title: BOT-4

city: Hautcharage

first: Gea

last: Guerriero

state: Luxembourg

address: 5, rue Bommel, Z.A.E. Robert Steichen, L-4940

department: Environmental Research and Innovation Department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology (LIST)

data_processing:
The raw sequences obtained were uploaded in CLC Genomics Workbench 9.0.1. Sequences were filtered as follows: sequences >35 bps, the sequence quality score was left as default value (0.05), the maximum number of ambiguities was set to 0. Trimming was performed using the Illumina adaptor sequences, then a hard trim of 14 bps at the 5′ end and 2 bps at the 3′ end was additionally carried out, resulting in a final sequence average length of 59 bps.
The reads were mapped back to the assembly with a mismatch, insertion and deletion cost of 3, and a length and similarity fraction of 0.95.
The expression values were subjected to an ANOVA statistical test with three groups (TOP, MID, BOT), each composed of four biological replicates and, subsequently, to a false discovery rate (FDR) correction. Only the genes showing a corrected p-value <0.05 were retained for downstream analysis.
The  data were further filtered by removing those genes showing a maximum value of the means <1 RPKM (this was done with the purpose of removing those contigs showing negligible changes in gene expression) and a maximum fold change (FC) >4 in absolute value.
The reads were mapped back to the assembly with a mismatch, insertion and deletion cost of 3, and a length and similarity fraction of 0.95.
Genome_build: The de novo assembly was therefore performed by merging the processed bast fibre reads with those generated from our previous study on hemp hypocotyls (Behr et al., 2016). The wording size was set to 20, the bubble size to 50 and minimum contig length of 300. The assembly was then annotated using Blast2GO PRO version 3.0 against the A. thaliana non-redundant database.
Supplementary_files_format_and_content: Table includes: contig number, FDR p-value, TAIR ID,  contig size, gene annotation; unique gene reads, RPKM values for each sample, average of the three biological replicates.

organism: Cannabis sativa

source_name: Bast fibres BOT biological replicate 4

growth_protocol: A hemp monoecious fibre variety (C. sativa cv. Santhica 27) was studied in this work. After six weeks of growth in controlled chambers, samples were taken along three stem regions localized at different heights with respect to the snap point.  At the time of sampling, the plants had ca. 6-7 internodes.

extract_protocol:
Total RNA was extracted using a modified CTAB extraction protocol combined with an RNeasy Plant Mini Kit (Qiagen). The RNA concentration and quality were measured by using a Nanodrop ND-1000 (Thermo Scientific) and a 2100 Bioanalyzer (Agilent), respectively. All the RNAs had a RIN value between 8 and 9.
Libraries were prepared from 3 μg of total RNA using the SMARTer Stranded RNA-Seq kit (Clontech). The isolation of mRNAs was performed using the Illumina beads and the TruSeq protocol (Illumina). The final elution of the mRNAs was performed using the Illumina elution buffer (19.5 μl). 10 ng mRNA were used for the cDNA synthesis and shearing. Indexing was performed using the Illumina indices 1-12. The enrichment step was carried out using 12 cycles of PCR. Subsequently, libraries were checked using 2100 Bioanalyzer (DNA-1000) to evaluate the mean fragment size. Quantification was done using the KAPA library quantification kit (KAPA Biosystems) using a ViiA7 Real-Time PCR System (Applied Biosystems).  The libraries were pooled at the concentration of 20 pM and sequenced on an Illumina MiSeq in five consecutive runs (MiSeq reagent kit V3, 150 cycles).

treatment_protocol: A segment of 2.5 cm was collected in the middle of each internode to avoid too much variation in gene expression, because of the varying developmental stages of the cell types. Fibres were separated from the shivs by peeling the cortical tissues and by quickly processing them in EtOH 80% with a mortar and a pestle.

tag: tissue

value: Bast fibres

tag: biological replicate

value: Bast fibres BOT4

tag: stem region

value: Two internodes below snap point


title: Cord blood CB9880 DNA methylation

status: Public on Jul 10 2017

type: SRA

city: Camden

first: Jaroslav

last: Jelinek

state: NJ

address: 403 Haddon Avenue

department: Research Labs

country: USA

institute: Coriell Institute for Medical Research

library_source: genomic

data_processing:
Illumina HiSeq 2500 paired ends sequencing
Raw sequencing data were converted to fastq.gz files.
bowtie2 --sensitive alignment of the reads in fastq files to hg19 and generating SAM files
generating sorted bam files from the sam files with samtools
counting methylated CCGGG signatures and unmethylated GGG at the reads aligned to CCCGGG sites
Adjusting methylation values based on the spiked in standards. At each SmaI/XmaI site, let Xma be the number of reads corresponding to methylated CpG (i.e., reads starting with CCGGG) and Sma be the number of reads corresponding to unmethylated CpG (i.e., reads starting with GGG), the methylation value was calculated as 100%*(c*(Xma+0.5)/(c*(Xma+0.5)+Sma+0.5)), where c was the correction factor calculated based on observed and expected methylation of spiked-in standards.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data are in tab-delimited text file. The columns of the file are: ID_SmaI_hg19 (CCCGGG site ID), chromosome (chromosome of the CCCGGG site), position (position of the CCCGGG site), meth_reads (observed number of reads corresponding to methylated CpG, Xma),  unmeth_reads (observed number of reads corresponding to unmethylated CpG, Sma), total_reads, raw_methylation (unadjusted methylation value), adjusted_methylation (methylation value adjusted based on the spiked in standards).

molecule: genomic DNA

organism: Homo sapiens

source_name: Human cord blood mononuclear cells

extract_protocol:
phenol-chloroform
Five micrograms of genomic DNA spiked with 20 ng of methylation standards with defined methylation levels of 0, 25, 50, and 100% were digested with 100 units of SmaI endonuclease (NEB) for 3 hours at 25°C. Subsequently, 100 units of XmaI endonuclease (NEB) were added and the digestion was continued for an additional 16 hours at 37°C. Digested DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA) and eluted in TRIS-HCl 10 mM pH 8.5 (EB). Eluted DNA was supplemented with NEB buffer #2, dCTP, dGTP and dATP (0.4 mM final concentration of each), 15 units of Klenow Fragment (3'→5' exonuclease deficient) DNA polymerase (NEB) and incubated for 30 minutes at 37°C. This step filled in the recesses at 3' DNA ends created by XmaI digestion and added 3' dA tails to all fragments. Illumina paired end (Quail et al. 2008) or barcoded Truseq (Illumina, San Diego, CA) sequencing adapters were then ligated at 10:1 adapter:fragment ratio using Rapid T4 DNA ligase (Enzymatics, Beverly, MA). The ligation mix was size selected by electrophoresis in 2% agarose. Two slices corresponding to 250-350 bp and 350-500 bp sizes based on a 100 bp DNA ladder (NEB) were cut out and DNA was extracted from agarose. DNA eluted from the slices was separately amplified with Illumina paired end PCR primers (Quail et al. 2008) using iProof high-fidelity DNA polymerase (Bio-Rad Laboratories, Hercules, CA) and 18 cycles of amplification. Resulting sequencing libraries were purified with AMPure magnetic beads (Agencourt, Beverly, MA).

tag: gender

value: Unknown

tag: age


title: W6h_rep2

city: Taipei

first: Meng-Chun

last: Lin

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Institute of Plant and Microbial Biology

library_source: transcriptomic

data_processing:
Sequence reads were adaptor-trimmed. Only reads with over 18 nt after adaptor removal were used for mapping.
Mapping were conducted using Bowtie (v1.0.0), with parameters set as: –f –n 0 –e 80 –l 18 –a –m 5 –best –strata
Transcripts per million reads (TPM, 20 - 24 nt) were calculated for normalization.
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel tables for the TPM of the sRNAs are attached.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 4d-old de-etiolating seedling

growth_protocol: Surface steriled seeds were stratified at 4 °C for 4 days on 1/2 MS medium. The stratified seeds were them applled 1 h of white light exposure to synchronize germination, then placed in dark for 4 days at 22 °C.

extract_protocol:
Total RNA was isolated from seedlings grown under the conditions listed above, and were isolated by using PureLink Plant RNA Reagent (Invitrogen), following manufacturer's instructions. Small RNAs sized between 17 - 30 bp were resolved by TBE-UREA gel and were sliced for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Tru-seq small RNA for sRNA sequencing replicate 1 and 2. sm ll RNA v1.5 for replicate 3. Degradome library construction has followed the protocol puclished in Methods. 2014 1;67(1):84-90.

treatment_protocol: The 4-d-old seedlings were applied for whilte light (100 mE) exposure for 0, 1, 3, 6, 12 and 24 h.

tag: ecotype

tag: time point

tag: genotype/variation

value: wild type

tag: light intensity


title: W12h_rep2


title: BOT-3

molecule: polyA RNA

source_name: Bast fibres BOT biological replicate 3

value: Bast fibres BOT3


title: BOT-2

source_name: Bast fibres BOT biological replicate 2

value: Bast fibres BOT2


title: H3K27ac_ChIP-Seq

city: Cambridge

first: Michael

last: Hemann

state: Massachusetts

address: 500 Main St, Building 76 Room 301

department: Koch Institute

institute: Massachusetts Institute of Technology

data_processing:
Illumina HiSeq 40nt single-end sequencing (40 cycles)
Bowtie 2 mapping of reads to reference genome (mm9) with maximum allowed number of mismatches in seed alignment set to 1
Removal of unmapped reads and conversion to BAM files using samtools
MACS 1.4.0 peak/summit calling and generation of WIG files with parameters: -p 1e-6 -m 10,30 -w -S --space=50
Genome_build: mm9
Supplementary_files_format_and_content: WIG files of ChIP-seq signal tracks; BED files of Phf6 and histone peaks/summits called by MACS

organism: Mus musculus

source_name: BCR-ABL1 transformed p19 null preB-ALL

growth_protocol: RPMI-1640 supplemented with 10% FBS, 4mM L-glutamine, 50µM 2-mercaptoethanol, 100U/mL penicillin and 100ug/mL streptomycin.

extract_protocol:
preB-ALL cells were crosslinked with formaldehyde solution. Nuclei were isolated as previously described and sonicated in lysis buffer. DNA was purified with phenol-chloroform extraction and ethanol precipitation.
Purified ChIP DNA was used to prepare Illumina multiplexed sequencing libraries. Libraries were prepared following the TruSeq DNA Sample Prep v2 Kit (Illumina). Amplified libraries were size-selected using a 2% gel cassette in the Pippin Prep system (Sage Science) set to capture fragments between 200-400 bp. Libraries were quantified by qPCR using the Illumina Library Quantification Kit (KAPA Biosystems) according to manufacturer guidelines. Libraries were sequenced on the Illumina HiSeq2500 for 40-nt in single read mode.

tag: strain

tag: cell type

value: pre-B cell leukemia

tag: genotype

value: BCR-ABL1 overexpressed p19 null

tag: antibody

value: H3K27ac (ab4729, abcam)


title: PHF6_ChIP-Seq

value: PHF6 (A301-451A, Bethyl)


title: Cab12: ES d7 PAR CHIRT-seq

city: Boston

first: Hsueh-Ping

last: Chu

state: MA

address: 185 Cambridge St

department: molecular biology

institute: MGH, Harvard Medical School

data_processing:
library strategy: CHIRT-seq
Basecalls performed using Illumina software, version 1.8. CHIRT-seq: Following the removal of adaptor sequences and PCR duplicates, paired-end 50 bp sequencing data was aligned to mouse reference genome (GRCm38/mm10) using the software Novoalign (v3.00.02) (http://www.novocraft.com/products/novoalign/). The coverage files were generated using R software library SPP software (Kharchenko et al., 2008) with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities. Controls include input, sense-CHIRT, and TERRA-CHIRT without RNase H elution (no RNase H).
Genome_build: mm10
Supplementary_files_format_and_content: CHIRT-seq: The processed data are the coverage files (bigwig) generated using R software library SPP software with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities. Input files are wig files generated by MACS software.

source_name: PAR-TERRA CHIRT-seq

growth_protocol: Cells were cultured in regular ES medium (15% FBS) without LIF

extract_protocol:
CHIRT-seq: Nuclei were crosslinked in 1% glutaraldehyde and chromatin were sheared to 0.5~3kb. Chromatin was incubated with biotinylated capture oligonucleotides that were complementary to PAR-TERRA RNA, and the hybridized material was captured by streptavidin beads. Enriched DNA was eluted by RNaseH digestion.
CHIRT-seq: Eluted genomic DNA or input samples were fragmented into a median size of 220 bp, and the sequencing libraries were constructed according to NEB ChIP-Seq library protocol.

treatment_protocol: d7 ES cells were cultured without LIF for 4 days under non-adherent conditions and plated for an additional 3 days.

tag: strain background

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells

tag: capture oligos

value: PAR-AS

tag: molecule subtype

value: PAR-TERRA enriched DNA


title: Cab12: ES d7 TERRA CHIRT-seq

value: TERRA-AS


title: W3h_rep2


title: BOT-1

source_name: Bast fibres BOT biological replicate 1

value: Bast fibres BOT1


title: Cab12: ES d7 input CHIRT-seq

value: input DNA


title: Cab12: ES d3 PAR CHIRT-seq

treatment_protocol: d3 ES cells were cultured without LIF for 3 days under non-adherent conditions.


title: Cab12: ES d3 TERRA CHIRT-seq


title: W1h_rep2


title: preB-ALL input DNA_ChIP-Seq


title: H3K27me3_ChIP-Seq

value: H3K27me3 (ab6002, abcam)


title: MID-3

source_name: Bast fibres MID biological replicate 3

value: Bast fibres

value: Bast fibres MID3

value: Internode containing snap point


title: MID-4

source_name: Bast fibres MID biological replicate 4

value: Bast fibres MID4


title: Cab12: ES d3 input CHIRT-seq


title: Cab11: MEF input CHIRT-seq

growth_protocol: Cells were cultured in regular fibroblast medium (1% Pen/Strep, high-glucose DMEM+GlutaMAX) with 10% FBS

value: Immortalized MEFs


title: W24h_rep1

value: wild type


title: Cab11: MEF noRNAseH CHIRT-seq

value: TERRA-AS,noRNaseH

value: no RNaseH control DNA


title: Cab11: MEF Sense CHIRT-seq

value: TERRA-sense

value: Sense control DNA


title: TOP-4

source_name: Bast fibres TOP biological replicate 4

value: Bast fibres TOP4

value: Internode above snap point


title: MID-2

source_name: Bast fibres MID biological replicate 2

value: Bast fibres MID2


title: W3h_rep1


title: W12h_rep1


title: MID-1

source_name: Bast fibres MID biological replicate 1

value: Bast fibres MID1


title: W6h_rep1


title: Cab11: MEF TERRA CHIRT-seq

source_name: PAR-TERRA ChIRT-seq

value: CAST/Ei x 129/Sv/Jae

value: TERRA-AS

value: PAR-TERRA enriched DNA


title: Phf6KD_rep2

description: pre-B cell leukemia cells with indicated genotype

data_processing:
Illumina pipeline version 1.8 used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

extract_protocol:
RNA from preB-ALL cells was prepared using Qiagen RNeasy Mini Kit.
cDNA for RNA-Seq libraries was prepared using Illumina TruSeq mRNA library Prep Kit.

value: pre-B cell leukemia

value: BCR-ABL1 overexpressed p19 null

tag: phf6 genotype

value: shRNA


title: TOP-3

source_name: Bast fibres TOP biological replicate 3

tag: tissue

value: Bast fibres

value: Bast fibres TOP3


title: W0h_rep1

value: wild type


title: Cab11: MEF PAR CHIRT-seq

value: Immortalized MEFs

value: PAR-AS


title: TOP-1

source_name: Bast fibres TOP biological replicate 1

tag: biological replicate

value: Bast fibres TOP1


title: TOP-2

source_name: Bast fibres TOP biological replicate 2

value: Bast fibres TOP2

tag: stem region


title: W1h_rep1


title: Degradome_light

data_processing:
Sequence reads were adaptor-trimmed. Only reads with over 18 nt after adaptor removal were used for mapping.
Mapping were conducted using Bowtie (v1.0.0), with parameters set as: –f –n 0 –e 80 –l 18 –a –m 5 –best –strata
Transcripts per million reads (TPM, 20 - 24 nt) were calculated for normalization.
Genome_build: TAIR10
Supplementary_files_format_and_content: Degradome analysis of sRNA-mediated cleavage under light


title: Th0 replicate 2

status: Public on Jul 09 2017

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

data_processing:
Sequencing data was processed to remove any adaptor, PCR primers and low quality transcripts using FASTQC and fastx.
These high quality, clean reads were aligned against mouse genome using tophat2 and bowtie2 packages (http://tophat.cbcb.umd.edu/).
Gene expression measurement was performed from aligned reads by counting the unique reads using htseq-count algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: Count Files

source_name: CD4+ T cell

growth_protocol: Sorted naïve T cells were activated and differentiated into Th0 and Th9 cells for 48 hrs. Breifely, cells were activated with plate bound anti-CD3 (2 microgram per ml) and anti-CD28 antibodies (2 microgram per ml) in the presence or absence of TGF-beta 1 (2 ng per ml) and IL-4 (20 ng per ml).

extract_protocol:
Total RNA was extracted from Th0 and Th9 cells using RNAeasy mini kit from Qiangen. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Differentiated CD4+ T cells

tag: cell subpopulation


title: Cab10: ES d0 PAR CHIRT-seq

data_processing:
library strategy: CHIRT-seq
Basecalls performed using Illumina software, version 1.8. CHIRT-seq: Following the removal of adaptor sequences and PCR duplicates, paired-end 50 bp sequencing data was aligned to mouse reference genome (GRCm38/mm10) using the software Novoalign (v3.00.02) (http://www.novocraft.com/products/novoalign/). The coverage files were generated using R software library SPP software (Kharchenko et al., 2008) with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities. Controls include input, sense-CHIRT, and TERRA-CHIRT without RNase H elution (no RNase H).
Genome_build: mm10
Supplementary_files_format_and_content: CHIRT-seq: The processed data are the coverage files (bigwig) generated using R software library SPP software with smoothing using 500 bp bins with a 100 bp step size to generate control-subtracted, normalized read densities.Input files are wig files generated by MACS software.

growth_protocol: Cells were cultured in regular ES medium (15% FBS) with LIF

value: Embryonic stem cells


title: Th9 replicate 3


title: Th0 replicate 1


title: Th9 replicate 1


title: Th9 replicate 2


title: Th0 replicate 3


title: Replicate B, timepoint 114

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

data_processing:
Adaptor and low quality trimming by TrimGalore
Tophat2  was used to align reads to the December 2011 release of the mouse reference genome (mm10)
Bam files for duplicated seq runs were combined
Read counts data corresponding to GENCODE vM2 transcript annotations were generated using HTSeq
counts data were background corrected and normalized for library size using edgeR,  then transformed using voom (‘variance modeling at the observational level’) for differential expression analysis using LIMMA
Genome_build: mm10
Supplementary_files_format_and_content: csv of voomed expression values on M2

source_name: ES cells_114 hrs

extract_protocol:
Trizol RNA Extraction
Agilent Stranded RNA

tag: strain backgroun

tag: cell line

value: embryonic stem cells (ES cells)

value: 114 hrs


title: Replicate B, timepoint 102

source_name: ES cells_102 hrs

tag: time point

value: 102 hrs


title: Replicate B, timepoint 108

source_name: ES cells_108 hrs

value: 108 hrs


title: Replicate B, timepoint 96

source_name: ES cells_96 hrs

value: 96 hrs


title: Replicate B, timepoint 90

source_name: ES cells_90 hrs

value: 90 hrs


title: Replicate B, timepoint 72

source_name: ES cells_72 hrs

value: 72 hrs


title: Replicate B, timepoint 78

source_name: ES cells_78 hrs

value: 78 hrs


title: Replicate B, timepoint 84

source_name: ES cells_84 hrs

value: 84 hrs


title: Replicate B, timepoint 54

source_name: ES cells_54 hrs

value: 54 hrs


title: Replicate B, timepoint 66

source_name: ES cells_66 hrs

value: 66 hrs


title: Replicate B, timepoint 42

source_name: ES cells_42 hrs

value: 42 hrs


title: Replicate B, timepoint 60

source_name: ES cells_60 hrs

value: 60 hrs


title: Replicate B, timepoint 36

source_name: ES cells_36 hrs

value: 36 hrs


title: W0h_rep2

source_name: 4d-old de-etiolating seedling

tag: ecotype

tag: genotype/variation

value: wild type


title: Replicate B, timepoint 18

source_name: ES cells_18 hrs

value: 18 hrs


title: Replicate B, timepoint 12

source_name: ES cells_12 hrs

value: 12 hrs


title: Replicate B, timepoint 24

source_name: ES cells_24 hrs

value: embryonic stem cells (ES cells)

value: 24 hrs


title: Replicate B, timepoint 30

source_name: ES cells_30 hrs

value: 30 hrs


title: Replicate B, timepoint 6

source_name: ES cells_6 hrs

value: 6 hrs


title: Replicate A, timepoint 114

source_name: ES cells_114 hrs

value: 114 hrs


title: Replicate A, timepoint 108

source_name: ES cells_108 hrs

value: 108 hrs


title: Replicate A, timepoint 102

source_name: ES cells_102 hrs

value: 102 hrs


title: Replicate B, timepoint 0

source_name: ES cells_0 hr

value: 0 hr


title: Replicate B, timepoint 120

source_name: ES cells_120 hrs

value: 120 hrs


title: Replicate A, timepoint 90

source_name: ES cells_90 hrs

value: 90 hrs


title: Replicate A, timepoint 120


title: Replicate A, timepoint 96

source_name: ES cells_96 hrs

value: 96 hrs


title: Replicate A, timepoint 60


title: Replicate A, timepoint 72

source_name: ES cells_72 hrs

value: 72 hrs


title: Replicate A, timepoint 78

source_name: ES cells_78 hrs

value: 78 hrs


title: Replicate A, timepoint 84

source_name: ES cells_84 hrs

value: 84 hrs


title: Replicate A, timepoint 54

source_name: ES cells_54 hrs

value: 54 hrs


title: Replicate A, timepoint 66

source_name: ES cells_66 hrs

value: 66 hrs


title: Replicate A, timepoint 48

source_name: ES cells_48 hrs

value: 48 hrs


title: Replicate B, timepoint 48

value: embryonic stem cells (ES cells)


title: BPA_Genistein_Rat_5

city: San Antonio

first: Rohit

middle: Ramakant

last: Jadhav

state: TX

address: Rm. 261 South Texas Research Facility, MC 8257 7703 Floyd Curl Drive

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

data_processing:
Single-end 50 bp reads were mapped to the UCSC rat transcriptome (rn5) by Bowtie with parameters -v 2 -best -k 10
Multiple matched reads were processed by LONUT, an algorithm developed originally to improve the detection of the enriched regions for ChIP-seq and MBD-seq data.
Those of the multiple matched reads close to peaks detected in the uniquely matched reads were retained and combined with uniquely matched reads. The combined reads were then binned by 100 bp bin-size and normalized by total reads of each sample.
The combined reads were then binned by 100 bp bin-size and normalized by total reads of each sample.
Genome_build: rn5
Supplementary_files_format_and_content: The bedgraph files were created using the genomecoverage function in bedtools.

organism: Rattus norvegicus

source_name: Mammary gland

growth_protocol: Seven week old female Sprague-Dawley rats were purchased from Charles River Laboratories (Wilmington, MA). Animals were housed in a temperature controlled facility with a 12-h light : dark cycle. These animals were bred with proven Sprague-Dawley studs, fed phytoestrogen-free AIN-76A diet (Harlan Teklad, Madison WS), housed in polypropylene cages and water provided via glass bottles (all polycarbonate/BPA free). On the day of birth (designated as PND zero), offspring were sexed and litters were culled to 10 offspring per lactating dam.

extract_protocol:
The fourth abdominal mammary glands were rapidly dissected from live ketamine/xylazine anesthetized animals (to minimize proteolysis), snap-frozen in liquid nitrogen, and stored at -80 ºC for later analysis. Methylated DNA was obtained by the MethylMiner Methylated DNA Enrichment Kit (Invitrogen).
Eluted DNA was used to generate libraries following the standard protocols from Illumina. Next, MBDCap-seq libraries were sequenced using the Illumina Genome Analyzer II as per manufacturer's instructions. Image analysis and base calling were performed with the standard Illumina pipeline.

treatment_protocol: From PND2 through PND20 only, the offspring nursed via the lactating dams. Animals were weaned at PND20 and provided AIN-76A diet and water without further treatment/exposure. GEN was provided by DSM Nutritional Products (Basel, Switzerland). BPA, sesame oil, and all other chemicals were from Sigma Chemical Co. (St. Louis, MO). Offspring were weaned at PND21 and fed AIN-76A diet. At PND100, female offspring were killed in the estrous phase.

tag: strain

value: Sprague-Dawley

tag: Sex

value: Female

tag: days after birth


title: Replicate A, timepoint 36

source_name: ES cells_36 hrs

tag: cell type

value: 36 hrs


title: BPA_Genistein_Rat_4


title: Replicate A, timepoint 30

source_name: ES cells_30 hrs

value: 30 hrs


title: Replicate A, timepoint 42

source_name: ES cells_42 hrs

value: 42 hrs


title: Replicate A, timepoint 24

source_name: ES cells_24 hrs

value: 24 hrs


title: BPA_Genistein_Rat_3


title: BPA_Genistein_Rat_2


title: Replicate A, timepoint 18

source_name: ES cells_18 hrs

value: 18 hrs


title: Replicate A, timepoint 6

source_name: ES cells_6 hrs

value: 6 hrs


title: Genistein_Rat_4


title: Replicate A, timepoint 12

source_name: ES cells_12 hrs

value: 12 hrs


title: Replicate A, timepoint 0

source_name: ES cells_0 hr

value: 0 hr


title: gm12878_dmso_replicate3

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

data_processing:
50 bp reads mapped using Bowtie to an index containing both human hg19 and EBV reference genomes.
Parameters allowed for up to two mismatches and only considered reads that mapped to a unique sequence.
The number of hits at each base was counted and then normalized per million mapped reads.
Nucleotide read counts for each lytic transcript were normalized to the total number of mapped reads and integrated only over exons spanning regions that did not overlap with another transcript based on version 6 of a published B95-8 annotation.
RNA-seq profiling for every condition was performed with three biological replicates and yielded ∼60–100 million mapped sequences each experiment with reproducible transcriptome profiles.
Genome_build: hg19
Supplementary_files_format_and_content: wig files

organism:
Homo sapiens
human gammaherpesvirus 4

extract_protocol:
We isolated RNA from 4 × 10^6 log phase cells homogenized with a QIAshredder spin column (Qiagen). Total RNA was purified by silica-based membrane affinity as packaged in the RNeasy Mini Kit (Qiagen). Preparations included the optional DNAse treatment step. Single primer isothermal linear amplification to cDNA was achieved using the Ovation RNA-Seq System V2 (NuGEN) and 20 ng of RNA. 3 μg of cDNA was then sheared in a 40 μL volume using a Covaris S2 Focused-ultrasonicator.
We prepared deep sequencing libraries by adaptor-mediated amplification as packaged in either the Encore NGS Library System I (NuGEN) or Ovation Ultralow Library System V2 (NuGEN).

treatment_protocol: For drug treatment, we added acyclovir (Sigma-Aldrich) to 200 µM from a 100X stock solution in DMSO. Acyclovir- and vehicle-treated cells were cultured in parallel and treatment replenished with every addition of new media for at least one week.

value: GM12878 [EBV+ B cell]

tag: treated with

value: DMSO (vehicle)


title: Genistein_Rat_1


title: Genistein_Rat_3


title: gm12878_dmso_replicate1


title: Genistein_Rat_2


title: gm12878_dmso_replicate2


title: gm12878_acy_replicate3

value: 200 µM acyclovir


title: BPA_Rat_5


title: Neuro2a_ChIPseq_input

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

description: Chromatin

data_processing:
Illumina Casava1.7 software used for basecalling.
GRO-seq and nuclear total RNA-seq mapping: The raw FASTQ files were mapped to the mouse mm10 genome by STAR using the parameters of “--outFilterMultimapNmax 1 --outFilterMismatchNmax 3”.
ATAC-seq mapping: The mate1 and mate2 files of the paired-end sequencing were mapped separately to the mm10 genome by bowtie2 using “-v 2 -m 1”. If both mates of a read pair were mapped to the opposite strands of the same chromosome and the distance in-between was less than 2 kb, the read pair was included for further analysis.
ChIP-seq mapping and peak calling: The ChIP-seq FASTQ files were mapped to the mouse mm10 genome by bowtie using “-v 2 -m 1”. Only uniquely mapped reads were included for further analysis. The Homer findPeaks function was used to call peaks from the H3K4me3 data sets using the parameters of “-style histone -minDist 2500”.
TAB-seq and WGBS mapping and analysis: Trim Galore was used to remove the adaptor contamination from the raw sequencing reads using “-stringency 2 --length 36”. The trimmed reads were mapped to mm10 genome by Bismark using parameters “-n 2 -l 40”. Clonal reads were excluded to avoid PCR artifacts. Methylation calling was performed by Binomial distribution followed by the Benjamini-Hochberg procedure to identify cytosine whose methylation level was significantly higher than the non-conversion rate, which is set to 0.02 for TAB-seq and 0.001 for WGBS. The cutoff was FDR < 0.0001. The hmC level for a cytosine was calculated as the number of methylated TAB-seq reads covering this cytosine divided by the total number of TAB-seq reads covering this cytosine. The mC level for a cytosine was calculated as the number of methylated WGBS reads covering this cytosine divided by the total number of WGBS reads covering this cytosine, then subtract the hmC level in this cytosine. The minimum mC level was set to zero.
Genome browser track files: Samtools was used to convert sam files into bam files and sorted the bam files. For GRO-seq, Bedtools genomecov was used to convert the bam files into bedGraph files using “-bga -split -strand”, and then bedGraphToBigWig was used to convert the bedGraph files into BigWig files. For ATAC-seq, IGVtools was used to generate the TDF files using “count -z 5 -w 25 --pairs”. For ChIP-seq, IGVTools was used to generate the TDF files using “count -z 5 -w 25 -e 250”.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Samtools was used to convert sam files into bam files and sorted the bam files. For GRO-seq, Bedtools genomecov was used to convert the bam files into bedGraph files using “-bga -split -strand”, and then bedGraphToBigWig was used to convert the bedGraph files into BigWig files. For ATAC-seq, IGVtools was used to generate the TDF files using “count -z 5 -w 25 --pairs”. For ChIP-seq, IGVTools was used to generate the TDF files using “count -z 5 -w 25 -e 250”. For TAB-seq and WGBS, bedGraph files include the methylation levels.

source_name: Neuro 2a cells, input

growth_protocol: All the mice used were in the C57BL/6 background, were housed in a 12h light/12h dark cycle, and were given enough amounts of food and water. All experiments were conducted in accordance with the ethical guidelines of the US National Institutes of Health and with the approval of the Institutional Animal Care and Use Committee of the University of Pennsylvania.

extract_protocol:
Neuro 2a cells were grown to confluency on 150 mm culture dishes. Cells were crosslinked directly on the dishes for 10 min at room temperature with 1% formaldehyde, followed by quenching with 0.125M glycine for 5 min. Cells were scraped, pelleted, and lysed in cell lysis buffer (50 mM HEPES (pH 7.5) 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.25% Triton X-100, 0.5% NP-40, 10% glycerol) for 10 min on ice. Nuclei were collected and lysed in 10 mM Tris pH 8.0, 1% SDS, 1 mM EDTA and 1 mM EGTA. The SDS concentration was diluted to 0.625% and DNA shearing was performed on a Bioruptor instrument (Diagenode; 5 ten-minute cycles, 30 sec on, 30 sec off). Buffer conditions were adjusted to contain 150 mM NaCl, 0.1% SDS, and 0.5% Triton X-100 and chromatin was precleared with Protein A Dynabeads (Invitrogen) for 2 h and an aliquot was saved as Input. Immunoprecipitation was performed using 32 ul Protein A Dynabeads and 5ul of H3K4me3 antibody (Millipore; 07-473) or 10ug H3K27ac antibody (Abcam; ab4729). Beads were washed twice with low-salt buffer (150 mM NaCl, 50 mM HEPES pH 7.5, 0.1% DOC, 1% Triton X-100, and 1 mM EDTA), once with high-salt buffer (500 mM NaCl, 0.1% DOC, 50 mM HEPES pH 7.5, 1% Triton X-100, and 1 mM EDTA), once with LiCl buffer (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 0.5% NP-40, 0.5% DOC, 1 mM EDTA), and twice with TE. Chromatin was eluted with elution buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, and 1% SDS, wt/vol) and reverse crosslinked overnight at 65º C, followed by treatment with RNase A for 30 min at 42º C and proteinase K for 3 hr at 55º C. DNA was extracted twice with phenol/chloroform, once with chloroform, and ethanol precipitated. 10 ng of ChIP DNA was used for library preparation.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: Albino strain A

value: Neuro 2a

tag: chip antibody


title: gm12878_acy_replicate2


title: BPA_Rat_3


title: Neuro2a_mRNAseq_rep2

description:
RNA-seq
mRNA

source_name: Neuro 2a cells

extract_protocol:
RNA-seq was performed in Neuro 2a cells using two replicates. RNA was extracted with Trizol reagent (Invitrogen) and purified using the RNeasy MinElute Clean-up kit (Qiagen cat. #74204).
2.5 ug of purified RNA was used for library construction using the TruSeq stranded mRNA Library Prep Kit (Illumina RS-122-2101).


title: Neuro2a_mRNAseq_rep1

description:
RNA-seq
mRNA


title: BPA_Rat_4


title: Neuro2a_GROseq

description:
GRO-seq
RNA

extract_protocol:
For ChIP-seq, chromatin of whole cortex from two 6-week-old C57BL/6 mice were used. For GRO-seq, nuclei were isolated from the Neuro 2a cells. For TAB-seq and WGBS, the genomic DNA was isolated from the nuclei of the cortical excitatory neurons. For ATAC-seq, the chromatin was isolated from the nuclei of the cortical excitatory neurons.
Libraries were prepared for sequencing using standard Illumina protocols.


title: Neuro2a_ChIPseq_H3K4me3

description:
ChIP-seq
Chromatin

source_name: Neuro 2a cells, H3K4me3 ChIP

value: H3K4me3 (Millipore 07-473, 5ul per IP)


title: gm12878_acy_replicate1


title: BPA_Rat_2


title: Neuro2a_ChIPseq_H3K27ac

description:
ChIP-seq
Chromatin

source_name: Neuro 2a cells, H3K27ac ChIP

value: H3K27ac (Abcam ab4729, 10ug per IP)


title: mutui_dmso_replicate3

value: MutuI [EBV+ Burkitt lymphoma]


title: Genistein_Rat_5

value: Sprague-Dawley

value: Female


title: BPA_Genistein_Rat_1


title: BPA_Rat_1


title: Control_Rat_4


title: mutui_acy_replicate3


title: Control_Rat_3


title: Control_Rat_5


title: mutui_dmso_replicate2


title: mutui_acy_replicate2


title: mutui_dmso_replicate1


title: mutui_acy_replicate1


title: VMS

city: Yangzhou

first: Biao

last: Jin

state: Jiangsu

address: Wenhui east road no. 48

department: College of Horticulture and Plant Protection

country: China

institute: Yangzhou University

data_processing:
an Illumina Hiseq2000 platform for sequencing
Clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated.
Reads remaining without annotation were used to predict potentially novel miRNAs using miREvo and mirdeep2 software, followed by a prediction of secondary structure using MFOLD  software (Zuker 2003)
We used the Web-based psRNATarget program and psRobot to identify putative targets for known and novel miRNAs.
Genome_build: miRNA_target.fa
Supplementary_files_format_and_content: The compressed files include miRNA read counts (.table and .fa) and targets (.table).

organism: Viburnum macrocephalum f. keteleeri

source_name: Viburnum macrocephalum f. keteleeri, sterile flower

growth_protocol: fertile and sterile flowers of V. macrocephalum f. keteleeri were obtained from mature healthy V. macrocephalum f. keteleeri tree growing under natural conditions in Yangzhou University, Jiangsu, Eastern China (32°39’N, 119°43'E).

extract_protocol:
Samples were collected in April 2014. Total RNAs of fertile and sterile flowers were extracted using MiniBEST Plant RNA Extraction Kit (Takara, Dalian, Liaoning, China), according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ

value: Flower

value: sterile flower

tag: growth condition

value: Healthy

tag: forma

value: keteleeri


title: VMF

source_name: Viburnum macrocephalum f. keteleeri, fertile flower

tag: tissue

value: fertile flower


title: BMM inf

status: Public on Jul 08 2017

city: Seongnam-si

first: Jee Soo

last: Son

state: Gyeonggi-do

address: Room 903, JungAng Induspia V, 137, Sagimakgol-ro, Jungwon-gu

country: South Korea

institute: iNtRON Biotechnology

data_processing:
Sequenced using Illumina HiSeq 2500
Data analysis was performed with bowtie
Differential gene expression analysis was performed with CLRNASeq software from Chunlab Inc., South Korea
Genome_build: NCBI RefSeq Brucella abortus 544 (PRJNA173507)
Supplementary_files_format_and_content: Supplementay_files_format_and_content: text files with normalization values and raw read counts

source_name: Bone marrow derived macrophage_I

growth_protocol: Bone marrow-derived macrophages (BMM) from female BALB/c mice were prepared and incubated at 37°C with 5% CO2 atmosphere. BMMs were cultured in cultivation dishes (100 mm x 20 mm) with 10 ml L-cell conditioned medium. After 5 days of incubation, 10 ml fresh medium without antibiotics was added and the cells were incubated further for 5 days. After 10 days of incubation, BMMs were washed three times with PBS and incubated with fresh RPMI 1640 medium containing 10% (v/v) heat-inactivated fetal bovine serum (FBS).

extract_protocol:
Total RNA from the uninfected or infected BMMs were isolated in accordance with the Qiagen RNeasy Mini kit “Animal Cells I” protocol (Qiagen). DNA was removed by using the “On-Column DNase Digestion” protocol.
The Ribo-Zero rRNA removal kit (Epicentre, USA) was used for ribosomal RNA depletion according to manufacturer’s instructions. Libraries for Illumina sequencing were made with the TruSeq Stranded mRNA sample prep kit (Illumina, USA) following the manufacturer’s protocol. RNA sequencing was performed on the Illumina HiSeq 2500 platform using single-end 50 bp sequencing.

treatment_protocol: The BMM cells were then infected with 107 CFU of the virulent strain Brucella abortus for 1 h at 37oC in 5% CO2. Washing was performed using RPMI 1640 medium and then incubated for 24 h with fresh RPMI 1640 medium containing 10% (v/v) FBS and gentamicin (30 µg/ml) to kill extracellular bacteria at 37oC in 5% CO2.

value: BALB/c

value: Bone marrow derived macrophage_I

tag: age

value: 24 hours post-infection at 10 days


title: Control_Rat_1


title: BMM con

source_name: Bone marrow derived macrophage_C


title: KD_Ino80_NC2

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

description:
Ino80NC2KD_vs_ctr_antisense_ratio.txt
Ino80NC2KD_vs_ctr_sense_ratio.txt

data_processing:
Fastq files were used to map reads to mouse genome(mm9) with TopHat v2.0.8
Use SAMMate to caclutate RPKM using accepted bam file from Tophat
Mapped reads were counted and  used to calculate the metagene profile for mutant and control
log2 ratio of mutant vs control was used for metagene profile
genome_build: mm9

source_name: ESC cells

growth_protocol: E14 cells were grown on feeder-free tissue culture plates (0.5% gelatin treated before use) in ESC media: knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibiting factor, L-glutamine, non-essential amino acids, penicillin/streptomycin and 2-mercaptoethanol. Cells were passaged at least twice before treatment.

extract_protocol: For RNA-seq, total RNA was extracted using TRIzol Reagent, followed by DNaseI treatment and a second round of TRIzol extraction.

treatment_protocol: Cells were transfected with siRNA following the protocol of Lipofectamine RNAiMAX Transfection Reagent. 72 hours post transfection, cells were harvested for experiments

value: ESC cells


title: KD_Mot1

description:
Mot1KD_vs_ctr_antisense_ratio.txt
Mot1KD_vs_ctr_sense_ratio.txt


title: KD_Mot1_Ino80

description:
Mot1Ino80KD_vs_ctr_antisense_ratio.txt
Mot1Ino80KD_vs_ctr_sense_ratio.txt


title: Mock_For_singleKD


title: KD_NC2

description:
Nc2KD_vs_ctr_antisense_ratio.txt
Nc2KD_vs_ctr_sense_ratio.txt


title: RNA150213LC_H8

city: Portland

first: Lisa

last: Coussens

state: Oregon

address: SW Sam Jackson Park Rd

institute: OHSU

description: No fpkms submitted for this sample because it was not included in current publication

data_processing:
Tophat version 2.0.12 for alignment
Cufflinks version 2.2.1 for transcript assembly
Cuffnorm from cufflinks version 2.2.1for library zise normalization
R preprocessCore version 1.34.0 for quantile normalization
R SVA (Combat) version3.30.0  batch effects correction
Genome_build: hg19
Supplementary_files_format_and_content: Text file with quantile normalized, batch corrected, fpkm measurement for each gene

source_name: Human breast adjacent normal

extract_protocol:
Qiagen RNAEasy isolation kit
Agilent SureSelect Stranded RNAseq

value: Adjacent normal

tag: tumor size

tag: grade

tag: histology

tag: node status (pos/total)

tag: er status

tag: pr status

tag: her2 status


title: Mock_For_doubleKD


title: RNA150213LC_G4


title: RNA150213LC_G3


title: RNA150213LC_G2


title: RNA150213LC_G12

source_name: Human Breast Normal

value: Normal Breast


title: RNA150213LC_H10

source_name: Human breast tumor

value: Breast tumor

value: Ductal

value: Whole human breast tumor


title: RNA150213LC_G1

source_name: No clinical information available

value: No clinical information available


title: RNA150213LC_H11

source_name: Prophylactic Mastectomy

value: Prophylactic Mastectomy


title: RNA150213LC_G7


title: RNA150213LC_F9


title: RNA150213LC_G8


title: RNA150213LC_H12

value: Lobular


title: Control_Rat_2

source_name: Mammary gland

tag: strain

value: Sprague-Dawley

tag: Sex

value: Female

tag: days after birth


title: RNA150213LC_F4

tag: cell type


title: RNA150213LC_F12


title: RNA150213LC_F7


title: RNA150213LC_F8


title: RNA150213LC_F11


title: RNA150213LC_F1


title: RNA150213LC_E5

value: Ductal and Micropapillary


title: KD_Ino80

description:
Ino80KD_vs_ctr_antisense_ratio.txt
Ino80KD_vs_ctr_sense_ratio.txt


title: RNA150213LC_F10


title: RNA150213LC_E3


title: RNA150213LC_E2


title: RNA150213LC_E11


title: RNA150213LC_E10


title: RNA150213LC_D8


title: IP_mIno80_replicate2

description: Sample 137

data_processing:
For mouse ChIP-seq
Fastq files were used to map reads to mouse genome(mm9) with  Bowtie 0.12.9
Mapped reads were counted and shuffled to similar reads.
Shuffled reads were used to calculate the p value and log2 ratio of Ip vs Input or histone modifications in knockdown vs control
log2 ratio of Ip vs input at significant windows were used to plot with metagene profiles or center with TSS
log2 ratio of H3K79Me3 in mutant vs control at all windowns was used for metagene profile
genome build: mm9

growth_protocol:
cells were harvested and crosslinked in suspension with 1% formaldehyde for 10 minute at room temperature.
E14 cells were grown on feeder-free tissue culture plates (0.5% gelatin treated before use) in ESC media: knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibiting factor, L-glutamine, non-essential amino acids, penicillin/streptomycin and 2-mercaptoethanol. Cells were passaged at least twice before treatment.

extract_protocol:
Crosslinked cells were lysed, sonicated and chromatin was collected for IP. 2-5 ug of antibody was used for each IP. IPed chromatin was captured by Protein A/G beads. After washing, bound complexes were eluted and crosslinking was reversed. DNA was extracted using phenol-chloroform and purified by ethanol precipitation.
For ChIP-seq, cells were harvested and crosslinked in suspension with 1% formaldehyde for 10 minute at room temperature. Crosslinked cells were lysed, sonicated and chromatin was collected for IP. 2-5 ug of antibody was used for each IP. IPed chromatin was captured by Protein A/G beads. After washing, bound complexes were eluted and crosslinking was reversed. DNA was extracted using phenol-chloroform and purified by ethanol precipitation.

tag: antibody

value: Anti Ino80 antibody from Proteintech (18810-1-AP)


title: IP_Pol II_KDMot1Ino80_replicate2

description: Sample 140

growth_protocol:
Cells were transfected with siRNA following the protocol of Lipofectamine RNAiMAX Transfection Reagent. 72 hours post transfection, Cells were harvested and crosslinked in suspension with 1% formaldehyde for 10 minute at room temperature.
E14 cells were grown on feeder-free tissue culture plates (0.5% gelatin treated before use) in ESC media: knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibiting factor, L-glutamine, non-essential amino acids, penicillin/streptomycin and 2-mercaptoethanol. Cells were passaged at least twice before treatment.

value: Anti Pol II antibody (QED Bioscience)


title: IP_mMot1_replicate2

description: Sample 136

value: Anti murine Mot1 antibody from Abcam (ab72285)


title: IP_Pol II_Mock_replicate2

description: Sample 139


title: RNA150213LC_D4


title: Input_For_MINC_replicate2

description: Sample 135


title: IP_mNC2_replicate2

description: Sample 138

value: Anti NC2 beta antibody from Abcam (ab50783)


title: chromatinRNA_mock_replicate2

description:
chromatinRNA (isolate chromatin fraction then isolate RNA)
Sample 107

data_processing:
For mouse RNA-seq
Fastq files were used to map reads to mouse genome(mm9) with TopHat v2.0.8
Use SAMMate to caclutate RPKM using accepted bam file from Tophat
Mapped reads were counted and  used to calculate the metagene profile for mutant and control
log2 ratio of mutant vs control was used for metagene profile
genome build: mm9

growth_protocol:
Cells were transfected with siRNA following the protocol of Lipofectamine RNAiMAX Transfection Reagent. 72 hours post transfection, cells were harvested for experiments
E14 cells were grown on feeder-free tissue culture plates (0.5% gelatin treated before use) in ESC media: knockout DMEM supplemented with 15% fetal bovine serum, leukemia inhibiting factor, L-glutamine, non-essential amino acids, penicillin/streptomycin and 2-mercaptoethanol. Cells were passaged at least twice before treatment.

extract_protocol:
For nascent-RNA, cells washed with DPBS and lysed in 200 µl of ice-cold lysis buffer (10 mM Tris-HCl [pH 7.5], 0.1% NP40, 150 mM NaCl). The cell lysate was gently layered over 500 µl of chilled sucrose cushion (24% RNAse-free sucrose in lysis buffer) in a new Eppendorf tube and centrifuged for 10 min at 4°C, 10,000xg. The supernatant (cytoplasmic fraction) was removed and the pellet (nuclei) was washed once with 200 ml of ice-cold 1× PBS/1 mM EDTA. The nuclear pellet was resuspended in 100 µl of prechilled glycerol buffer (20 mM Tris-HCl [pH 7.9], 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol) by gentle flicking of the tube. An equal volume (100 µl) of cold nuclei lysis buffer (10 mM HEPES [pH 7.6], 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40) was added. The mix was vortexed vigorously for 2 seconds. The sample was incubated for 2 min on ice, and then centrifuged for 2 min at 4°C and 10,000xg. The supernatant (nuclear fraction/nucleoplasm) was removed and the pellet (chromatin) was gently rinsed with ice-cold 1× PBS/1 mM EDTA. 1 ml of Trizol reagent was added to the chromatin and incubated for 30 min at 50 °C to dissolve it. Nascent RNA was extracted following the manufacturer’s manual.
For nascent-RNA-Seq, cells washed with DPBS and lysed in 200 µl of ice-cold lysis buffer (10 mM Tris-HCl [pH 7.5], 0.1% NP40, 150 mM NaCl). The cell lysate was gently layered over 500 µl of chilled sucrose cushion (24% RNAse-free sucrose in lysis buffer) in a new Eppendorf tube and centrifuged for 10 min at 4°C, 10,000xg. The supernatant (cytoplasmic fraction) was removed and the pellet (nuclei) was washed once with 200 ml of ice-cold 1× PBS/1 mM EDTA. The nuclear pellet was resuspended in 100 µl of prechilled glycerol buffer (20 mM Tris-HCl [pH 7.9], 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol) by gentle flicking of the tube. An equal volume (100 µl) of cold nuclei lysis buffer (10 mM HEPES [pH 7.6], 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40) was added. The mix was vortexed vigorously for 2 seconds. The sample was incubated for 2 min on ice, and then centrifuged for 2 min at 4°C and 10,000xg. The supernatant (nuclear fraction/nucleoplasm) was removed and the pellet (chromatin) was gently rinsed with ice-cold 1× PBS/1 mM EDTA. 1 ml of Trizol reagent was added to the chromatin and incubated for 30 min at 50 °C to dissolve it. Nascent RNA was extracted following the manufacturer’s manual.


title: chromatinRNA_KDMot1Ino80_replicate1

description:
chromatinRNA (isolate chromatin fraction then isolate RNA)
Sample 106


title: RNA150213LC_C6


title: RNA150213LC_C2


title: RNA150213LC_D3


title: chromatinRNA_mock_replicate1

description:
chromatinRNA (isolate chromatin fraction then isolate RNA)
Sample 105


title: KD_Ino80_NC2_replicate2

description:
Total RNA (RiboMinus)
Ino80NC2KD_vs_ctr_antisense_ratio.txt.gz
Ino80NC2KD_vs_ctr_sense_ratio.txt.gz
Sample 104

extract_protocol:
total RNA was extracted using TRIzol Reagent, followed by DNaseI treatment and a second round of TRIzol extraction.
For RNA-seq, total RNA was extracted using TRIzol Reagent, followed by DNaseI treatment and a second round of TRIzol extraction.


title: RNA150213LC_C11


title: Mock_For_doubleKD_replicate2

description:
Total RNA (RiboMinus)
Sample 102


title: chromatinRNA_KDMot1Ino80_replicate2

description:
chromatinRNA (isolate chromatin fraction then isolate RNA)
Sample 108


title: KD_NC2_replicate2

description:
Total RNA (RiboMinus)
Nc2KD_vs_ctr_antisense_ratio.txt.gz
Nc2KD_vs_ctr_sense_ratio.txt.gz
Sample 101


title: RNA150213LC_C10


title: KD_Mot1_Ino80_replicate2

description:
Total RNA (RiboMinus)
Mot1Ino80KD_vs_ctr_antisense_ratio.txt.gz
Mot1Ino80KD_vs_ctr_sense_ratio.txt.gz
Sample 103


title: RNA150213LC_B8


title: KD_Ino80_replicate2

description:
Total RNA (RiboMinus)
Ino80KD_vs_ctr_antisense_ratio.txt.gz
Ino80KD_vs_ctr_sense_ratio.txt.gz
Sample 100


title: RNA150213LC_B7


title: RNA150213LC_E12


title: RNA150213LC_B6


title: RNA150213LC_D11


title: RNA150213LC_D2


title: RNA150213LC_B3


title: RNA150213LC_B12


title: Mock_For_singleKD_replicate2

description:
Total RNA (RiboMinus)
Sample 98


title: IP_K79Me3_control_ForKDNC2

data_processing:
Fastq files were used to map reads to mouse genome(mm9) with  Bowtie 0.12.9
Mapped reads were counted and shuffled to similar reads.
Shuffled reads were used to calculate the p value and log2 ratio of Ip vs Input or histone modifications in knockdown vs control
log2 ratio of Ip vs input at significant windows were used to plot with metagene profiles or center with TSS
log2 ratio of H3K79Me3 in mutant vs control at all windowns was used for metagene profile
genome_build: mm9

extract_protocol: For ChIP-seq, cells were harvested and crosslinked in suspension with 1% formaldehyde for 10 minute at room temperature. Crosslinked cells were lysed, sonicated and chromatin was collected for IP. 2-5 ug of antibody was used for each IP. IPed chromatin was captured by Protein A beads. After washing, bound complexes were eluted and crosslinking was reversed. DNA was extracted using phenol-chloroform and purified by ethanol precipitation.

value: Anti H3K79Me3 antibody from Abcam (ab8898)


title: IP_K79Me3_KD_NC2

value: ESC cells


title: RNA150213LC_B11


title: RNA150213LC_B10


title: RNA150213LC_C12


title: IP_K79Me3_KD_Mot1


title: RNA150213LC_A9


title: IP_K79Me3_KD_Ino80


title: RNA150213LC_A7

value: Adjacent normal


title: RNA150213LC_A10


title: RNA150213LC_A8

source_name: Prophylactic Mammoplasty

value: Prophylactic Mammoplasty


title: RNA150213LC_A1

value: Breast tumor


title: Input_For_KDMot1Ino80


title: IP_Pol II_KDMot1Ino80


title: RNA140128LC_98

value: Ductal


title: RNA150213LC_A11


title: KD_Mot1_replicate2

description:
Total RNA (RiboMinus)
Mot1KD_vs_ctr_antisense_ratio.txt.gz
Mot1KD_vs_ctr_sense_ratio.txt.gz
Sample 99


title: RNA140128LC_88


title: Input_For_Pol II_Mock


title: IP_Med1_repeat2

value: Anti Med1 antibody (SC-5334x)


title: Input_For_Med1_repeat2


title: RNA140128LC_87


title: IP_K79Me3_control_ForKDIno80


title: IP_Med1_repeat1


title: IP_K79Me3_control_ForKDMot1


title: RNA140128LC_86


title: RNA140128LC_75


title: IP_mNC2


title: RNA140128LC_72

value: Whole human breast tumor


title: IP_Pol II_Mock


title: IP_Pol II_KDIno80NC2


title: IP_mIno80


title: IP_K79Me3_Mot1Ino80AA_replicate2

description:
YPD + RAP
Sample 134

data_processing:
For yeast ChIP-seq
Fastq files were used to map reads to yeast genome(saccer3) with or Bowtie 0.12.9
Mapped reads were counted and shuffled to similar reads.
Shuffled reads were used to calculate the p value and log2 ratio of Ip vs Input
log2 ratio of Ip vs input at significant windows were used to plot with metagene profiles or center with TSS or TTS
genome build: sacCer3

organism: Saccharomyces cerevisiae

source_name: Mot1-FRB, Ino80-FRB

growth_protocol:
Overnight incubated yeast cells were diluted in YPD and grow to exponential phase. Add  rapamycin to 8 ug/ml and treat for 24 hours, keep in log phase by dilution during treatment and crosslinked with 1% formaldehyde for 20 minutes.
Overnight incubated yeast cells were diluted in YPD and grow to exponential phase.

extract_protocol:
Samples were lysed with glass beads in lysis buffer, chromatin was collected by centrifugation, resuspended in lysis buffer and subjected to sonification. The supernatant from sonicated lysates were precleared with Protein A/G beads and ChIP was performed as described using commercial antibodies
Libraries were prepared with a KAPA LTP kit following the manufacturer’s protocol

treatment_protocol: Add  rapamycin to 8 ug/ml and treat for 24 hours, keep in log phase by dilution during treatment.

value: MJE7 Background

value: Anti H3K79Me3 antibody 644


title: RJY6249_nhp6a,bΔ

description: in YPD

data_processing:
Fastq files were used to map reads to yeast genome(saccer3) with TopHat v2.0.8 (for FPKM analysis, treat as single end)
Caclutate FPKM using accepted bam file from cuffdiff cuffdiff v2.0.2 for mRNA-Seq
mapped reads(sam file) were used to cacullate the mRNA level and log2 ratio of mutants vs WT using customed script
log2 ratio of mutants vs wt were used to plot with metagene profiles.
genome_build: = sacCer3

growth_protocol: Overnight incubated yeast cells were diluted in YPD and grow to exponential phase.

extract_protocol:
Total RNA was extracted with phenol, digested with DNase and further purified by Trizol
Libraries of mRNA were prepared with KAPA stranded mRNA-Seq Kits v2 following the manufacturer’s protocol

value: yeast cells

value: W303-1A Background


title: W303-1A_WT

description: in YPD

source_name: WT


title: IP_mMot1


title: RNA140128LC_69


title: Input_For_KDIno80NC2


title: RNA140128LC_62


title: Input_For_Med1_repeat1


title: Input_For_MINC


title: IP_K79Me3_Mot1Ino80AA_replicate1

description:
YPD + RAP
Sample 133


title: RNA140128LC_77

value: DCIS (Comedo)


title: IP_K79Me3_WT_replicate2

description:
YPD + RAP
Sample 132


title: RAP1AA_Rap_repeat1

description: in Rapamycin

treatment_protocol: Add DMSO or rapamycin to 8 ug/ml and treat for 8 hours, keep in log phase by dilution during treatment.


title: RNA140128LC_71


title: RNA140128LC_58


title: RNA140128LC_40


title: RNA140128LC_96


title: RNA140128LC_209


title: RAP1AA_Rap_repeat2

description: in Rapamycin


title: IP_K79Me3_WT_replicate1

description:
YPD + RAP
Sample 131


title: Nc2bAA&Ino80AA_Rap_repeat1

description: in Rapamycin

source_name: Nc2b-FRB, Ino80-FRB


title: YXY1077_RAP_IP_Ino80_TBPAA_replicate2

description:
YPD + RAP
Sample 130

source_name: bar1∆, TBP-FRB, Ino80-13Myc

growth_protocol: Cells were synchronized in G1 with a-factor in YPD (4hours treatment) and treat with rapamycin for 2 hours, harvested at O.D of 0.8-1.0 and crosslinked with 1% formaldehyde for 20 minutes.

value: Anti Myc antibody from Abcam (ab32)


title: YXY1075_RAP_IP_Mot1_TBPAA_replicate2

description:
YPD + RAP
Sample 126

source_name: bar1∆, TBP-FRB, MOT1-13Myc

treatment_protocol: Cells were synchronized in G1 with a-factor in YPD (4hours treatment) and treat with rapamycin for 2 hours, harvested at O.D of 0.8-1.0  and crosslinked with 1% formaldehyde


title: RNA140128LC_21


title: RNA140128LC_207


title: YXY1077_RAP_Input_TBPAA_replicate2

description:
YPD + RAP
Sample 129


title: Control_ForRAPAA_repeat1

description: in DMSO

source_name: TBP-FRB


title: RNA140128LC_202


title: Nc2bAA&Ino80AA_Rap_repeat2

description: in Rapamycin


title: YXY1076_RAP_IP_Nc2β_TBPAA_replicate2

description:
YPD + RAP
Sample 128

source_name: bar1∆, TBP-FRB, Nc2β-13Myc


title: RNA140128LC_201


title: SW480_N1

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

data_processing:
Adapter trimming BBDuk version 35.14
Alignment BWA mem -T 40 -B 2 -L 10 -CM -U 100 -p
PicardTools AddOrReplaceReadGroups
PicardTools ReorderSam
BisSNP BisulfiteRealignerTargetCreator
BisSNP BisulfiteIndelRealigner
PicardTools MarkDuplicates
BisSNP BisulfiteCountCovariates
BisSNP BisulfiteTableRecalibration
BisSNP BisulfiteCountCovariates
BisSNP BisulfiteGenotyper
BisSNP VCFpostprocess -trim5 5 -trim3 5 -mmq 30 -C CG,1
www.github.com/brucemoran/perl-tools/vcf2methylKit.sh
Genome_build: hg19
Supplementary_files_format_and_content: methylKit input format

source_name: Cell line SW480

extract_protocol:
Qiagen FFPE-DNA kit (FFPE), Qiagen DNAeasy kit (FF, cell lines)
KAPA LT-DNA (KK8320)

tag: material type

value: Cell line


title: YXY1076_RAP_Input_TBPAA_replicate2

description:
YPD + RAP
Sample 127


title: SW620_N2

source_name: Cell line SW620


title: YXY1008_DMSO_IP_Ino80_replicate2

description:
YPD + DMSO
Sample 124

source_name: MOT1-FRB, Ino80-13myc, bar1∆

growth_protocol: Cells were synchronized in G1 with a-factor in YPD (3hours treatment) and treat with DMSO for 2 hours, harvested at O.D of 0.8-1.0 and crosslinked with 1% formaldehyde for 20 minutes.


title: Nc2aAA&Ino80AA_Rap_repeat2

description: in Rapamycin

source_name: Nc2a-FRB, Ino80-FRB


title: RNA140128LC_208


title: YXY1008_DMSO_Input_replicate2

description:
YPD + DMSO
Sample 123

treatment_protocol: Cells were synchronized in G1 with a-factor in YPD (3hours treatment) and treat with DMSO for 2 hours, harvested at O.D of 0.8-1.0 and crosslinked with 1% formaldehyde


title: SW480_N2


title: YXY1075_RAP_Input_TBPAA_replicate2

description:
YPD + RAP
Sample 125


title: YXY1006_DMSO_IP_Nc2β_replicate2

description:
YPD + DMSO
Sample 122

source_name: INO80-FRB, Nc2β-13myc, bar1∆


title: Control_ForRAPAA_repeat2

description: in DMSO


title: S3_FF

source_name: Metastatic Colorectal Tumour

value: Fresh Frozen


title: Mot1AA&Ino80AA_Rap_repeat1

description: in Rapamycin


title: Nc2aAA&Ino80AA_Rap_repeat1

description: in Rapamycin


title: RNA140128LC_200

source_name: Human breast tumor


title: S2_FFPE

value: FFPE


title: Mot1AA&Ino80AA_Rap_repeat2

description: in Rapamycin


title: Nc2bAA-Rap_repeat1

description: in Rapamycin


title: SW620_N1


title: RNA140128LC_199


title: Nc2aAA-Rap_repeat2

description: in Rapamycin


title: RNA140128LC_198


title: S2_FF


title: RNA140128LC_196


title: Ino80AA-Rap_repeat2

description: in Rapamycin


title: Nc2aAA-Rap_repeat1

description: in Rapamycin


title: RNA140128LC_197


title: S1_FF


title: Ino80AA-Rap_repeat1

description: in Rapamycin


title: YXY1005_DMSO_Input_replicate2

description:
YPD + DMSO
Sample 119

source_name: INO80-FRB, Mot1-13myc, bar1∆


title: S3_FFPE


title: S1_FFPE


title: Mot1AA_Rap_repeat2

description: in Rapamycin


title: Forsubtelomere_YXY1007_Input_sir3del_replicate2

description:
in YPD
Sample 117

source_name: INO80-FRB, Nc2β-13myc, sir3∆

growth_protocol:
Log phase cells were crosslinked with 1% formaldehyde for 45 minutes.
Yeast cells were grown in YPD to exponential phase at OD600 around 0.8-1.

extract_protocol:
Cell were lysed with glass beads in lysis buffer  and chromatin were extensively washed. chromatin was sonicated for 4 minutes with 30s on and 1 min off on a Biodisruptor. The supernatant from sonicated lysates were precleared with Protein A beads and ChIP was performed as described using commercial antibodies
Cell were lysed with glass beads in lysis buffer  and chromatin were extensively washed. chromatin was sonicated for 4 minutes with 30s on and 1 min off on a Biodisruptor. The supernatant from sonicated lysates were precleared with Protein A/G beads and ChIP was performed as described using commercial antibodies
Libraries were prepared with a KAPA LTP kit following the manufacturer’s protocol

treatment_protocol: Cells were crosslinked with 1% formaldehyde.


title: Forsubtelomere_YXY1007_IP_Nc2β_sir3del_replicate2

description:
in YPD
Sample 118


title: RNA140128LC_195

value: Lobular


title: 12-dpi-Control-Rep 3_Tech 2

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

data_processing:
The quality of raw data from each library was controlled by CLC Genomic Workbench version 7.5.1.  Raw data were stripped of adapters and reads with quality score above 0.05 and less than 2 ambiguous nucleotides were retained. Reads without 3’ adapters and also reads with less than 16 nt were discarded from the libraries. Clean data considered as mappable reads for further analysis.
Tab separated files with the read sequences and their counts were used as input file for homologous miRNA analysis CLC genomic workbench.
Genome_build: Aedes aegypti genome ( GCA_000004015.1) was used
Supplementary_files_format_and_content: Excel files

organism: Aedes aegypti

source_name: Homogenized Adult Mosquitoes, Non Infected (Control)

extract_protocol:
Total RNA from cells was isolated using QIAzol Lysis Reagent (Qiagen), and subsequently treated with DNase before being used for reverse transcription. The procedure of RNA extraction was based on the manufacturer’s instructions, except that the isopropanol precipitation step was performed at -80°C for overnight.
samples submitted to the Australia Genome Research Facility (AGRF) for Illumina small RNA sequencing.

treatment_protocol: To obtain RNA samples from PCV infections, 4 day old Ae. aegypti mosquitoes (Townsville, Australia strain) were injected with 102.3 virus/ml (106 TCID50/ml) in 200 nl of stock PCV diluted in Opti-MEM medium (Gibco, Invitrogen Corporation, Grand Island, NY) with 3% FBS without antibiotics or antimycotics. Control group mosquitoes were injected with the same growth medium without PCV. Mosquitoes were collected and stored at -80°C on days 2, 6 and 12 post-inoculation.

value: Townsville, Australia strain

value: Whole body

tag: developmental stage

value: adult


title: RNA140128LC_194

value: Breast tumor


title: YXY1006_DMSO_Input_replicate2

description:
YPD + DMSO
Sample 121


title: RNA140128LC_193


title: 12-dpi-Control-Rep 3_Tech 1


title: Forsubtelomere_YXY920_IP_Nc2β_WT_replicate2

description:
in YPD
Sample 116

source_name: INO80-FRB, Nc2β-13myc


title: 12-dpi-Control-Rep 2_Tech 2


title: 12-dpi-Control-Rep 2_Tech 1


title: Forsubtelomere_YXY920_Input_WT_replicate2

description:
in YPD
Sample 115


title: RNA140128LC_191


title: YXY1005_DMSO_IP_Mot1_replicate2

description:
YPD + DMSO
Sample 120


title: WT_Rap_repeat2

description: in Rapamycin

source_name: WT


title: 12-dpi-Control-Rep 1_Tech 2


title: Forsubtelomere_YXY968_IP_Mot1_sir3del_replicate2

description:
in YPD
Sample 114

source_name: INO80-FRB, MOT1-13myc, sir3∆


title: RNA140128LC_189

value: Ductal


title: WT_Rap_repeat1

description: in Rapamycin


title: RNA140128LC_188


title: Forsubtelomere_YXY968_IP_Arp5_sir3del_replicate2

description:
in YPD
Sample 113

value: Anti Arp5 antibody from Abcam (ab12099).


title: RNA140128LC_186

value: Whole human breast tumor


title: 12-dpi-Control-Rep 1_Tech 1


title: Forsubtelomere_YXY968_Input_sir3del_replicate2

description:
in YPD
Sample 112

value: MJE7 Background


title: 12-dpi-PCV-Rep 3_Tech 2

source_name: Homogenized Adult Mosquitoes, PCV infected


title: RNA140128LC_183


title: Mot1AA_Rap_repeat1

description: in Rapamycin


title: 12-dpi-PCV-Rep 3_Tech 1


title: 12-dpi-PCV-Rep 2_Tech 1


title: Forsubtelomere_YXY919_IP_Arp5_WT_replicate2

description:
in YPD
Sample 110

source_name: INO80-FRB, MOT1-13myc


title: RNA140128LC_178


title: nhp6a,bΔ_replicate2

description:
in YPD
Sample 75

data_processing:
For yeast mRNA-seq
Fastq files were used to map reads to yeast genome(saccer3) with TopHat v2.0.8 (for FPKM analysis, treat as single end)
Caclutate FPKM using accepted bam file from cuffdiff cuffdiff v2.0.2 for mRNA-Seq
mapped reads(sam file) were used to cacullate the mRNA level and log2 ratio of mutants vs WT using customed script
log2 ratio of mutants vs wt were used to plot with metagene profiles.
genome build: sacCer3

growth_protocol:
Overnight incubated yeast cells were diluted in YPD and grow to exponential phase.
Overnight incubated yeast cells were diluted in YPD and grow to exponential phase.

extract_protocol:
Total RNA was extracted with phenol, digested with DNase and further purified by Trizol
Total RNA was extracted with phenol, digested with DNase and further purified by Trizol
Libraries of mRNA were prepared with KAPA stranded mRNA-Seq Kits v2 following the manufacturer’s protocol

value: SEY6210 Background


title: RNA140128LC_182


title: Forsubtelomere_YXY919_Input_WT_replicate2

description:
in YPD
Sample 109


title: 12-dpi-PCV-Rep 2_Tech 2


title: Nc2bAA-Rap_replicatet2

description:
in YPD
Sample 73

growth_protocol:
Overnight incubated yeast cells were diluted in YPD and grow to exponential phase. Add  rapamycin to 8 ug/ml and treat for 24 hours, keep in log phase by dilution during treatment.
Overnight incubated yeast cells were diluted in YPD and grow to exponential phase.


title: RNA140128LC_175


title: 12-dpi-PCV-Rep 1_Tech 2


title: 12-dpi-PCV-Rep 1_Tech 1


title: 6-dpi-Control-Rep 3_Tech 2


title: WT_replicate2

description:
in YPD
Sample 74


title: RNA140128LC_177


title: RNA140128LC_174


title: 6-dpi-Control-Rep 3_Tech 1


title: YXY1077_RAP_IP_Ino80_TBPAA

description: YPD + RAP

data_processing:
Fastq files were used to map reads to yeast genome(saccer3) with or Bowtie 0.12.9
Mapped reads were counted and shuffled to similar reads.
Shuffled reads were used to calculate the p value and log2 ratio of Ip vs Input
log2 ratio of Ip vs input at significant windows were used to plot with metagene profiles or center with TSS or TTS
genome_build: = sacCer3

source_name: bar1∆, TBP-FRB, Ino80-13Myc

extract_protocol:
Samples were lysed with glass beads in lysis buffer, chromatin was collected by centrifugation, resuspended in lysis buffer and subjected to sonification. The supernatant from sonicated lysates were precleared with Protein A beads and ChIP was performed as described using commercial antibodies
Libraries were prepared with a KAPA LTP kit following the manufacturer’s protocol

value: yeast cells


title: MJE7_Rap_for_NC2baa_replicate2

description:
in YPD
Sample 72


title: RNA140128LC_171


title: RNA140128LC_170


title: YXY1076_RAP_IP_Nc2β_TBPAA

description: YPD + RAP

source_name: bar1∆, TBP-FRB, Nc2β-13Myc


title: 6-dpi-Control-Rep 2_Tech 1


title: 6-dpi-Control-Rep 1_Tech 2


title: Forsubtelomere_YXY919_IP_Mot1_WT_replicate2

description:
in YPD
Sample 111


title: RNA140128LC_163


title: RNA140128LC_181


title: YXY1076_RAP_Input_TBPAA

description: YPD + RAP


title: RNA140128LC_155

source_name: Prophylactic Mastectomy

value: Prophylactic Mastectomy


title: YXY1075_RAP_IP_Mot1_TBPAA

description: YPD + RAP

source_name: bar1∆, TBP-FRB, MOT1-13Myc


title: RNA140128LC_147

source_name: Human breast adjacent normal

value: Adjacent normal


title: RNA140128LC_145

source_name: Human Breast Normal

value: Normal Breast


title: 6-dpi-PCV-Rep 3_Tech 1


title: YXY1075_RAP_Input_TBPAA

description: YPD + RAP


title: YXY1008_DMSO_Input

description: YPD + DMSO

source_name: MOT1-FRB, Ino80-13myc, bar1∆


title: 6-dpi-PCV-Rep 2_Tech 1


title: RNA140128LC_144


title: YXY1006_DMSO_IP_Nc2β

description: YPD + DMSO

source_name: INO80-FRB, Nc2β-13myc, bar1∆

value: Anti Myc antibody from Abcam (ab32)


title: YXY1008_DMSO_IP_Ino80

description: YPD + DMSO


title: YXY1077_RAP_Input_TBPAA

description: YPD + RAP


title: 6-dpi-PCV-Rep 1_Tech 2


title: YXY1006_DMSO_Input

description: YPD + DMSO


title: RNA140128LC_142

source_name: Human breast tumor


title: 6-dpi-Control-Rep 1_Tech 1


title: RNA140128LC_149


title: 2-dpi-Control-Rep 3_Tech 2


title: RNA140128LC_130


title: YXY1005_DMSO_Input

description: YPD + DMSO

source_name: INO80-FRB, Mot1-13myc, bar1∆


title: RNA140128LC_139


title: 6-dpi-PCV-Rep 2_Tech 2


title: 6-dpi-Control-Rep 2_Tech 2


title: 2-dpi-Control-Rep 3_Tech 1


title: RNA140128LC_128


title: RNA140128LC_125

value: Metaplastic


title: Forsubtelomere_YXY1007_IP_Nc2β_sir3del

description: in YPD

source_name: INO80-FRB, Nc2β-13myc, sir3∆

growth_protocol: Yeast cells were grown in YPD to exponential phase at OD600 around 0.8-1.

extract_protocol:
Cell were lysed with glass beads in lysis buffer  and chromatin were extensively washed. chromatin was sonicated for 4 minutes with 30s on and 1 min off on a Biodisruptor. The supernatant from sonicated lysates were precleared with Protein A beads and ChIP was performed as described using commercial antibodies
Libraries were prepared with a KAPA LTP kit following the manufacturer’s protocol


title: 2-dpi-Control-Rep 2_Tech 2

source_name: Homogenized Adult Mosquitoes, Non Infected (Control)


title: 2-dpi-Control-Rep 2_Tech 1


title: Forsubtelomere_YXY1007_Input_sir3del

description: in YPD


title: Forsubtelomere_YXY920_IP_Nc2β_WT

description: in YPD

source_name: INO80-FRB, Nc2β-13myc


title: RNA140128LC_112


title: RNA140128LC_102

value: Ductal with prominent lobular features


title: 2-dpi-Control-Rep 1_Tech 1


title: Forsubtelomere_YXY920_Input_WT

description: in YPD


title: 2-dpi-Control-Rep 1_Tech 2


title: 6-dpi-PCV-Rep 1_Tech 1


title: Forsubtelomere_YXY968_IP_Arp5_sir3del

description: in YPD


title: 2-dpi-PCV-Rep 3_Tech 1


title: YXY1005_DMSO_IP_Mot1

description: YPD + DMSO


title: 2-dpi-PCV-Rep 2_Tech 2


title: BRUA inf

organism: Brucella abortus 544

source_name: Brucella 544_I

growth_protocol: Brucella abortus was routinely cultured overnight in Brucella broth (BD Biosciences, USA) at 37℃ in a gyratory shaker (Waver Digital Platform; VWR International, USA) at 10 × g.

extract_protocol:
Free-living or intracellular B. abortus were washed with PBS and then incubated in 500 µl of RNA-free water for 30 min at room temperature. One milliliter RNA protect Bacteria Reagent (Qiagen) was added directly to sample and incubated for 5 min at room temperature. After centrifugation at 5,000 x g, bacteria were dissolved in 1 ml total solution containing 850 µl RNase-free water (Qiagen), either 150 µl 1% sodium dodecyl sulfate (SDS) or 10% SDS, and 10 µl proteinase K (Promega). The sample was then incubated at 37oC for 1 h, followed by adding 200 µl Chloroform (Sigma). The total RNA was isolated using Qiagen RNeasy Mini “Bacterial” protocol (Qiagen). DNA was removed by using the “On-Column DNase Digestion” protocol.
The Ribo-Zero rRNA removal kit (Epicentre, USA) was used for ribosomal RNA depletion according to manufacturer’s instructions. Libraries for Illumina sequencing were made with the TruSeq Stranded mRNA sample prep kit (Illumina, USA) following the manufacturer’s protocol. RNA sequencing was performed on the Illumina HiSeq 2500 platform using single-end 50 bp sequencing.

treatment_protocol: Brucella abortus were isolated as follows. BMMs were washed three times with PBS, lysed using sterile distilled water and incubated at 37oC for 5 min. Adherent lysed macrophages were scraped, pelleted at 14,000 x g for 2 min, and the supernatant was removed. To enzymatically digest the macrophage DNA, the pellet was resuspended in a 1 ml solution containing 890 µl sterile water, 100 µl RQ1 DNase Reaction Buffer (Promega), 10 µl RQ1 RNase –free DNase 1 u/µl (Promega). The solution was incubated for 30 min at 37oC and then centrifuged at 8,000 x g for 2 min. The supernatant was removed and the bacteria were pelleted at the bottom.

value: Brucella abortus

value: 24 hours post-infection at 10 days


title: RNA150213LC_C4

source_name: No clinical information available

value: No clinical information available


title: Forsubtelomere_YXY968_IP_Mot1_sir3del

description: in YPD

source_name: INO80-FRB, MOT1-13myc, sir3∆


title: 6-dpi-PCV-Rep 3_Tech 2

source_name: Homogenized Adult Mosquitoes, PCV infected

value: Townsville, Australia strain

value: Whole body

value: adult


title: 2-dpi-PCV-Rep 3_Tech 2


title: BRUA con

source_name: Brucella 544_C


title: Forsubtelomere_YXY919_IP_Arp5_WT

description: in YPD

source_name: INO80-FRB, MOT1-13myc

value: Anti Arp5 antibody from Abcam (ab12099).


title: Forsubtelomere_YXY919_IP_Mot1_WT

description: in YPD


title: 2-dpi-PCV-Rep 2_Tech 1


title: 2-dpi-PCV-Rep 1_Tech 1


title: Forsubtelomere_YXY919_Input_WT

description: in YPD


title: Forsubtelomere_YXY968_Input_sir3del

description: in YPD


title: 2-dpi-PCV-Rep 1_Tech 2


title: HeLa_KO38_RA1

status: Public on Jul 07 2017

city: Houston

first: Yue

last: Lu

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to the human genome (hg19) using TopHat (version 2.0.10).
The number of fragments in each gene from the RefSeq database (downloaded from UCSC Genome Browser on July 17, 2015) was enumerated using htseq-count from the HTSeq software package (version 0.6.0).
Genome_build: hg19
Supplementary_files_format_and_content: Number of fragments in each gene

source_name: cervical cancer HeLa S3

growth_protocol: 106 fibroblast cells were cultured 24 to 48 hr or until 90% confluent. 2 x 106 cells were treated for different periods with 10 µM all-trans retinoic acid (RA) in dimethyl sulfoxide (DMSO) or with DMSO only as a control. HeLa S3 cells were cultured in RPMI (Thermo Fisher Scientific) media with 10% FBS and 1% penicillin/streptomycin solution. HeLa cell lines were treated with 1 µM RA in DMSO or with DMSO only as a control. The final concentration of DMSO was 0.01% in the cell culture. The fibroblast cells were harvested with a cell scraper, centrifuged (1500 rpm = 485 x g, for 5 min at 4 ºC) and washed once with PBS. The pellets were quick-frozen and stored at -80 ºC.

extract_protocol:
HeLa cells were pelleted by centrifugation. The fibroblast cells were harvested with a cell scraper, centrifuged (1500 rpm = 485 x g, for 5 min at 4 ºC) and washed once with PBS. The pellets were quick-frozen and stored at -80 ºC. RNA was extracted from pellets using a QIAGEN RNA isolation kit for a qPCR assay.
Libraries were prepared using the Illumina TruSeq stranded mRNA kit according to the manufacturer’s protocol, except that eight PCR amplification cycles were used.

tag: retionoic acid treatment

value: 1 micromolar, 7 hr

tag: xpa function

value: inactive


title: HeLa_KO38_RA3

treatment_protocol: 2 x 106 cells were treated for different periods with 10 µM all-trans retinoic acid (RA) in dimethyl sulfoxide (DMSO) or with DMSO only as a control. HeLa S3 cells were cultured in RPMI (Thermo Fisher Scientific) media with 10% FBS and 1% penicillin/streptomycin solution. HeLa cell lines were treated with 1 µM RA in DMSO or with DMSO only as a control. The final concentration of DMSO was 0.01% in the cell culture.


title: HeLa_KO38_DMSO3


title: HeLa_WT_RA2

value: active


title: HeLa_WT_DMSO3


title: HeLa_WT_RA_1


title: HeLa_KO38_RA2


title: HeLa_WT_DMSO1


title: HeLa_KO142_RA_3

value: partially active (6 aa deletion)


title: HeLa_KO38_DMSO2


title: HeLa_KO142_DMSO_3


title: XPA/XP2OS_RA_1

source_name: skin fibroblasts, SV40-immortalized

value: 10 micromolar, 7 hr

value: active, complemented with XPA gene


title: XPA/XP2OS_RA_2


title: XPA/XP2OS_DMSO_3


title: HeLa_WT_RA3


title: HeLa_WT_DMSO2


title: HeLa_WT_RA_3


title: HeLa_KO38_DMSO1


title: XPA/XP2OS_DMSO_1


title: HeLa_WT_DMSO_1


title: HeLa_WT_RA_2


title: HeLa_WT_DMSO_3


title: XP2OS_RA_3


title: XP2OS_DMSO_1


title: XPA/XP12RO_RA_3


title: HeLa_KO142_DMSO_2


title: HeLa_KO142_RA_1


title: HeLa_KO142_DMSO_1


title: XPA/XP2OS_RA_3


title: XPA/XP12RO_DMSO_3


title: RNA140128LC_166

tag: tissue

value: Breast tumor

tag: age

value: Ductal

value: Whole human breast tumor


title: XPA/XP2OS_DMSO_2


title: XPA/XP12RO_DMSO_2


title: XP2OS_RA_2


title: HeLa_WT_DMSO_2


title: XP2OS_RA_1


title: XP2OS_DMSO_3


title: XP12RO_RA_2


title: XPA/XP12RO_RA_2


title: HeLa_WT_RA1


title: XP12RO_RA_3


title: HeLa_KO142_RA_2


title: XPA/XP12RO_RA_1


title: XP2OS_DMSO_2


title: XP12RO_RA_1


title: XPA/XP12RO_DMSO_1


title: XP12RO_DMSO_3


title: XP12RO_DMSO_1


title: XP12RO_DMSO_2


title: B58_03_Rep1

city: Singapore

first: Tze Hau

last: Lam

address: 70 Biopolis Street

country: Singapore

institute: Procter and Gamble

data_processing:
Raw sequencing reads with 70% of the base positions having a Phred score of <20 were removed prior to alignment using the NGS QC Toolkit
The processed reads were then mapped to the hg19 human genome assembly using TopHat2. Reads mapping to genomic features in the GENCODE release 19 (GRCh37.p13) gene annotation were summarized using featureCounts program in the Subread package.
The DESeq2 was used to normalize the RNA-Seq libraries and regularized log transformation was applied to the normalized raw counts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include regularized log transformation values for each sample

source_name: B-LCLs

extract_protocol:
The quality  and concentration of the total RNA, extracted using the RNeasy Mini Kit, were measured by Agilent Bioanalyzer 2100 and only samples with a RIN value of >7.0 were selected for RNA-Seq. Prior to library preparation, ribosomal RNA was removed from the samples using the human Ribo-ZeroTM rRNA Removal Kits. Paired-end RNA-Seq libraries were generated using the Illumina TruSeq RNA library preparation kit v2.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The B-LCLs cultures were stimulated with 200nM of phorbol 12-myristate 13-acetate (PMA, Sigma) and 125nM of ionomycin. The cultures were then harvested after 6 hours of incubation at 37°C to activate the cells.

tag: haplotype


title: B58_02_Rep2


title: B58_03_Rep2


title: B08_02_Rep2


title: B46_03_Rep1


title: B58_01_Rep2


title: B58_01_Rep1


title: B58_02_Rep1


title: B46_03_Rep2


title: B46_02_Rep1


title: B46_01_Rep1


title: B46_01_Rep2


title: B08_02_Rep1


title: B08_01_Rep2


title: neurons duplicate 2

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description:
neurons
Sample name: Neuron-S2

data_processing:
Illumina Casava 1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v1.2.0 with default settings. Aligned reads were used to generate pileup for each base with Samtools v0.1.18.
Read counts for each refseq gene were summarized using custom built R scripts. The exons in all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted using customized R script and Bioconductor package "ShortRead".
Genome_build: mm9
Supplementary_files_format_and_content: Counts for each refseq genes

source_name: Cortex

extract_protocol:
Heterozygous Nestin-GFP mice were bred with homozygous DCX-mRFP mice to yield GFP/RFP double positive embryos. The cortices derived from the double positive embryos were dissociated by trituration in HBSS with 2mM of EDTA and 25 ug/ml of DNase I. Cells were washed once with HBSS and re-suspended in DMEM/F12. Fluorescence-activated cell sorting (FACS) was used to acquire neural progenitor cells (NPCs, green color) and daughtor neurons (double color). Total RNA was extracted using TRIzol.
Following Illumina's True-seq RNA-seq library prep kit

value: cortex

value: neurons

value: Embryonic day 15.5


title: B08_01_Rep1


title: Neural progenitor cells duplicate 2

description:
Neural progenitor cells
Sample name: NPC-S2

value: Neural progenitor cells


title: Neural progenitor cells duplicate 1

description:
Neural progenitor cells
Sample name: NPC-S1


title: 8006577911_WT_Dok3

first: Eric

last: Schadt

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description: wild type

data_processing:
Illumina Casava1.82 software used for basecalling.
Short reads in fastQ format are processed using RAPiD, which is a RNA-Seq analysis framework developed and maintained by the Technology Development group at Icahn Institute for Genomics and MultiScale Biology. .
RAPiD uses STAR to map the short reads to the  [ MOUSE: mm10 ] reference and resultant alignment map in BAM format is quantified for gene level expression using featureCounts of the subreads package. Detailed QC metrics are generated using the RNASeQC package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count number reads per gene for each Sample.

growth_protocol: mouse models

extract_protocol:
RNA was prepared using the KAPA Stranded RNA-Seq with RiboErase sample preparation kit (kapabiosystems) in accordance with the manufacturer’s instructions.
Briefly, 500ng of total RNA was ribo depleted, fragmented and went under first and second strand synthesis, A tailing, adapter ligation and PCR amplification (using 11 cycles).  Final libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems), Qubit Fluorometer (Life Technologies) and Agilent 2100 BioAnalyzer.
Samples were sequenced on an Illumina HiSeq2500 sequencer (v4 chemistry) using 1 x 100bp cycles.

treatment_protocol: For each mouse line for: Gpsm3 (3% DSS), Aif1 (3% DSS), Nckap1l (Hem1), Dock2 (3% DSS), Dok3 (3.5% DSS) DSS treatment for five days followed by water for 5 days, (7 days for Nckap1l).  Tissue was collected at Day 10 (Day 12 for Nckap1l (HEM1))

value: M

tag: genotype

value: WT


title: 8006577914_HO_Dok3

description: homozygous knockout

value: HO


title: 8006577895_WT_Dok3

description: wild type


title: 8006577907_HO_Dok3

description: homozygous knockout


title: 8006577909_WT_Dok3

description: wild type


title: 8006577908_HO_Dok3

description: homozygous knockout


title: neurons duplicate 1

description:
neurons
Sample name: Neuron-S1


title: B46_02_Rep2


title: 8006577894_WT_Dok3

description: wild type


title: 8006577891_HO_Dok3

description: homozygous knockout


title: 8006577896_WT_Dok3

description: wild type


title: 8006577799_WT_Dok3

description: wild type


title: 8006577881_WT_Dok3

description: wild type


title: 8006577884_HO_Dok3

description: homozygous knockout


title: 8006577883_HO_Dok3

description: homozygous knockout


title: 8006577890_HO_Dok3

description: homozygous knockout


title: 8006577888_HO_Dok3

description: homozygous knockout


title: 8006577797_HO_Dok3

description: homozygous knockout


title: 8006577796_HO_Dok3

description: homozygous knockout


title: 8006577794_WT_Dok3

description: wild type


title: 8006577787_HO_Dok3

description: homozygous knockout


title: 8006577793_WT_Dok3

description: wild type


title: 8006577789_HO_Dok3

description: homozygous knockout


title: 8006577913_HO_Dok3

description: homozygous knockout


title: 8006577786_HO_Dok3

description: homozygous knockout


title: 8006577889_WT_Dok3

description: wild type


title: 8006577783_WT_Dok3

description: wild type


title: 8006577798_HO_Dok3

description: homozygous knockout


title: 8006577770_WT_Dok3

description: wild type


title: 8006577777_HO_Dok3

description: homozygous knockout


title: 8006577776_HO_Dok3

description: homozygous knockout


title: 8006577782_HO_Dok3

description: homozygous knockout


title: 8006577795_HO_Dok3

description: homozygous knockout


title: 8006577785_HO_Dok3

description: homozygous knockout


title: 8006577781_HO_Dok3

description: homozygous knockout


title: 8006577766_WT_Dok3

description: wild type


title: 8006577772_HO_Dok3

description: homozygous knockout


title: 8006577761_WT_Dok3

description: wild type


title: 8006577791_HO_Dok3

description: homozygous knockout


title: 8006577882_WT_Dok3

description: wild type


title: 8006577765_WT_Dok3

description: wild type


title: 8006577764_HO_Dok3

description: homozygous knockout


title: 8006577762_HO_Dok3

description: homozygous knockout


title: 8006577746_WT_AIF1

description: wild type


title: 8006577744_WT_AIF1

description: wild type


title: 8006577760_HO_Dok3

description: homozygous knockout


title: 8006577742_HO_AIF1

description: homozygous knockout


title: 8006577737_WT_AIF1

description: wild type


title: 8006577734_WT_AIF1

description: wild type


title: 8006577741_HO_AIF1

description: homozygous knockout


title: 8006577735_HO_AIF1

description: homozygous knockout


title: 8006577739_HO_AIF1

description: homozygous knockout


title: 8006577778_WT_Dok3

description: wild type


title: 8006577773_WT_Dok3

description: wild type


title: 8006577731_HO_AIF1

description: homozygous knockout


title: 8006577729_WT_AIF1

description: wild type


title: 8006577730_WT_AIF1

description: wild type


title: 8006577728_WT_GPSM3

description: wild type


title: 8006577722_HO_GPSM3

description: homozygous knockout


title: 8006577721_WT_GPSM3

description: wild type


title: 8006577717_WT_GPSM3

description: wild type


title: 8006577715_HO_GPSM3

description: homozygous knockout


title: 8006577763_WT_Dok3

description: wild type


title: 8006577713_WT_GPSM3

description: wild type


title: 8006577711_WT_GPSM3

description: wild type


title: 8006577710_HO_GPSM3

description: homozygous knockout


title: 8006577707_WT_GPSM3

description: wild type


title: 8006577705_HO_GPSM3

description: homozygous knockout


title: 8006577719_HO_GPSM3

description: homozygous knockout


title: 8006577667_HO_GPSM3

description: homozygous knockout


title: 8006577687_WT_GPSM3

description: wild type


title: 8006577692_HO_GPSM3

description: homozygous knockout


title: 8006577686_HO_GPSM3

description: homozygous knockout


title: 8006577685_WT_GPSM3

description: wild type


title: 8006577665_WT_GPSM3

description: wild type


title: 8006577630_WT_AIF1

description: wild type


title: 8006577625_WT_AIF1

description: wild type


title: 178063675_WT_HEM1

description: wild type

value: F


title: 8006577631_WT_AIF1

description: wild type


title: 8006577664_HO_GPSM3

description: homozygous knockout


title: 8006577724_WT_GPSM3

description: wild type


title: 8006577626_HO_AIF1

description: homozygous knockout


title: 178063667_HO_HEM1

description: homozygous knockout


title: 178063646_HO_HEM1

description: homozygous knockout


title: 178063657_HO_HEM1

description: homozygous knockout


title: 178063632_HO_HEM1

description: homozygous knockout


title: 8006577706_HO_GPSM3

description: homozygous knockout


title: 178063659_WT_HEM1

description: wild type


title: 8006577767_WT_Dok3

description: wild type


title: TIM_PER_cDNA_night_Rep_1

city: Edmonton

first: Kirst

last: King-Jones

state: AB

address: 77 University Campus

department: Biological Sciences

country: Canada

institute: University of Alberta

description: This sample is of UAS-Tim-cDNA;UAS-Per-cDNA ring gland of ZT18-22 and 18-20 hours L3. It is the first of two biological replicates used in this experiment.

data_processing:
de-multiplexing with Novobarcode into 32 files
Arraystar 4.0 was used to align reads to Drosophila reference genome
paired reads were merged and two biological replicates were used to generate RPKM values for each condition
Arraystar followed by export to Excel and Access
Supplementary_files_format_and_content: provided as RPKMs in a separate worksheet of this Excel file

organism: Drosophila melanogaster

source_name: phm22_Tim-cDNA;Per-cDNA  ring gland ZT18-22 and 18-20 hours L3

growth_protocol: Drosophila larvae were reared in 12 hours light and 12 hours dark cycle on yeast paste at 25°C.

extract_protocol:
Total RNA was extracted using TRIzol and the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen). RNA quality and concentration was determined by analysis with a NanoDrop-1000 spectrophotometer and an Agilent 2100 bioanalyzer at the Molecular Biology Service Unit (University of Alberta, Edmonton, Canada).
Encore Complete RNA-Seq IL Multiplex System 1-8 (Part No. 0312) and Encore Complete RNA-Seq IL Multiplex System 9-16 (Part No. 0313) each provide eight unique barcoded adaptors for multiplex sequencing (NuGEN) were used to prep the library .

treatment_protocol: Genotypes: Samples 1-4:  phantom-Gal4/w1118 (control cross). Samples 5-6: phantom-Gal4/Tim-RNAi (ZT0-4). Samples 7-8: phantom-Gal4/Per-RNAi (ZT0-4). Samples 9-10: phantom-Gal4/Tim-RNAi (ZT18-22). Samples 11-12: phantom-Gal4/Per-RNAi(ZT18-22). Samples 13-14: phantom-Gal4/Tim-cDNA overexpression (ZT18-22). Samples 15-16: phantom-Gal4/Tim-cDNA; Per-cDNA overexpression (ZT18-22).

value: Tim, Per ovexpression

tag: phenotype

value: lethality percentage not determined, but cross results in normal-looking adults

value: third instar ring gland


title: 178063571_WT_AIF1

description: wild type


title: 178063570_WT_AIF1

description: wild type


title: 178063572_HO_AIF1

description: homozygous knockout


title: PER_RNAi_night_Rep_2

description: This sample is of Per-RNAi ring gland of ZT18-22 and 18-20 hours L3. It is the second of two biological replicates used in this experiment.

source_name: phm22_Per-RNAi  ring gland ZT18-22 and 18-20 hours L3

value: Per-RNAi

value: developmental arrest


title: 178063559_WT_AIF1

description: wild type


title: PER_RNAi_night_Rep_1

description: This sample is of Per-RNAi ring gland of ZT18-22 and 18-20 hours L3. It is the first of two biological replicates used in this experiment.


title: 178063558_WT_AIF1

description: wild type


title: TIM_RNAi_night_Rep_1

description: This sample is of Tim-RNAi ring gland of ZT18-22 and 18-20 hours L3. It is the first of two biological replicates used in this experiment.

source_name: phm22_Tim-RNAi  ring gland ZT18-22 and 18-20 hours L3

value: Tim-RNAi


title: 178063499_HO_HEM1

description: homozygous knockout


title: PER_RNAi_day_Rep_2

description: This sample is of Per-RNAi ring gland of ZT0-4 and 2-4 hours L3. It is the second of two biological replicates used in this experiment.

source_name: phm22_Per-RNAi  ring gland ZT0-4 and 2-4 hours L3


title: PER_RNAi_day_Rep_1

description: This sample is of Per-RNAi ring gland of ZT0-4 and 2-4 hours L3. It is the first of two biological replicates used in this experiment.


title: 178063497_WT_HEM1

description: wild type


title: 178063640_HO_HEM1

description: homozygous knockout


title: TIM_RNAi_day_Rep_1

description: This sample is of Tim-RNAi ring gland of ZT0-4 and 2-4 hours L3. It is the first of two biological replicates used in this experiment.

source_name: phm22_Tim-RNAi  ring gland ZT0-4 and 2-4 hours L3


title: TIM_PER_cDNA_night_Rep_2

description: This sample is of UAS-Tim-cDNA;UAS-Per-cDNA ring gland of ZT18-22 and 18-20 hours L3. It is the second of two biological replicates used in this experiment.


title: 178063496_HO_HEM1

description: homozygous knockout


title: TIM_RNAi_day_Rep_2

description: This sample is of Tim-RNAi ring gland of ZT0-4 and 2-4 hours L3. It is the second of two biological replicates used in this experiment.


title: TIM_cDNA_night_Rep_2

description: This sample is of UAS-Tim-cDNA ring gland of ZT18-22 and 18-20 hours L3. It is the second of two biological replicates used in this experiment.

source_name: phm22_Tim-cDNA  ring gland ZT18-22 and 18-20 hours L3

value: Tim overexpression

value: 50% embryonic and larval lethality, but otherwise normal-looking adults


title: control_night_Rep_1

description: This sample is of wild-type ring gland of ZT18-22 18-20 hours L3. It is the first of two wild-type biological replicates used in this experiment.

source_name: phm22_w1118  control ring gland ZT18-22 and 18-20 hours L3

value: control Gal4 driver crossed to wildtype

value: normal


title: TIM_cDNA_night_Rep_1

description: This sample is of UAS-Tim-cDNA ring gland of ZT18-22 and 18-20 hours L3. It is the first of two biological replicates used in this experiment.


title: 178063494_WT_HEM1

description: wild type


title: 178063493_HO_HEM1

description: homozygous knockout


title: 178063569_WT_AIF1

description: wild type


title: 178063492_HO_HEM1

description: homozygous knockout


title: control_day_Rep_2

description: This sample is of wild-type ring gland  ZT0-4 of 2-4 hours L3. It is the second of two wild-type biological replicates used in this experiment.

source_name: phm22_w1118 control ring gland ZT0-4 and 2-4 hours L3


title: control_day_Rep_1

description: This sample is of wild-type ring gland  ZT0-4 of 2-4 hours L3. It is the first of two wild-type biological replicates used in this experiment.


title: 178063491_WT_HEM1

description: wild type


title: TIM_RNAi_night_Rep_2

description: This sample is of Tim-RNAi ring gland of ZT18-22 and 18-20 hours L3. It is the second of two biological replicates used in this experiment.


title: 178063498_HO_HEM1

description: homozygous knockout


title: control_night_Rep_2

description: This sample is of wild-type ring gland of ZT18-22 18-20 hours L3. It is the second of two wild-type biological replicates used in this experiment.


title: 178063389_WT_GPSM3

description: wild type


title: 178063391_HO_GPSM3

description: homozygous knockout


title: 178063495_WT_HEM1

description: wild type


title: 8006577775_WT_Dok3

description: wild type


title: 178063380_HO_GPSM3

description: homozygous knockout


title: 178063374_HO_GPSM3

description: homozygous knockout


title: 178063379_WT_GPSM3

description: wild type


title: RNAseq-hPN-ZIKVPR-3

city: Atlanta

first: Peng

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

description: Illumina HiSeq3000

data_processing:
RNA-seq reads were aligned using tophat v2.0.8 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: RNAseq gene expression value in cufflink fpkm_tracking file format

source_name: hPN

extract_protocol:
RNA was extracted by Trizol.
RNA-seq libraries were constructed with Illumina True-seq kit

tag: virus infection


title: RNAseq-hNCC-ZIKVPR-1  [HiSeq 3000]

description: Illumina HiSeq3000

source_name: hNCC


title: RNAseq-hNCC-mock-2  [HiSeq 3000]

description: Illumina HiSeq3000

value: mock


title: 178063373_WT_GPSM3

description: wild type


title: RNAseq-hPN-ZIKVPR-4

description: Illumina HiSeq3000


title: 178063371_WT_GPSM3

description: wild type


title: 178063370_WT_GPSM3

description: wild type


title: 178063365_HO_GPSM3

description: homozygous knockout


title: 178063360_WT_GPSM3

description: wild type


title: 178063364_WT_GPSM3

description: wild type