq: GRO-seq experiments were performed according to {Core, 2008 #1330} in the C2 ESC line grown in 2i media, with the following modifications: Nuclei were harvested by swelling trypsinized cells for 10 minutes in 50 mL cold lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM CaCl2, 2 mM MgCl2, 0.5% NP40, 5 mM DTT, 300 mM sucrose, 1 mM PMSF, 2 U/ml Superase IN, 5 tablets Roche protease inhibitors), then gently dounce homogenized, centrifuged and washed once with 50 mL lysis buffer.  Nuclei were resuspended in freezing buffer as in {Core, 2008 #1330} at the concentration of 5x106 nuclei per 100 uL, and stored at -80°C until use.     To avoid a bias against representation of C-rich regions in the data set, the final concentration of CTP (Roche) was increased in the run-on ten-fold above that used in {Core, 2008 #1330} to 10 uM. To permit a quick, reproducible stop to the run-on reaction, the reaction was terminated after 5 minutes by the addition of Trizol (Invitrogen). RNA-seq: Two distinct conditional NELF-B KO ESC clones were grown +/- 4OHT in 2i media. On day 5 after initiating recombination, total RNA was prepared using Trizol (Invitrogen) and manufacturer recommended methods. DNA contamination was removed using the RNeasy Mini Kit (Qiagen) per manufacturer’s instructions, and RNA quality was assessed using a Bioanalyser Nano ChIP (Agilent).
GRO-seq: Following base hydrolysis, primary Br-U immunoprecipitation and end repair, the libraries were made using the Illumina small RNA TruSeq kit except the 3’ adapter was ligated using T4 RNA Ligase II, truncated KQ enzyme (NEB).  A secondary BrU IP was performed before ligation of the 5’ adapter (Illumina) followed by a tertiary BrU IP to produce triple-selected run-on RNA.  RNA was reverse transcribed and amplified with 15 cycles of PCR (Illumina).  Libraries were PAGE purified, selecting for products larger than 140 bp. RNA-seq: Ribosomal RNA was removed prior to library construction by hybridizing to ribo-depletion beads that contain biotinylated capture probes (Ribo-Zero, Epicentre). RNA was then fragmented and libraries were prepared according to the TruSeq Stranded Total RNA Gold Kit (Illumina) using random hexamer priming. Illumina Spike-ins were used for normalization.

treatment_protocol: To activate Cre recombinase and recombine out the floxed NELF-B allele, NELF-BFl/Fl, CreER+/- ESCs were treated with 100 nM 4OHT (Sigma) for 4 days (unless otherwise indicated).  ESCs were then grown in 2i media without 4OHT for the completion of the experiment.

value: embryonic stem cell


title: Wild-type cortex sample 2

description: Animal was 6-weeks old at sacrifice

source_name: Wild-type CD-1 mice

value: CD-1 (outbred)

value: Wild-type CD-1


title: MeCP2IP_MeCP2_ChIP_Cerebellum1


title: Wild-type cortex sample 3

description: Animal was 6-weeks old at sacrifice


title: Heterozygous cortex sample 2


title: H3K56ac ChIP-Seq Sirt6 WT RA Treated

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Rm M640

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: H3K56ac ChIP-Seq in Sirt6 WT mESC after differentiation with RA Treatment

data_processing:
ChIP libraries were indexed, pooled, and sequenced on Illumina HiSeq-2500 sequencers at the Broad Institute sequencing center.
ChIP-seq reads were aligned to the mouse mm9 genome assembly using bwa version 0.5.9 with parameters '-q 5 -l 32 -k 2 -t 4 -o 1 -f' for the aln command and '-t 4 -T -P -f' for the sampe command.
ChIP-seq duplicate reads were marked with Picard Tools MarkDuplicates version number 1.764.
Peak calling with MACS2 version 2.0.10 and parameters '-g mm -f BAM -B -q 0.01'
Ran the IGVtools version 2.3.18 utility 'count' on aligned bam files to compute the average alignment over 25 base windows across the genome and generate binary tiled data .tdf files.
Genome_build: mm9
Supplementary_files_format_and_content: txt files are ChIP-Seq peak summary files from MACS2 in a tab delimited text file format.
Supplementary_files_format_and_content: tdf files are binary tiled data files of aligned ChIP-Seq data from the IGVtools count utility that conatin average alignment counts across the genome and can viewed in the IGV genome browser.

source_name: Embryonic stem cells (ESCs)

growth_protocol: Mouse ESCs (mESCs) derived from Sirt6 Sirt6 KO and WT 129 mouse strain were maintained on gamma-irradiated mouse embryonic fibroblasts (MEFs) in knocSirt6 KOut DMEM medium (GIBCO) containing 15% ES-qualified FBS, 0.1 mM each of nonessential amino acids, 2 mM L-glutamine, 0.1 mM beta-mercaptoethanol, 50 units/ml penicillin/streptomycin (Invitrogen) and supplemented with leukemia inhibiting factor (LIF). For all experiments described, cells were trypsinized and plated for 30 min on standard tissue culture dishes to remove feeder cells before floating ES cells were collected and re-plated on gelatin-coated dishes or wells prior differentiation towards EBs.

extract_protocol:
Chromatin immunoprecipitation (ChIP) steps were performed using a modified version of our previous protocols (e.g., Ram & Goren et. al. (2011) Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells. Cell. 147 (7). and Garber & Yosef et. al. (2012) A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals. Molecular Cell 47 (5).) adapted to the Bravo liquid handling platform (Agilent). Cells were crosslinked using formaldehyde (1%, 37oC for 10 min), and then quenched with glycine (5min at 37oC). The fixed cells were lysed in Lysis buffer (1% SDS, 10mM EDTA and 50mM Tris-HCl pH 8.1, containing protease inhibitors (Roche, 04693159001). Chromatin was sheared using Covaris E-220 at 4oC to a size range between 200 and 800 bp. 1 to 5µg of antibody were incubated 2 hours with a mix of Protein-A and Protein-G Dynabeads (Invitrogen, 100-02D and100-07D, respectively) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA). Beads were washed added to the chromatin lysate, and incubated overnight. Next, samples were washed 6 times with RIPA buffer, twice with RIPA buffer containing 500mM NaCl, twice with LiCl buffer (10mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), twice with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in ChIP-Elution Buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0) at 65oC, 4 hours, and then treated with RNaseA (Roche, 11119915001) for 30 min and Proteinase K (NEB, P8102S) for 2 hours.
Illumina Library construction reactions were performed as we described previously (Garber & Yosef et. al. 2012). SPRI (Solid-phase reversible immobilization; AMPure XP beads (Agencourt)) cleanup steps were done using the Bravo liquid handling platform (Agilent) and a modified version of (Fisher et al., 2011). After the final ChIP step, 120µl SPRI was added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant was separated from the beads using a 96-well magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. DNA was eluted in 40µl EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing (25 times). The remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) the SPRI cleanup involves addition of PEG buffer (20% PEG and 2.5 M NaCl) to the reaction products. Next, plates were transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are washed on the magnet with 150µl 70% ethanol and air dried for 4 minutes. The DNA is eluted with 40µl of EB buffer (mixing 25 times). Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27µl of a master mix (17µl master mix (5µl T4 buffer, 5µl BSA-1mg/ml, 5µl ATP-10mM -2µl dNTPs 10 mM)) plus 5µl T4 PNK enzyme, 5µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12oC for 15 min, 25 oC for 15 min, and finally cooled to 4 oC. The SPRI bead clean up method was used to purify the product (147µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40µl EB). The A-base addition was performed by adding 20µl master mix (17µl A-base add mix, 3µl Klenow to each well and incubated at 37oC for 30 min in a thermal cycler. Product was purified using 132µl PEG buffer and eluted in 19µl EB. Adaptor ligation: was performed by adding 34µl of a master mix (29µl 2x DNA ligase buffer, 5µl DNA ligase) and 5µl indexed oligo adaptors (0.75 uM ) followed by 15min incubation in 25oC in a thermal cycler. Next, ligated products were purified using SPRI bead clean up with size selection (15.5µl of PEG buffer) and eluted in 40µl EB.  The final step of PCR enrichment was was performed by adding 10µl of a master mix (2µl Forward/Reverse Index Primer, 0.5µl dNTP mix, 5µl 10x PfuUltra Buffer, 1µl PfuUltra-II Fusion, 1.5µl Nuclease free water) to each well. Using a thermal cycler, programed to 95C for 2 min, followed by 16 cycles of (95oC for 30 sec, 55oC for 30 sec, 72oC for 60 sec), and a final incubation at 72oC for 10 min. The last SPRI clean up was coupled to size selection (35µl SPRI beads were added to each sample and eluted in 40µl).

treatment_protocol: ChIP-Seq experiments used either untreated mouse ESCs or retinoic acid (RA) differentiated mouse ESCs. The mouse ESC differentiation protocol used RA was as follows: ESCs were grown in LIF(-) medium [DMEM + GlutMax TM-1 (invitrogen) medium + 15% Serum (w/o LIF)]. On the next day, the media was changed to RA-containing LIF(-) medium [DMEM + GlutMax TM-1 (invitrogen) medium + 15% Serum (w/o LIF) + retinoic acid (RA) at dilution 1:10000/10cm plate]. Two days later, the media was changed back to LIF(-) medium [DMEM + GlutMax TM-1 (invitrogen) medium + 15% Serum (w/o LIF)]. Cells were harvested the day after and processed for ChIP seq analysis as described above. The RA stock used 0.01 M All trans-RETINOIC ACID (Sigma Product number: R 2625) in DMSO (10000x solution) used following the instructions from manufacturer.

value: WT

value: RA Treated

value: H3K56ac (abcam, ab76307)


title: H3K9ac ChIP-Seq Sirt6 WT RA Treated

description: H3K9ac ChIP-Seq in Sirt6 WT mESC after differentiation with RA Treatment

value: H3K9ac (Millipore, 07-352)


title: H3K9ac ChIP-Seq Sirt6 WT

description: H3K9ac ChIP-Seq in Sirt6 WT mESC

value: No


title: Bl6_mESC_C2cells_2i_4OHT_RNA-seq_rep1


title: MeCP2IP_MeCP2_ChIP_Forebrain1


title: H3K9ac ChIP-Seq Sirt6 Sirt6 KO

description: H3K9ac ChIP-Seq in Sirt6 Sirt6 KO mESC

value: Sirt6 KO


title: Sirt6 1ul ChIP-Seq Sirt6 Sirt6 KO mESC

description: Sirt6 1ul ChIP-Seq in Sirt6 Sirt6 KO mESC

value: Sirt6 (Cell Signaling Technology, 12486 in a ratio of 1ml/2e7 cells)


title: H3K56ac ChIP-Seq Sirt6 WT

description: H3K56ac ChIP-Seq in Sirt6 WT mESC


title: H_1105

first: Richard

middle: H

last: Myers

address: 72 E Concord St, E301

department: Neurology

institute: Boston University School of Medicine

description: small RNA

data_processing:
Basecalls from CASAVA 1.7
QUALITY FILTERING: FASTX-toolkit version 0.0.13.2 fastq_quality filter with -Q 33  -q 20 -p 80; ADAPTER REMOVAL: cutadapt 1.2.1 with --minimum-length 15 option, READ COLLAPSING: FASTX-toolkit version 0.0.13.2 fastx_collapser
READ ALIGNMENT: bowtie-1.0.0 with no mismatches and 200 multimap limit using -v 0 -k 200; ANNOTATION: bedtools v2.2 intersectBed and miRBase v20
COUNTING: custom R-script counting miRNAs ±4 nucleotides from 5' annotated start location
DIFFERENTIAL EXPRESSION ANALYSIS: Using R: DESeq2 v1.40 for variance stabilizing transformation counts, ComBat (R package sva 3.10) for batch effect correction, LIMMA v3.20.8 with adjustment for death at death for statistical comparison between conditions
Genome_build: hg19
Supplementary_files_format_and_content: Processed files contain normalized counts for all samples, covariates file with additional sample information and differential expression results from LIMMA, in comma separated value format

source_name: prefrontal cortex (BA9)

extract_protocol:
QIAzol Lysis Reagent, miRNeasy purification
Illumina TruSeq Small RNA Preparation Kit

value: brain prefrontal cortex (Brodmann Area 9)

tag: condition

value: ASYM

tag: post-mortem interval

tag: age at death

tag: gender (1=male, 2=female)

tag: cag repeat size

tag: age of onset

tag: vonsattel grade

tag: hadzi-vonsattel striatal score

tag: hadzi-vonsattel cortical score


title: WCE Sirt6 WT mESC

description: WCE from Sirt6 WT mESC


title: Sirt6 ChIP-Seq Sirt6 WT mESC

description: Sirt6 ChIP-Seq in Sirt6 WT mESC


title: H3K56ac ChIP-Seq Sirt6 Sirt6 KO

description: H3K56ac ChIP-Seq in Sirt6 Sirt6 KO mESC


title: Wild-type cortex sample 1

description: Animal was 6-weeks old at sacrifice

value: Microdissected cortex

tag: genotype


title: H3K9ac ChIP-Seq Sirt6 Sirt6 KO RA Treated

description: H3K9ac ChIP-Seq in Sirt6 Sirt6 KO mESC after differentiation with RA Treatment

tag: treatment


title: H3K56ac ChIP-Seq Sirt6 Sirt6 KO RA Treated

description: H3K56ac ChIP-Seq in Sirt6 Sirt6 KO mESC after differentiation with RA Treatment


title: Sirt6 5ul ChIP-Seq Sirt6 Sirt6 KO mESC

description: Sirt6 5ul ChIP-Seq in Sirt6 Sirt6 KO mESC

value: Sirt6 (Cell Signaling Technology, 12486 in a ratio of 5ml/2e7 cells)


title: WCE Sirt6 Sirt6 KO mESC

description: WCE from Sirt6 Sirt6 KO mESC


title: H_0681

description: small RNA

value: HD


title: H_0689

description: small RNA


title: H_1104

description: small RNA


title: Homozygous cortex sample 2

description: Animal was 6-weeks old at sacrifice


title: H_0750

description: small RNA


title: H_0723

description: small RNA


title: H_0012

description: small RNA


title: H_0013

description: small RNA


title: H_0740

description: small RNA


title: H_0709

description: small RNA


title: H_0726

description: small RNA


title: H_0005

description: small RNA


title: H_0695

description: small RNA


title: H_0700

description: small RNA


title: H_0657

description: small RNA


title: H_0658

description: small RNA


title: H_0656

description: small RNA


title: H_0539

description: small RNA


title: H_0014

description: small RNA


title: H_0008

description: small RNA


title: H_0010

description: small RNA


title: C_0039

description: small RNA

value: Control


title: H_0009

description: small RNA


title: H_0003

description: small RNA


title: C_0033

description: small RNA


title: C_0025

description: small RNA


title: H_0001

description: small RNA


title: H_0007

description: small RNA


title: H_0002

description: small RNA


title: C_0087

description: small RNA


title: H_0513

description: small RNA


title: C_0070

description: small RNA


title: C_0049

description: small RNA


title: C_0021

description: small RNA


title: C_0017

description: small RNA


title: C_0047

description: small RNA


title: C_0037

description: small RNA


title: C_0038

description: small RNA


title: C_0013

description: small RNA


title: C_0036

description: small RNA


title: C_0016

description: small RNA


title: C_0032

description: small RNA


title: C_0035

description: small RNA


title: C_0034

description: small RNA


title: C_0011

description: small RNA


title: C_0009

description: small RNA


title: C_0031

description: small RNA


title: C_0029

description: small RNA


title: C_0004

description: small RNA


title: H_0006

description: small RNA


title: C_0024

description: small RNA


title: C_0023

description: small RNA


title: C_0020

description: small RNA


title: C_0022

description: small RNA


title: C_0014

description: small RNA


title: C_0018

description: small RNA


title: C_0008

description: small RNA


title: C_0015

description: small RNA


title: Adelman_Bl6_mESC_C2cells_2i_Ctrl_startRNA-seq_rep2

description:
startRNA-seq
Adelman_Bl6_mESC_C2cells_2i_Ctrl_startRNA-seq_5pr_allReps_norm_forward.bedgraph
Adelman_Bl6_mESC_C2cells_2i_Ctrl_startRNA-seq_5pr_allReps_norm_reverse.bedgraph

data_processing:
GRO-seq: GRO-seq reads were trimmed for quality and adapter sequence using cutadapt 1.2.1 , discarding pairs where either mate was trimmed shorter than 15 nt (-m 15 -q 10 --match-read-wildcards).  Read pairs originating from rRNA were filtered by aligning against an index consisting of the 45S and 5S transcripts using Bowtie 0.12.8, allowing two mismatches (-m1 -v2 -X1000 --un --max).  Unmapped pairs were subsequently aligned to the mm9 index, allowing two mismatches and retaining only uniquely aligned pairs (-m1 -v2 -X1000).  BedGraph files were generated from the combined alignments of all technical and biological replicates, reduced to their strand-specific 5’-end mapping locations (N=59,099,712 reads: individual samples had mappable read depths of 33,123,684 for Library#1, and 25,976,028 for Library #2. Agreement between replicates was strong (R2=0.96, fig. S1A), thus the data was combined for further analysis.
RNA-seq: Read pairs were filtered, requiring a mean quality score greater than or equal to 20, for both mates, then aligned to the mm9 reference genome using TopHat 2.0.4, reporting up to 10 alignments per read pair (-g 10).  Mean fragment sizes and standard deviations were determined using Picard Tools 1.86 CollectInsertSizeMetrics, based on a bowtie 0.12.8 alignment (-m1 -v2 -X10000) of a subset of one million reads to an index of RefSeq transcripts, and passed to TopHat using the --mate-inner-dist and --mate-std-dev parameters.  A total of 113,817,860 and 108,809,117 read pairs were successfully aligned for the Control and 4OHT/NELF-B KO samples, respectively. UCSC Browser tracks displaying read coverage normalized per million mappable fragments were generated from the combined replicates per condition.
startRNA-seq: Reads trimmed for adapter sequence using cutadapt 1.2.1, pairs containing reads shorter than 20 nt excluded (-q 10 -m 20, otherwise default), reads further trimmed to maximum length of 36 nt, remaining read pairs aligned to index containing spike-in RNAs (bowtie 0.12.8 -m1 -v2 -X1000 --best), unaligned read pairs mapped to mm9 using same parameters
Genome_build: mm9
Supplementary_files_format_and_content: GRO-seq: BedGraph files were generated from the combined alignments of all technical and biological replicates, reduced to their strand-specific 5’-end mapping locations
Supplementary_files_format_and_content: RNA-seq: bigWig tracks displaying read coverage normalized per million mappable fragments were generated from the combined replicates per condition.
Supplementary_files_format_and_content: startRNA-seq: BedGraph files for each treatment were generated from the combined alignments of all technical and biological replicates, reduced to their strand-specific 5'-end mapping locations; prior to combination, the member of each Ctrl/4OHT replicate pair with higher uniquely mappable read count was depth normalized to the lower, in agreement with observed spike-in ratios

extract_protocol:
GRO-seq: GRO-seq experiments were performed according to {Core, 2008 #1330} in the C2 ESC line grown in 2i media, with the following modifications: Nuclei were harvested by swelling trypsinized cells for 10 minutes in 50 mL cold lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM CaCl2, 2 mM MgCl2, 0.5% NP40, 5 mM DTT, 300 mM sucrose, 1 mM PMSF, 2 U/ml Superase IN, 5 tablets Roche protease inhibitors), then gently dounce homogenized, centrifuged and washed once with 50 mL lysis buffer.  Nuclei were resuspended in freezing buffer as in {Core, 2008 #1330} at the concentration of 5x106 nuclei per 100 uL, and stored at -80°C until use. To avoid a bias against representation of C-rich regions in the data set, the final concentration of CTP (Roche) was increased in the run-on ten-fold above that used in {Core, 2008 #1330} to 10 uM. To permit a quick, reproducible stop to the run-on reaction, the reaction was terminated after 5 minutes by the addition of Trizol (Invitrogen). RNA-seq: Two distinct conditional NELF-B KO ESC clones were grown +/- 4OHT in 2i media. On day 5 after initiating recombination, total RNA was prepared using Trizol (Invitrogen) and manufacturer recommended methods. DNA contamination was removed using the RNeasy Mini Kit (Qiagen) per manufacturer’s instructions, and RNA quality was assessed using a Bioanalyser Nano ChIP (Agilent). startRNA-seq: Total RNA was extracted from nuclei using Trizol reagent (Invitrogen)
GRO-seq: Following base hydrolysis, primary Br-U immunoprecipitation and end repair, the libraries were made using the Illumina small RNA TruSeq kit except the 3’ adapter was ligated using T4 RNA Ligase II, truncated KQ enzyme (NEB).  A secondary BrU IP was performed before ligation of the 5’ adapter (Illumina) followed by a tertiary BrU IP to produce triple-selected run-on RNA.  RNA was reverse transcribed and amplified with 15 cycles of PCR (Illumina).  Libraries were PAGE purified, selecting for products larger than 140 bp. RNA-seq: Ribosomal RNA was removed prior to library construction by hybridizing to ribo-depletion beads that contain biotinylated capture probes (Ribo-Zero, Epicentre). RNA was then fragmented and libraries were prepared according to the TruSeq Stranded Total RNA Gold Kit (Illumina) using random hexamer priming. Illumina Spike-ins were used for normalization. startRNA-seq: Start-RNA libraries were prepared as described in (Nechaev et al., Science 2010) except reads were size selected in the range 20-80 nt to exclude full length snRNA species.

tag: cell type

value: control


title: Adelman_Bl6_mESC_C2cells_2i_4OHT_startRNA-seq_rep2

description:
startRNA-seq
Adelman_Bl6_mESC_C2cells_2i_4OHT_startRNA-seq_5pr_allReps_norm_forward.bedgraph
Adelman_Bl6_mESC_C2cells_2i_4OHT_startRNA-seq_5pr_allReps_norm_reverse.bedgraph

value: embryonic stem cell


title: C_0012

description: small RNA


title: Adelman_Bl6_mESC_C2cells_2i_4OHT_startRNA-seq_rep1


title: Bl6_mESC_C2cells_2i_GRO-seq_rep2

description: library strategy: GRO-seq

value: untreated


title: Bl6_mESC_C2cells_2i_Ctrl_RNA-seq_rep2


title: C_0010

description: small RNA


title: C_0006

description: small RNA


title: duck 2

city: Shanghai

first: LIANG

last: YAN

address: NO 131, Dongan Road

institute: Fudan University

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  whole genome (PRJNA46621) using TopHat v2.0.12.
Cufflinks v2.2.1 software (http://cufflinks.cbcb.umd.edu/) was later used for analyses that included transcript assembly and FPKM value calculations to quantify gene expression.
Genome_build: PRJNA46621
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Anas platyrhynchos

source_name: primary duck hepatocytes

growth_protocol: Primary duck hepatocytes were cultured in Leibovitz’s L-15 medium supplemented with 5% fetal bovine serum, 100 units/ml penicillin-streptomycin, 1 mg/L insulin, and 10−5 M hydrocortisone-hemisuccinate.

extract_protocol:
Primary duck hepatocytes were cultured for 24 hours, 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: liver

tag: age

value: 1-day-old duckling

value: wild type


title: duck 3


title: D0_input

status: Public on Mar 11 2015

first: Naihe

last: Jing

state: Shanghai

address: 320 Yueyang road

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

description: undifferentiated hESCs

data_processing:
Mapping to the Genome using bowtie version 0.12.8
Creation Tag directories using HOMER, makeTagDirectory
UCSC visualization using makeUCSCfile
Finding enriched peaks using findPeaks which is a program contains in HOMER
Genome_build: hg19
Supplementary_files_format_and_content: text files with peak coordinates called by findPeaks/HOMER; bedgraph files of signal

source_name: undifferentiated hESCs

growth_protocol: ES cell–derived neural progenitor cells were generated by floating neural differentiation cultures

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.

value: undifferentiated hESCs


title: C_0003

description: small RNA


title: H3K9Ac ChIP-seq_D8

description: Day 8 differentiated cells

source_name: Day 8 differentiated cells

value: Day 8 differentiated cells

value: H3K9Ac (Millipore)


title: D8_input

description: Day 8 differentiated cells


title: H3K9Ac ChIP-seq_D0

description: undifferentiated hESCs


title: Adelman_Bl6_mESC_C2cells_2i_4OHT_startRNA-seq_rep3


title: Bl6_mESC_C2cells_2i_GRO-seq_rep1

description: library strategy: GRO-seq


title: Adelman_Bl6_mESC_C2cells_2i_Ctrl_startRNA-seq_rep3


title: Adelman_Bl6_mESC_C2cells_2i_Ctrl_startRNA-seq_rep1


title: D8/D4-8+TSA

description: Day 8 differentiated cells with TSA treatment during days 4-8

data_processing:
Aligns RNA-Seq reads to the genome using TopHat version 2.0.4
Assembles transcripts using Cufflinks version 2.0.2
Merges transcript assemblies using Cuffmerge
Finds differentially expressed genes and transcripts, detects differential splicing using Cuffdiff version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: text file include FPKM values for each Sample.

extract_protocol:
Total RNA was extracted with Trizol reagents.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 ng/ml TSA was supplemented during hESC neural differentiation at days 0-4 or 4-8.


title: C_0002

description: small RNA


title: H9/D4

description: Day 4 differentiated cells

source_name: Day 4 differentiated cells

value: Day 4 differentiated cells


title: Bl6_mESC_C2cells_2i_Ctrl_RNA-seq_rep1


title: C_0005

description: small RNA


title: dCas9-p300 core_rep3

city: Durham

first: Christopher

last: Vockley

state: NC

address: 101 science drive rm 2193

institute: Duke University

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the hg19 version of the human genome using bowtie2-align version 2.1.0, and the  -p 32 --end-to-end --very-sensitive t" alignment options
Reads were converted from .sam to .bam files using samtools view version 0.1.19-44428cd with the  "-bS" option
Bam files were sorted using Samtools sort version 0.1.19-44428cd with the options "32 -m 2G"
Bam files were indexed using Samtools Index version 0.1.19-44428cd
Duplicate reads were removed using samtools rmdup  version 0.1.19-44428cd  usint the "-s option"
Bam files were re-indexed after duplicates were removed using Samtools Index version 0.1.19-44428cd
Reads were counted using samtools idxstats version 0.1.19-44428cd
Differential expression was computed using R version 3.1.2 using the DEseq2 package version 1.6.2  with default settings
Genome_build: RefSeq transcripts from hg19
Supplementary_files_format_and_content: Counts of the number of reads aligned to each RefSeq transcript.

source_name: Cultured HEK293T cells

growth_protocol: HEK293T cells were obtained from the American Tissue Collection Center (ATCC) through the Duke University Cel Culture Facilities and were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Between 0.5-1 million cells were washed with PBS and then lysed using Qiagen RLT buffer. Total RNA was extracted using Qiagen RNeasy mini-columns with 1% β-mercaptoethanol in RLT buffer and a 15 min on column DNase digestion. mRNA was prepared using the Wafergen automated sample prep system with the Prep-x mRNA kit with 1 microgram of total RNA.
Libraries were prepared using the Apollo 324 liquid handling platform, as per manufacturer’s instruction using the prep-mRNAseq kit.

treatment_protocol: HEK293T cells were transfected with Lipofectamine 2000 (Invitrogen) according to manufacturer’s instructions. Transfection efficiencies were routinely higher than 80% as determined by fluorescence microscopy following delivery of a control eGFP expression plasmid. Cas9 expression plasmids were transfected at a mass ratio of 3:1 to the total amount of gRNA expression plasmids as in main text.

tag: cell line

tag: transfected gene

value: dCas9-p300 core

tag: guide rna at 4 sites


title: dCas9-p300 D1399Y_rep3


title: duck 1

tag: tissue


title: Ad-NOER, 10 nM E2, rep 3

city: Rochester

first: David

middle: George

last: Monroe

state: MN

address: 200 1st St SW

department: Endocrinology

institute: Mayo Clinic

data_processing:
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and count values for each Sample

source_name: hFOB 1.19 cells

growth_protocol: The hFOB 1.19 human fetal osteoblastic cell line (hFOB) was passaged in phenol red-free αMEM growth medium (Invitrogen, Carlsbad, CA) supplemented with 1X antibiotic/antimycotic (Invitrogen), 10% (v/v) fetal bovine serum (Hyclone, Logan, UT) and 300 ug/mL G418 selection antibiotic.

extract_protocol:
Total RNA was prepared using RNeasy minicolumns (Qiagen, Valencia, CA) and treated with RNase-free DNase (Qiagen) to remove potential contaminating DNA.
RNA libraries for RNAseq analysis were prepared from 100 ng of isolated total RNA from each sample using the manufacturer’s instructions. Unique indexes were incorporated at the adaptor ligation step for loading multiple samples per flow cell.  Three distinct indexed libraries were loaded per flow cell and sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8).  Base calling was performed using Illumina RTA (version 1.12.4.2).  An average of 130 million reads per sample was achieved resulting in ~96% mapped reads.

treatment_protocol: hFOB cells were plated in 10-cm culture dishes (n=6) at a final density of 2 × 10^4 cells/cm2.  Cells were infected at the time of plating at a multiplicity of infection (MOI) of 15 (Ad-ERα), 30 (Ad-NERKI) and 22.5 (Ad-NOER).  Following another 24 hour incubation to allow for complete infection, the cells were treated with either ethanol vehicle (0.1% v/v) or 10 nM 17-β-estradiol (0.1% v/v; Sigma-Aldrich) in the presence of media containing triple-stripped charcoal-treated FBS for an additional 24 hrs.

value: osteoblastic cell


title: D4/D0-4+TSA

description: Day 4 differentiated cells  with TSA treatment during days 0-4


title: H9/D8

description: Day 8 differentiated cells


title: hESC/D0

description: undifferentiated hESCs


title: Ad-NOER, 10 nM E2, rep 2


title: Ad-NERKI, Vehicle, rep 3


title: Ad-NOER, Vehicle, rep 2


title: Ad-Era, 10 nM E2, rep 3


title: p300+ALL IL1RN_rep2


title: Ad-NOER, Vehicle, rep 3


title: Ad-NERKI, 10 nM E2, rep 3


title: dCas9_rep3