title: Sample23_hESO_8_fib2

description: wt mtDNA

source_name: Differentiated IVF Derived Stem Cell

value: Differentiated IVF-ESC


title: Sample24_Leigh_iPS2_fib1

status: Public on Jul 16 2015

type: SRA

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

country: USA

institute: UCSD

description: mutant mtDNA

library_source: transcriptomic

data_processing:
RNA-Seq reads were trimmed and mapped to the GRCh37 reference using STAR (version 2.3.0.1). Four previously published IVF-ESC samples and four NT-ESC were added to increase statistical power and for quality control.
Samtools (version 0.1.17) was then used to sort, merge, and eliminate duplicate reads
Expression levels for each gene were quantified using the python script rpkmforgenes and annotated using Ensembl GRCh37 refGene. Genes that did not have at least one sample with at least five reads were removed from the analysis.
The data was normalized using the R (version 3.1.1) package DESeq2 (version 1.4.5). Eight samples were added for comparison: Four IVF-ESC samples: GSM1282324, GSM1378018,GSM1282325 and GSM1378019 and four NT-ESC samples: GSM1282320,GSM1378014, GSM1282321, GSM1378015. These have been re-accessioned and are included in this record.
DESeq2 uses negative binomial generalized linear models and shrinkage estimation for dispersions and fold changes to improve stability and interpretability of the estimates. It reports a p-value and an adjusted p-value using the Benjamini-Hochberg procedure.
Transcripts with an adjusted P-Value less than 0.05 were considered differentially expressed.
All enrichment analysis was performed using GREAT (v.2.0.2)
genome build: GRCH37
processed data files format and content: .txt file including DESeq2 normalized counts filtered for genes with at least 5 reads in at least one sample

molecule: total RNA

organism: Homo sapiens

source_name: Differentiated induced Pluripotent Stem Cell

growth_protocol: Leigh patient fibroblasts were acquired from Coriell Cell Repositories (catalogue no. GM13411) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated as described previously (Ma, H. et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature 511, 177-183, doi:10.1038/nature13551 (2014)). NT-ESC lines were produced from Leigh patient fibroblasts as described previously (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)). iPSC and NT-ESC lines were differentiated into fibroblasts as described previously (Paull, D. et al. Nuclear genome transfer in human oocytes eliminates mitochondrial DNA variants. Nature 493, 632-637, doi:10.1038/nature11800 (2013)).

extract_protocol:
RNA was isolated (TRIzol Reagent, Life Technologies, Inc.) quantified (Qubit RNA Assay Kit, Life Technologies, Inc.) and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent).
Approximately 500 ng was used as input for the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Inc.) and sequencing libraries were created according to the manufacturer’s protocol. Briefly, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented and copied into first strand cDNA using random primers and reverse transcriptase. Second strand cDNA synthesis was then done using DNA Polymerase I and RNase H. The cDNA was then ligated to adapters and enriched with PCR to create the final cDNA library. The library was then pooled and sequenced on a HiSeq 2000 (Illumina, Inc.) instrument as per manufacturer’s instructions. Sequencing was performed up to 2 X 101 cycles.

treatment_protocol: Sendai virus-based reprogramming was carried out using sendai virus vectors carrying OCT4, SOX2, KLF4, and MYC. Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated as described previously (Ma, H. et al. Abnormalities in human pluripotent cells due to reprogramming mechanisms. Nature 511, 177-183, doi:10.1038/nature13551 (2014)). NT-ESC lines were produced from Leigh patient fibroblasts as described previously (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)). iPSC and NT-ESC lines were differentiated into fibroblasts as described previously (Paull, D. et al. Nuclear genome transfer in human oocytes eliminates mitochondrial DNA variants. Nature 493, 632-637, doi:10.1038/nature11800 (2013)).

tag: cell type

value: Fibroblast

tag: cell line

value: Differentated iPSC

tag: sequenced molecule

value: polyA RNA


title: Sample_03-04_23_6_31_004

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequenced reads were mapped to the hg19 reference genome and GencdeV7 reference transcriptome using Tophat 1.3.1with parameters : -g 1 -p 4 -r 150 --coverage-search --no-novel-indels --microexon-search -G GFFfile --solexa-quals hg19 FASTQFILE1 FASTQFILE2
Gene expression estimates: Counts were calculated using the BEDTools 2.12.0 function coverageBed with parameters: -abam BAMfilename -b BEDfilename
BAM files were sorted using the samtols 0.1.18 function: samtools sort -n
BAM files were converted to SAM format using the samtols 0.1.18 function: samtools view -h
SAM files were converted to MRF format using the RSEQtools 0.6 function: sam2mrf
Gene expression estimates in RPKM were calculated using the RseqTools function mrfQuantifier with parameters: INTERVALfile multipleOverlap MRFfile
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files include gene expression estimates in RPKM (.rpkm) and COUNTS (.counts.txt) for each sample.

source_name: iPSC-derived neural progenitors, day 31, non-ASD

growth_protocol: Neuronal differentiation of iPSCs: iPSC colonies were dissociated and plated on AggrewellTM 800 plates (STEMCELL Technologies) in DMEM/F12-GLUTAMAX medium containing 4% B27 supplement without vitamin A (Invitrogen), 1% N2 supplement (Invitrogen), and 55 uM 2-mercaptoethanol, 5μM Y-27632 and 200ng/ml recombinant mouse Noggin (R&D Systems). After 2 days, embryoid bodies (EBs) were collected and plated onto 10-cm bacterial Petri dishes in neuronal medium as above. After two days (day 4), free-floating EBs were collected and plated in neuronal medium, supplemented with only Noggin, onto tissue culture dishes coated with growth factor-reduced Matrigel (BD Bioscience) to allow neural rosette formation. The neuronal medium was changed the next day and supplemented with 20 ng/ml FGF2, 200 ng/ml Noggin, and 200 ng/ml rhDkk1 (R&D Systems). After two or three days, the neural rosettes were manually dissected and replated as free-floating aggregates in 10-cm bacterial Petri dishes in neuronal medium supplemented with FGF2 (10ng/ml) and EGF (10ng/ml). After five days in suspension, free-floating aggregates were plated onto ultra low-attachment 96-well plates (Corning) in neuronal medium supplemented with FGF2 and EGF. Terminal differentiation was started the next day, using a NEUROBASAL-type medium supplemented with 1% N2, 2% B27, 15 mM HEPES, 1X Glutamax, 1X nonessential amino acids (NEAA) and 55 uM 2-mercaptoethanol, supplemented with 200 nM ascorbic acid, 10 ng/ml BDNF (R&D), 10 ng/ml GDNF (R&D) and 1 mM dibutyryl-cAMP (Sigma). Half of the medium was changed twice a week.

extract_protocol:
Cells were treated with Accutase and pelleted. Total RNA was extracted using the PicoPure kit (Life Technologies catalog # KIT0204).
RNA sequencing was performed using 50ng of total RNA with the SMARTer® Ultra Low RNA kit for Illumina® Sequencing according to the manufacturer's instructions. Samples were barcoded. Multiplex Paired-End RNA sequencing (2x75) was performed on an IIllumina HiSeq 2000 to an average depth of 30M reads per sample.

tag: donor's disease state

value: unaffected

tag: donor's gender

value: male

value: iPSC-derived neural progenitors

tag: number of days in vitro in terminal differentiation conditions

tag: donor id


title: Cdx1 MO - rep 1

city: London

first: Ferdinand

last: Marlétaz

address: Gower Street

department: Genetics, Evolution & Environment

country: United Kingdom

institute: University College London

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were mapped with Tophat with standard parameters
Read counts were obtained using Htseq-count and ENSEMBL gene models
Differentation expression and subsequent analyses were conduced in the R package using DESeq2 library
Genome_build: JGI 4.2/xenTro3
Supplementary_files_format_and_content: files containing read counts by gene models

organism: Xenopus tropicalis

source_name: Whole embryos

growth_protocol: standard Xenopus embryo culture

extract_protocol:
RNA was extracted with Tri-reagent (Sigma) and cleaned on Qiagen RNAeasy colmun according to manufacturer specification
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 20 ng MO per embryo (or 6.67ng for each MO for the triple) was injected at the 1- or 2-cell stage, in a total volume of 10 nL divided between each cell

tag: developmental stage

value: Stage 14 (early neurula)

tag: morpholino

tag: tissue

value: whole embryo


title: Sample_07-01_23_1_11_005

source_name: iPSC-derived neural progenitors, day 11, non-ASD


title: Sample21_hESO_7_fib2

description: wt mtDNA


title: Sample29_Melas_iPS3_fib2

description: mutant mtDNA


title: Sample_03-04_23_6_11_002


title: Sample_03-03_23_5_11_007

source_name: iPSC-derived neural progenitors, day 11, ASD

value: autism spectrum disorder with macrocephaly


title: Sample22_hESO_8_fib1

description: wt mtDNA


title: Sample_03-02_23_9_31_012

value: female


title: Sample_03-01_23_2_31_006


title: 24dd_DOX_minus_TRA_minus_Rep1

city: Boston

first: Shannan

last: Ho Sui

state: Massachusetts

address: 401 Park Drive, Level 3 East

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

library_source: genomic

data_processing:
Reads were aligned on build hg19 of the human genome with MAQ(Li, Ruan, & Durbin, 2008) in bisulfite alignment mode.
The methylation level at single CpGs was calculated as the fraction of reads with unconverted cytosines over the total number of reads at that position. The methylation level for promoters was calculated as the mean of the methylation levels of the CpGs within the promoter weighted by the number of reads covering each CpG.
Differentially methylated promoters were defined as those exhibiting a methylation difference of 0.2 or greater between any two conditions and used for standard k-means clustering.
Genome_build: hg19
Supplementary_files_format_and_content: chrom, chromstart, chromend, 'number methylated cytosines/number total cytosines', score, strand

molecule: genomic DNA

source_name: reprogramming intermediates of hiF-T cells

growth_protocol: hiF-T fibroblasts were expanded on gelatin-coated dishes in hiF medium composed of basal medium (DMEM-F12 Glutamax, 1X MEM-NEAA, 1X beta-ME, 0.2X P/S) supplemented with 10% ES-FBS and 16 ng/ml FGFbasic. HUES64 and hIPSC-T were expanded in feeder-free conditions using Essential 8 (E8) medium. The attachment matrix for PSC was either Matrigel (MTG) or Vitronectin (VTN) with no significant differences.

extract_protocol:
Genomic DNA was extracted with the QIAamp DNA Mini Kit (QIAGEN)
Reduced Representation Bisulfite Sequencing (RRBS) Illumina libraries were prepared according to a standard gel-free pipeline(Boyle et al., 2012) starting from 10ng of genomic DNA.

treatment_protocol: Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript.

tag: surface antigen enrichment

tag: treatment

value: DOX days 0-20


title: 24dd_DOX_plus_TRA_minus_Rep1

value: DOX days 0-24


title: 14dd_DOX_plus_SSEA3_neg_Rep1

value: DOX days 0-14


title: Sample_03-01_23_2_11_005


title: 24dd_DOX_minus_TRA_plus_Rep1


title: Sample_9_005


title: Sample_8_004

source_name: iPSC-derived neural progenitors, day 0, ASD


title: 14dd_DOX_plus_SSEA3_pos_Rep1


title: 24dd_DOX_plus_TRA_plus_Rep1


title: Sample_7_002

source_name: iPSC-derived neural progenitors, day 0, non-ASD


title: 14dd_DOX_plus_SSEA3_tot_Rep1


title: 10dd_DOX_plus_tot_Rep1

value: DOX days 0-10


title: 10dd_DOX_plus_SSEA3_pos_Rep1


title: Sample_6_012

source_name: iPSC-derived neural progenitors, day 31, ASD


title: 10dd_DOX_plus_SSEA3_neg_Rep1


title: Sample_03-03_23_5_31_012


title: Sample_5_007


title: Sample_24_012


title: Sample20_hESO_7_fib1

description: wt mtDNA


title: 5dd_DOX_plus_Rep1

value: DOX days 0-5


title: Sample_4_006


title: 2dd_DOX_plus_Rep1

value: DOX days 0-2


title: Sample_03-02_23_9_11_007


title: 2dd_DOX_minus_Rep1


title: hIPSC-T_MTG_Rep1

source_name: hIPSCs from reprogrammed hiF-T cells (hIPSC-T)

tag: passage (pre-reprogramming)


title: Sample_22_006


title: Sample_23_007


title: hiF-T_P14_Rep1

source_name: immortalized human inducible fibroblasts-like cells (hiF-T)


title: Sample_20_004


title: hESC_TRA_pos_Rep1 [H9]

source_name: human ESC


title: Sample_21_005


title: Sample_19_002


title: hIPSC_TRA_pos_Rep1 [IPSC11c]

source_name: human IPSC (hIPSC)


title: Sample_17_007


title: Sample_16_006


title: Sample_18_012


title: Sample_14_004


title: Sample_15_005


title: hIPSC-T_P10_VTN_Rep1_smallRNA

description: Secondary iPSC

data_processing:
Small RNA read were mapped to the human genome with TopHat 2.0.7 and Bowtie 2.1.0. Spliced alignment by TopHat was disabled by omitting the GENCODE annotation file and providing the -no-novel-juncs option, which forces all alignments to be unspliced. Sequencing adapters were clipped from the reads using fastx_clipper form the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), using the options "-a TGGAATTCTCGGGTGCCAATGAACTCCAG -l 18 -Q 33". Reads were mapped with TopHat, as opposed to Bowtie, because the resulting alignment files are properly formatted for direct input to Cuffdiff. Small RNA expression levels were estimated using Cuffdiff 2.2.0 by providing Cuffdiff with the small RNA records from the GENCODE annotation. The number of reads generated from each small RNA is directly proportional to abundance, and independent of small RNA length, so the option -no-length-correction was provided to Cuffdiff, disabling length-based normalization of read counts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sample

growth_protocol: Refer to the section Cell Culture and Reprogramming in the Supplemental Experimental Procedures of the related manuscript.

extract_protocol:
Total RNA, including the small RNA fraction, was obtained by organic extraction followed by miRNeasy purification (Qiagen).
RNA-Seq Illumina libraries for small RNA profiling were prepared from 1 ug of total RNA using the TruSeq Small RNA Sample Prep Kit (Illumina).

treatment_protocol: Reprogramming treatments were perfomed by doxycyclin administration to hiF-T cells in hiF media first and hES media (basal medium, 20% KSR, 8ng/ml) after. Reprogramming intermediates were collected by MEF depletion and eventual surface marker enrichment as needed. Refer to manuscript for detailed reprogramming and sampling procedures.


title: BJ_P12_Rep1_smallRNA

description: Fibroblasts

source_name: primary BJ fibroblasts


title: hIPSC-T_P10_MTG_Rep1_smallRNA

description: Secondary iPSC


title: hiF-T_P14_Rep1_smallRNA

description: Secondary line - with TERT


title: 24dd_TRA_pos_DOX_plus_Rep1_smallRNA

description: First reprogramming


title: Sample_11_007


title: 24dd_TRA_pos_DOX_minus_Rep1_smallRNA

description: First reprogramming

value: DOX days 0-19


title: 24dd_TRA_neg_DOX_plus_Rep1_smallRNA

description: First reprogramming


title: 24dd_TRA_neg_DOX_minus_Rep1_smallRNA

description: First reprogramming


title: Sample_12_012


title: Sample_10_006


title: 20dd_DOX_plus_TRA_plus_Rep1_smallRNA

description: Second reprogramming


title: 20dd_DOX_plus_TRA_minus_Rep1_smallRNA

description: Second reprogramming


title: 14dd_DOX_plus_tot_Rep1_smallRNA

description: Second reprogramming


title: GSM1378018_hESO7_2

description: Re-analyzed sample

molecule: polyA RNA

source_name: Human Embryonic Stem Cell

growth_protocol: Fetal origin human dermal fibroblasts (HDF) were acquired from ScienCell Research Laboratories (catalog # 2300) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Cells were transduced by retro virus-based iPSC vectors as previously reported (Lowry, W. E. et al. Generation of human induced pluripotent stem cells from dermal fibroblasts. Proceedings of the National Academy of Sciences of the United States of America 105, 2883-2888, doi:10.1073/pnas.0711983105 (2008)). Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated similar to NT-ESC and IVF-ESC protocols (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)).

value: Human Pluripotent Stem Cell

value: IVF Derived


title: GSM1378019_hESO8_2

description: Re-analyzed sample

value: polyA RNA


title: 14dd_DOX_plus_SSEA3_pos_Rep1_smallRNA

description: Second reprogramming


title: GSM1282325_hESO8

description: Re-analyzed sample


title: GSM1282324_hESO7

description: Re-analyzed sample


title: Sample19_Melas_iPS2_fib2

value: Fibroblast

value: Differentated iPSC


title: Sample18_Melas_iPS2_fib1


title: HUES64_P30_smallRNA

description: Human Embryonic Stem Cell line

source_name: human hESC


title: Sample_13_002

value: unaffected

value: male

value: iPSC-derived neural progenitors


title: 10dd_DOX_plus_SSEA3_pos_Rep1_smallRNA

description: Second reprogramming


title: Sample17_Melas_iPS2_2

source_name: induced Pluripotent Stem Cell

value: Sendai-Virus Derived


title: Sample16_Melas_iPS2_1


title: 8dd_DOX_plus_Rep1_smallRNA

description: First reprogramming

value: DOX days 0-8


title: 10dd_DOX_plus_SSEA3_neg_Rep1_smallRNA

description: Second reprogramming


title: Sample15_Melas_iPS1_fib2

source_name: Differentiated induced Pluripotent Stem Cell


title: Sample14_Melas_iPS1_fib1


title: 5dd_DOX_plus_Rep2_smallRNA

description: Second reprogramming


title: Sample13_Melas_iPS1_2


title: 5dd_DOX_plus_Rep1_smallRNA

description: First reprogramming


title: 2dd_DOX_plus_Rep2_smallRNA

description: Second reprogramming


title: Sample12_Melas_fib2

source_name: Human Dermal Fibroblast

value: Human Dermal Fibroblast

value: Tissue


title: 2dd_DOX_plus_Rep1_smallRNA

description: First reprogramming


title: Sample11_Melas_fib1


title: 2dd_DOX_minus_Rep2_smallRNA

description: Second reprogramming

value: no DOX


title: 2dd_DOX_minus_Rep1_smallRNA

description: First reprogramming


title: Sample8_Leigh_NT_2

source_name: Nuclear Transfer Stem Cell

value: Nuclear Transfer Derived


title: Sample9_Leigh_NT_fib1

source_name: Differentiated Nuclear Transfer Stem Cell

value: Differentiated NT-ESC


title: 14dd_DOX_plus_SSEA3_neg_Rep1_smallRNA

description: Second reprogramming

value: DOX days 0-14


title: Sample7_Leigh_NT_1


title: 10dd_DOX_plus_tot_Rep1_smallRNA

description: Second reprogramming

value: DOX days 0-10


title: hIPSC-T_P10_VTN_Rep1_mRNA

data_processing:
Reads were mapped with TopHat version 2.0.7 and Bowtie version 2.1.0 with default parameters against build hg19 of the human genome, and build 13 of the GENCODE human genome annotation
Samples were quantified with the Cufflinks package version 2.2.0.
Differential expression was performed using Cuffdiff 2.2.0 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA, including the small RNA fraction, was obtained by organic extraction followed by miRNeasy purification (Qiagen).
RNA-Seq Illumina libraries for mRNA profiling were prepared from 100 ng total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina).


title: hIPSC-T_P10_VTN_Rep2_mRNA


title: hIPSC-T_P10_MTG_Rep2_mRNA


title: Sample4_Leigh_iPS1_2

value: Human Pluripotent Stem Cell


title: Sample5_Leigh_iPS1_fib1


title: hIPSC-T_P10_MTG_Rep1_mRNA


title: Sample6_Leigh_iPS1_fib2


title: hIPSC_P15_Rep1_mRNA

source_name: hIPSCs from reprogrammed hiF cells (hIPSC)


title: 24dd_TRA_pos_DOX_plus_Rep4

source_name: reprogramming intermediates of hiF-T cells

value: DOX days 0-24


title: Sample3_Leigh_iPS1_1

value: polyA RNA


title: 24dd_TRA_pos_DOX_minus_Rep3_mRNA

value: DOX days 0-20


title: 24dd_TRA_pos_DOX_plus_Rep3_mRNA


title: 24dd_TRA_pos_DOX_minus_Rep4


title: Sample10_Leigh_NT_fib2

value: Fibroblast


title: Sample1_Leigh_fib1


title: 14dd_DOX_plus_TRA_plus_Rep1_mRNA (hiF)

source_name: reprogramming intermediates of hiF cells


title: Sample2_Leigh_fib2


title: 14dd_DOX_plus_TRA_plus_Rep2_mRNA (hiF)


title: BJ_P12_Rep1_mRNA


title: BJ_P12_Rep2_mRNA


title: hiF-T_P37_Rep1_mRNA


title: hiF-T_P15_Rep1_mRNA


title: MW47-Worker Allospecific (Polistes fuscatus) Nest Swap Trained to Faces

city: Ames

first: Ali

last: Berens

state: IA

address: 251 Bessey Hall

department: Ecology, Evolution, and Organismal Biology

institute: Iowa State University

data_processing:
Before transcriptome assembly, we removed extraneous adapter sequences and filtered for quality using Trimmomatic (v. 0.32; ILLUMINACLIP:TruSeq2-SE.fa:2:40:15 LEADING:3 TRAILING:  3 SLIDINGWINDOW:5:20 MINLEN:40).
We assembled the groomed transcriptomic short reads de novo using Trinity (default parameters, Version r20140717).
The final Trinity-produced Transcriptome Shotgun Assembly (TSA) was annotated with the mRNAmarkup protocol (Volker Brendel, unpublished; code available from http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php). mRNAmarkup: parameter option –F 5 5 10 10 90 60; MuSeqBox option –A 45 10 75
We aligned the raw paired-end reads to the TSA using Bowtie2 (default options, Version 2.2.4) and quantified the abundances of the transcripts for each library with eXpress (default options, Version 1.5.1)
Genome_build: TSA: Polistes metricus, transcriptome shotgun assembly GDHQ00000000.1 (GI:880915720)
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

organism: Polistes metricus

source_name: Worker Brain

extract_protocol:
Thirty minutes after the 40th test, wasps were freeze-killed in liquid nitrogen and stored at -80C until RNA extraction. We extracted total RNA from individual brains using an RNeasy Kit (Qiagen). 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

treatment_protocol: The foundresses samples were collected from P. metricus nests in Ann Arbor, MI in early spring 2012. We used a negative reinforced T-maze (previously described in Sheehan and Tibbetts (2011) Science) to train foundresses to two different sets of stimuli: simple patterns and P. fuscatus faces (since P. metricus have previously been shown to learn P. fuscatus faces than conspecific [Sheehan and Tibbetts (2011) Science]). To investigate social environment, we reared adult workers on non-natal nests (half conspecific, other half allospecific - P. fuscatus). After at least one week, these workers were tested on the T-maze using P. fuscatus faces as stimuli. Each wasp was trained in 40 sequential trials.

value: brain

tag: age

value: adult

tag: Sex

value: female

value: USA:Michigan:Ann Arbor


title: MW41-Worker Allospecific (Polistes fuscatus) Nest Swap Trained to Faces


title: MW32-Worker Allospecific (Polistes fuscatus) Nest Swap Trained to Faces


title: MW30-Worker Allospecific (Polistes fuscatus) Nest Swap Trained to Faces


title: Daxx_KO_RNA-seq

city: Bethesda

first: Gernot

last: Wolf

state: Maryland

address: 6 Center Drive

department: NICHD

institute: NIH

data_processing:
Reads were aligned to the mouse reference genome using JAGuaR v2.1 and BWA v0.7.10 for alignment to the reference transcriptome, allowing for alignment to annotated exon-exon junctions compiled from Ensembl 67.
For RNA-seq RPKM normalization, the number of exonic reads were calculated for protein coding genes, excluding mitochondrial and ribosomal genes, as well as the top 0.5% of expressed exons
RPKM expression values were calculated for all ERV families (annotated RepeatMasker LTR elements) with copy numbers above 100.
RPKM value for each family was calculated by normalizing agglomerated read coverage of all annotated genomic copies of that family in the reference genome to the agglomerated length of the family, as well as the total number of exonic reads.
Genome_build: mm9
Supplementary_files_format_and_content: normalized RPKM values

organism: Mus musculus

source_name: Daxx fl/fl Embryonic stem cell_tamoxifen-treated to induced Daxx -/-

growth_protocol: ES cells were grown on mitomycin C inactivated feeder cells in DMEM supplemented with 16% FBS, 104 U/mL LIF, HEPES, NEAA, L-glutamine, b-ME, and antibiotics

extract_protocol:
Total RNA was purified and depleted from genomic DNA using the RNeasy Plus minikit (Qiagen)
RNA libraries were prepared for sequencing using the TruSeq RNA Sample Prep Kit v2 (Illumina)

tag: strain

tag: genotype

value: Daxx fl/fl; RosaCreERT

value: 1 µM 4-hydroxytamoxifen for 48 hours followed by 3 days recovery


title: Daxx_WT_RNA-seq

source_name: Daxx fl/fl Embryonic stem cell_DMSO-treated

value: DMSO


title: Brg1-cKO-rep2

first: Brynn

middle: Nicole-Yoshiko

last: Akerberg

state: MA

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description: Nfatc1Cre;Brg1F/F mutant cardiac cushion (OFT/AVC valves) (repeat 2)

data_processing:
Reads were quality checked with FastX and low-quality reads were discarded (http://hannonlab.cshl.edu/fastx_toolkit/)
Quality-checked reads were aligned using mm10 reference genome with Bowtie 2 (Langmead and Salzberg., 2012), SAMtools (Li et al., 2009) and TopHat 2 (Roberts et al., 2012)
TopHat 2 output (mapped reads/accepted_hits) were used to generate a counts table with HTSeq (Anders et al., 2014)
Differential expression of wildtype and Brg1-mutant tissue was analyzed with EdgeR (paired samples) (Robinson et al., 2009)
Genome_build: mm10
Supplementary_files_format_and_content: EdgeRcountstable.txt

source_name: cardiac cushion

extract_protocol:
Embryos were harvested on ice and in sterile PBS and cardiac cushions were isolated using GFP signal from Cre-reporter. Tissue extracted was immediately flash frozen in Trizol and stored at -80 degrees.
Total RNA was rRNA-depleted using Ribo-Zero (EpiBio) kit and libraries were prepared using manufacturer's recommendations for ScriptSeq V2 RNA-seq Library (EpiBio) kit.

value: embryonic day 14.5

value: dissected cardiac cushion

tag: genotype/variation

value: Nfatc1Cre;Brg1F/F mutant


title: MW40-Worker Conspecific Nest Swap Trained to Faces


title: WT-rep2

description: Wildtype cardiac cushion (OFT/AVC valves) (repeat 2)

value: Wildtype


title: MW25-Worker Conspecific Nest Swap Trained to Faces


title: Brg1-cKO-rep1

description: Nfatc1Cre;Brg1F/F mutant cardiac cushion (OFT/AVC valves) (repeat 1)


title: WT-rep1

description: Wildtype cardiac cushion (OFT/AVC valves) (repeat 1)


title: M91-Foundress Trained to Faces

source_name: Foundress Brain


title: hiF_P7_Rep1_mRNA

source_name: human inducible fibroblasts-like cells (hiF)


title: hiF_P9_Rep3_mRNA


title: hiF_P5_Rep1_mRNA


title: hiF-T_P13_Rep1_mRNA

source_name: immortalized human inducible fibroblasts-like cells (hiF-T)


title: hiF_P9_Rep2_mRNA


title: 13dd_DOX_plus_LSD1_SSEA3_pos_Rep1_mRNA

value: DOX days 0-13; LSD1 inhibition


title: hiF-T_P12_Rep1_mRNA


title: hiF_P9_Rep1_mRNA


title: MW21-Worker Conspecific Nest Swap Trained to Faces


title: 13dd_DOX_plus_LSD1_TRA_pos_Rep1_mRNA


title: M79-Foundress Trained to Faces


title: MW42-Worker Conspecific Nest Swap Trained to Faces


title: M30-Foundress Trained to Faces


title: M5-Foundress Trained to Patterns


title: 5dd_DOX_plus_LSD1_Rep1_mRNA

value: DOX days 0-5; LSD1 inhibition


title: ER_ChIPSeq

city: Worcester

first: Richard

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

data_processing:
Basecalls performed using CASAVA version 1.8.3
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND in the CASAVA pipeline.
No duplicate filtering was applied.
Coverage track was generated by the ReadCoverage program of the USeq suite after extending reads to the fragment length estimated by the fragment-size-estimation.sh utility of SICER  (200 bp).
Genome_build: mm9
Supplementary_files_format_and_content: Values in coverage tracks are reads per million total reads (RPM).

source_name: splenic B cells

growth_protocol: B cells were isolated from spleens by depletion of RBCs by lysis in Gey's solution for 5 min on ice and by depletion of T cells with a cocktail of anti-T cell reagents, anti-CD4 (GK1.5), anti-CD8 (3.168), and anti-Thy1 (HO13.4 and J1J10), followed by anti–rat κ chain mAb (MAR18.5) and guinea pig complement (Pelfreeze Biochem).Viable cells were isolated by flotation on Ficoll/Hypaque gradients (δ = 1.09) and cultured in RPMI 1640 (BioWhittaker), with 10% FCS (Hyclone), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (all from GIBCO BRL), 50 µM 2-ME (Sigma Chemical Co.), and 50 ng/ml human BAFF/BLyS (Human Genome Sciences).

extract_protocol:
2 × 10e7 live cells were resuspended in SBSS and cross-linked with 1% formaldehyde for 5 min at 37°C. Cross-linking was quenched by addition of glycine to 125 mM and incubating for 5 min at room temperature. Cross-linked cells were sonicated on ice for twenty 10-sec bursts, cooling on ice for 15 sec between bursts. A total of 2 × 10e6 cell equivalents were used per ChIP. Lysates were incubated with the appropriate antibodies overnight at 4°C. Protein A or G Dynabeads (Invitrogen) were added to samples for 2 h,followed by washing with low-salt (150 mM NaCl), high-salt (500 mM NaCl), and LiCl salt buffers, and finally with TE. The complexes were then eluted overnight at 65°C in the presence of 1 mg/ml RNAse A (Sigma-Aldrich). The following day, the samples were incubated with 10 mg/ml proteinase K (Sigma-Aldrich) at 55 °C overnight. Following phenol:chloroform and chloroform extractions, DNA was precipitated using 1 mg/ml glycogen (Roche) and 95% ethanol overnight at −20°C.
DNA fragments were made blunt using the END-IT DNA repair kit (Epicentre) and a 3'-dA overhang added using Exo-Minus Klenow DNA Polymerase (Epicentre). Illumina paired-end (PE) adapters were added using the Fast-Link DNA Ligation kit (Epicentre), and the fragments were amplified twice using Illumina PE primers and PfuUltra II Fusion HS DNA polymerase (Stratagene). Each round of PCR was followed by gel purification and sizing of the fragments.

treatment_protocol: LPS (25 μg/ml) (Sigma-Aldrich) and anti–δ-dextran (10 ng/ml) was added to induce switching to IgG3.

value: spleen

tag: cell type

value: B cells

tag: chip antibody

value: anti-estrogen receptor (Santa Cruz Biotechnology sc-8002X)

value: wildtype


title: aidko_Nbs1_Exp2_ChIPSeq

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND in the CASAVA pipeline. Unaligned reads were aligned by Bowtie (v1.0.0) using the options -n2 -strata -m 1 --chunkmbs 128, and combined with the ELAND alignments.
Reads were filtered to allow only 2 duplicates.
Coverage track was generated by the ReadCoverage program of the USeq suite after extending reads to the fragment length estimated by the fragment-size-estimation.sh utility of SICER  (140 bp).
Genome_build: mm9
Supplementary_files_format_and_content: Values in coverage tracks are reads per million total reads (RPM).

value: anti-Nbs1 (Abcam, ab32074)

value: aid-/-


title: ER-Aid_ChIPSeq

data_processing:
Basecalls performed using CASAVA version 1.8.3
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND in the CASAVA pipeline.
No duplicate filtering was applied.
Coverage track was generated by the ReadCoverage program of the USeq suite after extending reads to the fragment length estimated by the fragment-size-estimation.sh utility of SICER  (235 bp).
Genome_build: mm9
Supplementary_files_format_and_content: Values in coverage tracks are reads per million total reads (RPM).


title: hiF_P7_Rep2_mRNA


title: WT_Nbs1_Exp2_ChIPSeq

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND in the CASAVA pipeline. Unaligned reads were aligned by Bowtie (v1.0.0) using the options -n2 -strata -m 1 --chunkmbs 128, and combined with the ELAND alignments.
Reads were filtered to allow only 2 duplicates.
Peaks were called using using HOMER findPeaks in factor mode, using fragment lengths estimated by the makeTagDirectory program. findPeaks was run with the corresponding aidko library as control using a window size of 500 bp and a fold change threshold of 2.0. An empirical filtering scheme based on total peak tag counts was applied to eliminate questionable calls. The filtering thresholds were (tag count, WT/aidko threshold, local background threshold): >52, 2.0, 6.0; >52, 2.2, 4.0; ≥22, 2.2, 6.0; ≥19, 4.0, 10.0. For subsequent downstream analyses, the peak coordinates were extended 1000 bp from the center.
Coverage track was generated by the ReadCoverage program of the USeq suite after extending reads to the fragment length estimated by the fragment-size-estimation.sh utility of SICER  (140 bp).  Stranded coverage tracks were generated by the makeUCSCfile program of HOMER.
Genome_build: mm9
Supplementary_files_format_and_content: Values in coverage tracks are reads per million total reads (RPM).


title: M4-Foundress Trained to Patterns

value: brain

value: adult

value: female


title: 24dd_TRA_pos_DOX_plus_Rep1_mRNA

value: DOX days 0-24


title: M15-Foundress Trained to Patterns

value: USA:Michigan:Ann Arbor


title: 24dd_TRA_pos_DOX_minus_Rep2_mRNA

value: DOX days 0-19


title: M67-Foundress Trained to Faces


title: M1-Foundress Trained to Patterns


title: 24dd_TRA_pos_DOX_minus_Rep1_mRNA


title: FW44-Worker Allospecific (Polistes metricus) Nest Swap Trained to Faces

data_processing:
Before transcriptome assembly, we removed extraneous adapter sequences and filtered for quality using Trimmomatic (v. 0.32; ILLUMINACLIP:TruSeq2-SE.fa:2:40:15 LEADING:3 TRAILING:  3 SLIDINGWINDOW:5:20 MINLEN:40).
We assembled the groomed transcriptomic short reads de novo using Trinity (default parameters, Version r20140717).
The final Trinity-produced Transcriptome Shotgun Assembly (TSA) was annotated with the mRNAmarkup protocol (Volker Brendel, unpublished; code available from http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php). mRNAmarkup: parameter option –F 5 5 10 10 90 60; MuSeqBox option –A 45 10 75
We aligned the raw paired-end reads to the TSA using Bowtie2 (default options, Version 2.2.4) and quantified the abundances of the transcripts for each library with eXpress (default options, Version 1.5.1)
Genome_build: TSA: Polistes fuscatus, transcriptome shotgun assembly GDFS00000000.1 (GI:856617606)
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

organism: Polistes fuscatus

source_name: worker brain

treatment_protocol: The foundresses samples were collected from P. fuscatus nests in Ann Arbor, MI in early spring 2012. We used a negative reinforced T-maze (previously described in Sheehan and Tibbetts (2011) Science) to train foundresses to two different sets of stimuli: simple patterns and P. fuscatus faces. To investigate social environment, we reared adult workers on non-natal nests (half conspecific, other half allospecific - P. metricus). After at least one week, these workers were tested on the T-maze using P. fuscatus faces as stimuli. Each wasp was trained in 40 sequential trials.


title: FW11-Worker Allospecific (Polistes metricus) Nest Swap Trained to Faces


title: 20dd_DOX_plus_TRA_plus_Rep2_mRNA

value: DOX days 0-20


title: FW32-Worker Allospecific (Polistes metricus) Nest Swap Trained to Faces


title: 20dd_DOX_plus_TRA_plus_Rep1_mRNA


title: RNA_pol2_ChIPSeq

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND in the CASAVA pipeline.
Reads were filtered to allow only 2 duplicates.
Peaks were called by SICER v1.1 using the parameters W200, G600, E1000.
Coverage track was generated by the ReadCoverage program of the USeq suite after extending reads to the fragment length estimated by MACS v1.4.1  (235 bp).
Genome_build: mm9
Supplementary_files_format_and_content: Values in coverage tracks are reads per million total reads (RPM).

value: anti-RNA polymerase II (Millipore, 04-1572)


title: FW47-Worker Conspecific Nest Swap Trained to Faces


title: 24dd_TRA_neg_DOX_plus_Rep1_mRNA


title: FW24-Worker Allospecific (Polistes metricus) Nest Swap Trained to Faces


title: 5dd_DOX_plus_Rep3_mRNA

value: DOX days 0-5; LSD1 control


title: 24dd_TRA_neg_DOX_minus_Rep1_mRNA


title: FW25-Worker Conspecific Nest Swap Trained to Faces


title: 14dd_DOX_plus_tot_Rep1_mRNA

value: DOX days 0-14


title: 14dd_DOX_plus_SSEA3_neg_Rep1_mRNA


title: FW28-Worker Conspecific Nest Swap Trained to Faces


title: F55-Foundress Trained to Faces

source_name: foundress brain


title: FW10-Worker Conspecific Nest Swap Trained to Faces


title: 10dd_DOX_plus_SSEA3_neg_Rep1_mRNA

value: DOX days 0-10


title: q5_0

data_processing:
Data processing was performed using the Tuxedo RNAseq suite (Trapnell et al., 2012). 52 single cells displayed more than 50% alignment rate and 100,000 reads per sample and were therefore considered for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

extract_protocol:
The single-cell RNA-seq libraries were prepared from MEF-depleted hiF-T cells at day 10 of reprogramming directly sorted in lysis buffer at single cell using an ARIA facs sorter (BD).
Library preparation was performed using SMART-seq2 protocol with minor modifications (Trombetta et al., 2014) on 96 cells

tag: well number

tag: reprogramming time point (day)


title: 14dd_DOX_plus_SSEA3_pos_Rep2_mRNA


title: 14dd_DOX_plus_SSEA3_pos_Rep1_mRNA


title: F42-Foundress Trained to Faces


title: F29-Foundress Trained to Faces


title: F35-Foundress Trained to Faces


title: 10dd_DOX_plus_SSEA3_pos_Rep2_mRNA


title: 10dd_DOX_plus_tot_Rep1_mRNA


title: 10dd_DOX_plus_SSEA3_pos_Rep1_mRNA


title: F25-Foundress Trained to Faces


title: F3-Foundress Trained to Patterns


title: 8dd_DOX_plus_Rep2_mRNA

value: DOX days 0-8


title: 5dd_DOX_plus_Rep2_mRNA

value: DOX days 0-5


title: 8dd_DOX_plus_Rep1_mRNA


title: F17-Foundress Trained to Patterns


title: F34-Foundress Trained to Patterns


title: F52-Foundress Trained to Patterns


title: insituDNaseHiC-WG-patski-rep2

city: Seattle

first: Xinxian

last: Deng

state: WA

address: 1959 NE Pacific St.

department: Laboratory Medicine and Pathology

institute: University of Washington

description: in situ DNase Hi-C experiment in Patski cells

data_processing:
First, we performed an exhaustive search and cleaning of the Illumina primer and adaptor sequences in the full-length reads and extracted the remaining read fragments of various lengths from 25-80 bp.
A pseudo-spretus genome was assembled by replacing available SNPs between C57BL/6J and M. spretus (Sanger) into the BL6 reference genome.
We then mapped each end of these cleaned paired-end reads separately to the C57BL/6J genome (mm9 assembly) and the pseudo-spretus genome using BWA/v0.5.9. We only retained the reads that mapped uniquely, allowing at most 3 mismatches and requiring mapping quality MAPQ >= 30. Only high-quality uniquely-mapped reads were used for assignment to each haploid genome based on available SNPs.
To eliminate the bias due to the PCR duplication step, we removed redundant paired-end reads. We define two reads as redundant if both ends of the reads are mapped to identical locations in the genome.
Genome_build: mm9
Supplementary_files_format_and_content: txt files, containing uniquely mapped and non-redundent read pairs. The files are tab-delimited. The columns are #1 read identifier, #2 strand of the 1st end, #3 mapped chr of the 1st end, #4 mapped coordinate of the 1st end, #5 allele of 1st read (ref: BL6; alt: spretus; both-ref; allele-uncertain reads), #6 sequence of 1st end, #7 strand of the 2nd end, #8 mapped chr of the 2nd end, #9 mapped coordinate of the 2nd end, #10 allele of 2nd read (ref: BL6; alt: spretus; both-ref; allele-uncertain reads), #11 sequence of 2nd end.

organism: Mus musculus x Mus spretus

source_name: Patski cells

extract_protocol: DNase Hi-C or in situ DNase Hi-C:  Cells are cross-linked with formaldehyde; chromatin is then randomly fragmented by DNase I. The resulting chromatin fragments are end-repaired and dA-tailed, then marked with a biotinylated internal adaptor; and proximity ligation is carried out inside individual nuclei to favor ligation events between the cross-linked DNA fragments. The resulting DNA sample contains ligation products consisting of chimeric DNA fragments that were originally in close spatial proximity in the nucleus, marked with biotin at the junction. A whole-genome chromatin interaction library is created by shearing the DNA and selecting the biotin-containing fragments with streptavidin magnetic beads. After linear library amplification, a DNase Hi-C library is generated and can be sequenced to identify whole-genome chromatin contacts.

tag: experiment

value: in situ DNase Hi-C

tag: replicate


title: 5dd_DOX_plus_Rep1_mRNA


title: insituDNaseHiC-WG-patski-rep1


title: 2dd_DOX_plus_Rep1_mRNA

value: DOX days 0-2


title: 2dd_DOX_minus_Rep1_mRNA

value: no DOX


title: insituDNaseHiC-WG-brain-rep1

description: in situ DNase Hi-C experiment in F1 hybrid mouse brain cells

source_name: brain cells


title: 2dd_DOX_minus_Rep2_mRNA


title: Eed_ff

status: Public on Jul 15 2015

city: Aurora

first: Tobias

last: Neff

state: CO

department: Pediatric Oncology

institute: University of Colorado Denver AMC

data_processing:
Basecalling was performed by Illumina’s RTA (Real-Time Analysis) software version 1.18.61 with QTable version 6.  CASAVA version 1.8.2 was used to demultiplex samples. Illumina Chastity quality filtering was performed.
Alignment was performed using GSNAP (version 2012-07-20): gsnap -d mm9 -v snp128_strict_wholeChrs --use-splicing=ucscRefGeneSpliceSites_mm9 --gunzip --max-mismatches=0.06 -i2 -n1 -Q --nofails -B5 -t12 -A sam *.fastq.gz > *.sam. Sam format was converted to Bam format using  Samtools. Bam-files were sorted using Samtools.
Differential gene expression was determined using Cuffdiff. Genes with low levels (<0.5 in both samples, or 0 in one and <5 in the other sample) were excluded. Genes with 'Fail' and 'Notest' Cuffdiff status were exluded.
For GSEA, a ranked genelist between 2 conditions was created using the Cuffdiff log2-value. miRNAs and snoRNA were excluded from the ranked genelist used for GSEA.
To generate FPKM-files, Cufflinks was performed using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output, including Gene Symbol, locus, FPKM-value (Tab-delimited text files).

source_name: Bone marrow

growth_protocol: Expanded in methylcellulose in the presence of IL3, IL6, SCF

extract_protocol:
RNA was isolated using Qiagen RNAeasy kit
Illumina Stranded mRNA kit

value: bone marrow

value: LSK-cells transformed with MLL-AF9


title: Eed_ko


title: TKO_DAXX_KO_groundState_RNA_Seq

city: Houston

first: Quanyuan

last: He

state: TX

address: One Baylor Plaza, Room S307

institute: Baylor College of Medicine

description: mRNA from DAXX knockout TKO cel cultured with ES medium with 2i and VC (ground state)

data_processing:
The mouse reference genome, transcriptome, and annotation data were downloaded from Illumina iGenomes (version: UCSC mm9, download time: 2015/3/10). Repetitive element definition and location were downloaded from UCSC genome tab browser (RepeatMasker).
Paired-end RNA-seq reads were aligned to the genome (mm9) using Tophat with default parameters (Bowtie2 (version 2.2.4) for alignment).
Transcript assembly was done by Cufflinks and then all the assembly files from each sample were merged to a reference annotation based transcript assembly for use in downstream differential analysis.
Differential analysis was done by Cuffdiff, which calculates expression in two or more samples and tests the statistical significance of each transcript. To compare the expression level of coding genes across samples, weused FPKM (fragments per kilobase of exon per million fragments mapped) calculated by Cufflinks to represent expression levels.
For expression analysis of repetitive elements, all elements <5Kbps in length were removed. The RPKMs (Reads Per Kilobase per Million mapped reads) for repetitive elements were calculated by a homemade R script.
Genome_build: mm9
Supplementary_files_format_and_content: gene FPKM

source_name: mouse ES cell (TKO)

growth_protocol: Cell were cultured in two mediums: 1) regular ES cell medium (regular state);  2) ES cell medium with 2i and VC (ground state). [2i: (MEK inhibitor PD0325901 at 1 μM  (StemRD, PD-10) and GSK3b inhibitor CHIR99021 at 3 μM (StemRD, CHIR-50)) and Vitamin C (L-ascorbic acid 2-phosphate, Sigma, A8960) at 100 μg/ml for 72hrs).

extract_protocol:
Cytoplasmic RNAs were extracted using the RNeasy Mini Kit (QIAGEN), with mRNAs captured using oligo-dT magnetic beads and then fragmented.
First-strand cDNAs were generated using random primers, and second-strand cDNAs were synthesized in the presence of dUTP.   The double-stranded cDNAs were end repaired, followed by addition of a 3’A and then Y-shaped adaptors to each end.

value: embryo stem cell

value: three DNMTs Knocktout

tag: medium

value: medium with 2i and VC


title: TKO_DAXX_KO_regularState_RNA_Seq

description: mRNA from DAXX knockout TKO cell cultured with ES medium without 2i and VC (regular state)

value: medium without 2i and VC


title: J1_DAXX_KO_groundState_RNA_Seq

description: mRNA from DAXX knockout J1 cel cultured with ES medium with 2i and VC (ground state)

source_name: mouse ES cell (J1)

value: WT


title: TKO_regularState_RNA_Seq

description: mRNA from TKO cell in ES medium without 2i and VC (regular state)


title: TKO_groundState_RNA_Seq

description: mRNA from TKO cell in ES medium with 2i and VC (ground state)


title: J1_DAXX_KO_regularState_RNA_Seq

description: mRNA from DAXX knockout J1 cell cultured with ES medium without 2i and VC (regular state)


title: J1_groundState_RNA_Seq

description: mRNA from J1 cell in ES medium with 2i and VC (ground state)


title: BEX_2

city: Stockholm

first: Nikolaos

last: Volakakis

address: Nobels vag 3

country: Sweden

institute: LICR

description:
Sample 16
DMSO_BEX.txt, DMSO_BEX_deseq.txt

data_processing:
For expression values, we aligned reads using bowtie 0.12.7, option --best, against the genome and transcriptome (Refseq) in mm9 coordinates
Non-uniquely mapped reads were removed
Rpkmforgenes options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE.
Analysis with DeSEQ (Anders & Huber 2010) for samples 12-19 and DeSeq2 (Love et al. 2014) for samples 1-11
Genome_build: mm9
Supplementary_files_format_and_content: RPKM_deseq_RFP_highSyn.txt: Gene expression values (tab-limited text) and Deseq analysis
Supplementary_files_format_and_content: RPKM_deseq_RFP_highSynNurr.txt: Gene expression values (tab-limited text) and Deseq analysis
Supplementary_files_format_and_content: DMSO_BEX.txt: Gene expression values (tab-limited text)
Supplementary_files_format_and_content: refseq_SCR_SHN.txt: Gene expression values (tab-limited text)
Supplementary_files_format_and_content: DMSO_BEX_deseq.txt: Gene expression values (tab-limited text) and Deseq analysis

source_name: primary E13.5 midbrain cultures

growth_protocol: Primary ventral midbrain cultures were obtained from E13.5 Pitx3eGFP/+ mouse embryos. The anlage of the substantia nigra was microdissected, dissociated with the neural tissue dissociation kit P from MACS (Miltenyi Biotec) and plated at 50000 cells/mm2 on poly-ornithine- and laminin- (Sigma) coated plates in attachment medium consisting of stock medium 1:1 DMEM/12:Neurobasal differentation medium (Gibco), 1x B27 (Gibco), 1x N2 (Gibco), 1 mM sodium pyruvate (Gibco), 0.25% bovine serum albumin (Sigma), 2 mM glutamine (Gibco), after addition of 3% FCS (PAA, GE Healthcare) and 20 ng/ml bFGF (R&D Systems). After 24 hr the medium was replaced with differentiation medium consisting of stock medium supplemented with 100 μM ascorbic acid (Sigma) and 1% FCS. The first 48 hr after adhesion, the stock medium was also supplemented with 10 ng/ml recombinant human GDNF (R&D systems) and 20 ng/ml recombinant human BDNF (R&D systems).

extract_protocol:
Total RNA was prepared using the RNeasy micro kit (Qiagen), treated with DNase (Qiagen).
For samples 1-11 RNA sequencing was performed using the SMARTER Ultra Low RNA kit for Illumina Sequencing (Clontech) and the generated cDNA was tagmentated, amplified and purified using the Nextera XT DNA sample preparation kit (Illumina), while for the rest of the libraries the Smart-Seq2 protocol (Picelli et al. 2013) was used.

value: primary E13.5 midbrain cultures

value: midbrain

value: treated with 100nM Bexarotene for 24 hr and FACS-sorted for GFP


title: SCR

description:
Sample 18
refseq_SCR_SHN.txt

source_name: primary E11.5 midbrain cultures

value: primary E11.5 midbrain cultures

value: infected with scrambled lentivirus for 48 hr and FACS-sorted for GFP


title: BEX_3

description:
Sample 17
DMSO_BEX.txt, DMSO_BEX_deseq.txt


title: SHN

description:
Sample 19
refseq_SCR_SHN.txt

value: infected with sh Nurr1 lentivirus for 48 hr and FACS-sorted for GFP


title: BEX_1

description:
Sample 15
DMSO_BEX.txt, DMSO_BEX_deseq.txt


title: J1_regularState_RNA_Seq

description: mRNA from J1 cell in ES medium without 2i and VC (regular state)


title: DMSO_1

description:
Sample 12
DMSO_BEX.txt, DMSO_BEX_deseq.txt

value: treated with DMSO for 24 hr and FACS-sorted for GFP


title: DMSO_2

description:
Sample 13
DMSO_BEX.txt, DMSO_BEX_deseq.txt


title: DMSO_3

description:
Sample 14
DMSO_BEX.txt, DMSO_BEX_deseq.txt


title: SYN_HIGH_NURR1_2

description:
Sample 10
RPKM_deseq_RFP_highSynNurr.txt

value: infected with a-synuclein and Nurr1 lentivirus for 5days


title: SYN_HIGH_NURR1_1

description:
Sample 9
RPKM_deseq_RFP_highSynNurr.txt


title: SYN_HIGH_NURR1_3

description:
Sample 11
RPKM_deseq_RFP_highSynNurr.txt


title: RFP2_3

description:
Sample 5
RPKM_deseq_RFP_highSyn.txt, RPKM_deseq_RFP_highSynNurr.txt

value: infected with RFP lentivirus for 5 days


title: SYN_HIGH_2

description:
Sample 7
RPKM_deseq_RFP_highSyn.txt

value: infected with a-synuclein and control lentivirus for 5days


title: RFP1_3

description:
Sample 3
RPKM_deseq_RFP_highSyn.txt, RPKM_deseq_RFP_highSynNurr.txt


title: RFP1_2

description:
Sample 2
RPKM_deseq_RFP_highSyn.txt, RPKM_deseq_RFP_highSynNurr.txt


title: RFP2_1

description:
Sample 4
RPKM_deseq_RFP_highSyn.txt, RPKM_deseq_RFP_highSynNurr.txt


title: RFP1_1

description:
Sample 1
RPKM_deseq_RFP_highSyn.txt, RPKM_deseq_RFP_highSynNurr.txt


title: SYN_HIGH_1

description:
Sample 6
RPKM_deseq_RFP_highSyn.txt


title: PRMT5 control 2

city: Miami

first: Fan

last: Liu

state: Florida

address: 1501 NW 10th Ave

department: Biochemistry and Molecular Biology

institute: University of Miami

data_processing:
Illumina Casava1.80 software used for basecalling.
tophat was used to do the alignment and mapped to mm10 mouse genome assembly
samtools was used to do the sort and index
wig files generated using python and bam2wig
Genome_build: mm10
Supplementary_files_format_and_content: wig files

extract_protocol:
RNA was isolated from hematopoietic stem and progenitor cells using the Qiagen RNeasy Micro kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hematopoetic stem and progenitor cells

value: control


title: PRMT5 knockout 2

value: PRMT5 knockout


title: mmu_Ezh2_RNASeq_1

city: Corvallis

first: David

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

description: RNA-Seq in Ezh2-/- mES cells, Replicate 1

data_processing:
RNA-Seq reads were aligned to mm10 with TopHat v2.0.9 using the parameters –-no-novel-juncs and --no-coverage-search and using a gtf file downloaded from UCSC Table browser for ensembl genes.
Comparison between wild-type and Ezh2-/- RNA-Seq reads was performed with Cuffdiff v2.2.1, the default parameters, and the ensembl gtf files from UCSC Table browser
genome_build: mm10

source_name: embryonic cells

growth_protocol: Mouse ES cell lines were maintained in ES medium: DMEM (Dulbecco’s modified Eagle’s medium- Life Technologies) supplemented with 15% fetal calf serum (Life Technologies), 0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Life Technologies), 0.1 mM nonessential amino acid (Life Technologies), 1% of nucleoside mix (Sigma), 1000 U/ ml recombinant leukemia inhibitory factor (LIF; Chemicon), and 50 U/ml penicillin/streptomycin (Life Technologies).

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
All mRNA libraries were prepared according to the manufacturer’s instructions (Directional (strand specific) mRNA-Seq sample preparation kit, Illumina).

treatment_protocol: None.


title: mmu_Eed_RNASeq_1

description: RNA-Seq in Eed-/- mES cells, Replicate 1

data_processing:
RNA-Seq reads were aligned to mm10 with TopHat v2.0.9 using the parameters –-no-novel-juncs and --no-coverage-search and using a gtf file downloaded from UCSC Table browser for ensembl genes.
Comparison between wild-type and Eed-/- RNA-Seq reads was performed with Cuffdiff v2.2.1, the default parameters, and the ensembl gtf files from UCSC Table browser
genome_build: mm10

value: Eed-/-


title: mmu_Ezh2_RNASeq_2

description: RNA-Seq in Ezh2-/- mES cells, Replicate 2


title: mmu_Eed_RNASeq_2

description: RNA-Seq in Eed-/- mES cells, Replicate 2


title: PRMT5 control 1


title: mESC_wt_RNASeq_2

description: RNA-Seq in wild-type mES cells, Replicate 2

data_processing:
RNA-Seq reads were aligned to mm10 with TopHat v2.0.9 using the parameters –-no-novel-juncs and --no-coverage-search and using a gtf file downloaded from UCSC Table browser for ensembl genes.
Comparison between wild-type and Ezh2-/-, Jarid2-/-, and Eed-/- RNA-Seq reads was performed with Cuffdiff v2.2.1, the default parameters, and the ensembl gtf files from UCSC Table browser
genome_build: mm10

value: wild-type


title: mESC_Jarid2_RNASeq_2

description: RNA-Seq in Jarid2-/- mES cells, Replicate 2

data_processing:
RNA-Seq reads were aligned to mm10 with TopHat v2.0.9 using the parameters –-no-novel-juncs and --no-coverage-search and using a gtf file downloaded from UCSC Table browser for ensembl genes.
Comparison between wild-type and Jarid2-/- RNA-Seq reads was performed with Cuffdiff v2.2.1, the default parameters, and the ensembl gtf files from UCSC Table browser
genome_build: mm10


title: SYN_HIGH_3

description:
Sample 8
RPKM_deseq_RFP_highSyn.txt


title: mESC_wt_RNASeq_1

description: RNA-Seq in wild-type mES cells, Replicate 1


title: mmu_ezh2_INPUT

description: INPUT DNA for Ezh2-/- mES cells

data_processing:
ChIP-Seq reads were aligned using Bowtie v0.12.9 to the mm9 genome index with the following parameters: -S -m 1 -a --best -q and with -l and -n parameters adjusted according to read length.
Significant peaks were identified with SICER v1.1, and the following parameters: FDR 0.05, redundancy threshold: 1, fragment size: 150, species: mm9, effective genome size: .79 for samples with aligned read length of 45, 46 or 50, .70 for those with aligned read length of 26
genome_build: mm9

extract_protocol:
Cross-linked cell pellet was resuspended in SDS-ChIP buffer and chromatin was sonicated to around 200-500 bp. Sonicated chromatin were incubated with 5-10 µg antibody overnight at 4oC. After overnight incubation, protein A or G agarose beads were added to the ChIP reactions and incubated for 2-3 hours at 4oC to IP chromatin. Subsequently, beads were washed twice with 1 ml of low salt wash buffer, once with 1 ml of high salt wash buffer, once with 1 ml of LiCl wash buffer, and twice with 1 ml of TE buffer. The chromatin was eluted and reverse-crosslinked at 65oC overnight in SDS elution buffer (300 µl). The next day, an equal volume of TE was added (300µl). ChIP DNA was treated with 1 µl of RNaseA (10 mg/ml) for 1 hour, and with 3 µl of proteinase K (20 mg/ml) for 3 hours at 37ºC, and purified using phenol-chloroform extraction, followed by QIAquick PCR purification spin columns (Qiagen). Finally, ChIP-DNA was eluted from the column with 40 µl of water. Input ChIP samples were reserved after the sonication and continued from reverse cross-linking step until the end, same as other ChIP samples.
Purified ChIP DNA was measured in Qubit (Invitrogen). 2-10 ng of purified ChIP DNA was used to prepare sequencing libraries, using NEB next generation ChIP sequencing Kit (NEB) and Illumina ChIP seq kit (illumina) according to the manufacture’s instructions. All libraries were checked through a Bio-analyzer for quality control purposes. ChIP sequencing was performed using illumina Hiseq 2000 sequencing system. Raw data were processed through the illumina software pipeline.

treatment_protocol: Cells were cross-linked directly on 15 cm dishes with 37% formaldehyde solution (Calbiochem) to a final concentration of 1% for 8 min at room temperature with gentle shaking. The reaction was quenched by adding 2.5M glycine to a final concentration of 0.125 M. Cells were washed twice with PBS, trypsinized and washed twice with PBS. Cells were either snap frozen or proceeded to next steps of ChIP protocol.


title: mESC_Jarid2_RNASeq_1

description: RNA-Seq in Jarid2-/- mES cells, Replicate 1


title: mmu_ezh2_PolII

description: ChIP-Seq for Pol-II in Ezh2-/- mES cells


title: mmu_wt_PolII

description: ChIP-Seq for Pol-II in wild-type mES cells


title: mmu_ezh2_H3K27ac_ChIPSeq

description: ChIP-Seq for H3K27ac in wild-type Ezh2-/- cells


title: mmu_wt_INPUT_2

description: INPUT DNA in wild-type mES cells, Replicate2


title: mmu_wt_INPUT_3

description: INPUT DNA in wild-type mES cells, Replicate3


title: mmu_wt_H3K4me3_ChIPSeq

description: ChIP-Seq for H3K4me3 in wild-type mES cells


title: mmu_wt_H3K27me3_ChIPSeq

description: ChIP-Seq for H3K27me3 in wild-type mES cells


title: mmu_wt_INPUT_1

description: INPUT DNA in wild-type mES cells, Replicate1


title: mmu_wt_H3K27ac_ChIPSeq

description: ChIP-Seq for H3K27ac in wild-type mES cells


title: PRMT5 knockout 1


title: H143 Yeast A

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

data_processing:
Filtering: Paired-end reads were pre-processed to remove high copy sequences that were not of interest; specifically, all read pairs were searched against the mitochondrial genome, a representative full length MAGGY transposon, and the 45S rDNA locus using bowtie2 version 2.0.0-beta7 with a minimum fragment length (-I) of 50 and a maximum fragment length (-X) of 800.
Alignment and abundance estimation: Relative abundances (reported as FPKM values) for each transcript in each sample were estimated by aligning read pairs to the transcriptome assembly for the corresponding genome with bowtie2 version 2.0.0-beta7 with a maximum fragment length (-X) of 800, allowing all alignments (-a), and submitting the output to eXpress version 1.3.1 specifying strand-specific read pairs (--fr-stranded).
Genome_build: The following sources of Hc genomic sequences were used: version 2 of the H88, H143, and G168AR genome assemblies from the BROAD Institute, retrieved on 6/15/2011 from http://www.broadinstitute.org/annotation/genome/dimorph_collab/MultiDownloads.html and the 11/30/2004 version of the G217B genome assembly from the Genome Sequencing Center at Washington University (GSC) as mirrored at http://histo.ucsf.edu/downloads/.  The transcriptomes used for read alignment in the data processing steps were assembled from the paired-end sequencing data using a genome-guided approach, as described in the manuscript, and are available from http://histo.ucsf.edu/downloads/.
Supplementary_files_format_and_content: For each sample, per-transcript abundance estimates and related statistics are given in eXpress results.xprs format, as documented on http://bio.math.berkeley.edu/eXpress/manual.html#output.  The eXpress target_id column corresponds to the transcript IDs for the corresponding transcriptomes at http://histo.ucsf.edu/downloads/.  Additionally, normalized expression ratios and annotations are supplied as a single matrix table: Supplementary_File_13.tdt. Each row corresponds to an assembled transcript orthogroup, containing at most one transcript from each of the four strains. The columns are as follows: "G217B gene name" and "G217B annotation" -- short gene names and gene annotations from Inglis et al. (Eukaryotic cell 12:828) for the predicted gene(s) with additional annotations added in this work, pipe delimited; [G217B, G186AR, H88, H143] transcript: (4 columns) assembled transcript name; [G217B, G186AR, H88, H143] predicted gene: (4 columns) GSC and BROAD predicted genes overlapping the assembled transcript. Where multiple predicted genes overlap a single transcript, they are pipe (|) delimited ; [G217B, G186AR, H88, H143] Pfam accession: (4 columns) Accessions for all unique Pfam-A hits to the protein sequence translated from the assembled transcript. Pipe delimited, no e-value threshold; [G217B, G186AR, H88, H143] Pfam name: (4 columns) Short domain names, corresponding to the above accessions, pipe delimited; [G217B, G186AR, H88, H143] Pfam description: (4 columns) Domain descriptions, corresponding to the above accessions, pipe delimited; [G217B, G186AR, H88, H143] signal peptide: (4 columns) "True" if Phobius predicts a signal peptide for the protein sequence translated from the assembled transcript, "False" otherwise; Enrichment: "YPS" for core yeast-enriched transcripts, "HPS" for core hyphal-enriched transcripts; Longer Leader: "Yeast" for transcripts with a longer leader in yeast for at least 3 of 4 strains, "Hyphae" for transcripts with a longer leader in hyphae for at least 3 of 4 strains; [G217B, G186AR, H88, H143] Y/H: (4 columns) median normalized log2 ratio of mean yeast and hyphal FPKMs as determined by eXpress for the assembled transcript.

organism: Histoplasma capsulatum

source_name: yeast

growth_protocol: G217B, G186AR, H88, and H143 yeast cells were inoculated from HMM agarose plates into HMM liquid medium for yeast-phase growth. Yeast cells were passaged at a 1:25 dilution three times and 2-day cultures of each strain were harvested for RNA collection after the third passage. For hyphal cells, G217B, G186AR, H88, and H143 hyphae were inoculated from Sabouraud dextrose agar plates grown at RT into HMM liquid medium. Hyphal cells were grown for 4 – 6 weeks with passaging 3 times (1:5 dilution) into fresh HMM medium at RT before reaching a sufficient density of cells for harvesting.

extract_protocol:
Hyphal and yeast cells were collected by centrifugation or filtration and total RNA was isolated using a guanidine thiocyanate lysis protocol as previously described (Hwang et al, Molecular Biology of the Cell 14:2314).
Paired-end RNA-seq libraries were made from biological duplicate cultures of G217B, G186AR, H88, and H143 for both yeast and hyphae. DNA was depleted from 10 – 20 μg of total RNA by 1 hour of DNaseI digestion at 37°C (Ambion by Life Technologies, Carlsbad, CA). Poly(A)+ RNA was selected from DNA-depleted RNA on oligo- dT25 DynaBeads (Invitrogen by Life Technologies) using 2 rounds of selection per the manufacturer’s instructions. Approximately 50 ng of poly(A)+ RNA was used as input for generating sequencing libraries with the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre, Madison, WI) per the manufacturer’s instructions with the following modifications.  After 11 cycles of the ScriptSeq v2 PCR cDNA amplification step, cDNA libraries were resolved on an 8% TBE gel (Invitrogen by Life Technologies) and a 350 – 500 bp range of cDNA library was excised, eluted, and precipitated from the gel. Seven additional PCR cycles were resumed following the ScriptSeq v2 Kit protocol. cDNA libraries were purified with AMPure XP beads (Beckman Coulter, Brea, CA) to deplete primers. Libraries were multiplexed and subjected to 100 bp paired-end sequencing using the Illumina HiSeq2000 sequencer (Illumina, San Diego, CA).

tag: growth phase

value: yeast


title: H143 Hyphae B

source_name: hyphae

value: hyphae


title: H88 Yeast B


title: H88 Yeast A


title: H88 Hyphae B


title: G186AR Yeast B


title: mmu_ezh2_H3K4me3_ChIPSeq

description: ChIP-Seq for H3K4me3 in wild-type Ezh2-/- cells


title: G186AR Yeast A


title: G186AR Hyphae B


title: G186AR Hyphae A


title: mmu_ezh2_H3K27me3_ChIPSeq

description: ChIP-Seq for H3K27me3 in wild-type Ezh2-/- cells


title: G217B Yeast A


title: G217B Hyphae A


title: Yeast D mRNA

description: matched mRNA-seq

data_processing:
Filtering: Reads were pre-processed by stripping 3' sequence matching the primer linker sequence, allowing 20% mismatches, filtering any reads that were less than 11 bp after linker stripping, and additionally filtering for matches to the mitochondrial genome, a representative full length MAGGY transposon, and the 45S rDNA locus using bowtie version 0.12.7 with default parameters.
Alignment: The remaining, linker-stripped sequences were mapped to the genome with bowtie, restricting the output to unique alignments (-k1) and post-filtered for full length alignments of the query sequences. We noted a strong bias for T mismatches in the first aligned position, consistent with previously observed terminal nucleotidyl transferase activity of reverse transcriptase (Chen and Patton BioTechniques 30:574); to address this, we removed all first position T mismatches, treating the second aligned position as the true 5' of the sampled fragment for the remaining steps. Other than this special treatment of the first position, all alignments were required to be perfect matches between query and genome sequence. Aligned sequences were required to be at least 22 bp and, for ribosome footprint samples only, no more than 32 bp.  For alignments passing the above criteria, the 13th aligned position, inferred to correspond to the ribosomal P-site for ribosome footprint samples, was taken as the location of the mapped read.
Abundance estimation: Assembled transcript FPKMs for each sample were calculated as the number of reads located in the CDS of that transcript, divided by the length of that CDS in kilobases and the total number of CDS-mapped reads for the sample in millions. The same formula was used for quantifying ribosome footprints in leader regions, defining the leader as all transcript sequence 5' of the first CDS position, and normalizing by the length of the leader and the total number of CDS-mapped reads (to allow direct comparison of CDS and leader FPKMs).
Genome_build: Reads were aligned to the 11/30/2004 version of the G217B genome assembly from the Genome Sequencing Center at Washington University (GSC) as mirrored at http://histo.ucsf.edu/downloads/.  Transcripts and CDS annotations used in the data processing steps were assembled from Hc G217B paired-end sequencing data using a genome-guided approach, as described in the manuscript, and are available from http://histo.ucsf.edu/downloads/.
Supplementary_files_format_and_content: Processed data for all samples are supplied as a single matrix table for all samples (Supplementary_File_27.tdt.txt).  Each row corresponds to an assembled transcript.  The columns are: "G217B transcript" -- unique ID of the transcript used for read mapping; "Pfam accession" -- Accessions for all unique Pfam-A hits to the protein sequence translated from the assembled transcript. Pipe delimited, no e-value threshold; "G217B predicted gene" -- gene name(s) for predicted genes from the 9/21/2005 predicted gene set from the Genome Sequencing Center at Washington University (GSC) (as mirrored at http://histo.ucsf.edu/downloads/) overlapping the transcript; "G217B gene name" and "G217B annotation" -- short gene names and gene annotations from Inglis et al. (Eukaryotic cell 12:828) for the predicted gene(s) with additional annotations added in this work, pipe delimited; "Longer Leader" -- morphological state for which the transcript contains a longer leader, based on analysis of paired-end RnaSeq data in four strains of Hc; Leader Category -- longer leader classification from the accompanying manuscript; [Y, H] [footprint, mRNA] counts: Combined read counts for yeast or hyphae footprint or mRNA samples; [Y, H] [footprint, mRNA] FPKM: FPKM values for the above counts; [Y, H] TE: Median normalized log2 (footprint/mRNA) ratios of yeast or hyphae FPKMs; mRNA Y/H: Median normalized log2 (yeast/hyphae) ratio of mRNA FPKMs.

growth_protocol: Biological duplicates of G217B yeast cells were grown at 37°C in HMM liquid medium to mid-log phase. Biological duplicates of G217B hyphal cells were grown for 4 – 6 weeks with passaging three times (1:5 dilution) into fresh HMM medium at RT before reaching a sufficient density of cells for harvesting.

extract_protocol:
Hyphal and yeast cells were treated with 100 μg/mL cycloheximide for 2 minutes (MP Biomedicals, Santa Ana, CA) before harvesting of cells by filtration. Total RNA for mRNA library preparation was isolated from a small fraction of the total yeast or hyphal cells collected for ribosome profiling using a guanidine thiocyanate lysis protocol as previously described (Hwang et al, Molecular Biology of the Cell 14:2314).
Ribosome profiling and matched mRNA-seq sample preparation and library building were performed as described (Ingolia et al Science 324:218), except that the 3′ linker ligation strategy was used instead of poly(A) tailing for marking and capturing the 3’ RNA end (Dunn et al eLife 2:e01179). Libraries were multiplexed and subjected to 50 bp single-end sequencing with an Illumina HiSeq2000 sequencer (Illumina).


title: G217B Hyphae B


title: Yeast D footprint

description: ribosome profiling


title: H143 Yeast B


title: H143 Hyphae A


title: Hyphae D mRNA

description: matched mRNA-seq


title: Yeast C mRNA

description: matched mRNA-seq


title: Hyphae D footprint

description: ribosome profiling


title: HBG Guide Control Rep1

first: George

last: Chruch

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Reads were combined from the four different flow cells using a custom script
Reads were aligned to the hg19 UCSC Known Genes annotations using RSEM v1.2.1
Using paired end setting (not strand specific)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file of RSEM output with TPM, Counts, FPKM

growth_protocol: HEK-293T cells were cultivated in Dulbecco’s Modified Eagle Medium (Life Technologies) with 10% FBS (Life Technologies) and Penicillin/Streptomycin (Life Technologies). Incubator conditions were 37 oC and 5% CO2.

extract_protocol:
Samples were lysed and RNA was extracted using the RNeasy Plus Mini Kit (Qiagen). For each sample, 200 ng of total RNA was polyA selected using Dynabeads mRNA Purification Kit (Life Technologies). The RNA was then DNAse treated with Turbo DNase (Life Technologies) and cleaned up with Agenocourt RNAClean XP Beads (Beckman Coulter).
RNA-Seq Libraries were made using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs) according to manufacturer’s instructions with NEBNext Multiplex Oligos (New England BioLabs).

treatment_protocol: Cells were transfected with Lipofectamine 2000 (Life Technologies)

tag: transfection

tag: cell line


title: HBG Guide Control Rep2


title: HBG_VPR 14nt Rep2

value: dCas9-VPR and a gRNA of length 14nt targeting HBG1/2


title: Yeast C footprint

description: ribosome profiling


title: Hyphae C mRNA

description: matched mRNA-seq


title: HBG_VPR 14nt Rep1


title: H88 Hyphae A


title: Hyphae C footprint

description: ribosome profiling


title: HBG_VPR 20nt Rep2

value: dCas9-VPR and a gRNA of length 20nt targeting HBG1/2


title: HBG_VPR 16nt Rep1

value: dCas9-VPR and a gRNA of length 16nt targeting HBG1/2


title: HBG_VPR 20nt Rep1


title: Miat_VPR 16nt Rep2

value: dCas9-VPR and a gRNA of length 16nt targeting MIAT


title: Miat_VPR 14nt Rep1

value: dCas9-VPR and a gRNA of length 14nt targeting MIAT


title: Miat Guide Control Rep1


title: Miat_VPR 14nt Rep2


title: 2dd_DOX_plus_Rep2_mRNA

data_processing:
Reads were mapped with TopHat version 2.0.7 and Bowtie version 2.1.0 with default parameters against build hg19 of the human genome, and build 13 of the GENCODE human genome annotation
Samples were quantified with the Cufflinks package version 2.2.0.
Differential expression was performed using Cuffdiff 2.2.0 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: reprogramming intermediates of hiF-T cells

tag: treatment

value: DOX days 0-2


title: G217B Yeast B


title: Miat_VPR 20nt Rep2

value: dCas9-VPR and a gRNA of length 20nt targeting MIAT


title: Miat_VPR 16nt Rep1


title: T2D-10B (type 2 diabetic 5)

city: Philadelphia

first: Diana

last: Bernstein

address: 3400 Civic Center Blvd Bldg 421

department: Department of Genetics, IDOM

institute: University of Pennsylvania

description: BisPCRSeq

data_processing:
DNA libraries were sequenced on the Illumina MiSeq with 150 base pair paired-end reads
DNA sequencing data was aligned to an in silico bisulfite converted human genome with the BS Seeker program, and was processed by the Next Generation Sequencing Core at the University of Pennsylvania (Philadelphia, PA)
Data was reported as the fraction of reads that were methylated, calculated as the ratio of cytosine bases (indicating methylated CpGs) to total reads for each CpG coordinate.  Unmethylated cytosines are ultimately converted to thymine bases during the bisulfite conversion and PCR amplification process.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files of loci, fraction of methylated Cytosines and total read count.

source_name: pancreatic islets

extract_protocol:
Genomic DNA was extracted using the Qiagen AllPrep DNA/RNA Micro kit, and was then bisulfite converted with the Qiagen Epitect Bisulfite Kit.
Libraries were prepared by the reported BisPCR2 protocol which includes bisulfite conversion followed by two rounds of PCR, for target enrichment and sample barcoding.  Libraries were sequenced on an Illumina MiSeq with 150 base pair paired-end reads.  Data was analyzed by the Next Generation Sequencing Core at the University of Pennsylvania (Philadelphia, PA)

tag: tissue

value: pancreatic islets

tag: disease status

value: type 2 diabetes


title: Miat_VPR 20nt Rep1


title: ACTC1_VPR 14nt Rep1

value: dCas9-VPR and a gRNA of length 14nt targeting ACTC1


title: ACTC1_VPR 14nt Rep2


title: T2D-9 (type 2 diabetic 4)

description: BisPCRSeq


title: ACTC1_VPR 16nt Rep2

value: dCas9-VPR and a gRNA of length 16nt targeting ACTC1


title: T2D-7 (type 2 diabetic 2)

description: BisPCRSeq


title: ACTC1_VPR 16nt Rep1


title: T2D-8B (type 2 diabetic 3)

description: BisPCRSeq


title: HBG_VPR 16nt Rep2


title: T2D-6B (type 2 diabetic 1)

description: BisPCRSeq


title: ACTC1_VPR 20nt Rep1

value: dCas9-VPR and a gRNA of length 20nt targeting ACTC1


title: Control-4 (non-diabetic 4)

description: BisPCRSeq

value: healthy


title: Control-5 (non-diabetic 5)

description: BisPCRSeq


title: Miat Guide Control Rep2


title: Control-2 (non-diabetic 2)

description: BisPCRSeq


title: Control-3C (non-diabetic 3)

description: BisPCRSeq


title: Control-1 (non-diabetic 1)

description: BisPCRSeq


title: ACTC1 Guide Only Control Rep2


title: ACTC1 Guide Only Control Rep1


title: SR024

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

description:
Infected 24 hours + AraC
Replicate 3

data_processing:
Total reads were assessed for quality using fastQC and adapter primers removed using cutadapt v1.1 (parameters: -O 9 -m 16 -n 4 -q 20)
Using simple scripts, fasta sequences of 16 or more nucleotides were extracted from the primer-trimmed reads and collapsed to generate a non-redundant set of sequences within each sample
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contain the non-redundant sequences from each sample.

source_name: Infected 24 hours + AraC

growth_protocol: Human cervix carcinoma epithelioid cells (HeLa) and Chinese Hamster Ovary (CHO) cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) (Life Technologies) containing 50 IU/ml penicillin, 50 g/ml streptomycin (Sigma) and 10% foetal bovine serum (FBS) (Life Technologies). Cells were incubated at 37C in a 5% CO2 incubator. The experiments presented here were carried out with sucrose gradient-purified IMV form of VACV strain Western Reserve or Modified Vaccinia virus Ankara (MVA), a kind gift from Tim Connelly (University of Edinburgh).

extract_protocol: RNA was extracted using the miRNAeasy kit (Qiagen), the integrity of the RNA measured as 10 for all samples based on the Bioanalyzer (Agilent) and 10 ug of RNA was gel purified (20-40 nt) by 15% UREA PAGE prior to library preparation with the TrueSeq kit (Illumina).

treatment_protocol: Confluent 175cm2 flasks of HeLa cells were infected with VACV at an MOI of 10 for 1 h at 37oC. The inoculum was removed (time point 0 h), cells were washed with medium and incubated with 2.5% DMEM. At 6 and 24 h pi cells were washed once with ice cold PBS then collected into an appropriate volume of QIAzol lysis reagent (Qiagen) and frozen at -80⁰C. AraC (40μg/ml) was added at time point 0 h to a parallel set of samples.

value: HeLa


title: SR023

description:
Infected 24 hours + AraC
Replicate 2


title: SR022

description:
Infected 24 hours + AraC
Replicate 1


title: SR019

description:
Infected 24 hours
Replicate 1

source_name: Infected 24 hours


title: SR021

description:
Infected 24 hours
Replicate 3


title: SR018

description:
Uninfected 24 hours + AraC
Replicate 3

source_name: Uninfected 24 hours + AraC


title: SR015

description:
Uninfected 24 hours
Replicate 3

source_name: Uninfected 24 hours


title: SR017

description:
Uninfected 24 hours + AraC
Replicate 2


title: SR016

description:
Uninfected 24 hours + AraC
Replicate 1


title: SR014

description:
Uninfected 24 hours
Replicate 2


title: ACTC1_VPR 20nt Rep2


title: SR012

description:
Infected 6 hours + AraC
Replicate 3

source_name: Infected 6 hours + AraC


title: SR011

description:
Infected 6 hours + AraC
Replicate 2


title: SR009

description:
Infected 6 hours
Replicate 3

source_name: Infected 6 hours


title: SR013

description:
Uninfected 24 hours
Replicate 1


title: SR008

description:
Infected 6 hours
Replicate 2


title: SR006

description:
Uninfected 6 hours + AraC
Replicate 3

source_name: Uninfected 6 hours + AraC


title: SR005

description:
Uninfected 6 hours + AraC
Replicate 2


title: SR004

description:
Uninfected 6 hours + AraC
Replicate 1


title: SR001

description:
Uninfected 6 hours
Replicate 1

source_name: Uninfected 6 hours


title: SR003

description:
Uninfected 6 hours
Replicate 3


title: SR002

description:
Uninfected 6 hours
Replicate 2


title: mmu_eed_smRNA_1

description: small-RNA-Seq in Eed-/- mES cells, Replicate 1

data_processing:
for the Small RNA sequencing, 3' adapters were trimmed using cutadapt, and the command: cutadapt --trim-primer -z -c -e 0.3 -a 330201030313112312 -m 10 -o reads.fastq reads.csfasta reads.qual
Small RNA reads were aligned with bowtie using the command: bowtie -C -S -a -k 10 -m 10 --best -l 20 -q mm9 c reads.fastq > reads.sam
genome_build: mm9

extract_protocol:
Total RNA was isolated from cells using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. 10 µg of total RNA was size selected to 18-40 nucleotides on a denaturing polyacrylamide gel, eluted in 0.3M NaCl for overnight and then ethanol precipitated. Small RNAs (18-40 nt) precipitate were dissolved into water.
Small RNA libraries were prepared according to manufacturer’s instructions (SOLiD small RNA library preparation kit, Life Technologies). All libraries were sequenced using SOLiD instrument (Life Technologies).

value: Eed-/-


title: mmu_eed_smRNA_2

description: small-RNA-Seq in Eed-/- mES cells, Replicate 2


title: SR020

description:
Infected 24 hours
Replicate 2


title: mmu_ezh2_smRNA_2

description: small-RNA-Seq in Ezh2-/- mES cells, Replicate 2


title: mmu_ezh2_smRNA_1

description: small-RNA-Seq in Ezh2-/- mES cells, Replicate 1


title: mmu_wt_smRNA_1

description: small-RNA-Seq in wild-type mES cells, Replicate 1

value: wild-type


title: mmu_wt_smRNA_2

description: small-RNA-Seq in wild-type mES cells, Replicate 2


title: PolII_ChIa-PET_rep1

city: Cambridge

last: Gifford

address: 32 Vassar St.

department: Computer Science and Artificial Intelligence Laboratory

institute: Massachusetts Institute of Technology

description: RNA Polymerase II

data_processing:
ChIA-PET sequence reads were aligned to the mouse genome (version mm10) using Bowtie
RNA-Seq sequence read pairs were aligned to the mouse genome (version mm10) using STAR
TSS-based interactions were called using GERM
FPKM values were computed using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files contain either FPKM values (RNA-Seq) or interaction information (pmn_tss_based_interactions.txt). The file esc_tss_based_interactions.txt is based on raw data published by another group.

source_name: motor neuron progenitors

growth_protocol: ESCs were cultured over a layer of neomycin resistant Mitomycin-C–treated fibroblasts (Millipore) in EmbryoMax D-MEM (Millipore) supplemented with 15% ESC-grade fetal bovine serum (Thermo Fisher), l-glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U ml-1 leukemia inhibitory factor. ESCs were trypsinized (Invitrogen) and seeded at 5 x 105 cells per ml in ANDFK medium (Advanced DMEM/F12:Neurobasal (1:1) Medium, 10% Knockout- SR (vol/vol), Pen/Strep, 2 mM l-glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (day 0). Medium was exchanged on day 2. Patterning of embryoid bodies was induced by supplementing media on day 2 with 1 muM all-trans retinoic acid (Sigma) and 0.5 muM Smo agonist of hedgehog signaling (SAG, Calbiochem).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
DNA was end polished with T4 DNA polymerase (NEB). To assess the degree of intermolecular proximity ligation end polished DNA was divided into 2 aliquots and each ligated to linkers (A or B). The two samples were then joined together for proximity ligation under dilute conditions. Following ligation samples were treated with Mme1 to release paired end tag (PET) constructs. PET constructs were amplified and submitted to sequencing on Illumina Genome Analyzer II.

value: ESC-derived motor neuron progenitors


title: TKO_IgG_CHIP

description: ChIP with rabbit IgG in DNMTs TKO embryonic stem cell

data_processing:
Low quality reads were filtered and adaptor sequence were trimmed using our in-house perl script.
Alignment of short reads (100bp) to the mouse genome (mm9 release, USCS) was carried out using Bowtie 2 with a sensitive-local, paired-end model.
All PCR duplicates were removed using Picard.
The MACS software was used to recognize peak candidates using IgG samples as controls (the e-value cutoffs are as following: 1e-5 for J1DAXX, 1e-7 for J1ATRX, TKODAXX, TKOATRX), which were further filtered by fold-enrichment of >2 as cutoff.
Annotation of the identified peaks was carried out using the UCSC genome database for genomic features.Promoters were defined as +/- 0.5kb relative to the start of UCSC gene transcription start sites. The definition of mouse ancestral simple repeat sequences were downloaded from Repbase.
Genome_build: mm9
Supplementary_files_format_and_content: txt/bed file containing peaks identified by MACS

source_name: mouse ES cell (TKO)

growth_protocol: All of these cell growth in ES cell medium containing 2i (MEK inhibitor PD0325901 at 1 μM  (StemRD, PD-10) and GSK3b inhibitor CHIR99021 at 3 μM (StemRD, CHIR-50))

extract_protocol:
Briefly, about 1 × 107 mES cells were fixed and permeabilized with 4% paraformaldehyde for 10 min in 4℃ following by cell lysis and sonication. Sonicated and pre-cleared lysates were incubated with appropriate antibodies (e.g., anti-ATRX (SC-15408), anti-DAXX (SC-7152), and anti-RAP1 (A300-306A) antibodies), before the addition of Protein A agarose beads.
DNA libraries were prepared from whole-genome ChIP experiments using the DNA Sample Kit (Illumina), with ~10ng of precipitated DNA end-repaired and ligated to Illumina adaptors. The quantity and size distribution of the libraries were determined using the PicoGreen fluorescence assay and the Agilent 2100 Bioanalyzer, respectively.

value: DNMTs Knocktout mES cell

value: ES medium with 2i

tag: antibody

value: Rabbit IgG


title: SR010

description:
Infected 6 hours + AraC
Replicate 1


title: PolII_Chia-PET_rep2

description: RNA Polymerase II

tag: strain


title: ESC_RNA-Seq

description: Truseq RNA-Seq

source_name: embryonic stem cells

growth_protocol: ESCs were cultured over a layer of neomycin resistant Mitomycin-C–treated fibroblasts (Millipore) in EmbryoMax D-MEM (Millipore) supplemented with 15% ESC-grade fetal bovine serum (Thermo Fisher), l-glutamine (Gibco), 0.1 mM beta-mercaptoethanol and 100 U ml-1 leukemia inhibitory factor.

extract_protocol:
Total RNA from mouse embryonic stem cells or motor neuron progenitors was isolated using Trizol Reagent (Invitrogen).
mRNA was isolated and strand specific RNA-Seq was performed following the Illumina Truseq protocol.

value: embryonic stem cells


title: TKO_ATRX_CHIP

description: ChIP with ATRX antibody (SC-15408) in DNMTs TKO embryonic stem cell

value: ATRX antibody (SC-15408)


title: SR007

description:
Infected 6 hours
Replicate 1


title: repo_micro_rep1

city: Mainz

first: Ari

last: Waisman

address: Obere Zahlbacher Straße 67

country: Germany

institute: Institute for Molecular Medicine

data_processing:
Sequenced reads were mapped to the mouse genome reference sequence (mm10, retrieved from Illumina iGenomes); TopHat version 2.0.10, combined with Bowtie2 (2.1.0.0) was used for this purpose. Default parameters were used to perform the alignment.
Quantification of gene expression was performed with the htseq-count tool from the HTSeq software suite. The corresponding annotation was also retrieved from the Illumina iGenomes archive.
Differential expression analysis was performed by using DESeq (version 1.14.0). A False Discovery Rate (FDR) cutoff of 0.05 was selected.
Genome_build: mm10
Supplementary_files_format_and_content: Tag-delimited text file, containing normalized read counts, stored in a NxM matrix (N genes, M samples) with a header line

source_name: Repopulating microglia

extract_protocol:
Mice were anesthetized and perfused with NaCl and organs were excised out. Brains were either fixed with 4% of PFA for histology, snap frozen in liquid nitrogen for RNA preparation, or digested according to manufacturer’s guidelines supplied in the MACS tissue dissociation kit Papain (Miltenyi Biotec). The tissue homogenate was loaded on a 30:70% Percoll gradient for enrichment of CNS infiltrates. The interphasic cellular ring was collected for further investigation. The different microglia samples were FACS sorted (FACS Aria) and immediately centrifuged down for 15 mins and 400 x g. RNA was isolated with the RNeasy® Plus Micro Kit (Qiagen) according to the manufacturer’s instructions. RNA amounts were measured by Q-bit 2.0 fluorometer (Life Technologies) and the quality was assessed on a Bioanalyzer (Agilent) using a High Sensitivity Chip. Samples with a RNA integrity number (RIN) > 8 were used for library preparation with TruSeq® RNA Sample Prep v2 Kit (Illumina) according to the manufacturer’s manual. Library size distribution was assessed on a Bioanalyzer 2100 using a High Sensitivity DNA Chip (Agilent).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tamoxifen (TAM; Sigma) was suspended on 37°C in olive oil for 60 mins (MP Biomedicals). 2 mg Tamoxifen was administered subcutaneously (s.c.) twice on postnatal days 12 and 14. For microglia depletion, mice were injected intraperitoneally (i.p.) with 500ng diphtheria toxin (DT; Merck Millipore) three times, with a one-day interval between each injection.

value: Repopulating microglia

tag: genotype

value: DTRmg


title: repo_micro_rep3


title: wt_micro_rep2

source_name: Wild-type microglia

value: Wild-type microglia

value: DTR


title: repo_micro_rep2


title: J1_IgG_CHIP

description: ChIP with rabbit IgG in WT (J1) embryonic stem cell

source_name: mouse ES cell (J1)

value: WT mES cell (J1)


title: wt_micro_rep1


title: bm_micro_rep3

source_name: Bone-marrow macrophages

value: Bone-marrow macrophages


title: J1_DAXX_CHIP

description: ChIP with DAXX antibody (SC-7152) in WT (J1) embryonic stem cell

value: DAXX antibody (SC-7152)


title: TKO_DAXX_CHIP

description: ChIP with DAXX antibody (SC-7152) in DNMTs TKO embryonic stem cell


title: bm_micro_rep1


title: bm_micro_rep2


title: mmu_jarid2_smRNA_1

description: small-RNA-Seq in Jarid2-/- mES cells, Replicate 1

source_name: embryonic cells

tag: genotype/variation


title: J1_ATRX_CHIP

description: ChIP with ATRX antibody (SC-15408) in WT (J1) embryonic stem cell

tag: cell type


title: PMN_RNA-Seq

description: Truseq RNA-Seq


title: inflamed region of patient with B2/stricturing Crohn's disease [ncRNA-Seq, 440_CD_IF_B2]

city: Chapel Hill

first: Bailey

last: Peck

state: NC

address: 120 Mason Farm Rd, 5100H Genetic Medicine Bldg

institute: University of North Carolina at Chapel Hill

data_processing:
Small RNA-seq data was aligned using methodology described in Baran-Gale et al. (PLOS ONE, 2012)
Reads were trimmed by cutAdapt to remove adaptor remnants. Trimmed reads of 14-41 nt are first mapped exactly (no mismatches) using Bowtie. Windows are determined using these mapped reads, and the unmapped reads, are realigned to these windows using SHRiMP2 with mismatches allowed (See Baran-Gale et al, 2012), these would be considered edits & isomiRs, and are named based on the canonical miRNA (miRbase).
Reads were normalized using Reads per Million Mapped (RPMM). We pulled out miRNAs and isomiRs with at least 100 RPMM in at least 1 sample for downstream analyses.
Genome_build: Hg19
Supplementary_files_format_and_content: Multiple sample Tab-delimited file with RPMMs of all miRNAs & isomiRs that reached 100 RPMM in at least one sample analyzed.

source_name: Colon

extract_protocol:
RNA was isolated from fresh-frozen human colon tissues using the Qiagen RNeasy Mini Kit
Small RNA libraries were generated using Illumina TruSeq Small RNA Sample Preparation Kit

tag: age

tag: Sex

value: male

tag: disease

value: Crohn's Disease

tag: inflamed

value: Yes

tag: montreal classification


title: inflamed region of patient with B1/non-stricturing, non-penetrating Crohn's disease [ncRNA-Seq, 431_CD_IF_B1]

value: female

value: B1/non-strictuing, non-penetrating


title: E2-siNCAPD3_GROseq

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

description:
nascent RNA
cells were transfected with siNCAPD3, after 1hr treatment with 100nM E2, subjected to GRO-seq,
library strategy: GRO-seq

data_processing:
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18

source_name: beast cancer cell line

growth_protocol: MCF7 obtained from ATCC were cultured in ?-MEM media supplemented with 10% FBS in a 5% CO2 humidified incubator.

extract_protocol:
MCF7 cells were subjected to nuclear run-on for 5minutes at 30 degree with BrU labeling. The run-on RNAs were pull down by BrU beads and subjected to library preparation for deep sequencing.
We followed a previous published protocol (Ingolia et al., 2009 Science; Wang et al., 2011 Nature; Li et al., 2013 Nature). Briefly, the run-on RNA were first added with a polyA tracts by RNA polyA polymerase. This polyA tail enables the run-on RNA to be reverse transcribed into single strand cDNA by Reverse Transcriptase. The cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1, subsequently subjected to PCR amplification and deep sequencing.

treatment_protocol: Before experiment, the cells were changed to deficient MEM plus 5% charcoal treated phenol red free medium to culture for 3 days, followed by treatemnt of either 100nM 17-?-estrodial or ethanol for 1hr.


title: E2-siCTL_repeat2_GROseq (v.s. E2-siNCAPD3_GROseq)

description:
nascent RNA
cells were transfected with siCTL, after 1hr treatment with 100nM E2, subjected to GRO-seq, serves as a control for cells with siNCAPD3 and 100nM E2 treatment (v.s. E2-siNCAPD3_GROseq)
library strategy: GRO-seq


title: EtOH-siNCAPD3_GROseq

description:
nascent RNA
cells were transfected with siNCAPD3, after 1hr treatment with ethanol, subjected to GRO-seq,
library strategy: GRO-seq


title: inflamed region of patient with B1/non-stricturing, non-penetrating Crohn's disease [ncRNA-Seq, 413_CD_IF_B1]


title: E2-siNCAPG_GROseq

description:
nascent RNA
cells were transfected with siNCAPG, after 1hr treatment with 100nM E2, subjected to GRO-seq,
library strategy: GRO-seq


title: inflamed region of patient with B3/penetrating Crohn's disease [ncRNA-Seq, 434_CD_IF_B3]


title: EtOH-siNCAPG_GROseq

description:
nascent RNA
cells were transfected with siNCAPG, after 1hr treatment with ethanol, subjected to GRO-seq,
library strategy: GRO-seq


title: inflamed region of patient with B1/non-stricturing, non-penetrating Crohn's disease [ncRNA-Seq, 408_CD_IF_B1]


title: inflamed region of patient with B3/penetrating Crohn's disease [ncRNA-Seq, 407_CD_IF_B3]


title: B3/penetrating Crohn's disease [ncRNA-Seq, 64_CD_NI_B3]

value: No


title: B1/non-strituring, non-penetrating Crohn's disease [ncRNA-Seq, 63_CD_NI_B1]


title: B3/penetrating Crohn's disease [ncRNA-Seq, 62_CD_NI_B3]


title: E2-siCTL_repeat1_GROseq (v.s. E2-siNCAPG_GROseq)

description:
nascent RNA
cells were transfected with siCTL, after 1hr treatment with 100nM E2, subjected to GRO-seq, serves as a control for cells with siNCAPG and 100nM E2 treatment (v.s. E2-siNCAPG_GROseq)
library strategy: GRO-seq


title: EtOH-siCTL_repeat2_GROseq (v.s. EtOH-siNCAPD3_GROseq)

description:
nascent RNA
cells were transfected with siCTL, after 1hr treatment with ethanol, subjected to GRO-seq, serves as a control for cells with siNCAPD3 and EtOH treatment (v.s. EtOH-siNCAPD3_GROseq)
library strategy: GRO-seq


title: B1/non-strituring, non-penetrating Crohn's disease [ncRNA-Seq, 54_CD_NI_B1]


title: B3/penetrating Crohn's disease [ncRNA-Seq, 450_CD_NI_B3]


title: H3K27Ac-EtOH-siNCAPH_ChIP-Seq

description: cells transfected with siNCAPH, and 1hr treatment with ethanol, crosslinked with 1% formaldehyde, H3K27ac Mnase nucleasome ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using Bowtie version 2.0.1.
The bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18

growth_protocol: MCF7 obtained from ATCC were cultured in α-MEM media supplemented with 10% FBS in a 5% CO2 humidified incubator.

extract_protocol:
Lysates were crosslinked with 1% of formaldehyde or double-crosslinked with DSG first followed by 1% of formaldehyde, clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The extracted ChIP DNA was ligated to specific adaptors of Truseq system from Illumina, according to the manufacturer’s instructions.

treatment_protocol: Before experiment, the cells were changed to deficient MEM plus 5% charcoal treated phenol red free medium to culture for 3 days, followed by treatemnt of either 100nM 17-β-estrodial or ethanol for 1hr.

tag: chip antibody

tag: antibody vendor/catalog#

value: Ab4729, Abcam


title: B2/stricturing Crohn's disease [ncRNA-Seq, 440_CD_NI_B2]


title: H3K27Ac-EtOH-siCTL_ChIP-Seq

description: cells transfected with siCTL, and 1hr treatment with ethanol, crosslinked with 1% formaldehyde, H3K27ac Mnase nucleasome ChIP-seq


title: H3K27Ac-E2-siNCAPH_ChIP-Seq

description: cells transfected with siNCAPH, and 1hr treatment with 100nM E2, crosslinked with 1% formaldehyde, H3K27ac Mnase nucleasome ChIP-seq


title: H3K27Ac-E2-siNCAPG_ChIP-Seq

description: cells transfected with siNCAPG, and 1hr treatment with 100nM E2, crosslinked with 1% formaldehyde, H3K27ac Mnase nucleasome ChIP-seq


title: NCAPG-mitoticMCF7-E2_ChIPSeq

description: Enriched mitotic MCF7 cells after hormone stripping was treated with 1hr of 100nM E2, then was subjected to NCAPG ChIPseq

value: NCAPG

value: A300-602A, Bethyl


title: B2/stricturing Crohn's disease [ncRNA-Seq, 51_CD_NI_B2]