title: ChIPseq_Spt5-dCTR_I_input

data_processing:
Mapping using Bowtie2 first to S. pombe and then S. cerevisiae genomes.
WIG density tracks produced by SPP software functions select.informative.tags, remove.local.tag.anomalies, and get.smoothed.tag.density. The latter function was used with parameters control.tags=input (for ChIP), bandwidth=25,step=10,tag.shift = cross-correlation profile peak. Input samples were not background-subtracted.
Genome_build: S. pombe ASM294v2, S. cerevisiae R64-1-1
Supplementary_files_format_and_content: bedGraph track files for S. pombe tag-shifted density, sampled every 10bp, library-size-normalized, background-subtracted if ChIP-samples.

source_name: ChIPseq_Spt5-dCTR, input

growth_protocol: S. pombe strains were grown in EMM complete media at 30°C.

extract_protocol:
Samples were prepared as described in (PMID:24100010)
ChIP-seq libraries were prepared as described in (PMID:24100010). For the spike-in control, S. cerevisiae chromatin was added to S. pombe chromatin before immunoprecipitation with the relevant antibodies. S. cerevisiae chromatin corresponding to 2.5% of S. pombe chromatin, as estimated by Bradford assay (Bio-Rad), was used. Libraries were sequenced on the Illumina HiSeq platform at the Tufts University Core Facility.

treatment_protocol: Spt5 depletion experiments were performed by adding NAA (0.5mM in DMSO, napthaleneacetic acid, Sigma, N0640) and thiamine (100nM, thiamine hydrochloride, Sigma, T4625), to cells grown to a density of 10^7 cells/ml (O.D.600 ~ 0.5). Cultures were incubated with shaking at 30°C for 4.5 hours.

value: EMM

value: 2.5% S. cerevisiae chromatin

value: GCAGCC

value: CTR deleted

tag: chip antibody


title: ChIPseq_Spt5-WT_I_input

status: Public on Mar 30 2017

type: SRA

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

country: USA

institute: Harvard Medical School

library_source: genomic

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: ChIPseq_Spt5-WT, input

tag: strain

value: GTCTAC

value: wild type


title: ChIPseq_Spt5-dCTR_II_input

value: TCGCGT


title: ChIPseq_Spt5-WT_II_input

value: GAGTTA


title: BF1 brain (MeDIP-seq)

city: ShenZhen

first: Jinmin

last: Lian

address: Building No.11, Beishan Industrial Zone, Yantian District

country: China

institute: BGI-ShenZhen

data_processing:
TopHat (v1.4.1) was employed to map the RNA-seq reads to the naked mole rat reference genome (Heter_glaber.v1.7.fa.gz from http://mr.genomics.org.cn) with a segment length of 25 bp. Two mismatches were allowed in each segment. Only RNA-seq reads that were uniquely mapped to the genome and overlapped with annotated exons (gene-reads) in the naked mole rat gene set were kept. Gene expression levels were measured by RPKM (reads per kilobase per million mapped exonic reads). RPKMs in all the sequenced samples were adjusted by a scaling normalization method based on TMM (trimmed mean of M values).
MeDIP-seq reads were aligned to the naked mole rat reference genome using BWA (v0.5.9-r16), allowing two mismatches and one indel. Multiple reads mapping to the same position were regarded as PCR duplicates, and only one of them was kept. Reads mapping to more than one position were discarded. Differentially methylated regions (DMRs) between breeders and subordinates of the same sex were detected using edgeR integrated in the Bioconductor package MEDIPS (v.1.10.0) with a window size of 200 bp and default settings. P-values were adjusted for multiple testing by applying FDR, and windows with adjusted p-values < 0.05 were considered as DMRs. Differentially methylated genes (DMGs) were defined as genes containing DMRs in their putative promoter regions (TSS -2 kb to +500 bp) or gene body regions (exons + introns).
Genome_build: Heter_glaber.v1.7.fa.gz from http://mr.genomics.org.cn
Supplementary_files_format_and_content: Tab-delimited text file includes gene expression levels in terms of RPKM and gene annotations for each samples.

organism: Heterocephalus glaber

source_name: breeding female

growth_protocol: Naked mole rats were housed in the laboratory of Rochelle Buffenstein.

extract_protocol:
For MeDIP-seq libraries construction, 5 μg DNA was cut into 100 - 500 bp fragments with a Bioruptor sonicator (Diagenode), followed by end repair, 3’-end addition of dA, and adapter ligation according to Illumina’s protocols. Adaptor-ligated DNA was then immunoprecipitated by a monoclonal anti-methylcytidine antibody. The specificity of the enrichment was confirmed by qPCR using SYBR green mastermix (Applied Biosystems) with primers for positive and negative internal control DNA of non-human samples supplied in the Magnetic Methylated DNA Immunoprecipitation kit (Diagenode). The enriched fragments were purified on ZYMO DNA Clean & Concentrator-5 columns following the manufacturer’s instructions, followed by amplification via 10 adaptor mediated PCR cycles to yield the MeDIP-seq libraries.
All MeDIP-seq libraries were subjected to 50 bp paired-end sequencing on an Illumina HiSeq 2000 platform.
We analyzed brains from all eight individuals separately, but female ovaries were only large enough for individual analysis in breeders, whereas subordinate ovaries were so small that 3–5 of them had to be pooled for gene expression analyses. The testes of breeding and non-breeding males were not visually different, but breeder status was known because these males had previously sired pups. RNA and DNA were isolated as described in Kim, et al. Nature (2011).

treatment_protocol: Tissues were obtained from male (n = 2) and female (n = 2) breeders as well as male (n = 2) and female (n = 2) non-breeders (subordinates).

tag: age (year)

tag: tissue

value: brain

tag: gender

value: female


title: ChIPseq_Spt5-T4.5_I_input

description: Strain_FWP486_genotype_nmt81-Spt5-V5-IAA17

source_name: ChIPseq_Spt5-T4.5, input

tag: treatment

value: thiamine + 1-Napthaleneacetic acid (NAA)

tag: treatment time

value: AACCGT


title: patient_1_gastric_tissue

city: Kiel

first: Simonas

last: Juzenas

address: Am Botanischen Garten 11

department: Institute of Clinical Molecular Biology

country: Germany

institute: Christian-Albrechts-University of Kiel

description: small RNA

library_source: transcriptomic

data_processing:
Trimming of adapter sequences: cutadapt -b TGGAATTCTCGGGTGCCAAGG -m 18 -q 30 –discard-untrimmed (cutadapt v1.9.dev6)
Filtering of reads mapped to viral genome (RefSeq), human tRNAs, rRNAs, snRNAs and sRNAs (Rfam) : blastn  -word_size=18 (BLASTN v2.2.30)
Quantification of miRNAs: miraligner -sub 1 -trim 3 -add 3 -s hsa -i $reads -db miRBase_v21 -o "isomir_$sample" -freq (SeqBuster)
Supplementary_files_format_and_content: tab-delimited text files include miRNA and iso-miRNA counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: gastric tissue

extract_protocol:
The RNA extraction was performed using standard protocol of commercial miRNeasy FFPE Kit miRNeasy FFPE Kit by QIAGEN
Small RNA libraries were prepared using standard protocol of TruSeq Small RNA Sample Preparation Kit by Illumina

value: Female

tag: age


title: BF1 brain (RNA-seq)

extract_protocol:
For RNA-seq library construction, 2 μg total RNA per sample was treated with DNase I (New England BioLabs) to remove possible contamination with genomic DNA. Then poly (A+) mRNA was purified from the total RNA using the Dynabeads mRNA Purification Kit (Invitrogen), followed by fragmentation using the RNA fragmentation kit (Ambion). Next, the first cDNA strand was synthesized using random hexamer primers and reverse transcriptase (Invitrogen), and second-strand cDNA was synthesized using DNA polymerase I (New England BioLabs). After that, the synthetic double-stranded cDNA was end repaired, followed by 3’-end addition of dA, adapter ligation and size selection according to Illumina’s protocols. Finally, the selected products were amplified by 15 PCR cycles to yield the RNA-seq libraries.
All RNA-seq libraries were subjected to 90 bp paired-end sequencing on an Illumina HiSeq 2000 platform.
We analyzed brains from all eight individuals separately, but female ovaries were only large enough for individual analysis in breeders, whereas subordinate ovaries were so small that 3–5 of them had to be pooled for gene expression analyses. The testes of breeding and non-breeding males were not visually different, but breeder status was known because these males had previously sired pups. RNA and DNA were isolated as described in Kim, et al. Nature (2011).


title: ChIPseq_Spt5-T4.5_II_input

value: CTCTGT


title: ChIPseq_Spt5-dCTR_I_chip

source_name: ChIPseq_Spt5-dCTR, chip

value: GATCAG

value: anti-Rpb1, clone 8WG16 (BioLegend, previously Covance catalog #MMS-126R)


title: ChIPseq_Spt5-dCTR_II_chip

value: TAGCTT


title: ChIPseq_Spt5-T0_I_input

source_name: ChIPseq_Spt5-T0, input

value: EMM

value: 0 hr

value: ATATAG


title: ChIPseq_Spt5-T0_II_input

value: 2.5% S. cerevisiae chromatin

value: AGGTCA


title: ChIPseq_Spt5-WT_II_chip

source_name: ChIPseq_Spt5-WT, chip

value: ACTTGA

value: wild type


title: SF1 brain (RNA-seq)

source_name: subordinate female


title: ChIPseq_Spt5-T4.5_II_chip

source_name: ChIPseq_Spt5-T4.5, chip

value: TGACCA


title: ChIPseq_Spt5-WT_I_chip

value: CAGATC


title: ChIPseq_Spt5-T4.5_I_chip

value: CGATGT


title: ChIPseq_Spt5-T0_I_chip

source_name: ChIPseq_Spt5-T0, chip

value: ATCACG


title: ChIPseq_Spt5-T0_II_chip

value: TTAGGC


title: BM1 brain (RNA-seq)

source_name: breeding male

value: brain

value: male


title: mus_heart_MI_JQ1_3

city: San Francisco

first: Saptarsi

last: Haldar

address: 1650 Owens St

institute: Gladstone Institute of Cardiovascular Disease

description:
Mice were subjected to Permanent Ligation of the Left Anterior Descending Coronary Artery. Beginning from post-op day 6, JQ1 at 25 mg/kg/d was given via I.P. for 6 days and then increased to 50 mg/kg/d for additional 16 days.
MI_TAC_raw_counts.txt

data_processing:
Adapters and barcodes were trimmed, and low-quality reads were filtered using Fastq-mcf
High quality sequences were aligned to mm10 (mouse) with Tophat 2.0.13 and assigned to Ensembl genes and counted using "featureCounts" part of the Subread suite
the entry for ENSMUSG00000092329/Gm20388 was removed from the murine Gencode vM4 annotations we used before counting to avoid the artifactual loss of other transcripts, including Acta1, within its ~4Mb boundaries.
Raw counts were used as inputs to DESeq (v.1.25.0)
Genome_build: mm10
Supplementary_files_format_and_content: text files with raw counts

organism: Mus musculus

source_name: Left vetricle of heart

extract_protocol:
Hearts were removed, stored in RNALater. Total RNA was isolated using Trizol reagent and the Aurum purification kit (BioRad, 732-6830)
Paired-end libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold rRNA depletion (Illumina). Single-end libraries were prepared using TruSeq Stranded polyA kit (Illumina)

tag: Sex

value: sacrificed at 16 week-old


title: mus_heart_MI_JQ1_2


title: mus_heart_MI_JQ1_1


title: mus_heart_MI_veh_3

description:
Method: Adult C57Bl/6 mice (male, 10 wks) were subjected to Permanent Ligation of the Left Anterior Descending Coronary Artery. Beginning from post-op day 6, vehcle injection was given via I.P. for 22 days.
MI_TAC_raw_counts.txt


title: ChIP-seq_Spt5-V5-IAA17_noTreat_INPUT_r2

data_processing:
Demultiplexing, 5' barcode removal, and 3' trimming of initial 75bp sequence to 60bp resulted in the attached FASTQs.
Alignment using Bowtie 1.1.1 (parameter -m 1 for unique mapping) to a concatenated S. pombe and S. cerevisiae genome.
Split resulting BAMs by organism, then counted reads to produce ratios for spike-in normalization.
Determined cross-correlations via SPP which recommended tag shift of ~180bp for all ChIP samples.
bedGraph track files produced for S. pombe of 180bp tag-shifted density with bandwidth 20, sampled every 10bp, spike-in-normalized.
Genome_build: S. pombe ASM294v2 concatenated to S. cerevisiae R64-1-1
Supplementary_files_format_and_content: bedGraph track files for S. pombe tag-shifted density with bandwidth 20, sampled every 10bp, spike-in-normalized.

extract_protocol:
Samples were prepared as described in (PMID:24100010)
ChIP-seq libraires were prepared as described in (PMID:24100010). For the spike-in control, S. cerevisiae chromatin was added to S. pombe chromatin before immunoprecipitation with the relevant antibodies. S. cerevisiae chromatin corresponding to 10% of S. pombe chromatin, as estimated by Bradford assay (Bio-Rad), was used. Libraries were sequenced on the Illumina NextSeq 500 platform at the Harvard Bauer Core facility.

value: 10% S. cerevisiae chromatin

value: TGACGCATT

tag: antibody

value: INPUT

tag: replicate


title: ChIP-seq_noTag_noTreat_INPUT_r2

value: EMM

value: GTTGTCCCAT

value: noTag


title: mus_heart_TAC_JQ1_3

description:
Mice were subjected to TAC surgery with a 27 gauge needle. Starting at the beginning of post-op week 4, JQ1 at 50 mg/kg/d was adminstrated via I.P. injections and continue for another 6 weeks.
MI_TAC_raw_counts.txt

value: sacrificed at 20 week-old


title: RNAseq_Spt5-WT_I

description:
RNAseq_Spt5-FWP10_I
Strain_FWP10_WT

data_processing:
Trimming with custom script of adapter CTGTAGGCACCATCAAT
Alignment with TopHat 2.0.10 with minimum and maximum intron lengths 20 and 5000, respectively (-i 20 -I 500”), to a 'genome' of ASM294v2 plus sequences of ERCC spike-ins.
Spike-in normalization factors were obtained by calculating all pairwise linear model slopes for ERCC spike-ins, then deconvoluting to a vector of normalization factors. Coverage values were linearly transformed by these scaling factors.
WIGs were produced by sampling every 10bp.
Genome_build: ASM294v2
Supplementary_files_format_and_content: WIG track files, sampled every 10bp on each strand.

molecule: polyA RNA

extract_protocol:
RNA was extracted using the hot phenol method (PMID: 12854975 )
For RNA-seq libraries, 200 µg of total RNA from each strain was spiked-in with 10 µl of 1:100 diluted ERCC control RNA(). Then, poly(A)+ RNA was enriched by two rounds of Dynabeads Oligo (dT)25 (Invitrogen) purification, followed by alkaline fragmentation and size selection of fragments  40-70 nucleotides. Size-selected RNA was dephosphorylated and ligated to an RNA linker at the 3’ end. First-strand cDNA was synthesized using a primer with sequence complementary to the 3’-linker and an additional adapter sequence, using Superscript III reverse transcriptase (Invitrogen). cDNA was circularized using CircLigase (Epicentre). The library was amplified with 8-14 cycles of PCR, using primers specific for the adaptor sequence and the products were gel purified. Library size distributions and concentrations were determined using an Agilent Bioanalyzer. All strains were done in duplicate. RNA-seq libraries were sequenced on the Illumina HiSeq platform at the Tufts University Core Facility.

value: ERCC

value: CTTGTA


title: RNAseq_Spt5-T0_II

description:
RNAseq_Spt5-T0-167_II
Strain_FWP486_genotype_nmt81-Spt5-V5-IAA17

value: 0 hr

value: GCCAAT


title: mus_heart_MI_veh_1


title: RNAseq_Spt5-T0-untagged_II

description:
RNAseq_Spt5-T0-21104_II
Strain_FWP484_genotype_untagged

value: TAGCTT

value: wild type


title: RNAseq_Spt5-T0-untagged_I

description:
RNAseq_Spt5-T0-21104_I
Strain_FWP484_genotype_untagged

value: ACTTGA


title: RNAseq_Spt5-T4.5-untagged_II

description:
RNAseq_Spt5-T4-5-21104_II
Strain_FWP484_genotype_untagged

value: thiamine + 1-Napthaleneacetic acid (NAA)

value: GGCTAC


title: RNAseq_Spt5-T4.5_II

description:
RNAseq_Spt5-T4-5-167_II
Strain_FWP486_genotype_nmt81-Spt5-V5-IAA17

value: CAGATC


title: RNAseq_Spt5-T4.5-untagged_I

description:
RNAseq_Spt5-T4-5-21104_I
Strain_FWP484_genotype_untagged

value: GATCAG


title: RNAseq_Spt5-WT_II

description:
RNAseq_Spt5-FWP10_II
Strain_FWP10_WT

value: TTAGGC


title: RNAseq_Spt5-dCTR_I

description:
RNAseq_Spt5-CTR-243_1
Strain_FWP488_genotype_spt5∆CTR

value: CGATGT

value: CTR deleted


title: ChIP-seq_Spt5-deg_NAA+T_INPUT_r2

value: EMM

value: 10% S. cerevisiae chromatin

value: CAGGAGGCGT

value: INPUT


title: ChIP-seq_Spt5-V5-IAA17_noTreat_INPUT_r1

value: TTGAGTGTT


title: ChIP-seq_Spt5-deg_DMSO_INPUT_r2

value: DMSO

value: ACTAACTGCT


title: RNAseq_Spt5-dCTR_II

description:
RNAseq_Spt5-CTR-243_2
Strain_FWP488_genotype_spt5∆CTR

value: ERCC

value: TCAAGG


title: mus_heart_TAC_JQ1_2

value: male

value: sacrificed at 20 week-old


title: RNAseq_Spt5-T4.5_I

description:
RNAseq_Spt5-T4-5-167_I
Strain_FWP486_genotype_nmt81-Spt5-V5-IAA17

value: thiamine + 1-Napthaleneacetic acid (NAA)

value: ACATGT


title: ChIP-seq_noTag_noTreat_INPUT_r1

value: GGTCCTTGAT

value: noTag


title: ChIP-seq_Spt5-deg_NAA+T_INPUT_r1

value: CCTTTACAGT


title: mus_heart_MI_veh_2

value: sacrificed at 16 week-old


title: ChIP-seq_Spt5-V5-IAA17_noTreat_Spt5_r2

value: EMM

value: TGCGGTTAT


title: mus_heart_TAC_veh_3


title: ChIP-seq_Spt5-deg_DMSO_INPUT_r1

value: 10% S. cerevisiae chromatin

value: AACACCTACT


title: ChIP-seq_noTag_noTreat_Pol2_r2

value: TATACCGTT


title: ChIP-seq_noTag_noTreat_S5P_r2

value: TCGCGTACT


title: P0 wild-type (EG6089) treated with anti-GFP RNAi R3

city: Tel-Aviv

first: Itamar

last: Lev

address: Dr George Wise

country: Israel

institute: Tel-Aviv University

data_processing:
Adapter trimming - cutadapt
Filtering - Reads that were not cut or were less than 19bp long, were removed
Quality examination - fastQC
Alignment - Bowtie2
Counting - HTseq_count
Comparisons - DESeq2
Genome_build: WBcel235/ce11
Supplementary_files_format_and_content: HTseq_count output files

organism: Caenorhabditis elegans

source_name: P0 treated with anti-GFP RNAi

extract_protocol:
TRIZOL
NEBNext® Multiplex Small RNA Library Prep Set for Illumina® or TruSeq Small RNA Library Prep Kit

treatment_protocol: RNAi by feeding/regular growth on emtpy vector bacteria

value: wild-type (EG6089)

tag: developmental stage

value: day 1 adult

value: whole animal


title: ChIP-seq_noTag_noTreat_S2P_r2

value: GCAGCCTCT


title: F3 wild-type (EG6089) treated with anti-GFP RNAi R3

source_name: F3 treated with anti-GFP RNAi


title: F3 wild-type (EG6089) control R3

source_name: F3 control


title: mus_heart_TAC_veh_1

value: male

value: sacrificed at 20 week-old


title: mus_heart_TAC_veh_2


title: P0 wild-type (EG6089) control R3

source_name: P0 control


title: ChIP-seq_Spt5-deg_NAA+T_Spt5_r2

value: thiamine + 1-Napthaleneacetic acid (NAA)

value: GAGTTAACT


title: P0 met-2(n4256);set-25(n5021);EG6089 treated with anti-GFP RNAi R3


title: mus_heart_sham_JQ1_2

description:
Mice were subjected to sham surgery and received JQ1 at 50 mg/kg/d or veichle for 6 weeks starting post-op week 4.
Sham_raw_counts.txt


title: mus_heart_sham_JQ1_3


title: ChIP-seq_Spt5-deg_DMSO_Pol2_r2

value: DMSO

value: AGGTCAGTT


title: ChIP-seq_Spt5-deg_NAA+T_Pol2_r2

value: GTCTACATT


title: ChIP-seq_Spt5-deg_NAA+T_S5P_r2

value: EMM

value: CGCATTAAT


title: F3 met-2(n4256);set-25(n5021);EG6089 treated with anti-GFP RNAi R3


title: ChIP-seq_Spt5-deg_DMSO_S5P_r2

value: 10% S. cerevisiae chromatin

value: AACCGTGTT


title: mus_heart_sham_JQ1_1


title: ChIP-seq_Spt5-deg_DMSO_S2P_r2

value: ATATAGGAT


title: mus_heart_TAC_JQ1_1


title: ChIP-seq_Spt5-deg_NAA+T_S2P_r2

value: CCATACACT


title: F3 met-2(n4256);set-25(n5021);EG6089 control R3


title: mus_heart_sham_veh_6


title: ChIP-seq_noTag_noTreat_Pol2_r1

value: GGCTACT

value: noTag


title: ChIP-seq_Spt5-V5-IAA17_noTreat_Spt5_r1

value: CTTGTAT


title: P0 wild-type (EG6089) treated with anti-GFP RNAi R2

value: wild-type (EG6089)

value: day 1 adult

value: whole animal


title: ChIP-seq_noTag_noTreat_S5P_r1

value: TAGCTTT


title: mus_heart_sham_veh_5

value: male

value: sacrificed at 20 week-old


title: ChIP-seq_Spt5-deg_DMSO_Spt5_r2

value: DMSO

value: CTCTGTCTT


title: ChIP-seq_noTag_noTreat_S2P_r1

value: EMM

value: GATCAGT


title: P0 met-2(n4256);set-25(n5021);EG6089 control R3


title: F3 wild-type (EG6089) treated with anti-GFP RNAi R2


title: P0 wild-type (EG6089) control R2


title: mus_heart_sham_veh_3

description:
Mice were subjected to sham surgery and received vehicle injection for 6 weeks starting post-op week 4.
MI_TAC_raw_counts.txt


title: ChIP-seq_Spt5-deg_DMSO_Spt5_r1

value: 10% S. cerevisiae chromatin

value: TGACCAT


title: F3 wild-type (EG6089) control R2


title: mus_heart_sham_veh_4


title: P0 met-2(n4256);set-25(n5021);EG6089 treated with anti-GFP RNAi R2


title: mus_heart_sham_veh_1


title: ChIP-seq_Spt5-deg_DMSO_S5P_r1

value: CGATGTT


title: F3 met-2(n4256);set-25(n5021);EG6089 treated with anti-GFP RNAi R2


title: ChIP-seq_Spt5-deg_DMSO_S2P_r1

value: ATCACGT


title: ChIP-seq_Spt5-deg_NAA+T_Pol2_r1

value: thiamine + 1-Napthaleneacetic acid (NAA)

value: CAGATCT


title: ChIP-seq_Spt5-deg_NAA+T_Spt5_r1

value: ACTTGAT


title: mus_heart_sham_veh_2


title: ChIP-seq_Spt5-deg_DMSO_Pol2_r1

value: TTAGGCT


title: cho2_YPL_rep2

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

description:
cho2_YPL_2
Processed data file: Expression_deseq.txt

data_processing:
50 bp single-end reads were mapped using Bowtie against yeast genome SacCer2 (bowtie -5 3 -3 5 -p 12 --best ./index/saccer2). The number of reads overlapping yeast genes was calculated in R using the countOverlaps function from the GenomicRanges package. Differential expression was analyzed by DESeq.
Genome_build: SacCer2
Supplementary_files_format_and_content: Expression_deseq.txt: Tab-delimited text file. Each row represents one gene and each column represents normalized read counts from one sample. The standard DESeq command was used to normalize the read counts.

organism: Saccharomyces cerevisiae

source_name: yeast cells, cho2-delta, YPL

growth_protocol:
Cells growing logarithmically in YPL are washed with and switched to SL when A600 reached 1.0. Samples were collected for RNA-seq before and 1 or 3 hours after the switch.
YPL: 1% yeast extract, 2% peptone and 2% lactate; SL: 0.17% yeast nitrogen base without amino acids containing 0.5% ammonium sulfate (Difco), 2% lactate.

extract_protocol:
RNA isolation of five OD600 units of cells under different growth conditions was carried out following the manufacturer's manual using MasterPure yeast RNA purification kit (Epicentre).
4 µg of total DNase-treated RNA are then prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. Poly-A RNA is purified and fragmented before strand specific cDNA synthesis. cDNA are then A-tailed and indexed adapters are ligated. After adapter ligation, samples are PCR amplified and purified with Ampure XP beads, then validated again on the Agilent 2100 Bioanalyzer. Samples are quantified by Qubit before being normalized and pooled, then run on the Illumina HiSeq 2500 using SBS v3 reagents.

value: CEN.PK, cho2-delta::KanMX, MAT a

tag: medium

value: YPL

tag: timepoint

value: before medium switch


title: cho2_SL_1h_rep2

description:
cho2_SL1h_2
Processed data file: Expression_deseq.txt

source_name: yeast cells, cho2-delta, SL, 1h

value: SL

value: 1h after medium switch


title: MethylC-seq_prefrontal_ctx_rep2

city: San Diego

first: Eran

middle: A

last: Mukamel

state: United States

address: 9500 Gilman Dr.

department: Cognitive Science

institute: University of California-San Diego

data_processing:
Data was mapped to the Mus musculus reference genome (mm10, C57) and a pseudo genome for Spretus (mm10 modified with ~42 Million SNPs from Sanger Institute)
Allele-specific read sorting and analysis for RNA-seq and MethylC-seq datasets were performed as described in Keown et al., 2016 (in submission)
RNA-seq: Five base pairs were trimmed from the 5'-end of all reads to remove possible adaptor contamination (seqtk trimfq -b 5)
RNA-seq: Trimmed reads were aligned to the C57 and pseudo Spretus genomes using TOPHAT2 v2.0.9, guided by protein coding gene annotation from Gencode version 5 level 3
RNA-seq: Gene expression levels were estimated using Cufflinks v2.1.1
RNA-seq: Visualization tracks were generated by counting genome-wide coverage of reads (BEDTOOLS v2.2.4 genomecov -bg) and converted to bigWig format (bedGraphToBigWig).
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (https://bitbucket.org/schultzmattd/methylpy/ and Lister et al., 2013) for alignment and mC calling
MethylC-seq: DMRs were identified using methylpy (https://bitbucket.org/schultzmattd/methylpy/). For DMR calling, data from this study was combined across replicates.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig tracks for visualization of RNA-seq
Supplementary_files_format_and_content: tab delimited text files of gene expression levels estimated using Cufflinks v2.1.1 and Htseq v0.6.0
Supplementary_files_format_and_content: tab delimited text files of methylcytosine calls; columns in allc files are: column 1 - chromosome; column 2 - position; column 3 - strand; column 4 - class; column 5 - mC reads; column 6 - total reads; column 7 - methylated (Boolean value indicating the result of statistical test for methylated cytosines)
Supplementary_files_format_and_content: tab delimited text files of DMRs; columns in DMRs files are: column 1 - chromosome; column 2 - start; column 3 - end; column 4 -methylation C57; column 5 - methylation spretus

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
Animals were anesthetized with CO2 followed by cervical dislocation. Brains were removed and rinsed in cold PBS. For dissection, whole brains were placed in cold DMEM supplemented with 10% FBS. The prefrontal cortex (PFC) was obtained by first removing the cerebellum, followed by slicing coronally at Bregma 1 mm and carefully isolating the frontal cortical tissue under a dissecting microscope. PFC samples were rapidly frozen on dry ice until processing. DNA and RNA were isolated from pooled PFC samples obtained from two individuals from separate litters.
Genomic DNA was extracted from ground, frozen tissue using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). Two µg of genomic DNA was spiked with 10 ng unmethylated cl857Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 150-200 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were religated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure X P beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450ng) was subjected to sodium bisulfite conversion using the Methyl Code kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by four cycles of PCR with the following reaction composition: 25µL of Kapa Hi Fi Hotstart Uracil+Readymix (Kapa Biosystems, Woburn, MA) and 5µl TruSeq PCR Primer Mix (Illumina) (50µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 4 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure X P beads. Two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding two independent libraries from the same biological sample.
RNA-seq: Animals were anesthetized with CO2 followed by cervical dislocation. Brains were removed and rinsed in cold PBS. For dissection, whole brains were placed in cold DMEM supplemented with 10% FBS. The prefrontal cortex (PFC) was obtained by first removing the cerebellum, followed by slicing coronally at Bregma 1 mm and carefully isolating the frontal cortical tissue under a dissecting microscope. PFC samples were rapidly frozen on dry ice until processing. DNA and RNA were isolated from pooled PFC samples obtained from two individuals from separate litters.
RNA-seq: Ribosomal RNA was removed from samples using Ribo-Zero rRNA Removal kit (Illumina, San Diego, CA). mRNA-Seq libraries were then generated using the TruSeq Stranded RNA LT kit (Illumina, San Diego, CA) as per manufacturer’s instructions.
Bisulfite-Seq (MethylC-seq): Animals were anesthetized with CO2 followed by cervical dislocation. Brains were removed and rinsed in cold PBS. For dissection, whole brains were placed in cold DMEM supplemented with 10% FBS. The prefrontal cortex (PFC) was obtained by first removing the cerebellum, followed by slicing coronally at Bregma 1 mm and carefully isolating the frontal cortical tissue under a dissecting microscope. PFC samples were rapidly frozen on dry ice until processing. DNA and RNA were isolated from pooled PFC samples obtained from two individuals from separate litters.
Bisulfite-Seq (MethylC-seq): Genomic DNA was extracted from ground, frozen tissue using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). Two µg of genomic DNA was spiked with 10 ng unmethylated cl857Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 150-200 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were religated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure X P beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450ng) was subjected to sodium bisulfite conversion using the Methyl Code kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by four cycles of PCR with the following reaction composition: 25µL of Kapa Hi Fi Hotstart Uracil+Readymix (Kapa Biosystems, Woburn, MA) and 5µl TruSeq PCR Primer Mix (Illumina) (50µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 4 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure X P beads. Two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding two independent libraries from the same biological sample.

value: 14 weeks

value: female

tag: genotype

value: mutation of long noncoding RNA Xist on Maternal allele

value: brain (prefrontal cortex)


title: cho2_SL_3h_rep2

description:
cho2_SL3h_2
Processed data file: Expression_deseq.txt

source_name: yeast cells, cho2-delta, SL, 3h

value: 3h after medium switch


title: WT_SL_3h_rep2

description:
WT_SL3h_2
Processed data file: Expression_deseq.txt

source_name: yeast cells, WT, SL, 3h

value: CEN.PK, MAT a


title: MethylC-seq_prefrontal_ctx_rep1


title: WT_YPL_rep2

description:
WT_YPL_2
Processed data file: Expression_deseq.txt

source_name: yeast cells, WT, YPL


title: cho2_SL_3h_rep1

description:
cho2_SL3h_1
Processed data file: Expression_deseq.txt


title: P0 wild-type (EG6089) treated with anti-GFP RNAi R1

value: wild-type (EG6089)

value: day 1 adult

value: whole animal


title: RNA-seq_prefrontal_ctx_rep2

extract_protocol:
Animals were anesthetized with CO2 followed by cervical dislocation. Brains were removed and rinsed in cold PBS. For dissection, whole brains were placed in cold DMEM supplemented with 10% FBS. The prefrontal cortex (PFC) was obtained by first removing the cerebellum, followed by slicing coronally at Bregma 1 mm and carefully isolating the frontal cortical tissue under a dissecting microscope. PFC samples were rapidly frozen on dry ice until processing. DNA and RNA were isolated from pooled PFC samples obtained from two individuals from separate litters.
Ribosomal RNA was removed from samples using Ribo-Zero rRNA Removal kit (Illumina, San Diego, CA). mRNA-Seq libraries were then generated using the TruSeq Stranded RNA LT kit (Illumina, San Diego, CA) as per manufacturer’s instructions.
RNA-seq: Animals were anesthetized with CO2 followed by cervical dislocation. Brains were removed and rinsed in cold PBS. For dissection, whole brains were placed in cold DMEM supplemented with 10% FBS. The prefrontal cortex (PFC) was obtained by first removing the cerebellum, followed by slicing coronally at Bregma 1 mm and carefully isolating the frontal cortical tissue under a dissecting microscope. PFC samples were rapidly frozen on dry ice until processing. DNA and RNA were isolated from pooled PFC samples obtained from two individuals from separate litters.
RNA-seq: Ribosomal RNA was removed from samples using Ribo-Zero rRNA Removal kit (Illumina, San Diego, CA). mRNA-Seq libraries were then generated using the TruSeq Stranded RNA LT kit (Illumina, San Diego, CA) as per manufacturer’s instructions.
Bisulfite-Seq (MethylC-seq): Animals were anesthetized with CO2 followed by cervical dislocation. Brains were removed and rinsed in cold PBS. For dissection, whole brains were placed in cold DMEM supplemented with 10% FBS. The prefrontal cortex (PFC) was obtained by first removing the cerebellum, followed by slicing coronally at Bregma 1 mm and carefully isolating the frontal cortical tissue under a dissecting microscope. PFC samples were rapidly frozen on dry ice until processing. DNA and RNA were isolated from pooled PFC samples obtained from two individuals from separate litters.
Bisulfite-Seq (MethylC-seq): Genomic DNA was extracted from ground, frozen tissue using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). Two µg of genomic DNA was spiked with 10 ng unmethylated cl857Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 150-200 bp, followed by end repair and addition of a 3’ A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were religated to the sonicated DNA at 16˚C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure X P beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (≤450ng) was subjected to sodium bisulfite conversion using the Methyl Code kit (Life Technologies, Carlsbad, CA) as per manufacturer’s instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by four cycles of PCR with the following reaction composition: 25µL of Kapa Hi Fi Hotstart Uracil+Readymix (Kapa Biosystems, Woburn, MA) and 5µl TruSeq PCR Primer Mix (Illumina) (50µl final). The thermocycling parameters were: 95˚C 2 min, 98˚C 30 sec, then 4 cycles of 98˚C 15 sec, 60˚C 30 sec and 72˚C 4 min, ending with one 72˚C 10 min step. The reaction products were purified using AMPure X P beads. Two separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding two independent libraries from the same biological sample.


title: WT_SL_1h_rep2

description:
WT_SL1h_2
Processed data file: Expression_deseq.txt

source_name: yeast cells, WT, SL, 1h


title: cho2_SL_1h_rep1

description:
cho2_SL1h_1
Processed data file: Expression_deseq.txt


title: ChIP-seq_Spt5-deg_NAA+T_S5P_r1

value: EMM

value: thiamine + 1-Napthaleneacetic acid (NAA)

value: 10% S. cerevisiae chromatin

value: GCCAATT


title: RNA-seq_prefrontal_ctx_rep1


title: WT_SL_1h_rep1

description:
WT_SL1h_1
Processed data file: Expression_deseq.txt


title: F3 wild-type (EG6089) control R1


title: WT_SL_3h_rep1

description:
WT_SL3h_1
Processed data file: Expression_deseq.txt


title: P0 met-2(n4256);set-25(n5021);EG6089 treated with anti-GFP RNAi R1


title: F3 met-2(n4256);set-25(n5021);EG6089 treated with anti-GFP RNAi R1


title: cho2_YPL_rep1

description:
cho2_YPL_1
Processed data file: Expression_deseq.txt

value: CEN.PK, cho2-delta::KanMX, MAT a

value: YPL


title: P0 met-2(n4256);set-25(n5021);EG6089 control R2


title: LowZG_longExpos_2

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description:
Genter-14
100 µM zinc gluconate exposure for 24 hours
undifferentiated Odora

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq sequences were aligned to rn4 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: rn4
Supplementary_files_format_and_content: raw counts with genes in rows and samples in columns

organism: Rattus norvegicus

source_name: Odora cell line (rat olfactory neuron)_100 µM zinc gluconate exposure for 24 hours

extract_protocol:
not provided.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Odora

tag: cell type

value: olfactory neuron


title: LowZG_longExpos_3

description:
Genter-15
100 µM zinc gluconate exposure for 24 hours
undifferentiated Odora


title: P0 met-2(n4256);set-25(n5021);EG6089 control R1


title: F3 met-2(n4256);set-25(n5021);EG6089 control R2


title: HighZG_shortExpos_3

description:
Genter-12
200 µM zinc gluconate exposure for 6 hours
undifferentiated Odora

source_name: Odora cell line (rat olfactory neuron)_200 µM zinc gluconate exposure for 6 hours


title: F15 wild-type (SX1263) treated with anti-GFP RNAi R3

source_name: F15 treated with anti-GFP RNAi

value: wild-type (SX1263)


title: HighZG_shortExpos_2

description:
Genter-11
200 µM zinc gluconate exposure for 6 hours
undifferentiated Odora


title: HighZG_shortExpos_1

description:
Genter-10
200 µM zinc gluconate exposure for 6 hours
undifferentiated Odora


title: LowZG_medExpos_3

description:
Genter-9
100 µM zinc gluconate exposure for 12 hours
undifferentiated Odora

source_name: Odora cell line (rat olfactory neuron)_100 µM zinc gluconate exposure for 12 hours


title: LowZG_medExpos_1

description:
Genter-7
100 µM zinc gluconate exposure for 12 hours
undifferentiated Odora


title: P0 wild-type (EG6089) control R1


title: WT_YPL_rep1

description:
WT_YPL_1
Processed data file: Expression_deseq.txt

value: before medium switch


title: F3 wild-type (EG6089) treated with anti-GFP RNAi R1


title: LowZG_medExpos_2

description:
Genter-8
100 µM zinc gluconate exposure for 12 hours
undifferentiated Odora


title: F15 wild-type (SX1263) control R3

source_name: F15 control


title: LowZG_shortExpos_3

description:
Genter-6
100 µM zinc gluconate exposure for 6 hours
undifferentiated Odora

source_name: Odora cell line (rat olfactory neuron)_100 µM zinc gluconate exposure for 6 hours


title: LowZG_shortExpos_2

description:
Genter-5
100 µM zinc gluconate exposure for 6 hours
undifferentiated Odora


title: F15 met-2(n4256) control R3


title: Control3

description:
Genter-3
Control
undifferentiated Odora

source_name: Odora cell line (rat olfactory neuron)_Control


title: LowZG_shortExpos_1

description:
Genter-4
100 µM zinc gluconate exposure for 6 hours
undifferentiated Odora


title: Control2

description:
Genter-2
Control
undifferentiated Odora


title: Control1

description:
Genter-1
Control
undifferentiated Odora


title: F15 wild-type (SX1263) treated with anti-GFP RNAi R2


title: Dam_can_Rep2_Pc_Control

city: Novosibirsk

first: Petr

last: Laktionov

address: Lavrenitev ave 8/2

country: Russia

institute: Institute of molecular and cellular biology SD RAS

description:
Pc DamID/can-mut testes control sample
Pc_can_Testes_track.wig.gz

data_processing:
Library strategy: DamID
Sequenced reads were trimmed for adaptor sequence using cutadapt v1.7
The reads obtained were mapped to BDGP R5 Drosophila genome assembly using MOSAIK software with following parameters: -m all -mmp 0.1 -act 20 -a single
For further analysis, only the reads that started with GATC sequence were retained. The number of reads for each genomic fragment between the neighboring GATC sites (GATC fragments) was summed up.
The data were filtered for reproducibility: all GATC fragments were sorted according to the total read count in two biological samples. This list was binned into groups of 200 fragments having similar read counts. For each GATC fragment, a difference in read counts was calculated between the replicates. Those fragments that showed the difference above 2 standard deviations in the particular group were filtered out.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: wig

organism: Drosophila melanogaster

growth_protocol: The flies were kept at 23°C

extract_protocol:
Testes were collected from 3day-old males. For each biological replicate, 50 pairs of testes were used. Standard phenol-chloroform extraction method was used to isolate genomic DNA from the collected material. 0.5-1 ug DNA was used in each DamID experiment. Genomic DNA was digested by DpnI endonuclease. Digested DNA was ligated with double-stranded DNA adapters and then digested with DpnII endonuclease. Next, methylated fragments were selectively amplified using adapter-specific primer. Before the preparation of libraries for Illumina DamID-Seq, the adapters used in DamID procedure were cut with DpnII enzyme. No further fragmentation was performed.
One microgram of genomic DNA was processed for library preparation using the DNA TruSeq kit. The libraries were sequenced on the Illumina MiSeq system.

value: yw

value: male

value: 3 days old

value: adult testes


title: F15 wild-type (SX1263) control R2


title: F3 met-2(n4256);set-25(n5021);EG6089 control R1


title: F15 met-2(n4256) treated with anti-GFP RNAi R2


title: LowZG_longExpos_1

description:
Genter-13
100 µM zinc gluconate exposure for 24 hours
undifferentiated Odora


title: DamPc_can_Rep1

description:
DamPc/can-mutant testes
Pc_can_Testes_track.wig.gz


title: Dam_bam_Rep2_Pc_Control

description:
Pc DamID/bam-mut testes control sample
Pc_bam_Testes_track.wig.gz


title: F15 met-2(n4256) control R2


title: Dam_can_Rep1_Pc_Control


title: Dam_bam_Rep1_Pc_Control


title: DamPc_bam_Rep2

description:
DamPc/bam-mutant testes
Pc_bam_Testes_track.wig.gz


title: DamPc_aly_Rep2

description:
DamPc/aly-mutant testes
Pc_aly_Testes_track.wig.gz


title: F15 met-2(n4256) treated with anti-GFP RNAi R3


title: F15 wild-type (SX1263) treated with anti-GFP RNAi R1


title: Dam_WT_Rep2_Mip40_Control

description:
Mip40 DamID/WT testes control sample
Mip40_WT_Testes_track.wig.gz


title: DamPc_aly_Rep1


title: F15 met-2(n4256) treated with anti-GFP RNAi R1


title: F15 wild-type (SX1263) control R1


title: DamPc_bam_Rep1


title: Dam_WT_Rep1_Mip40_Control


title: DamMip40_WT_Rep2

description:
DamMip40/WT testes
Mip40_WT_Testes_track.wig.gz


title: F15 met-2(n4256) control R1


title: F3 wild-type (SX1263) treated with anti-GFP RNAi R3


title: DamPc_can_Rep2


title: Dam_can_Rep1_Mip40_Control

description:
Mip40 DamID/can-mut testes control sample
Mip40_can_Testes_track.wig.gz


title: NETseq_Spt5_T4.5_II

description: Strain_FWP487_genotype_nmt81-Spt5-V5-IAA17_Rpb3-3xFLAG

data_processing:
Library strategy: NET-Seq
Experiment 1 (T0_I): Custom removal of adapter sequence (oLSC007: ATCTCGTATGCCGTCTTCTGCTTG).
Exp. 1: Filter-mapping against a "genome" of tRNA, rRNA, snRNA, and snoRNA to filter out noise that should not come down with Pol II via Bowtie1 with parameters -m1 (unique mapping) -n3 (allowing 3 mismatches) -e 120 (allowing three full mismatches) --max (dumping non-unique mappers in another file). Unmapped reads are kept for next step.
Exp. 1: Mapping to S. pombe genome using Bowtie1 with parameters -m1 -n3 -e 120.
Exp. 1: Remove all PCR duplicates from SAM via R: unique() (custom script) on concatenated strand, chr, position, and sequence.
Exp. 1: Remove all splicing intermediates (exon, intron 3' positions) and non-nuclear chromosomes via custom R script.
Exp. 1: Normalize to total remaining counts in library, produce WIG track file (custom R script).
Experiment 2 (T0_II, T4.5_I, T4.5_II):  Cutadapt (1.8.3) removal of adapter sequence (oLSC007: ATCTCGTATGCCGTCTTCTGCTTG).
Exp. 2: Prinseq to clean file (-no_qual_header -min_len 7 -min_qual_mean 20 -trim_right 1 -trim_ns_right 1 -trim_qual_right 20 -trim_qual_type min -trim_qual_window 1 -trim_qual_step 1)
Exp. 2: Removal of hexameric molecular barcode via custom script. Placed in FASTQ header.
Exp. 2: Filter-mapping barcode-removed reads against a combined S. cerevisiae + S. pombe 'genome' composed only of t/r/sn/snoRNA using Tophat 2 with parameters --read-mismatches 3  --read-gap-length 1 --read-edit-dist 3 --min-anchor-length 8 --splice-mismatches 1 --min-intron-length 25 --max-intron-length 1200 --max-insertion-length 3 --max-deletion-length 3 --library-type fr-firststrand --segment-mismatches 3 --no-coverage-search --segment-length 25 --min-coverage-intron 50 --max-coverage-intron 100000 --min-segment-intron 50 --max-segment-intron 500000 --b2-sensitive.
Exp. 2: Mapping barcode-removed reads to combined S. pombe + S. cerevisiae 'genome' using Tophat 2 with same parameters as above plus the following to drive unique mapping: --prefilter-multihits --max-multihits 1 --transcriptome-max-hits 1
Exp. 2: Mapping barcode-containing reads (post-Prinseq input to barcode removal, above) using Tophat 2 with same parameters as barcode-removed immediately above. The purpose of this is to eventually filter out reads that map without barcode removal.
Exp. 2: From barcode-removed mapping, remove artefactual reads presumably arising from reverse transcription mispriming that map when the barcode is not removed. (Custom script).
Exp. 2: Remove all splicing intermediates and non-nuclear chromosomes via custom script.
Exp. 2: Split BAM into S. cerevisiae and S. pombe reads via custom script that calls bash samtools, grep, sed.
Exp. 2: Check whether spike-in normalization shows effect (it didn't: ratio of Sc/Sp similar in all samples). Custom script.
Exp. 2: Normalize to total remaining counts in library, produce WIG track file (custom R script).
Genome_build: Exp. 1: S. pombe ASM294v2; Exp. 2: S. pombe ASM294v2 concatenated to S. cerevisiae R64-1-1
Supplementary_files_format_and_content: WIG: track files of transcript 3' ends, from which RNA Pol II single-base-resolution active site position is inferred.

extract_protocol:
One liter cultures of S. pombe at 10^7 cells/ml were spiked-in with S. cerevisiae (10% by cell number), and the cells were collected by filtration. One of the libraries used for our analysis (T0_I, before depletion of Spt5) did not have S. cerevisiae as spike-in. Cells were flash frozen by forcing the cells through a syringe into liquid nitrogen. The frozen cells were mixed with 4 ml of frozen (by dropping 50 µl drops into liquid nitrogen) lysis-buffer without MnCl2 and protease inhibitors   and lysed in a mixer-mill using 8 cycles at 15 Hz (Lysis buffer: 20mM HEPES, 110mM KOAc, 0.5% Triton X-100, 0.1% Tween 20, 10mM MnCl2, 1X protease inhibitors Roche EDTA-free). This lysate was thawed on ice and 1 ml lysis buffer with 50mM MnCl2 and 5x protease inhibitor, was added to the lysate along with 660 µl of DNAseI (RQ1, Promega) and incubated on ice for 30 minutes. Solubilized RNAPII was then immunoprecipitated along with the associated RNA using  FLAG M2 Affinity gel (SIGMA), and eluted using 3X-FLAG peptide (SIGMA). RNA was extracted from the eluate using Qiagen miRNEasy kit.
Library prep was performed as previously described (PMID: 21248844) except that a modified linker-1 with a randomized hexamer was used for all libraries from experiment 2.

treatment_protocol: Spt5 depletion experiments were performed by adding NAA (0.5mM in DMSO, napthaleneacetic acid, Sigma, N0640) and thiamine (100nM, thiamine hydrochloride34, Sigma, T4625), to cells grown to a density of 10^7 cells/ml (O.D.600 ~ 0.5). Cultures were incubated with shaking at 30°C for 4.5 hours.

tag: genotype/variation

value: S cerevisiae

tag: rip antibody

value: anti-FLAG M2 Affinity gel (SIGMA, catalog #A2220)

value: CAGATC


title: DamMip40_can_Rep2

description:
DamMip40/can-mutant testes
Mip40_can_Testes_track.wig.gz

tag: strain


title: F3 wild-type (SX1263) control R3

value: day 1 adult

tag: tissue

value: whole animal


title: NETseq_Spt5_T4.5_I

value: thiamine + 1-Napthaleneacetic acid (NAA)

value: TAGCTT


title: RNAseq_Spt5-T0_I

description:
RNAseq_Spt5-T0-167_I
Strain_FWP486_genotype_nmt81-Spt5-V5-IAA17

value: EMM

value: 0 hr

value: ERCC

value: TGACCA


title: DamMip40_can_Rep1

tag: gender


title: NETseq_Spt5_T0_II

value: CTTGTA


title: Dam_bam_Rep2_Mip40_Control

description:
Mip40 DamID/bam-mut testes control sample
Mip40_bam_Testes_track.wig.gz


title: NETseq_Spt5_T0_I

value: ACAGTG


title: F3 met-2(n4256) treated with anti-GFP RNAi R3


title: Dam_bam_Rep1_Mip40_Control

value: yw


title: ChIP-seq_Spt5-deg_NAA+T_S2P_r1

tag: treatment

value: 10% S. cerevisiae chromatin

value: ACAGTGT


title: F3 met-2(n4256);set-25(n5021) treated with anti-GFP RNAi R3


title: DamMip40_bam_Rep1

description:
DamMip40/bam-mutant testes
Mip40_bam_Testes_track.wig.gz

value: male

value: 3 days old

value: adult testes


title: DamMip40_bam_Rep2


title: DamMip40_WT_Rep1


title: Dam_aly_Rep2_Mip40_Pc_Control

description:
Mip40 and Pc DamID/aly-mut testes control sample
Mip40_aly_Testes_track.wig.gz


title: F3 met-2(n4256) control R3


title: F3 wild-type (SX1263) treated with anti-GFP RNAi R2

value: wild-type (SX1263)


title: Dam_aly_Rep1_Mip40_Pc_Control


title: Dam_can_Rep2_Mip40_Control


title: DamMip40_aly_Rep1

description:
DamMip40/aly-mutant testes
Mip40_aly_Testes_track.wig.gz


title: F3 set-25(n5021) treated with anti-GFP RNAi R2

value: day 1 adult


title: DamMip40_aly_Rep2


title: F3 set-25(n5021) control R2

value: whole animal


title: F3 set-25(n5021) treated with anti-GFP RNAi R3


title: Dam_Rep2_CG9879_Control

description:
CG9879 DamID control sample
CG9879_WT_Testes_track.wig.gz


title: F3 met-2(n4256) treated with anti-GFP RNAi R2


title: F3 met-2(n4256);set-25(n5021) treated with anti-GFP RNAi R2


title: Dam_Rep1_CG9879_Control


title: F3 set-25(n5021) control R3


title: DamCG9879_Rep1

description:
DamCG9879/ WT testes
CG9879_WT_Testes_track.wig.gz


title: DamCG9879_Rep2


title: F3 met-2(n4256);set-25(n5021) control R2


title: F3 met-2(n4256) control R2


title: Dam_Rep2_Can_Control

description:
Can DamID control sample
Can_WT_Testes_track.wig.gz


title: F3 wild-type (SX1263) treated with anti-GFP RNAi R1


title: Dam_Rep1_Can_Control


title: DamCan_Rep2

description:
DamCan/ WT testes
Can_WT_Testes_track.wig.gz

source_name: DamCan


title: F3 wild-type (SX1263) control R1


title: F3 met-2(n4256);set-25(n5021) control R3


title: F3 wild-type (SX1263) control R2


title: DamCan_Rep1


title: F3 set-25(n5021) control R1


title: Dam_Rep2_Comr_Control

description:
Comr DamID control sample
Comr_WT_Testes_track.wig.gz


title: F3 set-25(n5021) treated with anti-GFP RNAi R1

source_name: F3 treated with anti-GFP RNAi


title: Nup98-3

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Raw fastq files were trimmed to remove low quality base calls using Trimmomatic, with parameter "LEADING:3 TRAILING:3 SLIDINGWINDOW:3:3 MINLEN:30".
Trimmed reads were aligned to dm3 using Bowtie2, allowing for only uniquely aligned reads (MAPQ > 10) to be reported.
Duplicate reads and mitochondria reads were removed using Samtools and Bedtools.
Significant peaks were called using MACS2, with parameter "--qvalue 0.05 -m 2 50".
Bedgraphs were generated using the command "bedtools genomecov", library sizes were normalized to 10 million reads per sample.
BigWig files were then converted from bedgraph files using command "bedGraphToBigWig".
Genome_build: dm3
Supplementary_files_format_and_content: bigwig files were converted from bedgraph files, which were generated using Bedtools. Scores were normalized to 10 million reads per sample.

source_name: brains

extract_protocol:
Lysates from embryonic cells or 3rd instar brains were clarified from sonicated nuclei and histone-DNA or Nup-DNA complexes were isolated with specific antibody
Libraries were prepared according to Illumina's instructions for NextSeq® 500/550 High Output Kit v2 (FC-404-2005).

value: 3rd instar larva

value: brains

tag: chip antibody

value: Nup98 (Capelson et al., (2010))

value: wild type


title: F3 met-2(n4256) treated with anti-GFP RNAi R1


title: Dam_Rep1_Comr_Control

tag: age


title: F3 met-2(n4256);set-25(n5021) treated with anti-GFP RNAi R1


title: DamComr_Rep1

description:
DamComr/ WT testes
Comr_WT_Testes_track.wig.gz

source_name: DamComr


title: DamComr_Rep2


title: Nup98-1


title: Nup98-2


title: F3 met-2(n4256) control R1

source_name: F3 control


title: P0 wild-type (SX1263) treated with anti-GFP RNAi R3

source_name: P0 treated with anti-GFP RNAi


title: WT_Rep2

data_processing:
Reads were aligned on D.melanogaster BDGP R6/dm6 genome assembly (https://genome-euro.ucsc.edu/) using TopHat (–r 200 –mate-std-dev 50) .
Transcript assembly was performed by Cufflinks (BDGP R6/dm6).
Genome_build: BDGP R6/dm6
Supplementary_files_format_and_content: gene abundance

source_name: WT

extract_protocol:
50 adult testes were dissected in PBS. Total RNA was isolated from testes, using TRIZol (Invitrogen) reagent, according to the manufacturer’s instructions.
One microgram of total RNA was processed for library preparation using the RNA TruSeq kit. The libraries were sequenced on the Illumina MiSeq system.


title: P0 wild-type (SX1263) control R3

source_name: P0 control


title: Nup93-3

value: Nup93 (This study)


title: Su(var)3-9_Rep2


title: WT_Rep1


title: Nup93-2


title: P0 set-25(n5021) treated with anti-GFP RNAi R3


title: Input-4

description: control for Nup93, Elys and H3K27m3 ChIP


title: Su(var)3-9_Rep1


title: P0 set-25(n5021) control R3


title: Input-2

description: control for Nup98 and H3K27ac ChIP


title: Input-3


title: Input-1

description: control for Nup98 and H3K27ac ChIP


title: wt_Rep1

description: control sample

data_processing:
Reads were aligned on D.melanogaster BDGP R5/dm3 (or BDGP R6/dm6) genome assembly (https://genome-euro.ucsc.edu/) using TopHat (–r 200 –mate-std-dev 50) .
Transcript differential expression testing between samples was performed with Cuffdiff  using geometric normalization, pooled dispersion estimation and FDR 0.05
Transcript assembly was performed by Cufflinks (BDGP R6/dm6).
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: gene abundance and log2(fold_change)

source_name: wt


title: mip40/bam_Rep2

description: Mip40_bam_vs_bam_CuffDiff_Output_BDGP5.txt


title: wt_Rep2

description: control sample


title: P0 met-2(n4256);set-25(n5021) treated with anti-GFP RNAi R3


title: P0 met-2(n4256) treated with anti-GFP RNAi R3


title: IgG-2

value: IgG (Santa Cruz #2027)


title: mip40/bam_Rep1


title: P0 met-2(n4256);set-25(n5021) control R3


title: F3 met-2(n4256);set-25(n5021) control R1


title: P0 met-2(n4256) control R3


title: mip40_Rep2


title: P0 set-25(n5021) treated with anti-GFP RNAi R2


title: P0 wild-type (SX1263) control R2


title: H3K27m3-2

value: H3K27m3 (Active Motif #39155)


title: mip40_Rep1


title: Nup93-1


title: P0 set-25(n5021) control R2


title: H3K27m3-1


title: H3K27ac-2

value: H3K27ac (Active Motif #39133)


title: P0 met-2(n4256) treated with anti-GFP RNAi R2


title: CG9879_Rep1


title: P0 met-2(n4256);set-25(n5021) treated with anti-GFP RNAi R2


title: CG9879_Rep2


title: can_Rep2

source_name: can

value: can


title: can_Rep1


title: P0 met-2(n4256);set-25(n5021) control R2


title: Elys-1

value: Elys (This study)


title: P0 met-2(n4256) control R2


title: comr_Rep2

source_name: comr

value: comr


title: P0 wild-type (SX1263) treated with anti-GFP RNAi R1


title: comr_Rep1

value: male


title: bam_Rep2

source_name: bam

value: bam

value: 3 days old


title: stage_9_Input_DNA

city: Irvine

first: Rebekah

middle: M

last: Charney

state: CA

address: 4410 Natural Sciences II

department: Developmental and Cell Biology

institute: University of California, Irvine

data_processing:
ChIP-seq reads were aligned to the Xenopus tropicalis genome v7.1 using Bowtie v1.0.0 (Langmead et al., 2009). All multimapping reads were discarded.
Foxh1 and Smad2/3 ChIP-seq peaks were called using the Irreproducibility Discovery Rate (IDR) framework (Li et al., 2011) and MACS2 v2.0.10 (Zhang et al., 2008). All other samples were peak-called using MACS2 v2.0.10. MACS2 'callpeak' command was used against the stage-matched inut control.
Genome_build: Xenopus tropicalis v7.1
Supplementary_files_format_and_content: Bedgraph files were created using Samtools (Li et al., 2009) and Homer v4.7 (Heinz et al., 2010). Duplicate reads were removed from sorted BAM files using the ‘rmdup’ command in Samtools and biological replicates were concatenated. Bedgraph files were created using HOMER after first making a tag directory. Default conditions were applied for the generation of the bedgraph files (http://homer.salk.edu/homer/ngs/ucsc.html).

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were cultured in 1/9x MMR at 25° until the indicated stage.

extract_protocol:
The fixed embryos were homogenized in RIPA buffer and incubated on ice for 10 minutes. Samples were then microfuged at 14,000rpm for 15 minutes at 4°C. Pellets were resuspended in RIPA buffer and sonicated on ice to an average size of 200-500bp. The resulting samples were microfuged at 14,000 rpm for 20 minutes at 4°C to remove insoluble cellular debris. The sheared chromatin was “pre-cleared” by incubating with Protein A-coated Dynabeads (Invitrogen) for 2 hour at 4°C with rotation. Antibodies were pre-bound to blocked Protein A Dynabeads by incubating at 4°C for 30 min. A sample of sheared chromatin was frozen for use as input control. Pre-cleared chromatin was added to antibody-bound Dynabeads, and incubated overnight at 4°C on an end-over-end rotator. The next day, the beads were washed, and DNA was eluted off the beads with TE buffer containing 1% SDS, and reverse-crosslinked at 65°C overnight. Sonicated input control was diluted 3-fold with elution buffer and also incubated at 65°C. All samples were treated with RNAse A, Proteinase K, phenol/chloroform extracted, and ethanol precipitated overnight. DNA pellets were resuspended in Qiagen EB solution.
10-30ng of DNA was used for library construction using the Bioo Scientific NEXTflex™ ChIP-seq Kit (Bioo Scientific #5143-01). Stage 8 Tle library was constructed using the TruSeq ChIP Sample Prep kit (Illumina).

treatment_protocol: Embryos were fixed in 1% formaldehyde in 1/9XMMR at room temperature for 45 minutes with gentle rocking. Crosslinking reactions were neutralized by the removal of the formaldehyde solution and incubation with 1ml 0.125M glycine solution for 10 minutes on ice. Embryos were then washed twice with cold RIPA buffer (50 mM Tris-HCl pH7.4, 150mM NaCl, 1mM EDTA, 0.25% sodium deoxycholate, 1% NP40, 0.1% SDS, 0.5 mM DTT, and Roche cOmplete protease inhibitor cocktail). Embryos were flash-frozen in liquid nitrogen and stored at -80°C.

value: Nigerian

tag: Stage

value: st. 9


title: IgG-1


title: stage_8_Input_Tle_DNA

value: st. 8


title: bam_Rep1

value: adult testes


title: P0 wild-type (SX1263) control R1

value: wild-type (SX1263)

value: day 1 adult

value: whole animal


title: stage_10.25_Foxa_ChIP

value: Foxa (Santa Cruz Biotechnology, sc-6554)


title: stage_8_Tle_ChIP

value: TLE (Santa Cruz Biotechnology, sc-13373)


title: stage_8_Input_DNA


title: stage_10.25_RNA_Pol_II_ChIP_rep1&2

description: rep 1 and rep 2

value: RNA Pol II (BioLegend, MMS-126R)


title: H3K27ac-1

value: 3rd instar larva

value: brains

value: H3K27ac (Active Motif #39133)

value: wild type


title: P0 set-25(n5021) treated with anti-GFP RNAi R1


title: P0 set-25(n5021) control R1


title: P0 met-2(n4256);set-25(n5021) treated with anti-GFP RNAi R1


title: H3K27me3_in_comr_testes_Rep1

data_processing:
The reads were mapped to BDGP R5/dm3 Drosophila genome assembly using MOSAIK software with the following parameters: -m all -mmp 0.1 -act 20 -a single. Paired reads were combined.
For each genomic position, the RPM (reads per million) value was calculated for ChIP sample and input sample.
Log2 of the ChIP to input ratio was used as a measure of local H3K27me3 enrichment. To build the whole genome profile, the data were processed using a 1kb sliding window, step 100 bp. Occupancy profiles were quantile normalized.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: .txt files report occupancy profiles

extract_protocol:
To perform H3K27me3 ChIP-seq, we used the True MicroChIP & MicroPlex Library Preparation™ Package (Diagenode), according to manufacturer’s recommendations. 400 adult testes of comr or can homozygotes were used as a starting material for two biological replicates. Abcam anti-H3K27me3 antibodies (#6002) were used for chromatin immunoprecipitation. Chromatin was sheared using BioRuptor instrument (Diagenode).
DNA from precipitated material and input were used for library preparation using MicroPlex Library Preparation protocol. The libraries were sequenced on the Illumina MiSeq system.

value: comr

value: male

value: anti-H3K27me3 (Abcam, catalog #6002)


title: H3K27me3_in_comr_testes_Rep2

value: 3 days old


title: Input_for_H3K27_in_comr_Rep2

description:
Input sample for the Replicate2 of comr-mutants ChIP-Seq
comr_H3K27me3_1kb_QN.txt.gz


title: P0 met-2(n4256);set-25(n5021) control R1


title: P0 met-2(n4256) treated with anti-GFP RNAi R1


title: Elys-2

value: Elys (This study)


title: Input_for_H3K27_in_can_Rep2

description:
Input sample for the Replicate2 of can-mutants ChIP-Seq
can_H3K27me3_1kb_QN.txt.gz

value: can


title: stage_9_RNA_Pol_II_ChIP_rep1&2

description: rep 1 and rep 2

value: Nigerian

value: st. 9


title: stage_8_RNA_Pol_II_ChIP_rep1&2

description: rep 1 and rep 2

value: st. 8


title: H3K27me3_in_can_testes_Rep2

value: adult testes


title: H3K27me3_in_can_testes_Rep1


title: stage_7_RNA_Pol_II_ChIP

value: st. 7


title: Input_for_H3K27_in_can_Rep1

description:
Input sample for the Replicate1 of can-mutants ChIP-Seq
can_H3K27me3_1kb_QN.txt.gz


title: stage_8_Foxh1_ChIP_rep1&2

description: rep 1 and rep 2

value: xtFoxh1 (custom)


title: stage_9_Foxh1_ChIP_rep1&2

description: rep 1 and rep 2


title: Input_for_H3K27_in_comr_Rep1

description:
Input sample for the Replicate1 of comr-mutants ChIP-Seq
comr_H3K27me3_1kb_QN.txt.gz


title: hnRNPU_shCTL

status: Public on Mar 29 2017

city: Cambridge

first: Juan

middle: R

last: Alvarez-Dominguez

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: total RNA minus rRNA

data_processing:
Reads were mapped to mm9 using TopHat v2.0.11 (Trapnell et al. 2009) with “--min-anchor 5 --no-novel-juncs” parameters. Gene expression was quantified from the mapped reads using HTSeq (Anders et al. 2015) on “union” mode based on Ensembl version 67 gene annotations
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files containing Htseq output for each sample

source_name: fetal liver

growth_protocol: Erythroid progenitors were purified from E14.5 mouse fetal livers by magnetic-assisted cell sorting (Flygare et al., 2011) and cultured for 24hrs in erythropoietin-containing media to induce terminal proliferation and differentiation (Zhang et al., 2003).

extract_protocol:
For RNA-seq, total RNA was isolated using the miRNeasy kit (QIAGEN) according to the manufacturer’s instructions. Ribosomal RNA was depleted from 4ug total RNA using the Ribo-Zero Gold Kit (Epicentre, Madison, WI).
Strand-specific cDNA libraries were prepared using a dUTP marking protocol (Borodina et al., 2011) and sequenced on an Illumina HiSeq2000 platform.

value: fetal liver


title: Bloodlinc_vector

description: total RNA minus rRNA


title: hnRNPU_sh1

description: total RNA minus rRNA


title: hnRNPU_sh2

description: total RNA minus rRNA


title: Empty_vector

description: total RNA minus rRNA


title: Bloodlinc_shCTL

description: total RNA minus rRNA


title: Bloodlinc_sh2

description: total RNA minus rRNA


title: Input_ChIRP-seq

data_processing:
Library strategy: ChIRP-seq
Reads were mapped to mm9 using bowtie2 (Langmead and Salzberg 2012). Peak calling was performed on uniquely-mapped reads relative to input control using MACS (Zhang et al. 2008) with default parameters and “--bw=300 --mfold 10 30”. High-confidence peaks were identified based on several criteria. First, peak coverage was quantified using BEDTools (Quinlan and Hall 2010), and only peaks with an average perbase coverage greater than 2 reads were considered. Then peaks whose read density enrichment was at least 10-fold greater than the background model were considered enriched. Finally, peaks in the experimental sample overlapping peaks in the input control were excluded from further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Uniquely-mapped reads in bigwig format. Peaks in text format.

source_name: MEL

growth_protocol: 40 million MEL cells were harvested after 5 days of 2% DMSO-induced differentiation

extract_protocol:
ChIRP-seq was conducted as described (Chu et al. 2011; Chu et al. 2012).
Non-strand-specific cDNA libraries were sequenced on an Illumina HiSeq2000 platform.

tag: protocol

value: 2% DMSO day 5

value: MEL


title: Bloodlinc_sh1

description: total RNA minus rRNA


title: Bloodlinc_ChIRP-seq


title: D7_WT

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: Barcode: ITAGCTT

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: Immature mouse chondrocytes

growth_protocol: Chondrocytes were isolated from the femoral head, femoral condyles and tibial plateau as previously described (Gosset et al 2008). Chondrocytes were maintained in DMEM 2% FBS, 1% anti-mycotic/antibiotic.

extract_protocol:
IMC were isolated at days 3, 7, and 14 of culture. Micromasses were washed with PBS and mechanically disrupted with a scalpel, and Qiazol was added to lyse cells. Total RNA was extracted using the miRNeasy MicroKit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wildtype and Ezh2-deficient chondrocytes were differentiated micromass culture in growth media supplemented with Insulin-Transferrin-Selenium solution, 0.05mg/mL ascorbic acid and 10mM β-glycerol phosphate.

value: C57BL/6 - mix

value: wildtype

value: post-natal day 5

value: Immature mouse chondrocytes

tag: time

value: day 7 of differentiation


title: D3_WT

description: Barcode: IGATCAG

value: day 3 of differentiation


title: D7_Ezh2_cKO

description: Barcode: ITTAGGC


title: D14_WT

description: Barcode: IGGCTAC

value: day 14 of differentiation


title: P0 met-2(n4256) control R1

tag: developmental stage

value: day 1 adult

value: whole animal


title: HDAC3-KO Exercise_RNA-seq 3

first: Bin

last: Fang

address: 3400 Civic Center Blvd, Bldg 42

data_processing:
RNA-seq: Tophat 2 was used to align RNA-seq samples to mm9 genome, followed by cuffdiff to measure normalized abundance and differential gene expression.
GRO-seq: Bowtie 1 was used to align GRO-seq samples to mm9 genome, followed by generation of tag directories and ucsc visualization tracks using HOMER, and enhancer-RNA calling using a custom script.
Genome_build: mm9

source_name: HDAC3-KO Exercise_quadriceps muscle

growth_protocol: C57BL/6 mice were fed normal chow on normal light/dark schedule

extract_protocol:
RNA is extracted using Qiagen kits
Library contruction follows illumina kits
Standard illumina method was used

treatment_protocol: Mice were subjected to 3 bouts of treadmill running, with each bout lasting for 1h at 10 m/min and 1 h rest interval inbetween runnings. Tissues were harvested at 2h after the 3rd running.

tag: strain background

value: 4-months old male

value: quadriceps muscle


title: WT Rest_GRO-seq 1

data_processing:
library strategy: GRO-seq
RNA-seq: Tophat 2 was used to align RNA-seq samples to mm9 genome, followed by cuffdiff to measure normalized abundance and differential gene expression.
GRO-seq: Bowtie 1 was used to align GRO-seq samples to mm9 genome, followed by generation of tag directories and ucsc visualization tracks using HOMER, and enhancer-RNA calling using a custom script.
Genome_build: mm9

source_name: WT Rest_quadriceps muscle

value: wild type

tag: molecule subtype

value: nascent RNA


title: HDAC3-KO Exercise_RNA-seq 2


title: WT Exercise_RNA-seq 3

source_name: WT Exercise_quadriceps muscle


title: WT Exercise_RNA-seq 2


title: HDAC3-KO Rest_GRO-seq 1

source_name: HDAC3-KO Rest_quadriceps muscle


title: WT Exercise_RNA-seq 1


title: HDAC3-KO Rest_RNA-seq 3


title: HDAC3-KO Exercise_RNA-seq 1


title: HDAC3-KO Rest_RNA-seq 2


title: WT Rest_RNA-seq 3


title: U2OS_input

city: Swarthmore

first: Dawn

last: Carone

address: 500 College Ave

department: Biology

institute: Swarthmore College

data_processing:
Illumina software used for basecalling
ChIP-seq reads were aligned to the hg19 human genome assembly using Bowtie using -maxins 1500
input files were rerun due to low read density and input files were merged prior to Bowtie sequence alignment to generatea single BAM alignment
BAM files were analyzed using SeqMonk2 (http://www.bioinformatics.babraham.ac.uk.projects/seqmonk) for Chip-seq analysis
Genome_build: hg19

source_name: U2OS osteosarcoma cells

growth_protocol: Both cell lines were maintained in 5% CO2 at 37°C in MEM medium containing 15% FBS and supplemented with 1% L-glutamine prior to harvesting for chromatin immunoprecipitation.

extract_protocol:
DNA was extracted with phenol:chloroform and precipitated with 0.1X volume 3M NaOAc, pH 5.2 and 2.5X volume 100% EtOH overnight at -20°C.
Preparation of Illumina paired end deep sequencing ChIP libraries was performed as previously described (Yildirim et al., 2011).

treatment_protocol: ChIP-seq was performed as previously described (Yildirim et al., 2011) with some modification. Approximately 1x106 cells were crosslinked with formaldehyde to a final concentration of 1% for 10 minutes at room temperature and stopped by the addition of 125mM glycine.  Cells were washed twice with 1xPBS containing protease inhibitors (Roche complete Mini protease inhibitor tablets) and pelleted at 100rpm at 4°C for 5 min.  Cell pellets were resuspended in SDS lysis buffer (1%SDS, 10mM EDTA, 50mM Tris-Cl pH 8.1) with protease inhibitors and incubated on ice for 10 min.  Cells were then sonicated at 10% duty, setting 2 for 10 minutes to a fragment size of 150-500nt followed by centrifugation at 3000rpm for 10 min at 4°C.  Supernatant was collected and 100uL chromatin was incubated with an antibody against Ubiquityl Histone H2A (UbH2A, Cell Signaling #8240) as per manufacturer’s recommended concentrations at 4°C overnight with rotation in IP Buffer (.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-Cl, pH 8.1, 167mM NaCl) + 0.5% BSA.  50uL protein G magnetic beads (Cell Signaling, #9006) was added to antibody-chromatin complex for 4 hours at 4°C with rotation.  ChIP washes were as follows:  2X IP Buffer, 2X RIPA buffer (0.1% SDS, 10mM Tris, pH 7.6, 1mM EDTA, 0.1% Na-deoxycholate, 1% Triton X-100), 2X RIPA buffer + 0.3M NaCl., 1X LiCl Buffer (0.25M LiCl, 0.5% NP-40, 0.5% Na-deoxycholate), 1X TE.  Crosslinks were reversed overnight at 65°C in 1X TE with the addition of 3% SDS, 1mg/mL proteinase K, 200mM NaCl.

value: osteosarcoma

tag: passages

value: unknown

tag: antibody

value: none -input


title: Tig_UbH2A Chip-seq

source_name: Tig-1 fibroblasts

tag: cell type

value: fibroblast

value: UbH2A, Cell Signaling #8240


title: U2OS_UbH2A Chip-seq


title: WT Rest_RNA-seq 2

tag: genotype/variation


title: Tig_input


title: D14_Ezh2_cKO

description: Barcode: IACTTGA

value: C57BL/6 - mix


title: WT Rest_RNA-seq 1


title: HDAC3-KO Exercise_GRO-seq 2


title: WT Exercise_GRO-seq 2


title: R46_IA_X_30m_h3k27ac

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: ChIP-Seq using Abcam ab4729 (rabbit polyclonal anti-H3K27Ac)

data_processing:
Base calls were performed using bcl2fastq v1.8.4 software (Illumina, San Diego, CA, USA).
Reads were aligned to Amel_4.5 (OGS v. 3.2 annotation set) using Bowtie2 v. 2.1.0 with default settings
Mapped sequence data were analyzed using HOMER (Hypergeometric Optimization of Motif EnRichment) v4.7. Samples were converted into Tag Directories, and QC was performed using read mapping and GC bias statistics.
Genome_build: Amel_4.5 (OGS v. 3.2 annotation)
Supplementary_files_format_and_content: BigWiggle pileup files were generated using HOMER’s makeBigWig.pl script with default settings.  Individual technical replicate IP samples were combined into pooled bigWig files.

organism: Apis mellifera

source_name: pooled whole brain (10 bees)

growth_protocol: Honey bee (Apis mellifera) workers were obtained from colonies maintained in apiaries according to standard commercial methods by the University of Illinois Bee Research Facility, Urbana, IL, from June to August 2013 and 2014. For the ChIP-Seq experiment, we used two colonies, each headed by a queen that was instrumentally inseminated with semen from a single (different) drone (Single Drone Inseminated colony, “SDI”); because of hapolodiploidy, the resulting female worker offspring were highly related to each other (average coefficient of relatedness, r = 0.75), thus decreasing within-trial genetic variation. One-day-old adult bees were obtained by removing frames of honeycomb containing pupae from colonies, placing them in an incubator (34°C, 50% relative humidity), and then monitoring their emergence every 24 h.

extract_protocol:
Bee heads were separated from bodies on dry ice and placed in a dissection dish with pure ethanol and dry ice to prevent degradation during dissection. The cuticle of the head capsule was removed and each head was placed in PBS + Protease Inhibitor Cocktail (Roche) at -20ºC for 14 to 18 h. The heads were then opened, the hypopharyngeal glands removed, and the whole brain removed.  The brains were placed in a new 1.5ml tube and kept frozen (-80°C) until ChIP. ChIP was performed with a Diagenode iDeal ChIP kit and the standard protocol using Abcam ab4729 (rb polyclonal anti-H3K27Ac) antibodies. 1/10 volume input  DNA samples were collected from each aliquot and pooled and used as a background control for peak calling
ChIP-Seq libraries were constructed with KAPA LTP library kits (KK8230) The libraries were pooled in equimolar concentration as per instructions and each pool was quantitated by qubit (invitrogen). Single-end sequencing (read length = 100nt) was performed on an Illumina HiSeq2000 using a TruSeq SBS sequencing kit version 3.

treatment_protocol: Groups were created by dividing emerged bees into groups of ten, individually marking on their thoraces with a spot of paint (Testor’s PLA), and keeping them in clear plastic Petri dishes (100 x 20 mm). The dishes were supplied with one 2 ml tube of 30% sucrose solution and one small piece of honeycomb containing honey (containing about 6 cells). Groups were held in the incubator for 7 days prior to the beginning of the experiment. Behavioral assays were performed in an observation room under conditions (28°C, 30% relative humidity) that are within the normal range that occurs in our locality at the hive entrance, where colony defense normally occurs. The dishes of bees were placed in the observation room for at least 30 min prior the beginning of the behavioral assay for acclimatization. To start the behavioral assay, an unrelated intruder bee was introduced to each group for 5 min, during which the response of each bee toward the intruder was recorded. Detailed scan sampling observations of each bee were made every 10 s for the entire 5-min introduction period, according to a well-established scoring system. Five different behaviors were recorded and scored based on their relative aggression intensity ranking as follows: 1- Antennation and/or Trophallaxis; 2- Opening of the mandibles; 3- Chasing and/or Lunging; 4- Biting the Intruder; and 5- Attempting to Sting or Stinging. Inter-observer assays were conducted to ensure that all observers involve in this study scored the behaviors similarly. Bees were assigned randomly to experimental or control treatments. For groups assigned to the experimental treatment, the intruder assay was performed as described above. For groups assigned to the control treatment, a small tube (200µl) similar in size to a worker bee was introduced to the group; although bees occasionally inspected the object, its presence did not elicit aggression or alter their behavior in any discernable way. To prevent odors from accumulating, each tube was used only once. The intruder bee and the control tube were introduced simultaneously (each to its respective group) and removed at the end of the 5-min assay. The resident bees were then left undisturbed for 30 or 120 min. The most aggressive bee in each experimental group (responding with at least biting and/or stinging attempts for more than 30 sec) was selected for transcriptomic analysis, and a randomly selected bee from the control group was collected at the same time for comparison. These bees were frozen immediately in liquid nitrogen and individually placed in a 1.5ml tube stored in a -80°C freezer for further analysis. For ChIP-Seq profiling, 10 bees for each unique combination of time point, colony, and social challenge were collected.

tag: challenge

value: X

tag: colony


title: R46_IA_X_120m_h3k27ac


title: R41_IA_X_30m_h3k27ac


title: R41_IA_X_120m_h3k27ac


title: R46_IA_C_30m_h3k27ac

value: C


title: R41_IA_C_30m_h3k27ac


title: R41_IA_C_120m_h3k27ac


title: X_60m_cR21_p05_9_CGCTCATT-CAGGACGT_L001_R1_001

data_processing:
Base calls were performed using CASAVA v. 1.8.2
Reads were aligned to Amel_4.5 (OGS v. 3.2 annotation set) using TopHat2 v. 2.0.10 with Bowtie2 v. 2.1.0 and Samtools v. 0.1.19
Deformed Wing Virus (DWV) alignments were calculated by aligning to the Pennsylvania variant of the DWV genome (GenBank accession: AY292384) using Bowtie 2 v. 2.1.0, and filtering took place during downstream bioinformatic analysis
Tags were counted using htseq-count in HTSeq v. 0.6.1
Genome_build: Amel_4.5 (OGS v. 3.2 annotation) with Pennsylvania build of DWV (GenBank accession: AY292384)
Supplementary_files_format_and_content: tab-delimited tag counts were generated using htseq-count.

source_name: mushroom body

growth_protocol: Honey bee (Apis mellifera) workers were obtained from colonies maintained in apiaries according to standard commercial methods by the University of Illinois Bee Research Facility, Urbana, IL, from June to August 2013 and 2014. For the RNA-Seq experiment, we used three colonies, each headed by a queen that was instrumentally inseminated with semen from a single (different) drone (Single Drone Inseminated colony, “SDI”); because of hapolodiploidy, the resulting female worker offspring were highly related to each other (average coefficient of relatedness, r = 0.75), thus decreasing within-trial genetic variation. One-day-old adult bees were obtained by removing frames of honeycomb containing pupae from colonies, placing them in an incubator (34°C, 50% relative humidity), and then monitoring their emergence every 24 h.

extract_protocol:
Bee heads were separated from bodies on dry ice and placed in a dissection dish with pure ethanol and dry ice to prevent RNA degradation during dissection. The cuticle of the head capsule was removed and each head was placed in RNAlaterICE (Life Technologies) at -20ºC for 14 to 18 h. The heads were then opened, the hypopharyngeal glands removed, and the whole brain removed. Using a fine scalpel, the optic lobes were removed and a horizontal incision was made across the midbrain through the posterior protocerebral lobe. The lower part of the midbrain containing the antennal lobes and the subesophageal ganglion were removed. The upper part of the midbrain containing mostly the mushroom bodies (MB) and the central brain was used for gene expression analysis. The MBs were placed in a new 1.5ml tube and kept frozen (-80°C) until RNA extraction. RNA extraction was performed with a PicoPure RNA Isolation Kit (Applied Biosystems; Lot #: 1210063) and the standard protocol, including DNase treatment (QIAGEN) to remove genomic DNA contamination. 500 ng RNA from each sample (except for 5 samples that yielded 350- 500 ng) were used for whole mRNA expression analysis.
RNA-Seq libraries were constructed with the TruSeq® Stranded mRNA HT (high throughput kit, Illumina cat #: RS-122-2103) using an ePMotion 5075 robot (Eppendorf) The libraries were pooled in equimolar concentration as per instructions and each pool was quantitated by qPCR. Single-end sequencing (read length = 100nt) was performed on an Illumina HiSeq2000 using a TruSeq SBS sequencing kit version 3.

treatment_protocol: Groups were created by dividing emerged bees into groups of ten, individually marking on their thoraces with a spot of paint (Testor’s PLA), and keeping them in clear plastic Petri dishes (100 x 20 mm). The dishes were supplied with one 2 ml tube of 30% sucrose solution and one small piece of honeycomb containing honey (containing about 6 cells). Groups were held in the incubator for 7 days prior to the beginning of the experiment. Behavioral assays were performed in an observation room under conditions (28°C, 30% relative humidity) that are within the normal range that occurs in our locality at the hive entrance, where colony defense normally occurs. The dishes of bees were placed in the observation room for at least 30 min prior the beginning of the behavioral assay for acclimatization. To start the behavioral assay, an unrelated intruder bee was introduced to each group for 5 min, during which the response of each bee toward the intruder was recorded. Detailed scan sampling observations of each bee were made every 10 s for the entire 5-min introduction period, according to a well-established scoring system. Five different behaviors were recorded and scored based on their relative aggression intensity ranking as follows: 1- Antennation and/or Trophallaxis; 2- Opening of the mandibles; 3- Chasing and/or Lunging; 4- Biting the Intruder; and 5- Attempting to Sting or Stinging. Inter-observer assays were conducted to ensure that all observers involve in this study scored the behaviors similarly. Bees were assigned randomly to experimental or control treatments. For groups assigned to the experimental treatment, the intruder assay was performed as described above. For groups assigned to the control treatment, a small tube (200µl) similar in size to a worker bee was introduced to the group; although bees occasionally inspected the object, its presence did not elicit aggression or alter their behavior in any discernable way. To prevent odors from accumulating, each tube was used only once. The intruder bee and the control tube were introduced simultaneously (each to its respective group) and removed at the end of the 5-min assay. The resident bees were then left undisturbed for 30, 60 or 120 min. The most aggressive bee in each experimental group (responding with at least biting and/or stinging attempts for more than 30 sec) was selected for transcriptomic analysis, and a randomly selected bee from the control group was collected at the same time for comparison. These bees were frozen immediately in liquid nitrogen and individually placed in a 1.5ml tube stored in a -80°C freezer for further analysis. For transcriptomic profiling, 10 pairs of experimental bees and matched control bees were used for each time point, summing to a total of 60 bees per colony. The experiment was repeated with three different colonies, summing to a total sample size of 180 bees (26 were excluded later as result of infection by Deformed Wing Virus, see below).

tag: pair

tag: replicate

tag: index

value: CGCTCATT-CAGGACGT

tag: lane


title: X_60m_cR21_p06_10_CGCTCATT-GTACTGAC_L002_R1_001

description: excluded from analysis due to high DWV content

value: CGCTCATT-GTACTGAC


title: X_60m_cR21_p04_7_CGCTCATT-TAATCTTA_L006_R1_001

value: CGCTCATT-TAATCTTA


title: X_60m_cR21_p02_5_CGCTCATT-GGCTCTGA_L004_R1_001

value: CGCTCATT-GGCTCTGA


title: X_60m_cR21_p09_15_ATTCAGAA-CCTATCCT_L003_R1_001

value: ATTCAGAA-CCTATCCT


title: X_60m_cR21_p08_12_ATTCAGAA-ATAGAGGC_L002_R1_001

value: ATTCAGAA-ATAGAGGC


title: X_60m_cR21_p07_11_ATTCAGAA-TATAGCCT_L001_R1_001

value: ATTCAGAA-TATAGCCT


title: X_60m_cR21_p03_6_CGCTCATT-AGGCGAAG_L005_R1_001

value: CGCTCATT-AGGCGAAG


title: X_60m_cR21_p01_3_CGCTCATT-CCTATCCT_L003_R1_001

value: CGCTCATT-CCTATCCT


title: X_60m_cR03_p08_62_CTGAAGCT-TAATCTTA_L00M_R1_001

value: CTGAAGCT-TAATCTTA


title: X_60m_cR03_p10_66_CTGAAGCT-GTACTGAC_L00M_R1_001

value: CTGAAGCT-GTACTGAC


title: X_60m_cR03_p07_61_CTGAAGCT-AGGCGAAG_L00M_R1_001

value: CTGAAGCT-AGGCGAAG


title: X_60m_cR03_p09_65_CTGAAGCT-CAGGACGT_L00M_R1_001

value: CTGAAGCT-CAGGACGT


title: R46_IA_C_120m_h3k27ac


title: X_60m_cR03_p05_57_CTGAAGCT-CCTATCCT_L00M_R1_001

value: CTGAAGCT-CCTATCCT


title: X_60m_cR03_p06_60p_CTGAAGCT-GGCTCTGA_L00M_R1_001

value: CTGAAGCT-GGCTCTGA


title: X_60m_cR03_p04_56_CTGAAGCT-ATAGAGGC_L00M_R1_001

value: X

value: CTGAAGCT-ATAGAGGC


title: X_60m_cR03_p01_50B_ATTCAGAA-CAGGACGT_L00M_R1_001

value: ATTCAGAA-CAGGACGT


title: X_60m_cR03_p03_55_CTGAAGCT-TATAGCCT_L00M_R1_001

value: CTGAAGCT-TATAGCCT


title: X_60m_cR03_p02_53p_ATTCAGAA-GTACTGAC_L00M_R1_001

value: ATTCAGAA-GTACTGAC


title: X_60m_cR02_p09_42_ATTACTCG-TATAGCCT_L00M_R1_001

value: ATTACTCG-TATAGCCT


title: X_60m_cR02_p10_43_ATTACTCG-ATAGAGGC_L00M_R1_001

value: ATTACTCG-ATAGAGGC


title: X_60m_cR02_p08_39_TCTCGCGC-GTACTGAC_L006_R1_001

value: TCTCGCGC-GTACTGAC


title: HDAC3-KO Rest_RNA-seq 1

tag: age

value: 4-months old male

tag: tissue

value: quadriceps muscle


title: X_60m_cR02_p07_38_TCTCGCGC-CAGGACGT_L006_R1_001

value: TCTCGCGC-CAGGACGT


title: X_60m_cR02_p04_30p_TCTCGCGC-GGCTCTGA_L004_R1_001

value: TCTCGCGC-GGCTCTGA


title: X_60m_cR02_p06_35_TCTCGCGC-TAATCTTA_L005_R1_001

value: TCTCGCGC-TAATCTTA


title: X_60m_cR02_p05_31_TCTCGCGC-AGGCGAAG_L005_R1_001

value: TCTCGCGC-AGGCGAAG


title: X_60m_cR21_p10_16_ATTCAGAA-GGCTCTGA_L004_R1_001

value: ATTCAGAA-GGCTCTGA


title: X_60m_cR02_p03_28_TCTCGCGC-CCTATCCT_L004_R1_001

value: TCTCGCGC-CCTATCCT


title: X_60m_cR02_p01_23_TCTCGCGC-TATAGCCT_L003_R1_001

value: TCTCGCGC-TATAGCCT


title: X_30m_cR21_p10_18_CGCTCATT-ATAGAGGC_L002_R1_001

value: X

value: CGCTCATT-ATAGAGGC


title: X_60m_cR02_p02_26_TCTCGCGC-ATAGAGGC_L003_R1_001

value: TCTCGCGC-ATAGAGGC


title: X_30m_cR21_p09_16_CGCTCATT-TATAGCCT_L001_R1_001

value: CGCTCATT-TATAGCCT


title: X_30m_cR21_p05_8_ATTACTCG-AGGCGAAG_L005_R1_001

value: ATTACTCG-AGGCGAAG


title: X_30m_cR21_p04_7_ATTACTCG-GGCTCTGA_L004_R1_001

value: ATTACTCG-GGCTCTGA


title: X_30m_cR21_p02_2_ATTACTCG-ATAGAGGC_L002_R1_001

value: ATTACTCG-ATAGAGGC


title: X_30m_cR03_p08_63_ATTCAGAA-GGCTCTGA_L00M_R1_001


title: X_30m_cR03_p06_59p_ATTCAGAA-ATAGAGGC_L00M_R1_001

value: ATTCAGAA-ATAGAGGC


title: X_30m_cR03_p07_61p_ATTCAGAA-CCTATCCT_L00M_R1_001

value: ATTCAGAA-CCTATCCT


title: X_30m_cR03_p05_58p_ATTCAGAA-TATAGCCT_L00M_R1_001

value: ATTCAGAA-TATAGCCT


title: X_30m_cR21_p07_13_ATTACTCG-CAGGACGT_L001_R1_001

value: ATTACTCG-CAGGACGT


title: X_30m_cR03_p01_52p_CGCTCATT-AGGCGAAG_L00M_R1_001

value: CGCTCATT-AGGCGAAG


title: X_30m_cR03_p03_54p_CGCTCATT-CAGGACGT_L00M_R1_001

value: CGCTCATT-CAGGACGT


title: X_30m_cR02_p09_40_CGGCTATG-CAGGACGT_L006_R1_001

value: CGGCTATG-CAGGACGT


title: X_30m_cR02_p08_38_CGGCTATG-TAATCTTA_L005_R1_001

value: CGGCTATG-TAATCTTA


title: X_30m_cR03_p04_55p_CGCTCATT-GTACTGAC_L00M_R1_001

value: CGCTCATT-GTACTGAC


title: X_30m_cR21_p08_14_ATTACTCG-GTACTGAC_L002_R1_001

value: ATTACTCG-GTACTGAC


title: X_30m_cR02_p10_43_CGGCTATG-GTACTGAC_L006_R1_001

value: X

value: CGGCTATG-GTACTGAC


title: X_30m_cR03_p02_53p_CGCTCATT-TAATCTTA_L00M_R1_001

value: CGCTCATT-TAATCTTA


title: X_30m_cR02_p07_36_CGGCTATG-AGGCGAAG_L005_R1_001

value: CGGCTATG-AGGCGAAG


title: X_30m_cR21_p01_1_ATTACTCG-TATAGCCT_L001_R1_001

value: ATTACTCG-TATAGCCT


title: X_30m_cR02_p04_33_CGGCTATG-ATAGAGGC_L003_R1_001

value: CGGCTATG-ATAGAGGC


title: X_30m_cR02_p02_27_CTGAAGCT-GTACTGAC_L002_R1_001

value: CTGAAGCT-GTACTGAC


title: X_30m_cR02_p03_29_CGGCTATG-TATAGCCT_L003_R1_001

value: CGGCTATG-TATAGCCT


title: X_30m_cR21_p03_5_ATTACTCG-CCTATCCT_L003_R1_001

value: ATTACTCG-CCTATCCT


title: X_120m_cR21_p09_16_CTGAAGCT-AGGCGAAG_L005_R1_001

value: CTGAAGCT-AGGCGAAG


title: X_120m_cR21_p10_17_CTGAAGCT-TAATCTTA_L006_R1_001

value: CTGAAGCT-TAATCTTA


title: X_30m_cR02_p01_26_CTGAAGCT-CAGGACGT_L001_R1_001

value: CTGAAGCT-CAGGACGT


title: X_30m_cR03_p09_66p_ATTCAGAA-AGGCGAAG_L00M_R1_001

value: ATTCAGAA-AGGCGAAG


title: X_30m_cR21_p06_12_ATTACTCG-TAATCTTA_L006_R1_001

value: ATTACTCG-TAATCTTA


title: X_120m_cR21_p08_13_CTGAAGCT-GGCTCTGA_L004_R1_001

value: CTGAAGCT-GGCTCTGA


title: X_120m_cR21_p07_12_CTGAAGCT-CCTATCCT_L003_R1_001

value: CTGAAGCT-CCTATCCT


title: X_30m_cR03_p10_67p_ATTCAGAA-TAATCTTA_L00M_R1_001

value: ATTCAGAA-TAATCTTA


title: X_120m_cR21_p06_11_CTGAAGCT-ATAGAGGC_L002_R1_001

value: X

value: CTGAAGCT-ATAGAGGC


title: X_120m_cR21_p05_10_CTGAAGCT-TATAGCCT_L001_R1_001

value: CTGAAGCT-TATAGCCT


title: X_120m_cR21_p03_7_ATTCAGAA-CAGGACGT_L001_R1_001

value: ATTCAGAA-CAGGACGT


title: X_120m_cR21_p04_8_ATTCAGAA-GTACTGAC_L002_R1_001

value: ATTCAGAA-GTACTGAC


title: X_120m_cR21_p01_3_ATTCAGAA-AGGCGAAG_L005_R1_001


title: X_120m_cR21_p02_5_ATTCAGAA-TAATCTTA_L006_R1_001


title: X_120m_cR03_p10_69p_AGCGATAG-AGGCGAAG_L001_R1_001

value: AGCGATAG-AGGCGAAG


title: X_120m_cR03_p09_67p_AGCGATAG-GGCTCTGA_L001_R1_001

value: AGCGATAG-GGCTCTGA


title: X_120m_cR03_p07_59_CGGCTATG-CAGGACGT_L00M_R1_001

value: CGGCTATG-CAGGACGT


title: X_120m_cR03_p05_55p_CGGCTATG-AGGCGAAG_L00M_R1_001

value: CGGCTATG-AGGCGAAG


title: X_120m_cR03_p06_57_CGGCTATG-TAATCTTA_L00M_R1_001

value: CGGCTATG-TAATCTTA


title: X_120m_cR03_p08_64p_AGCGATAG-CCTATCCT_L001_R1_001

value: AGCGATAG-CCTATCCT


title: X_120m_cR02_p07_32_CGCTCATT-TATAGCCT_L00M_R1_001

value: CGCTCATT-TATAGCCT


title: X_120m_cR02_p08_34_CGCTCATT-ATAGAGGC_L00M_R1_001

value: CGCTCATT-ATAGAGGC


title: X_120m_cR02_p05_30_ATTACTCG-CAGGACGT_L00M_R1_001

value: ATTACTCG-CAGGACGT


title: X_120m_cR02_p09_39_CGCTCATT-CCTATCCT_L00M_R1_001

value: CGCTCATT-CCTATCCT


title: X_120m_cR03_p01_50_CGGCTATG-TATAGCCT_L00M_R1_001

value: CGGCTATG-TATAGCCT


title: X_120m_cR02_p02_25_ATTACTCG-GGCTCTGA_L00M_R1_001

value: ATTACTCG-GGCTCTGA


title: X_120m_cR02_p04_29_ATTACTCG-TAATCTTA_L00M_R1_001

value: X

value: ATTACTCG-TAATCTTA


title: X_120m_cR03_p02_51_CGGCTATG-ATAGAGGC_L00M_R1_001

value: CGGCTATG-ATAGAGGC


title: X_120m_cR03_p03_52_CGGCTATG-CCTATCCT_L00M_R1_001

value: CGGCTATG-CCTATCCT


title: X_120m_cR02_p03_26B_ATTACTCG-AGGCGAAG_L00M_R1_001

value: ATTACTCG-AGGCGAAG


title: C_60m_cR21_p10_16_GAATTCGT-GGCTCTGA_L004_R1_001

value: C

value: GAATTCGT-GGCTCTGA


title: C_60m_cR21_p09_15B_GAATTCGT-CCTATCCT_L003_R1_001

value: GAATTCGT-CCTATCCT


title: X_120m_cR03_p04_54p_CGGCTATG-GGCTCTGA_L00M_R1_001

value: CGGCTATG-GGCTCTGA


title: shCUX1-B.rep2_ChIP-seq

city: Chicago

first: Megan

middle: E.

last: McNerney

state: Illinois

address: 900 East 57th Street, KCBD 5128

department: Pathology

institute: The University of Chicago

description:
processed data file:
DiffBindResults.txt

data_processing:
RNA-seq reads were aligned to hg19 with Tophat .2.10 using default parameters. Reads with quality scores >30 were counted using HTseq-tools and analyzed with EdgeR
ChIP-seq reads were aligned to hg19 using bwa (version 0.7.5) and peaks called using Q.
Genome_build: Hg19
Supplementary_files_format_and_content: RNA-seq text file contains EdgeR results for Gene ID, log fold change, log counts per million, p value and q values for control versus knockdown.  ChIP-seq text file contains DiffBind results for peak location, mean occupancy in the control, mean ocupancy in the knockdown, fold change in occupancy, p value, and FDR for control versus knockdown.

growth_protocol: K562 cells were grown in RPMI with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
RNA was isolated using Trizol. Genomic DNA was isolated follwing the Myers Lab ChIP-seq Protocol v042211.2 (www.encodeproject.org),
Barcoded RNA-seq libraries were generated using the standard Illumina TruSEQ kit. Barcoded ChIP-seq libraries were made with Ovation Ultralow Library kit (NuGEN).

treatment_protocol: For RNA-seq experiments, cells were treated with 2 ug/mL of doxycycline for four days.

tag: cell line

value: myeloid leukemia cell line

tag: shRNA

tag: chip-antibody

value: CUX1 sc-6327 Santa Cruz


title: shCUX1-A.rep2_ChIP-seq


title: C_60m_cR21_p08_12_GAATTCGT-ATAGAGGC_L002_R1_001

tag: time

value: GAATTCGT-ATAGAGGC


title: Control shRNA.rep2_ChIP-seq

source_name: K562_Control shRNA

value: control shRNA


title: X_120m_cR02_p10_42_CGCTCATT-GGCTCTGA_L00M_R1_001

value: CGCTCATT-GGCTCTGA


title: C_60m_cR21_p07_11_GAATTCGT-TATAGCCT_L001_R1_001

value: GAATTCGT-TATAGCCT


title: C_60m_cR21_p06_10_GAGATTCC-GTACTGAC_L002_R1_001

value: GAGATTCC-GTACTGAC


title: X_120m_cR02_p06_31_ATTACTCG-GTACTGAC_L00M_R1_001

value: ATTACTCG-GTACTGAC


title: C_60m_cR21_p05_9_GAGATTCC-CAGGACGT_L001_R1_001

value: GAGATTCC-CAGGACGT


title: Control shRNA.rep1_ChIP-seq


title: X_120m_cR02_p01_21_ATTACTCG-CCTATCCT_L00M_R1_001

value: X

value: ATTACTCG-CCTATCCT


title: C_60m_cR21_p04_7_GAGATTCC-TAATCTTA_L006_R1_001

value: GAGATTCC-TAATCTTA


title: Input.rep2_ChIP-seq


title: C_60m_cR21_p03_6_GAGATTCC-AGGCGAAG_L005_R1_001

value: GAGATTCC-AGGCGAAG


title: input.rep1_ChIP-seq


title: shCUX1-B.rep1_ChIP-seq


title: C_60m_cR21_p02_5_GAGATTCC-GGCTCTGA_L004_R1_001

value: C

value: GAGATTCC-GGCTCTGA


title: shCUX1-A.rep1_ChIP-seq


title: X_30m_cR02_p06_35_CGGCTATG-GGCTCTGA_L004_R1_001


title: C_60m_cR21_p01_3_GAGATTCC-CCTATCCT_L003_R1_001

value: GAGATTCC-CCTATCCT


title: E13.5 Mutant Minus 2

first: Andrew

last: Potter

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

description:
Gene expression of FACS-purified PTC2- cells
E13.5_Mutminus925

data_processing:
Samples were aligned to the mm9 genome using TopHat v2.0.5. Known junctions from the RefSeq database were provided to TopHat with the -G option.
Gene expression was quantified using Cufflinks v.2.0.0
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadsheet including NRPKM values for each sample in Series.

source_name: PTC2- cells from kidney-ureter junction

extract_protocol:
RNA was purified using the Qiagen Rneasy Micro Kit (Qiagen, 74004)
The initial amplification step for all  samples was done with the NuGEN Ovation RNA-Seq System v2. The assay was used to amplify RNA samples to create double stranded cDNA. The concentrations were measured using the Qubit dsDNA BR assay. Libraries were then created for all samples. Specifically, the Illumina protocol, the Nextera XT DNA Sample Preparation Kit, was used to create DNA library templates from the double stranded cDNA. The concentrations were measured using the Qubit dsDNA HS assay. The size of the libraries for each sample was measured using the Agilent HS DNA chip. The samples were placed in a pool. The concentration of the pool is optimized to acquire at least  15-20 million reads per sample.

tag: strain

value: E13.5 Mutant Ptc2-


title: E13.5 Mutant Plus 2

description:
Gene expression of FACS-purified PTC2+ cells
E13.5_Mutplus925

source_name: PTC2+ cells from kidney-ureter junction

value: E13.5 Mutant Ptc2+


title: E13.5 Mutant Plus 1

description:
Gene expression of FACS-purified PTC2+ cells
E13.5_Mutplus918


title: C_60m_cR03_p09_65_TAATGCGC-CAGGACGT_L00M_R1_001

value: TAATGCGC-CAGGACGT


title: E13.5 Mutant Minus 1

description:
Gene expression of FACS-purified PTC2- cells
E13.5_Mutminus918


title: C_60m_cR03_p07_61_TAATGCGC-AGGCGAAG_L00M_R1_001

value: TAATGCGC-AGGCGAAG


title: SAM24294908 Intestine Small DT1_EpCAM_48h bulk AKVPL 48h DT

city: South San Francisco

first: Robert

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

description:
timepoint: 48h
treatment_name: DT

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: small intestine

extract_protocol: After FACS, cells were centrifuged at 1200rpm for 5 minutes. RNA was extracted from samples using the RNeasy Micro kit (cat # 74004; Qiagen) according to the manufacturer’s instructions and resuspended in a volume of 14ul. RNA quality was evaluated using Bioanalyzer.

value: Intestine Small

tag: sort

value: bulk

tag: genotype

value: AKVPL


title: C_60m_cR03_p06_60_TAATGCGC-GGCTCTGA_L00M_R1_001

value: TAATGCGC-GGCTCTGA


title: SAM24294911 Intestine Small DT4_EpCAM_48h bulk AKVPL 48h DT

description:
timepoint: 48h
treatment_name: DT


title: SAM24294906 Intestine Small S3_EpCAM_48h bulk AKVPL 48h Saline

description:
timepoint: 48h
treatment_name: Saline


title: C_60m_cR03_p04_56_TAATGCGC-ATAGAGGC_L00M_R1_001

value: TAATGCGC-ATAGAGGC


title: C_60m_cR03_p05_57_TAATGCGC-CCTATCCT_L00M_R1_001

value: TAATGCGC-CCTATCCT


title: SAM24294909 Intestine Small DT2_EpCAM_48h bulk AKVPL 48h DT

description:
timepoint: 48h
treatment_name: DT


title: C_60m_cR03_p03_55_TAATGCGC-TATAGCCT_L00M_R1_001

value: TAATGCGC-TATAGCCT


title: C_60m_cR03_p02_53_GAATTCGT-GTACTGAC_L00M_R1_001

value: GAATTCGT-GTACTGAC


title: C_60m_cR03_p10_66_TAATGCGC-GTACTGAC_L00M_R1_001

value: TAATGCGC-GTACTGAC


title: SAM24294910 Intestine Small DT3_EpCAM_48h bulk AKVPL 48h DT

description:
timepoint: 48h
treatment_name: DT