title: dwil_dana_dyak_HD_f_r3.ERCC

description: ERCC SetB

tag: replicate


title: SMARTer CA2 LCM QIAGEN

status: Public on Jun 02 2017

type: SRA

city: Roanoke

first: Shannon

last: Farris

state: VA

address: 2 Riverside Circle

department: Fralin Biomedical Research Institute

country: USA

institute: Virginia Tech

description: NuGEN_vs_SMARTer_Exon_countMatrix.xlsx, NuGEN_vs_SMARTer_gene_countMatrix.xlsx

library_source: transcriptomic

data_processing:
Reads were trimmed using Sickle and only paired reads with a quality score >20 and a minimum length of 20 bp were aligned to the GENCODE (M9) gene models and the mm10 mouse genome assembly index using STAR (v 2.4.1d) with the recommended ENCODE RNAseq parameters.
Transcript abundance was quantified using FeatureCounts given GENCODE (M9) gene models.
Samples were normalized with DESeq2 using total read counts mapped to annotated exons.
Genome_build: mm10
Supplementary_files_format_and_content: excel files of DESeq2 normalized counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: hippocampal CA2 neurons

extract_protocol:
RNA was extracted using either the QIAGEN RNeasy® Micro kit (cat #74004) or the Picopure® RNA isolation kit (Thermo Fisher Scientific, cat #KIT0204) according to the manufacturer's instructions. All samples were subjected to on-column DNase-treatment (Qiagen, cat#79254).
Libraries were generating using either the NuGEN Ovation Universal RNA-Seq Systems 1-16 for Model Organisms (mouse, cat# 0348) or Clontech SMARTer Stranded RNA-Seq Kit (cat# 634837) with the Clontech RiboGone mammalian kit (cat# 634847) according to the manufacturer's instructions.

treatment_protocol: Naive mice were deeply anesthetized with Fatal Plus (50mg/kg) before decapitation and swift removal of the brain (<3 min). Brains were bisected in the sagittal plane and individually flash frozen in 22 x 22mm disposable cryomold (Polysciences, Inc.) filled with Tissue-Tek Optimal Cutting Temperature (O.C.T., Sakura Finetek) compound and submerged in isopentane cooled to -20°C in a dry ice and ethanol slurry.

tag: strain

value: Amigo2-GFP C57BL/6

tag: tissue

value: brain

tag: age

value: 6 weeks

tag: Sex

value: male

tag: rna extraction kit

value: QIAGEN

tag: library generation kit

value: Clontech


title: DM_48hr_Myod1_KO_H3K27ac

city: Guangzhou

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

country: China

institute: Southern Medical University

library_source: genomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads by ChIP-seq were mapped to mm9 genome using SOAP2 with parameters: -v 2 -r 0 -m 0 -p 20
Peaks were called using MACS2 (v2.1.0), a p-value of 10^-4 was used as the cutoff
Annotations of the peaks were perfomed using in-house programs against the RefSeq gene annotation. Overlapping analysis was performed using in-house programs and the maximum distance limitation was set to 1000bp.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files were generated by MACS, scores represent -10*log(p)

molecule: genomic DNA

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were grown in growth medium containing DMEM, 10% FBS and 1% pen/strep.

extract_protocol:
Chromatins from myoblasts and myotubes were isolated and sonicated to 100-300nt for immunoprecipitation with antibodies
ChIP-seq libraries were constructed closely according to the standard illumina pair-end ChIP-seq procedure
After the attachment of anchor sequences, fragments were PCR-amplified using Illumina primers.

treatment_protocol: C2C12 myoblasts were induced to differentiate by culturing in differentiation medium (DMEM, 2% horse serum and 1% pen/strep)

tag: cell line

tag: cell type

value: myoblasts

tag: developmental stage; time in differentiation medium

value: DM 48 hours

tag: antibody

value: H3K27ac (Abcam ab4729)


title: DM_48hr_WT_H3K27ac


title: dwil_dana_dyak_TX_f_r1.ERCC

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: ERCC SetA

data_processing:
De-multiplexed reads (Chastity > 0.6) were generated by Illumina CASAVA (v.1.8.2) as fastq files.  For the single-species samples (i.e., D. melanogaster genitalia samples), we provided the raw de-multiplexed fastq files without processing.  For the multi-species samples, we first made merged genome and annotation of appropriate Drosophila species plus corrected ERCC standards (Lee et al., Journal of Genomics, 2016, PMID 27512518).  Additionally, we added a four-letter prefix for each chromosome or scaffold in the merged genome or annotation (e.g., 2L => dmel_2L).  ERCC names were unchanged due to their specific prefix.  The de-multiplexed reads from the multi-species samples were then mapped to the appropriate merged genome and annotation using STAR (v2.4.2a) (Doblin et al., Bioinformatics, 2012, PMID 23104886) with default parameters.  We used an in-house python script to fetch the prefix of read names in the bam alignments, and obtained all uniquely-mapped and multi-hit (2-10 hits) reads (in bam format) that were mapped exclusively to a single species or exclusively to ERCC.  We converted the bam reads to fastq reads by BEDTools (2.25.0; bamtofastq) (Quinlan and Hall, 2010, Bioinformatics, PMID 20110278).  After this step, reads of each multi-species sample were split into five categories – species 1, species 2, species 3, ERCC, and leftover, which includes unmapped reads and reads mapped to multiple species (or multiple species plus ERCC).  For multi-species samples, the original fastq file can be restored by merging the reads of appropriate three species as well as the ERCC and leftover reads.
We provide both STAR (SRR5639* and SRR6181*) and HiSAT2 (SRR724*) fastq and associated matrices of raw gene-level read counts in this GEO entry. For STAR read count files, we used the FlyBase (FB) annotations (version 2017_03). For HiSAT2 read count files, we used both FB and updated (YO) annotations (data in Supplementary Files of this GEO). For the latter one, we also provide two extra columns in the expression matrix, showing the maximum exon-level Jaccard index overlap between our YO annotation gene IDs and FlyBase ones. In addition, we provided bigWig tracks for all samples (replicated merged), YO annotation files (in both gtf and gff3 format), ortholog look up table (among YO gene ID, FlyBase gene ID, and dmel gene), gene-level normalized read counts based on either YO or FlyBase annotation, and transcript-level transcripts per million (TPM) based on YO or FlyBase annotation.
Supplementary_files_format_and_content: counts

molecule: polyA RNA

organism: synthetic construct

source_name: ERCC that merged to the multi-species sample (Drosophila willistoni; Drosophila ananassae; Drosophila yakuba)

growth_protocol: D. melanogaster stocks were obtained from the Drosophila Stock Center (Bloomington IN, NIH P40OD018537, http://fly.bio.indiana.edu), and were reared at the NIH (Bethesda MD).  Fly food for D. melanogaster was a medium of water (8.5 L), agar (79 g), torumel yeast (275 g), cornmeal (520 g), granulated sugar (1,100 g), p-hydroxy-benzoic acid methyl ester (23.8 g), and 95% ethanol (91.8 mL) (LabExpress, Ann Arbor MI).  All non-melanogaster flies were reared and dissected at the Drosophila Species Stock Center (San Diego CA, NSF CSBR 1351502, https://stockcenter.ucsd.edu).  D. yakuba, D. ananassae, D. pseudoobscura, D. willistoni, and D. virilis were grown on a medium of de-ionized water (28 L), agar (300 g), soy flour (700 g), cornmeal (2,940 g), molasses (2,230 g), yeast (860 g), propionate (135 g), and nipogen (200 g) (https://stockcenter.ucsd.edu/info/food_cornmeal.php).  D. persimilis and D. mojavensis were grown on a medium of agar (85 g), yeast (165 g), methylparaben (13.4 g), blended bananas (825 g), syrup (570 g), liquid malt extract (180 g), and 100% ethanol (134 mL) (https://stockcenter.ucsd.edu/info/food_banana_Opuntia.php).  All flies were reared at 23-25 oC.

extract_protocol:
Flies were anesthetized using CO2, and all samples were dissected in phosphate buffered saline solution (PH 7.4, Life Technologies, Carlsbad CA) and transferred to 56 or 112 μL of RNAlater (Life Technologies, Carlsbad CA) in 96-well 1.5 mL plates at room temperature after being macerated with forceps.  Plates were stored at -80 oC at the NIH after dissection (melanogaster samples) or after dissection and shipping (non-melanogaster samples).  For RNA extraction, we added 20-30 1.0 mm glass beads (BioSpec Products, Bartlesville OK) to each sample and added RLT buffer from the RNeasy 96 kit (Qiagen, Valencia CA) to 712 μL (final volume).  We homogenized the samples three times for 60 seconds each with a mini-beadbeater (Biospec Products, Bartlesville OK).  Extraction of total RNA was performed using the RNeasy 96 kit (spin version), except that we used 712 μL of 70% ethanol due to the increased volumes of RNAlater/RLT mixture.  RNA was quantified using Quant-iT RiboGreen (Life Technologies, Carlsbad CA).  We spot checked RNA integrity by capillary electrophoresis on a TapeStation 2200 (Agilent Technologies, Santa Clara CA) and found that the rRNA bands were distinct.  We used 33 ng aliquots of RNA of three genetically distant species for each library, except for thorax, where we used 17 ng due to lower yield.  The mixing of RNA was performed using a pipetting robot (Andrew Alliance, Vernier CH).  RNA from D. melanogaster genitalia was not mixed with tissues of the other species.
We used 100 ng of total RNA as input (except thorax samples: 50 ng), and followed the TruSeq PolyA+ stranded mRNA kit protocol with half volume reactions (Illumina, San Diego CA).  For each sample, we also added 10 pg Standard Reference Material 2374 beta (Pool 78A or 78B) ERCC spike-ins (Lee et al., Journal of Genomics, 2016, PMID 27512518) to the Fragment-Prime-Finish Mix during the mRNA fragmentation step.  We used 96-plex molecular barcoding (Kozarewa and Turner, Methods in Molecular Biology, 2011, PMID 21431778) from the Illumina TruSeq kit for all samples.  Libraries were quantified with Quant-iT PicoGreen (Life Technologies, Carlsbad CA).  For each sample, we conducted RNA-seq for the three libraries with the highest DNA concentration out of four libraries.  The quality (i.e., no overt primer dimers or low complexity) of all selected libraries were confirmed by capillary electrophoresis on a TapeStation 2200 (Agilent Technologies, Santa Clara CA).  We performed single-end 76 bp PolyA+ sequencing on the HiSeq2000 Sequencing System (Illumina, San Diego CA).

tag: flybase species id

value: not applicable

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: illumina barcode

value: CGGCTATG-GGCTCTGA

tag: plate and well id

tag: ercc infomation

value: ERCC SetA


title: dwil_dana_dyak_HD_m_r1.ERCC

description: ERCC SetA

tag: tissue

tag: replicate

value: CGGCTATG-ATAGAGGC


title: DM_48hr_H3_KO_H3K27ac


title: Parental cells

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

data_processing:
Illumina Casava1.7 software (illumina)  used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg9 whole genome using  TopHat.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated. Differential expression was calculated at a significance of p<0.05 after Benjamini and Hochberg correction using a null model.
Genome_build: hg9
Supplementary_files_format_and_content: TXT file (File1 Vasu_Normalized RPKM values_ RNAseq_Agus .txt) include RPKM values for each Sample.

organism: Homo sapiens

source_name: cell line

growth_protocol: The NSCLC cell lines HCC827 and H3255 were grown in DMEM media (Invitrogen) containing 1% of dialyzed fetal bovine serum (Invitrogen) and 13C-lysine (100 mg/L) or 12C -lysine (100 mg/L) for six passages according the standard SILAC protocol. Incorporation of 13C-lysine exceeded 95% of the total protein lysine content. Debris were removed by centrifugation at 5,000 x g and then by filtration through a 0.22-μm filter.

extract_protocol: RNA extracted from cells was polyA+ labelled and used to generate libraries  following the manufacturer’s protocols (Illumina).  The modified cDNA molecules were subjected to sequencing by Illumina Hiseq 2000 system

treatment_protocol: HCC827 cells were co-cultured in 10 nM gefitinib for 1 month. The concentration of gefitinib was increased threefold every month. At 1 micro M gefitinib, the cells maintained growth with kinetics equal to that of the parental line. Three individual colonies from the HCC827

value: Parental HCC827 cells


title: dwil_dana_dyak_HD_f_r1.ERCC

description: ERCC SetA

tag: Sex


title: dwil_dana_dyak_GO_m_r3.ERCC

description: ERCC SetB

value: AGCGATAG-TAATCTTA

value: ERCC SetB


title: DM_48hr_H34_KO_H3K27ac


title: DM_48hr_H23_KO_H3K27ac


title: dwil_dana_dyak_GO_m_r2.ERCC

description: ERCC SetA

value: TCCGCGAA-TAATCTTA


title: DM_48hr_H1_KO_H3K27ac


title: dwil_dana_dyak_GO_m_r1.ERCC

description: ERCC SetA

value: CGGCTATG-TAATCTTA


title: dwil_dana_dyak_GO_f_r3.ERCC

description: ERCC SetB


title: NuGEN CA2 LCM Pico

tag: strain

value: Amigo2-GFP C57BL/6

value: brain

tag: age

tag: rna extraction kit

value: PicoPure

value: NuGEN


title: dwil_dana_dyak_GO_f_r2.ERCC

description: ERCC SetB

value: TCTCGCGC-TAATCTTA


title: DM_48hr_CRISPR_CTRL_H3K27ac

tag: cell line

tag: cell type

value: myoblasts


title: dwil_dana_dyak_WB_m_r1.ERCC

description: ERCC SetA

value: CGGCTATG-TATAGCCT


title: orgR_dmoj_dper_WB_m_r3.leftover

description: mixed-species [D. melanogaster (Oregon-R), D. mojavensis, and D. persimilis] RNA preparation

organism:
Drosophila melanogaster
Drosophila mojavensis
Drosophila persimilis

source_name: whole body

value: adult

value: whole body

value: Male

value: GAGATTCC-TATAGCCT

value: without ERCC


title: dwil_dana_dyak_DG_m_r3.ERCC

description: ERCC SetB

value: not applicable

value: AGCGATAG-GTACTGAC


title: dwil_dana_dyak_HD_f_r2.ERCC

description: ERCC SetA

value: TCCGCGAA-ATAGAGGC

value: ERCC SetA


title: dwil_dana_dyak_DG_m_r2.ERCC

description: ERCC SetB

value: TCTCGCGC-GTACTGAC

value: ERCC SetB


title: orgR_dmoj_dper_WB_f_r3.leftover

value: Female

value: TAATGCGC-TATAGCCT


title: dwil_dana_dyak_RE_f_r1.ERCC

description: ERCC SetA

value: CGGCTATG-CAGGACGT


title: dwil_dana_dyak_DG_f_r3.ERCC

description: ERCC SetB


title: orgR_dmoj_dper_WB_f_r2.leftover

value: CTGAAGCT-TATAGCCT


title: dwil_dana_dyak_AC_m_r3.ERCC

description: ERCC SetB

value: AGCGATAG-AGGCGAAG


title: dwil_dana_dyak_DG_f_r2.ERCC

description: ERCC SetB


title: orgR_dmoj_dper_WB_f_r1.leftover

value: ATTCAGAA-TATAGCCT


title: dwil_dana_dyak_DG_f_r1.ERCC

description: ERCC SetA

value: CGGCTATG-GTACTGAC


title: dwil_dana_dyak_AC_m_r2.ERCC

description: ERCC SetA

value: TCCGCGAA-AGGCGAAG


title: orgR_dmoj_dper_WB_m_r2.leftover

value: adult

value: whole body

value: Male

value: TCCGGAGA-TATAGCCT


title: orgR_dmoj_dper_TX_m_r3.leftover

source_name: thorax without digestive system

value: thorax without digestive system

value: GAGATTCC-CCTATCCT

value: without ERCC


title: dwil_dana_dyak_GO_f_r1.ERCC

description: ERCC SetA

value: not applicable

value: CGGCTATG-TAATCTTA

value: ERCC SetA


title: dwil_dana_dyak_AC_f_r3.ERCC

description: ERCC SetB

value: ERCC SetB


title: orgR_dmoj_dper_TX_m_r2.leftover

value: CGCTCATT-CCTATCCT


title: dwil_dana_dyak_AC_m_r1.ERCC

description: ERCC SetA

value: CGGCTATG-AGGCGAAG


title: orgR_dmoj_dper_TX_f_r3.leftover

value: Female

value: TAATGCGC-CCTATCCT


title: orgR_dmoj_dper_TX_m_r1.leftover

value: TCCGGAGA-CCTATCCT


title: dwil_dana_dyak_AC_f_r1.ERCC

description: ERCC SetA


title: dwil_dana_dyak_AC_f_r2.ERCC

description: ERCC SetA

value: TCCGCGAA-AGGCGAAG


title: orgR_dmoj_dper_WB_m_r1.leftover

value: adult

value: ATTACTCG-TATAGCCT


title: dwil_dana_dyak_DG_m_r1.ERCC

description: ERCC SetA

value: CGGCTATG-GTACTGAC


title: orgR_dmoj_dper_RE_m_r3.leftover

source_name: reproductive system without gonad and genitalia; reproductive system without gonad

value: Male

value: GAGATTCC-TAATCTTA


title: orgR_dmoj_dper_TX_f_r1.leftover

value: thorax without digestive system

value: ATTCAGAA-CCTATCCT


title: orgR_dmoj_dper_RE_m_r2.leftover

value: reproductive system without gonad and genitalia; reproductive system without gonad

value: CGCTCATT-TAATCTTA

value: without ERCC


title: orgR_dmoj_dper_RE_m_r1.leftover

value: ATTACTCG-TAATCTTA


title: dvir_WB_m_r2

description: mixed-species [D. melanogaster (w1118), D. pseudoobscura, and D. virilis] RNA preparation

organism: Drosophila virilis

value: whole body

value: TCCGGAGA-TATAGCCT


title: orgR_dmoj_dper_TX_f_r2.leftover

value: Female

value: CTGAAGCT-CCTATCCT


title: dvir_WB_m_r1


title: orgR_dmoj_dper_RE_f_r3.leftover

value: TAATGCGC-TAATCTTA


title: orgR_dmoj_dper_RE_f_r2.leftover

value: GAATTCGT-TAATCTTA


title: dvir_WB_f_r3

value: adult

value: TAATGCGC-TATAGCCT


title: orgR_dmoj_dper_RE_f_r1.leftover

value: ATTCAGAA-TAATCTTA


title: dvir_WB_f_r1

value: ATTCAGAA-TATAGCCT


title: orgR_dmoj_dper_HD_m_r3.leftover

source_name: head

value: head

value: Male

value: GAGATTCC-ATAGAGGC


title: dvir_TX_m_r3

value: thorax without digestive system

value: GAGATTCC-CCTATCCT


title: dvir_TX_m_r2

value: CGCTCATT-CCTATCCT

value: without ERCC


title: orgR_dmoj_dper_HD_m_r2.leftover

value: CGCTCATT-ATAGAGGC


title: dvir_WB_f_r2

value: whole body

value: GAATTCGT-TATAGCCT


title: dvir_WB_m_r3

value: CGCTCATT-TATAGCCT


title: orgR_dmoj_dper_HD_f_r3.leftover

value: Female

value: CTGAAGCT-ATAGAGGC


title: orgR_dmoj_dper_HD_f_r2.leftover

value: adult

value: GAATTCGT-ATAGAGGC


title: dvir_TX_m_r1

value: ATTACTCG-CCTATCCT


title: dvir_TX_f_r3

value: TAATGCGC-CCTATCCT


title: orgR_dmoj_dper_GO_m_r3.leftover

source_name: gonad

value: gonad

value: GAGATTCC-AGGCGAAG


title: orgR_dmoj_dper_HD_f_r1.leftover

value: head

value: ATTCAGAA-ATAGAGGC


title: w1118_dpse_dvir_WB_m_r3.leftover

organism:
Drosophila melanogaster
Drosophila pseudoobscura
Drosophila virilis

value: Male


title: dvir_TX_f_r2

value: thorax without digestive system

value: CTGAAGCT-CCTATCCT


title: w1118_dpse_dvir_WB_m_r2.leftover

value: TCCGGAGA-TATAGCCT

value: without ERCC


title: dvir_RE_m_r3

source_name: reproductive system without gonad

value: reproductive system without gonad

value: CGCTCATT-TAATCTTA


title: orgR_dmoj_dper_GO_m_r2.leftover

value: CGCTCATT-AGGCGAAG


title: orgR_dmoj_dper_GO_m_r1.leftover

value: TCCGGAGA-AGGCGAAG


title: w1118_dpse_dvir_WB_f_r3.leftover

value: adult

value: whole body

value: Female

value: TAATGCGC-TATAGCCT


title: w1118_dpse_dvir_WB_f_r2.leftover

value: GAATTCGT-TATAGCCT


title: dvir_RE_m_r2

value: TCCGGAGA-TAATCTTA


title: dvir_RE_m_r1

value: ATTACTCG-TAATCTTA


title: orgR_dmoj_dper_GO_f_r3.leftover

value: gonad

value: TAATGCGC-AGGCGAAG


title: orgR_dmoj_dper_HD_m_r1.leftover

value: head

value: Male

value: ATTACTCG-ATAGAGGC


title: w1118_dpse_dvir_TX_m_r1.leftover

value: thorax without digestive system

value: ATTACTCG-CCTATCCT

value: without ERCC


title: orgR_dmoj_dper_GO_f_r1.leftover

value: ATTCAGAA-AGGCGAAG


title: w1118_dpse_dvir_TX_f_r3.leftover

value: TAATGCGC-CCTATCCT


title: dvir_RE_f_r3

value: adult

value: reproductive system without gonad

value: TAATGCGC-TAATCTTA


title: dvir_RE_f_r2

value: Female

value: CTGAAGCT-TAATCTTA


title: dvir_RE_f_r1

value: ATTCAGAA-TAATCTTA


title: w1118_dpse_dvir_TX_f_r1.leftover

value: GAATTCGT-CCTATCCT


title: w1118_dpse_dvir_RE_m_r2.leftover

value: reproductive system without gonad and genitalia; reproductive system without gonad

value: TCCGGAGA-TAATCTTA


title: orgR_dmoj_dper_DG_m_r3.leftover

source_name: digestive plus excretory system

value: digestive plus excretory system

value: GAGATTCC-GTACTGAC


title: dvir_TX_f_r1


title: w1118_dpse_dvir_WB_m_r1.leftover

value: whole body

value: Male

value: ATTACTCG-TATAGCCT


title: w1118_dpse_dvir_RE_m_r1.leftover

value: ATTACTCG-TAATCTTA

value: without ERCC


title: orgR_dmoj_dper_DG_m_r2.leftover

value: CGCTCATT-GTACTGAC


title: orgR_dmoj_dper_DG_m_r1.leftover

value: adult

value: TCCGGAGA-GTACTGAC


title: w1118_dpse_dvir_RE_f_r2.leftover


title: dvir_HD_m_r2

value: head

value: CGCTCATT-ATAGAGGC


title: w1118_dpse_dvir_WB_f_r1.leftover

value: Female

value: ATTCAGAA-TATAGCCT


title: orgR_dmoj_dper_GO_f_r2.leftover

value: gonad

value: GAATTCGT-AGGCGAAG


title: w1118_dpse_dvir_HD_m_r3.leftover

value: GAGATTCC-ATAGAGGC


title: w1118_dpse_dvir_RE_f_r3.leftover

value: reproductive system without gonad and genitalia; reproductive system without gonad

value: TAATGCGC-TAATCTTA


title: w1118_dpse_dvir_TX_m_r3.leftover

value: thorax without digestive system

value: GAGATTCC-CCTATCCT


title: w1118_dpse_dvir_TX_m_r2.leftover

value: Male

value: CGCTCATT-CCTATCCT


title: orgR_dmoj_dper_DG_f_r3.leftover

value: digestive plus excretory system

value: TAATGCGC-GTACTGAC

value: without ERCC


title: w1118_dpse_dvir_TX_f_r2.leftover

value: adult

value: CTGAAGCT-CCTATCCT


title: w1118_dpse_dvir_HD_m_r2.leftover

value: head

value: CGCTCATT-ATAGAGGC


title: dvir_HD_m_r1

value: TCCGGAGA-ATAGAGGC


title: w1118_dpse_dvir_RE_f_r1.leftover

value: Female

value: ATTCAGAA-TAATCTTA


title: w1118_dpse_dvir_HD_m_r1.leftover


title: orgR_dmoj_dper_DG_f_r2.leftover

value: GAATTCGT-GTACTGAC


title: w1118_dpse_dvir_HD_f_r3.leftover

value: TAATGCGC-ATAGAGGC


title: orgR_dmoj_dper_DG_f_r1.leftover

value: ATTCAGAA-GTACTGAC


title: w1118_dpse_dvir_HD_f_r1.leftover

value: ATTCAGAA-ATAGAGGC


title: w1118_dpse_dvir_HD_f_r2.leftover

value: CTGAAGCT-ATAGAGGC


title: dvir_HD_f_r2


title: w1118_dpse_dvir_GO_m_r2.leftover

value: gonad

value: Male

value: CGCTCATT-AGGCGAAG


title: orgR_dmoj_dper_AC_m_r3.leftover

source_name: abdomen without digestive or reproductive system

value: GAGATTCC-GGCTCTGA


title: w1118_dpse_dvir_GO_m_r1.leftover

value: TCCGGAGA-AGGCGAAG

value: without ERCC


title: w1118_dpse_dvir_GO_f_r3.leftover

value: adult

value: TAATGCGC-AGGCGAAG


title: w1118_dpse_dvir_GO_f_r2.leftover

value: CTGAAGCT-AGGCGAAG


title: orgR_dmoj_dper_AC_m_r1.leftover

value: abdomen without digestive or reproductive system

value: ATTACTCG-GGCTCTGA


title: dvir_HD_f_r1

value: head

value: Female


title: w1118_dpse_dvir_DG_m_r3.leftover

value: digestive plus excretory system

value: CGCTCATT-GTACTGAC


title: orgR_dmoj_dper_AC_f_r3.leftover

value: TAATGCGC-GGCTCTGA


title: w1118_dpse_dvir_GO_f_r1.leftover

value: ATTCAGAA-AGGCGAAG


title: dvir_HD_f_r3

value: TAATGCGC-ATAGAGGC


title: orgR_dmoj_dper_AC_f_r2.leftover

value: CTGAAGCT-GGCTCTGA


title: dvir_GO_f_r3

value: gonad


title: dvir_GO_m_r1

value: Male


title: w1118_dpse_dvir_DG_m_r1.leftover

value: ATTACTCG-GTACTGAC


title: orgR_dmoj_dper_AC_f_r1.leftover

value: ATTCAGAA-GGCTCTGA

value: without ERCC


title: w1118_dpse_dvir_DG_f_r2.leftover

value: adult

value: CTGAAGCT-GTACTGAC


title: w1118_dpse_dvir_DG_f_r3.leftover

value: TAATGCGC-GTACTGAC


title: w1118_dpse_dvir_GO_m_r3.leftover

value: GAGATTCC-AGGCGAAG


title: dvir_GO_f_r2

value: CTGAAGCT-AGGCGAAG


title: w1118_dpse_dvir_DG_f_r1.leftover

value: Female

value: GAATTCGT-GTACTGAC


title: w1118_dpse_dvir_AC_m_r3.leftover

value: abdomen without digestive or reproductive system

value: GAGATTCC-GGCTCTGA


title: dwil_dana_dyak_WB_m_r3.leftover

description: mixed-species (D. willistoni, D. ananassae, and D. yakuba) RNA preparation

organism:
Drosophila ananassae
Drosophila yakuba
Drosophila willistoni

value: whole body

value: TCTCGCGC-TATAGCCT


title: dvir_GO_f_r1

value: ATTCAGAA-AGGCGAAG


title: w1118_dpse_dvir_AC_m_r2.leftover

value: CGCTCATT-GGCTCTGA


title: orgR_dmoj_dper_AC_m_r2.leftover

value: Male


title: dvir_GO_m_r2

value: gonad

value: CGCTCATT-AGGCGAAG


title: w1118_dpse_dvir_AC_m_r1.leftover

value: ATTACTCG-GGCTCTGA

value: without ERCC


title: dwil_dana_dyak_WB_m_r2.leftover

value: adult

value: TCCGCGAA-TATAGCCT


title: dvir_DG_m_r3

value: digestive plus excretory system

value: CGCTCATT-GTACTGAC


title: w1118_dpse_dvir_DG_m_r2.leftover

value: TCCGGAGA-GTACTGAC


title: w1118_dpse_dvir_AC_f_r2.leftover

value: Female

value: GAATTCGT-GGCTCTGA


title: w1118_dpse_dvir_AC_f_r3.leftover

value: abdomen without digestive or reproductive system

value: CTGAAGCT-GGCTCTGA


title: w1118_dpse_dvir_AC_f_r1.leftover

value: ATTCAGAA-GGCTCTGA


title: dwil_dana_dyak_WB_m_r1.leftover

value: whole body

value: CGGCTATG-TATAGCCT


title: dwil_WB_m_r3

organism: Drosophila willistoni

value: Male

value: TCTCGCGC-TATAGCCT


title: dwil_dana_dyak_WB_f_r3.leftover

value: AGCGATAG-TATAGCCT


title: dvir_DG_m_r1

value: ATTACTCG-GTACTGAC


title: w1118_dpse_dvir_RE_m_r3.leftover

value: reproductive system without gonad and genitalia; reproductive system without gonad

value: CGCTCATT-TAATCTTA

value: without ERCC


title: dvir_DG_m_r2

value: adult

value: digestive plus excretory system


title: dwil_WB_m_r1


title: dvir_HD_m_r3

value: head

value: GAGATTCC-ATAGAGGC


title: dwil_dana_dyak_WB_f_r2.leftover

value: Female

value: TCCGCGAA-TATAGCCT


title: dwil_WB_f_r3


title: dwil_dana_dyak_WB_f_r1.leftover


title: dvir_DG_f_r3

value: TAATGCGC-GTACTGAC


title: dwil_WB_f_r2


title: dvir_DG_f_r2

value: CTGAAGCT-GTACTGAC


title: dwil_dana_dyak_TX_m_r3.leftover

value: thorax without digestive system

value: AGCGATAG-GGCTCTGA


title: dwil_TX_m_r3

value: Male


title: dwil_WB_f_r1

value: whole body

value: CGGCTATG-TATAGCCT


title: dvir_DG_f_r1

value: GAATTCGT-GTACTGAC


title: dvir_GO_m_r3

value: gonad

value: GAGATTCC-AGGCGAAG


title: dwil_TX_m_r2

value: TCTCGCGC-GGCTCTGA

value: without ERCC


title: dwil_TX_m_r1

value: adult

value: CGGCTATG-GGCTCTGA


title: dwil_dana_dyak_TX_m_r2.leftover


title: dwil_TX_f_r3


title: dwil_dana_dyak_TX_m_r1.leftover


title: dwil_dana_dyak_TX_f_r3.leftover


title: dvir_AC_m_r2

value: abdomen without digestive or reproductive system

value: CGCTCATT-GGCTCTGA


title: dwil_TX_f_r2

value: Female

value: TCCGCGAA-GGCTCTGA


title: dwil_TX_f_r1


title: dwil_WB_m_r2

value: TCCGCGAA-TATAGCCT


title: dwil_dana_dyak_TX_f_r2.leftover

value: thorax without digestive system


title: dwil_RE_m_r2

value: reproductive system without gonad

value: TCTCGCGC-CAGGACGT


title: dwil_RE_m_r1

value: Male

value: TCCGCGAA-CAGGACGT


title: dwil_RE_m_r3

value: AGCGATAG-CAGGACGT


title: dvir_AC_m_r1

value: ATTACTCG-GGCTCTGA


title: dvir_AC_f_r3

value: CTGAAGCT-GGCTCTGA


title: dwil_RE_f_r3


title: dwil_RE_f_r1

value: CGGCTATG-CAGGACGT


title: dwil_HD_m_r3

value: head

value: AGCGATAG-ATAGAGGC

value: without ERCC


title: dvir_AC_f_r1

value: adult

value: abdomen without digestive or reproductive system

value: ATTCAGAA-GGCTCTGA


title: dwil_dana_dyak_TX_f_r1.leftover

value: Female

value: CGGCTATG-GGCTCTGA


title: dwil_HD_m_r2

value: TCCGCGAA-ATAGAGGC


title: dwil_RE_f_r2

value: reproductive system without gonad


title: dvir_AC_f_r2

value: GAATTCGT-GGCTCTGA


title: dwil_HD_f_r3


title: dwil_dana_dyak_RE_m_r1.leftover

value: Male


title: w1118_WB_m_r3

organism: Drosophila melanogaster

value: whole body

value: CGCTCATT-TATAGCCT


title: dvir_AC_m_r3

value: GAGATTCC-GGCTCTGA


title: dwil_dana_dyak_RE_m_r3.leftover

value: AGCGATAG-CAGGACGT


title: dwil_HD_m_r1

value: CGGCTATG-ATAGAGGC


title: dwil_HD_f_r2

value: head


title: dwil_dana_dyak_RE_m_r2.leftover

value: TCTCGCGC-CAGGACGT


title: w1118_WB_m_r2

value: TCCGGAGA-TATAGCCT

value: without ERCC


title: dwil_GO_m_r3

value: adult

value: gonad

value: AGCGATAG-TAATCTTA


title: dwil_HD_f_r1

value: Female


title: dwil_dana_dyak_RE_f_r3.leftover


title: dwil_GO_m_r1

value: CGGCTATG-TAATCTTA


title: w1118_WB_f_r3

value: TAATGCGC-TATAGCCT


title: w1118_WB_m_r1

value: ATTACTCG-TATAGCCT


title: dwil_dana_dyak_RE_f_r1.leftover

value: reproductive system without gonad

value: CGGCTATG-CAGGACGT


title: dwil_GO_f_r2

value: TCTCGCGC-TAATCTTA


title: dwil_GO_f_r3


title: dwil_dana_dyak_HD_m_r3.leftover

value: Male

value: AGCGATAG-ATAGAGGC


title: w1118_WB_f_r2

value: whole body

value: GAATTCGT-TATAGCCT


title: dwil_dana_dyak_HD_m_r1.leftover

value: head

value: CGGCTATG-ATAGAGGC


title: w1118_WB_f_r1

value: ATTCAGAA-TATAGCCT

value: without ERCC


title: dwil_DG_f_r3

value: adult

value: digestive plus excretory system

value: AGCGATAG-GTACTGAC


title: dwil_DG_m_r1

value: CGGCTATG-GTACTGAC


title: w1118_TX_m_r3

value: thorax without digestive system

value: GAGATTCC-CCTATCCT


title: dwil_DG_f_r2

value: Female

value: TCTCGCGC-GTACTGAC


title: dwil_dana_dyak_HD_f_r3.leftover


title: dwil_DG_f_r1


title: dwil_AC_m_r3

value: abdomen without digestive or reproductive system

value: AGCGATAG-AGGCGAAG


title: dwil_AC_m_r2

value: Male

value: TCCGCGAA-AGGCGAAG


title: dwil_AC_m_r1

value: CGGCTATG-AGGCGAAG


title: dwil_GO_m_r2

value: gonad

value: TCCGCGAA-TAATCTTA


title: dwil_dana_dyak_RE_f_r2.leftover

value: reproductive system without gonad

value: TCTCGCGC-CAGGACGT


title: w1118_TX_f_r3

value: adult

value: TAATGCGC-CCTATCCT

value: without ERCC


title: dwil_dana_dyak_HD_f_r2.leftover

value: head

value: TCCGCGAA-ATAGAGGC


title: dwil_dana_dyak_HD_f_r1.leftover

value: CGGCTATG-ATAGAGGC


title: dwil_AC_f_r2

value: Female


title: w1118_TX_f_r2

value: thorax without digestive system

value: CTGAAGCT-CCTATCCT


title: dwil_dana_dyak_GO_m_r3.leftover

value: AGCGATAG-TAATCTTA


title: dwil_AC_f_r1

value: abdomen without digestive or reproductive system


title: dwil_GO_f_r1

value: CGGCTATG-TAATCTTA


title: w1118_TX_m_r1

value: Male

value: ATTACTCG-CCTATCCT


title: dwil_DG_m_r2

value: digestive plus excretory system

value: TCTCGCGC-GTACTGAC


title: w1118_RE_m_r3

source_name: reproductive system without gonad and genitalia

value: CGCTCATT-TAATCTTA


title: dwil_dana_dyak_GO_m_r1.leftover

value: adult

value: gonad


title: w1118_TX_m_r2

value: CGCTCATT-CCTATCCT

value: without ERCC


title: dwil_dana_dyak_GO_f_r2.leftover

value: TCTCGCGC-TAATCTTA


title: dwil_dana_dyak_GO_f_r3.leftover


title: w1118_RE_m_r1

value: reproductive system without gonad and genitalia

value: ATTACTCG-TAATCTTA


title: w1118_RE_f_r3

value: Female

value: TAATGCGC-TAATCTTA


title: dwil_dana_dyak_GO_f_r1.leftover


title: w1118_RE_m_r2

value: TCCGGAGA-TAATCTTA


title: dwil_dana_dyak_DG_m_r2.leftover


title: dwil_dana_dyak_DG_m_r1.leftover

value: CGGCTATG-GTACTGAC


title: w1118_RE_f_r2

value: CTGAAGCT-TAATCTTA


title: dwil_dana_dyak_DG_f_r3.leftover

value: AGCGATAG-GTACTGAC


title: dwil_dana_dyak_DG_f_r2.leftover


title: dwil_dana_dyak_GO_m_r2.leftover

value: Male

value: TCCGCGAA-TAATCTTA


title: w1118_HD_m_r3

value: head

value: GAGATTCC-ATAGAGGC


title: dwil_dana_dyak_AC_m_r3.leftover

value: adult

value: abdomen without digestive or reproductive system

value: AGCGATAG-AGGCGAAG


title: w1118_TX_f_r1

value: thorax without digestive system

value: GAATTCGT-CCTATCCT

value: without ERCC


title: w1118_HD_m_r1

value: TCCGGAGA-ATAGAGGC


title: w1118_RE_f_r1

value: reproductive system without gonad and genitalia

value: Female

value: ATTCAGAA-TAATCTTA


title: dwil_dana_dyak_DG_f_r1.leftover

value: digestive plus excretory system

value: CGGCTATG-GTACTGAC


title: w1118_HD_f_r1

value: ATTCAGAA-ATAGAGGC


title: dwil_dana_dyak_AC_m_r2.leftover

value: Male

value: TCCGCGAA-AGGCGAAG


title: w1118_HD_f_r2

value: head

value: CTGAAGCT-ATAGAGGC


title: w1118_GO_m_r3

value: adult

value: gonad

value: GAGATTCC-AGGCGAAG


title: dwil_dana_dyak_AC_f_r2.leftover

value: abdomen without digestive or reproductive system


title: dwil_dana_dyak_AC_f_r1.leftover

value: CGGCTATG-AGGCGAAG


title: dwil_dana_dyak_AC_m_r1.leftover

value: without ERCC


title: dwil_dana_dyak_AC_f_r3.leftover

value: AGCGATAG-AGGCGAAG


title: w1118_GO_m_r1

value: TCCGGAGA-AGGCGAAG


title: w1118_GO_m_r2

value: CGCTCATT-AGGCGAAG


title: w1118_GO_f_r3

value: Female

value: TAATGCGC-AGGCGAAG


title: w1118_HD_m_r2

value: CGCTCATT-ATAGAGGC


title: 293_Fish_D_E5_120_input_GTAGAG_L004_R1_001

city: Urbana

first: Alison

last: Bell

state: Illinois

address: Justin Smith Morrill Hall, 505 S Goodwin Ave #393

department: Animal Biology

institute: University of Illinois at Urbana Champaign

data_processing:
Base calling and demultiplexing into FASTQ files was done using bcl2fastq v1.8.4 software (Illumina, San Diego, CA, USA).
Sequence data were aligned with Bowtie2 (Langmead and Salzberg 2012) to the stickleback genome (v. 75), using default settings.
Aligned sequence data were analyzed for peaks using HOMER (Hypergeometric Optimization of Motif EnRichment) v4.7 (Heinz et al. 2010).
After peak calling, peak files were annotated to the stickleback genome using HOMER’s annotation script to assign peaks to genes, and associate peaks with differential expression data.
BigWiggle pileup files were generated using HOMER’s makeBigWig.pl script with default settings.
Genome_build: Gasterosteus aculeatus reference genome (the repeat masked reference genome, Ensembl release 75).
Supplementary_files_format_and_content: BigWig files were generated using HOMER's makeBigWig.pl script with default settings.  Scores represent read depth.  BigWig files for inputs represent single samples.  The remaining BigWig files represent the pooled read depth for the two samples with the same brain region, timepoint, control or treatment, and ChIP antibody.

organism: Gasterosteus aculeatus

extract_protocol:
For tissue intended for ChIP-Seq, brain tissue from regions of interest was pooled and kept at 4° C until homogenization in PBS with protease inhibitor cocktail (PIC, Roche, Basel, Switzerland). Fresh brains were homogenized in pools of five on ice by motorized pestle. Homogenized brains were fixed in PBS with 1% formaldehyde for 10 minutes. Fixing reaction was stopped with addition of Glycine to 0.125M. Fixed cells were washed 3x with PBS+PIC to remove formaldehyde. Washed cells were lysed to nuclei with lysis solution – 50 mM Tris-HCl (pH 8.0), 2 mM EDTA, 0.1% v/v NP-40, 10% v/v glycerol, and PIC – for 30 minutes on ice. Cell debris was washed away with PBS with PIC. Nuclei were pelleted and flash-frozen on dry ice.  Frozen nuclei were thawed on ice in lysis solution (1% SDS, 10mM EDTA, 50mM Tris, pH 8.1 with protease inhibitor cocktail). Nuclei were counted using a hemocytometer. Nuclei were sonicated at high power for 7 x 7 minute cycles (30 s on, 30 s off) in a BiorupterTM UCD-200 (Diagenode, Liège, Belgium) sonicator. Remaining cellular debris was pelleted by centrifugation for 10 minutes at 13,000 x g.
Fragmented chromatin was processed for histone H3K27Ac ChIP (Abcam ab4729) with Diagenode iDeal ChIP kits (Diagenode #C01010051, Liège, Belgium), according to manufacturer’s specifications with minor adjustments. One million nuclei were used for each IP. 25 µl of each IP was reserved for input samples. Technical replicate inputs were pooled to 50 µl. 2 ug of h3k27ac antibody was used for each IP. An additional wash in TE buffer was performed after the initial four IP washes. Chromatin was processed for ESRRA ChIP using a customized protocol. Briefly, sonicated samples were pre-incubated with Protein G Dynabeads (Invitrogen 10009D) for three hours. Beads were removed and 10 µg of ESRRA antibody (SC-66882, Santa Cruz Biotechnology, Dallas, TX, USA) was added overnight with rotation at 4° C. Protein G beads were added for 3 hours to bind antibodies. Beads were washed with high salt, low salt, LiCl, and TE buffers for 5 minutes each in succession. Precipitated chromatin was eluted in ChIP elution buffer (1% SDS, 0.1 M NaHCO3) for 15 minutes twice in 25 µl. Samples were reverse cross-linked at 65° C with 1,300 rpm rotation overnight. Samples were phenol-chloroform extracted with standard methods and eluted into 20 µl of nuclease-free water.  After ChIP, immunoprecipitated DNA was quantified using a Qubit 2.0 (Life Technologies, Carlsbad, CA, USA) with a dsDNA HS Assay kit (Life Technologies #Q32854). Libraries were prepared using KAPA LTP library kits (KK8230), with protocol as written, using Bioo Scientific index adapters. Libraries were size selected using AmpureXP beads (Beckman Coulter, Brea, CA, USA), with protocol as written, selecting for DNA between 200-500bp in size. Library quality was checked by Qubit 2.0 and Bioanalyzer (Agilent 2100). Samples were sequenced with an Illumina HiSeq 2500 sequencer using a TruSeq SBS sequencing kit, version 4. All samples were sequenced in single end format with fragment length of 100 bp.

tag: brain region

value: Diencephalon

tag: timepoint (min after the flask was introduced)

tag: sample group

value: Experiment

tag: chip antibody


title: w1118_GO_f_r1

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

tag: age post eclosion (days)

value: ATTCAGAA-AGGCGAAG


title: HCT116_genome_PE125bp

first: Christophe

middle: E

last: Redon

address: 37 Convent Drive

institute: NIH

description: Random shear /sequenced DNA from HCT116 used as control for peak calling

data_processing:
For RepID ChIP, the MACS peak calling program was used comparing reads from the ChIP –seq experiment to genomic input reads from the same cell line, with default parameters, and a p-value = 1e-9.
For nascent strand peak calling the SICER program was used. Nascent strand reads were called by comparison to HCT116 genomic reads using a window size of 200bp, gap size of 600pb, and FDR of 0.00001. For ChiP sequencing peak calling, the SICER program was used except for H4K16Ac ChIP, which are called peaks by broad MACS. For peak calling, used same length sequenced genomic control (101bp or 125bp)
Illumina single read 105bp or 125bp sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq

source_name: Control Reads (random shear) from HCT116

growth_protocol: Cancer cells were grown in DMEM medium, 10% FBS

extract_protocol:
DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. DNA from asynchronous cell cultures was isolated, size fractionated and subject to exunuclease digestion as described in Aladjem et al., Science 281, 1005, 1998. and Wang et al., Molecular and Cellular Biology 24:3373-86, 2004. For ChipSeq, DNA molecules were enriched using each antibodies. Enriched DNA molecules were then amplified randam primer with klenow fragment and sequenced by Illumina Genome Analyzer IIx.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).

value: Colon carcinoma


title: dwil_AC_f_r3

tag: fly culture temperature (oc)

tag: illumina barcode

tag: plate and well id

tag: ercc infomation


title: w1118_GE_m_r3

description: single-species [D. melanogaster (w1118)] RNA preparation

source_name: genitalia

tag: tissue

value: genitalia

tag: Sex

value: Male

tag: replicate

value: CGCTCATT-CAGGACGT

value: ERCC SetB


title: K562_G2_S139_pMCM2

description: ChipSeq for phosphprylated MCM2(S139) cell fractionated to G2 phase by elutriation

source_name: ChipSeq reads from K562 wt G2 phase

tag: cell line

value: Chronic myelogenous leukemia

value: anti-S139 phosphorylated MCM2 antibody (12958S, Cell signaling)


title: K562_lateS_S139_pMCM2

description: ChipSeq for phosphprylated MCM2(S139) cell fractionated to late S phase by elutriation

source_name: ChipSeq reads from K562 wt late S phase

tag: cell type


title: w1118_GO_f_r2

value: adult

value: gonad

value: CTGAAGCT-AGGCGAAG

value: without ERCC


title: K562_genome_control

description: Random shear /sequenced DNA from K562 used as control for peak calling

source_name: Control Reads (random shear) from K562

value: Cultured cancer cell line


title: w1118_GE_m_r2

value: TCCGGAGA-CAGGACGT

value: ERCC SetA


title: K562_T530_pSIRT1

description: ChipSeq for phosphprylated SIRT1(T530)

source_name: ChipSeq reads from K562 wt

value: anti-T530 phosphorylated SIRT1 antibody (ab156585, Abcam)


title: 291_Fish_D_E5_120_H3k27ac_ATGTCA_L001_R1_001

description:
processed data file:
291+292_Fish_D_E5_120_H3k27ac_S1.ucsc.bigWig

tag: brain region

value: Diencephalon

value: Experiment

value: H3k27ac; abcam ab4729


title: K562_earlyS_S139_pMCM2

description: ChipSeq for phosphprylated MCM2(S139) cell fractionated to early S phase by elutriation

source_name: ChipSeq reads from K562 wt early S phase


title: 290_Fish_D_C5_120_input_AGTTCC_L002_R1_001

tag: timepoint (min after the flask was introduced)

value: Control


title: w1118_GE_m_r1

value: genitalia

value: Male

value: ATTACTCG-CAGGACGT


title: K562_G1_S139_pMCM2

description: ChipSeq for phosphprylated MCM2(S139) cell fractionated to G1 phase by elutriation

source_name: ChipSeq reads from K562 wt G1 phase

value: Chronic myelogenous leukemia


title: 289_Fish_D_C5_120_H3k27ac_AGTCAA_L001_R1_001

description:
processed data file:
288+289_Fish_D_C5_120_H3k27ac_S1.ucsc.bigWig

tag: sample group


title: K562_lateS_T530_pSIRT1

description: ChipSeq for phosphprylated SIRT1(T530) cell fractionated to late S phase by elutriation

tag: chip antibody


title: 288_Fish_D_C5_120_H3k27ac_GGCTAC_L001_R1_001


title: w1118_HD_f_r3

tag: flybase species id

value: head

value: Female

value: TAATGCGC-ATAGAGGC


title: w1118_GE_f_r2

tag: strain (strain name or flybase id or drosophila species stock center id)

value: adult

value: GAATTCGT-CAGGACGT


title: HCT116_S139_pMCM2

description: ChipSeq for phosphprylated MCM2(S139)

source_name: ChipSeq reads from HCT116 wt

value: Colon carcinoma

value: anti-S139 phosphorylated MCM2 antibody (12958S, Cell signaling)


title: K562_G1_T530_pSIRT1

description: ChipSeq for phosphprylated SIRT1(T530) cell fractionated to G1 phase by elutriation


title: w1118_GE_f_r1

tag: developmental stage

value: ATTCAGAA-CAGGACGT

value: ERCC SetA


title: K562_earlyS_NS

description: Fractionated early S phase K562 nascent strand

data_processing:
Library strategy: nascent DNA
For RepID ChIP, the MACS peak calling program was used comparing reads from the ChIP –seq experiment to genomic input reads from the same cell line, with default parameters, and a p-value = 1e-9.
For nascent strand peak calling the SICER program was used. Nascent strand reads were called by comparison to HCT116 genomic reads using a window size of 200bp, gap size of 600pb, and FDR of 0.00001. For ChiP sequencing peak calling, the SICER program was used except for H4K16Ac ChIP, which are called peaks by broad MACS. For peak calling, used same length sequenced genomic control (101bp or 125bp)
Illumina single read 105bp or 125bp sequencing
Genome_build: hg19
Supplementary_files_format_and_content: Bed file format of replication initiation peaks and ChipSeq

source_name: Nascent strands reads from K562


title: K562_middleS_S139_pMCM2

description: ChipSeq for phosphprylated MCM2(S139) cell fractionated to middle S phase by elutriation

source_name: ChipSeq reads from K562 wt middle S phase


title: HCT116_H4K16Ac

description: ChipSeq for acetylated Histone H4 (K16)

value: anti-Histone H4 acetyl lysine16 antibody (07-329, Millipore)


title: 260Fish_D_E4_input_GATCAG_L005_R1_001

value: Diencephalon

value: Experiment


title: HCT116_T530_pSIRT1

description: ChipSeq for phosphprylated SIRT1(T530)

value: anti-T530 phosphorylated SIRT1 antibody (ab156585, Abcam)


title: K562_middleS_NS

description: Fractionated middle S phase K562 nascent strand


title: HCT116_SIRT1_depleted_rescued T530A_SIRT1_NS

description: HCT116 SIRT1 depleted and T530A mutant SIRT1 rescued clone nascent strand

source_name: Nascent strands reads from HCT116


title: K562_middleS_T530_pSIRT1

description: ChipSeq for phosphprylated SIRT1(T530) cell fractionated to middle S phase by elutriation


title: K562_earlyS_T530_pSIRT1

description: ChipSeq for phosphprylated SIRT1(T530) cell fractionated to early S phase by elutriation


title: w1118_DG_m_r3

description: mixed-species [D. melanogaster (w1118), D. pseudoobscura, and D. virilis] RNA preparation

value: digestive plus excretory system

tag: age post eclosion (days)

value: CGCTCATT-GTACTGAC

value: without ERCC


title: 257Fish_D_E4_H3k27ac_ATCACG_L005_R1_001

description:
processed data file:
256+257_Fish_D_E4_30_H3k27ac_S1.ucsc.bigWig

value: H3k27ac; abcam ab4729


title: w1118_DG_m_r2

value: Male

tag: fly culture temperature (oc)

value: TCCGGAGA-GTACTGAC


title: 252Fish_D_C4_H3k27ac_TGACCA_L005_R1_001

description:
processed data file:
251+252_Fish_D_C4_30_H3k27ac_S1.ucsc.bigWig

value: Control


title: K562_G2_T530_pSIRT1

description: ChipSeq for phosphprylated SIRT1(T530) cell fractionated to G2 phase by elutriation

value: Chronic myelogenous leukemia


title: w1118_DG_m_r1

value: adult

tag: illumina barcode

value: ATTACTCG-GTACTGAC


title: HCT116_SIRT1_depleted_NS

description: HCT116 SIRT1 depleted clone nascent strand

value: Colon carcinoma


title: w1118_DG_f_r3

value: Female

value: TAATGCGC-GTACTGAC

tag: plate and well id


title: w1118_GE_f_r3

description: single-species [D. melanogaster (w1118)] RNA preparation

value: genitalia

value: TAATGCGC-CAGGACGT

tag: ercc infomation

value: ERCC SetB


title: dwil_dana_dyak_DG_m_r3.leftover

description: mixed-species (D. willistoni, D. ananassae, and D. yakuba) RNA preparation

tag: tissue

value: AGCGATAG-GTACTGAC


title: 256Fish_D_E4_H3k27ac_CTTGTA_L005_R1_001

value: Diencephalon

value: Experiment


title: K562_lateS_NS

description: Fractionated late S phase K562 nascent strand


title: HCT116_WT_APH24hr_REL24hr_NS

description: HCT116 wt nascent strand DNA treated 200nM Aphidicolin for 24hrs and released into freshmedium, then culutured another 24hrs


title: w1118_DG_f_r2

value: digestive plus excretory system

tag: Sex

value: CTGAAGCT-GTACTGAC

value: without ERCC


title: 9T_120_E

data_processing:
Fastq files were generated with the software Casava 1.8.2 (Illumina)
read alignment: Tophat 2.0.8, default parameters
read quantification: Reads inside of exon features were counted in union mode using htseq version 0.6.1.
differential expression: Done in R using the Bioconductor package edgeR.
Genome_build: Gasterosteus aculeatus reference genome (the repeat masked reference genome, Ensembl release 75)
Supplementary_files_format_and_content: gacu_mrsb_counts_raw_03.13.2017.txt: Tab delimited text file of the matrix of raw read counts mapped to the mouse genome (Ensembl annotation of the NCBIM37 version of the mouse genome) as created by the edgeR function readDGE. TopHat2 version 2.0.8 (Kim et al. 2013) was used to align reads.  Reads inside of exon features were counted in union mode using htseq version 0.6.1 (Anders et al. 2015).

extract_protocol:
Heads were flash frozen in liquid nitrogen and the telencephalon and diencephalon were carefully dissected and placed individually in Eppendorf tubes containing 500 μL of TRIzol Reagent (Life Technologies). Total RNA was isolated immediately using TRIzol Reagent according to the manufacturer’s recommendation and subsequently purified on columns with the RNeasy kit (QIAGEN). RNA was eluted in a total volume of 30 μL in RNase-free water. Samples were treated with DNase (QIAGEN) to remove genomic DNA during the extraction procedure. RNA quantity was assessed using a Nanodrop spectrophotometer (Thermo Scientific), and RNA quality was assessed using the Agilent Bioanalyzer 2100 (RIN 7.5-10). RNA was immediately stored at −80 °C until used in sequencing library preparation.
Poly-A RNA was enriched from 1–2 μg of total RNA by using Dynabeads Oligo(dT)25 (Life Technologies), following the manufacturer’s protocol. Two rounds of poly(A) enrichment were performed with a final elution in 14μL of water. The poly-A–enriched RNA was used to prepare RNAseq libraries, using the NEXTflex Directional RNA-seq Kit (dUTP based) with Illumina compatible adaptors (Bioo Scientific). Manufacturer’s instructions were followed and 13–15 cycles of PCR amplification were performed depending on the starting input of total RNA. Libraries were quantified on a Qubit fluorometer, using the dsDNA High Sensitivity Assay Kit (Life Technologies), and library size was assessed on a Bioanalyzer High Sensitivity DNA chip (Agilent). Libraries were pooled and diluted to a final concentration of 10 nM. Final library pools were quantified using real-time PCR, using the Illumina compatible kit and standards (KAPA) by the W. M. Keck Center for Comparative and Functional Genomics at the Roy J. Carver Biotechnology Center (University of Illinois). Single-end sequencing was performed on an Illumina HiSeq 2500 instrument by the W. M. Keck Center for Comparative and Functional Genomics at the Roy J. Carver Biotechnology Center (University of Illinois). The samples were sequenced on 20 lanes.

tag: FISH id

value: male

tag: timepoint in minutes

value: Telencephalon


title: HCT116_SIRT1_depleted_rescued wt_SIRT1_NS

description: HCT116 SIRT1 depleted and wtSIRT1 rescued clone nascent strand

tag: cell line

tag: cell type


title: 8T_60_C

value: Control


title: 9D_120_E

value: adult


title: dyak_WB_m_r3

organism: Drosophila yakuba

source_name: whole body

value: whole body

value: Male

tag: replicate

value: TCTCGCGC-TATAGCCT


title: dyak_WB_m_r2

value: TCCGCGAA-TATAGCCT


title: 251Fish_D_C4_H3k27ac_CGATGT_L005_R1_001

tag: brain region

tag: timepoint (min after the flask was introduced)

tag: sample group

value: H3k27ac; abcam ab4729


title: w1118_AC_m_r3

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

value: abdomen without digestive or reproductive system

value: GAGATTCC-GGCTCTGA


title: w1118_DG_f_r1

tag: developmental stage

value: Female

tag: age post eclosion (days)

value: GAATTCGT-GTACTGAC


title: dyak_WB_f_r2

tag: fly culture temperature (oc)

tag: illumina barcode


title: dyak_WB_f_r1

value: CGGCTATG-TATAGCCT

tag: plate and well id

tag: ercc infomation


title: dyak_TX_m_r1

source_name: thorax without digestive system

tag: tissue

value: thorax without digestive system

tag: Sex

value: CGGCTATG-GGCTCTGA


title: dyak_TX_m_r2

value: TCTCGCGC-GGCTCTGA

value: without ERCC


title: 7T_60_E

tag: FISH id

value: male

tag: timepoint in minutes

value: Experiment

value: Telencephalon


title: w1118_AC_m_r1

value: adult

value: ATTACTCG-GGCTCTGA


title: dyak_WB_f_r3

value: whole body

value: AGCGATAG-TATAGCCT


title: w1118_AC_m_r2

value: Male

value: CGCTCATT-GGCTCTGA


title: dyak_TX_f_r3


title: w1118_AC_f_r3

value: abdomen without digestive or reproductive system

value: CTGAAGCT-GGCTCTGA


title: dyak_TX_f_r2

value: Female

value: TCCGCGAA-GGCTCTGA


title: dyak_WB_m_r1

value: CGGCTATG-TATAGCCT


title: dyak_TX_f_r1

value: thorax without digestive system

value: CGGCTATG-GGCTCTGA


title: dyak_RE_m_r3

source_name: reproductive system without gonad

value: reproductive system without gonad

value: AGCGATAG-CAGGACGT

value: without ERCC


title: 8D_60_C

value: male

value: Control

value: Diencephalon


title: dyak_TX_m_r3

value: adult

value: AGCGATAG-GGCTCTGA


title: w1118_AC_f_r2

source_name: abdomen without digestive or reproductive system

value: GAATTCGT-GGCTCTGA


title: 292_Fish_D_E5_120_H3k27ac_CCGTCC_L004_R1_001

description:
processed data file:
291+292_Fish_D_E5_120_H3k27ac_S1.ucsc.bigWig

value: Experiment

tag: chip antibody

value: H3k27ac; abcam ab4729


title: 5T_30_C

value: Telencephalon


title: 5D_30_C


title: w1118_AC_f_r1

value: abdomen without digestive or reproductive system

value: Female

tag: replicate

value: ATTCAGAA-GGCTCTGA


title: 7D_60_E


title: orgR_WB_m_r3

description: mixed-species [D. melanogaster (Oregon-R), D. mojavensis, and D. persimilis] RNA preparation

value: Oregon-R  (FBst0005905)

value: whole body

value: Male

value: GAGATTCC-TATAGCCT


title: dyak_RE_m_r1

value: reproductive system without gonad

value: TCCGCGAA-CAGGACGT

value: without ERCC


title: dyak_RE_f_r2

value: TCTCGCGC-CAGGACGT


title: dyak_RE_f_r3

value: adult

value: AGCGATAG-CAGGACGT


title: dyak_HD_m_r3

source_name: head

value: head

value: AGCGATAG-ATAGAGGC


title: dyak_RE_f_r1

value: CGGCTATG-CAGGACGT


title: dyak_RE_m_r2


title: dyak_HD_m_r1

value: CGGCTATG-ATAGAGGC


title: orgR_WB_m_r1

value: ATTACTCG-TATAGCCT


title: 3T_60_C

value: male

value: Control

value: Telencephalon


title: dyak_HD_m_r2

value: TCCGCGAA-ATAGAGGC


title: 4T_60_E

value: Experiment


title: orgR_WB_m_r2

value: Oregon-R  (FBst0005905)

value: whole body

value: Male

value: TCCGGAGA-TATAGCCT


title: dyak_HD_f_r2

value: Female

value: without ERCC


title: orgR_WB_f_r3

value: adult

value: TAATGCGC-TATAGCCT


title: dwil_DG_m_r3

source_name: digestive plus excretory system

value: digestive plus excretory system

value: AGCGATAG-GTACTGAC


title: dwil_dana_dyak_HD_m_r2.leftover

value: head


title: dyak_HD_f_r3

value: AGCGATAG-ATAGAGGC


title: dyak_HD_f_r1

value: CGGCTATG-ATAGAGGC


title: 3D_60_C

value: male

value: Control

value: Diencephalon


title: dyak_GO_m_r3

source_name: gonad

value: gonad

value: AGCGATAG-TAATCTTA


title: dyak_GO_m_r1

value: CGGCTATG-TAATCTTA


title: dyak_GO_m_r2

value: Male

value: TCCGCGAA-TAATCTTA


title: dyak_GO_f_r3

value: Female


title: 38D_30_E

value: Experiment


title: orgR_WB_f_r2

value: Oregon-R  (FBst0005905)

value: adult

value: whole body

value: CTGAAGCT-TATAGCCT

value: without ERCC


title: 36D_60_E


title: dyak_GO_f_r1


title: dyak_DG_m_r3

value: digestive plus excretory system

value: AGCGATAG-GTACTGAC


title: dyak_GO_f_r2

value: TCTCGCGC-TAATCTTA


title: dyak_DG_m_r2

value: TCTCGCGC-GTACTGAC


title: 38T_30_E

value: male

value: Telencephalon


title: orgR_TX_m_r3

value: thorax without digestive system

value: GAGATTCC-CCTATCCT


title: 4D_60_E

value: Diencephalon


title: orgR_TX_m_r2

value: Male

value: CGCTCATT-CCTATCCT


title: orgR_WB_f_r1

value: Female

value: ATTCAGAA-TATAGCCT


title: dyak_DG_f_r3

value: adult


title: orgR_TX_f_r3

value: Oregon-R  (FBst0005905)

value: TAATGCGC-CCTATCCT


title: dyak_DG_f_r2

value: without ERCC


title: orgR_TX_m_r1

value: TCCGGAGA-CCTATCCT


title: dyak_DG_m_r1

value: digestive plus excretory system

value: CGGCTATG-GTACTGAC


title: 35D_60_C

value: Control


title: dyak_DG_f_r1


title: 34T_30_E

value: male

value: Experiment


title: dyak_AC_m_r3

value: abdomen without digestive or reproductive system

value: AGCGATAG-AGGCGAAG


title: orgR_TX_f_r2

value: thorax without digestive system

value: CTGAAGCT-CCTATCCT


title: 36T_60_E

value: Telencephalon


title: dyak_AC_f_r3

value: Female


title: orgR_TX_f_r1

value: ATTCAGAA-CCTATCCT


title: dyak_AC_m_r1

value: adult

value: Male

value: CGGCTATG-AGGCGAAG


title: 34D_30_E

value: Diencephalon


title: 33D_30_C


title: orgR_RE_m_r3

source_name: reproductive system without gonad and genitalia

value: Oregon-R  (FBst0005905)

value: GAGATTCC-TAATCTTA

value: without ERCC


title: dyak_AC_f_r2

value: TCCGCGAA-AGGCGAAG


title: dyak_AC_f_r1


title: 35T_60_C

value: male

value: Control


title: orgR_RE_m_r2

value: reproductive system without gonad and genitalia

value: CGCTCATT-TAATCTTA


title: 32T_120_C


title: PAPTRAP1

city: St Louis

first: Joseph

middle: D

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

data_processing:
Trimmomatic V0.32
Deplete rRNA with bowtie2
Align to genome with STAR
Count reads with HTSeq
Genome_build: mouse ensembl175
Supplementary_files_format_and_content: .count files. Ensembl id and count #

source_name: Peripheral Astrocyte Process TRAP: Immunoprecipitation of GFP from synaptoneurosome fraction of Aldh1L1 bacTRAP cortex and hippocampus

extract_protocol:
Cortex and hippocampus homogenate from Aldh1L1::RPL10a-eGFP mice was homogenized and layered onto a sucrose density gradient (Westmark et al, JOVE 2011) and the synaptoneurosome layer was extracted. TRAP (Heiman et al, 2008) was performed on this layer.
cDNA was made from 2ng RNA and amplified using SPIA (Nugen). Illumina libraries were made from 500ng cDNA fragments (~200BP, after Covaris sonication) using NEB Next library prep.

treatment_protocol: Cycloheximide (1ug/mL), TTX (1mM)

tag: strain

tag: age

value: Post natal day 21

tag: cell type

value: astrocytes


title: PAPTRAP3


title: 32D_120_C

tag: sample group


title: orgR_RE_f_r3

tag: flybase species id

tag: strain (strain name or flybase id or drosophila species stock center id)

value: TAATGCGC-TAATCTTA


title: 33T_30_C

tag: developmental stage

value: Telencephalon


title: PAPTRAP2


title: PAPpre1

source_name: Synaptoneurosome fraction of Aldh1L1 bacTRAP cortex and hippocampus, before immunoprecipitation


title: dyak_AC_m_r2

value: abdomen without digestive or reproductive system

tag: age post eclosion (days)

tag: fly culture temperature (oc)


title: 30T_30_C

value: adult


title: orgR_RE_f_r2

value: Female

tag: illumina barcode

value: GAATTCGT-TAATCTTA

tag: plate and well id


title: orgR_RE_f_r1

tag: tissue

value: ATTCAGAA-TAATCTTA

tag: ercc infomation


title: 255Fish_D_C4_input_CAGATC_L005_R1_001

tag: brain region

value: Diencephalon

tag: timepoint (min after the flask was introduced)

value: none (input)


title: CtxTRAP1

source_name: Cortex TRAP: Immunoprecipitation sample of GFP from Aldh1l1 bacTRAP mouse (cortex and hippocampus)


title: 30D_30_C

tag: FISH id

tag: Sex

tag: timepoint in minutes


title: CtxTRAP3

tag: strain

tag: age


title: CtxPre2

source_name: Input to Cortex TRAP before immunoprecipitation

tag: cell type


title: PAPpre3


title: CtxPre3


title: orgR_RE_m_r1

tag: flybase species id

value: Oregon-R  (FBst0005905)

value: Male

tag: replicate

value: ATTACTCG-TAATCTTA

value: without ERCC


title: orgR_HD_m_r3

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

value: head

value: GAGATTCC-ATAGAGGC


title: CtxPre1

value: Post natal day 21


title: 29T_120_E

value: male

tag: sample group

value: Experiment


title: PAPpre2

value: astrocytes


title: 2T_120_C

value: Control

value: Telencephalon


title: 2D_120_C

value: adult


title: CEBPe Chipseq (GTX)-Whole bone marrow-CEBPe KO mouse

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

country: Canada

institute: Memorial University of Newfoundland

data_processing:
Images analysis, base calling and barre code removal were done using the Illumina pipeline.
Fastq files from same experiment (2 lanes) were combined and aligned against hg19 using BWA aln/samse with the following parameters: bwa aln  -t 10 -n 2.
bedgraph files were generated using the “makeUCSCfile” module from Homer package.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph, ChIPseq Signals

source_name: bone marrow

growth_protocol: primary C57BL/6 bone marrow cells without culture

extract_protocol:
Magna ChIP™ A - Chromatin Immunoprecipitation Kit, Cat# 17-610 (EMD Millipore)
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 1000 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Illumina Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: chip antibody

value: CEBPe GTX109155 (GeneTex)

value: primary whole bone marrow cells

tag: genotype

value: C/EBPepsilon knock-out


title: Input-Whole bone marrow-CEBPe KO mouse

description: Input-Whole bone marrow-CEBPe KO mouse

value: Input Control


title: orgR_HD_f_r3

value: Oregon-R  (FBst0005905)

tag: tissue

value: Female

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: illumina barcode

value: CTGAAGCT-ATAGAGGC

tag: plate and well id


title: orgR_HD_m_r1

tag: Sex

value: Male

value: ATTACTCG-ATAGAGGC

tag: ercc infomation

value: without ERCC


title: CEBPe Chipseq (SC158)-Whole bone marrow-CEBPe KO mouse

value: CEBPe SC-158 (Santa Cruz Biotechnology)

tag: strain


title: CEBPe Chipseq (SC158)-Whole bone marrow-B6 mouse

value: wild type


title: 28T_60_E

tag: FISH id

value: male

tag: timepoint in minutes

value: Experiment


title: dper_WB_m_r3

organism: Drosophila persimilis

tag: flybase species id

value: whole body

value: GAGATTCC-TATAGCCT


title: 29D_120_E

value: adult

value: Diencephalon


title: orgR_HD_f_r2

value: head

tag: replicate

value: GAATTCGT-ATAGAGGC


title: CEBPe Chipseq (GTX)-Whole bone marrow-B6 mouse

value: CEBPe GTX109155 (GeneTex)

tag: cell type

value: primary whole bone marrow cells


title: dper_WB_m_r2

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

value: TCCGGAGA-TATAGCCT


title: orgR_HD_f_r1

value: Oregon-R  (FBst0005905)

value: Female

value: ATTCAGAA-ATAGAGGC


title: CtxTRAP2

tag: age

value: Post natal day 21

value: astrocytes


title: dper_WB_f_r3

value: TAATGCGC-TATAGCCT

value: without ERCC


title: orgR_HD_m_r2

value: Male

value: CGCTCATT-ATAGAGGC


title: dper_WB_m_r1

value: whole body

value: ATTACTCG-TATAGCCT


title: 27T_60_C

value: male

value: adult

tag: sample group

value: Control

value: Telencephalon


title: orgR_GO_m_r3

tag: tissue

value: gonad

value: GAGATTCC-AGGCGAAG


title: dper_WB_f_r1

tag: age post eclosion (days)

value: ATTCAGAA-TATAGCCT


title: Input-Whole bone marrow-B6 mouse

description: Input-Whole bone marrow-B6 mouse

tag: chip antibody

value: Input Control

value: primary whole bone marrow cells

tag: genotype

value: wild type


title: dper_TX_m_r3

value: thorax without digestive system

tag: fly culture temperature (oc)

tag: illumina barcode

value: GAGATTCC-CCTATCCT

tag: plate and well id


title: dper_TX_m_r2

tag: Sex

value: CGCTCATT-CCTATCCT

tag: ercc infomation

value: without ERCC


title: dper_WB_f_r2

value: Female

value: CTGAAGCT-TATAGCCT


title: orgR_GO_m_r2

value: Oregon-R  (FBst0005905)

value: Male

value: CGCTCATT-AGGCGAAG


title: 25T_120_C

tag: FISH id

value: male

value: adult

tag: timepoint in minutes

value: Control


title: dper_TX_f_r3

tag: flybase species id

tag: replicate

value: TAATGCGC-CCTATCCT


title: dper_TX_f_r1

tag: strain (strain name or flybase id or drosophila species stock center id)

value: ATTCAGAA-CCTATCCT


title: dper_TX_f_r2

tag: developmental stage

value: CTGAAGCT-CCTATCCT


title: 23T_30_E

value: Experiment

value: Telencephalon


title: orgR_GO_f_r3

value: gonad

value: TAATGCGC-AGGCGAAG


title: orgR_GO_f_r2

value: GAATTCGT-AGGCGAAG


title: orgR_GO_m_r1

value: TCCGGAGA-AGGCGAAG

value: without ERCC


title: dper_RE_m_r3

value: reproductive system without gonad

value: GAGATTCC-TAATCTTA


title: dper_RE_m_r2

value: Male

value: CGCTCATT-TAATCTTA


title: 28D_60_E

value: male

value: Diencephalon


title: orgR_GO_f_r1

value: Oregon-R  (FBst0005905)

value: adult

value: Female

value: ATTCAGAA-AGGCGAAG


title: 23D_30_E

value: Experiment


title: dper_RE_m_r1

value: ATTACTCG-TAATCTTA


title: dper_RE_f_r3

value: TAATGCGC-TAATCTTA


title: dper_RE_f_r1

value: ATTCAGAA-TAATCTTA


title: dper_RE_f_r2

value: GAATTCGT-TAATCTTA


title: 21T_60_E

value: Telencephalon


title: orgR_GE_m_r3

description: single-species [D. melanogaster (Oregon-R)] RNA preparation

source_name: genitalia

value: genitalia

value: GAGATTCC-CAGGACGT

value: ERCC SetB


title: orgR_GE_m_r2

value: Male

value: CGCTCATT-CAGGACGT


title: 27D_60_C

value: male

value: Control


title: 21D_60_E

value: Diencephalon


title: dper_HD_m_r3

value: adult

value: head

value: GAGATTCC-ATAGAGGC

value: without ERCC


title: dper_HD_m_r2

value: CGCTCATT-ATAGAGGC


title: dper_TX_m_r1

value: thorax without digestive system

value: TCCGGAGA-CCTATCCT


title: orgR_GE_m_r1

value: Oregon-R  (FBst0005905)

value: TCCGGAGA-CAGGACGT

value: ERCC SetA


title: 25D_120_C


title: dper_HD_m_r1

value: ATTACTCG-ATAGAGGC


title: 20T_120_C

value: Telencephalon


title: orgR_GE_f_r3

value: genitalia

value: Female

value: TAATGCGC-CAGGACGT

value: ERCC SetB


title: 20D_120_C

value: male

value: Control

value: Diencephalon


title: 1T_120_E

value: adult

value: Experiment


title: dper_HD_f_r2

value: head

value: GAATTCGT-ATAGAGGC

value: without ERCC


title: orgR_GE_f_r2

value: Oregon-R  (FBst0005905)

value: CTGAAGCT-CAGGACGT


title: dper_HD_f_r3

value: CTGAAGCT-ATAGAGGC


title: dper_HD_f_r1

value: ATTCAGAA-ATAGAGGC


title: 1D_120_E


title: dper_GO_m_r2

value: gonad

value: Male

value: CGCTCATT-AGGCGAAG


title: dper_GO_m_r3

value: GAGATTCC-AGGCGAAG


title: 19T_120_E

value: Telencephalon


title: orgR_DG_m_r3

value: digestive plus excretory system

value: GAGATTCC-GTACTGAC


title: orgR_GE_f_r1

value: genitalia

value: Female

value: GAATTCGT-CAGGACGT

value: ERCC SetA


title: 19D_120_E

value: male

value: adult

value: Experiment

value: Diencephalon


title: dper_GO_m_r1

value: TCCGGAGA-AGGCGAAG

value: without ERCC


title: dper_GO_f_r2

value: gonad

value: GAATTCGT-AGGCGAAG


title: orgR_DG_m_r1

value: Oregon-R  (FBst0005905)

value: Male

value: TCCGGAGA-GTACTGAC


title: dper_GO_f_r3

value: TAATGCGC-AGGCGAAG


title: orgR_DG_f_r3

value: digestive plus excretory system

value: TAATGCGC-GTACTGAC


title: 18D_30_E


title: 18T_30_E

value: Telencephalon


title: dper_GO_f_r1

value: Female

value: ATTCAGAA-AGGCGAAG


title: orgR_DG_f_r2

value: GAATTCGT-GTACTGAC


title: 17T_30_C

value: male

value: adult

value: Control


title: dper_DG_m_r3

value: GAGATTCC-GTACTGAC


title: dper_DG_m_r2

value: CGCTCATT-GTACTGAC

value: without ERCC


title: 17D_30_C

value: Diencephalon


title: orgR_DG_f_r1

value: Oregon-R  (FBst0005905)

value: ATTCAGAA-GTACTGAC


title: orgR_AC_m_r3

value: abdomen without digestive or reproductive system

value: Male

value: GAGATTCC-GGCTCTGA


title: 15T_60_C


title: DM_72hr_H3K27ac

source_name: C2C12 myoblasts

tag: cell line

tag: cell type

value: myoblasts

tag: developmental stage; time in differentiation medium

value: DM 72 hours

tag: antibody

value: H3K27ac (Abcam ab4729)


title: dper_DG_m_r1

tag: tissue

value: digestive plus excretory system

tag: age post eclosion (days)

value: TCCGGAGA-GTACTGAC


title: DM_24hr_H3K27ac

value: DM 24 hours


title: orgR_AC_m_r2

value: adult

tag: fly culture temperature (oc)

value: CGCTCATT-GGCTCTGA


title: dper_DG_f_r3

value: Female

tag: illumina barcode

value: TAATGCGC-GTACTGAC


title: 15D_60_C

value: male

tag: sample group

value: Control


title: orgR_AC_m_r1

value: Oregon-R  (FBst0005905)

tag: Sex

value: ATTACTCG-GGCTCTGA

tag: plate and well id

value: without ERCC


title: dper_DG_f_r2

value: GAATTCGT-GTACTGAC

tag: ercc infomation


title: orgR_DG_m_r2

value: Male

value: CGCTCATT-GTACTGAC


title: DM_12hr_H3K27ac

value: myoblasts

value: DM 12 hours


title: 13T_120_E

tag: FISH id

tag: timepoint in minutes

value: Experiment

value: Telencephalon


title: DM_6hr_H3K27ac

value: DM 6 hours

value: H3K27ac (Abcam ab4729)


title: 13D_120_E

value: adult

value: Diencephalon


title: orgR_AC_f_r3

tag: flybase species id

value: abdomen without digestive or reproductive system

value: Female

tag: replicate

value: TAATGCGC-GGCTCTGA


title: dper_DG_f_r1

tag: strain (strain name or flybase id or drosophila species stock center id)

tag: developmental stage

value: digestive plus excretory system

value: ATTCAGAA-GTACTGAC


title: DM_0hr_H3K27ac

tag: cell line

tag: cell type

value: DM 0 hour


title: orgR_AC_f_r2

value: Oregon-R  (FBst0005905)

value: CTGAAGCT-GGCTCTGA

value: without ERCC


title: 12T_30_C

value: male

value: Control


title: dper_AC_m_r3

value: Male

value: GAGATTCC-GGCTCTGA


title: DM_minus24hr_H3K27ac

value: myoblasts

tag: developmental stage; time in differentiation medium

value: DM -24 hours

tag: antibody


title: orgR_AC_f_r1

value: adult

tag: tissue

tag: age post eclosion (days)

value: ATTCAGAA-GGCTCTGA


title: 12D_30_C

value: Diencephalon


title: dper_AC_m_r2

value: abdomen without digestive or reproductive system

tag: fly culture temperature (oc)

tag: illumina barcode

value: CGCTCATT-GGCTCTGA


title: Gal_NO_B

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

data_processing:
mapping of reads was done using: bowtie2  -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Genome and plasmids:
Genome_build: gi|87159837|ref|NC_007790.1| Staphylococcus aureus subsp. aureus USA300_FPR3757 plasmid pUSA01, complete sequence       3125
Genome_build: gi|87159843|ref|NC_007791.1| Staphylococcus aureus subsp. aureus USA300_FPR3757 plasmid pUSA02, complete sequence       4439
Genome_build: gi|87159847|ref|NC_007792.1| Staphylococcus aureus subsp. aureus USA300_FPR3757 plasmid pUSA03, complete sequence       37136
Genome_build: gi|87159884|ref|NC_007793.1| Staphylococcus aureus subsp. aureus USA300_FPR3757 chromosome, complete genome     2872769
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: S. aureus cells

growth_protocol: S. aureus was cultured on chemically defined medium (CDM) containing galactose as carbon source (20 mM), phosphate buffer, trace minerals, vitamins, nucleobases, nitrogen and sulfur sources and amino acids using the concentrations previously described (Ferreira et al., 2013). Cultures were started at an initial OD600 of 0.05-0.1 by addition of preculture cells harvested in exponential phase (OD600 of 1).

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
RNA libraries were prepared for sequencing using standard Ion Proton Sequencer protocols

treatment_protocol: Cells were grown to OD600 of 0.4 and then left untreated or exposed to spermine NONOate (250 μM, Sigma) for 3h.

tag: strain

value: S. aureus USA300_FPR3757


title: 11T_30_E

tag: Sex

tag: sample group

value: Experiment

value: Telencephalon


title: dper_AC_m_r1

value: ATTACTCG-GGCTCTGA

tag: plate and well id

tag: ercc infomation


title: Gal_NO_A

organism: Staphylococcus aureus subsp. aureus USA300_FPR3757


title: dper_AC_f_r3

tag: flybase species id

value: Female

value: TAATGCGC-GGCTCTGA


title: rny1

city: Portland

first: Jens

last: Kreth

state: OR

address: 3181 SW Sam Jackson Park Rd., #L595

department: Restorative Dentistry

institute: Oregon Health and Science University

data_processing:
Bowtie2 was used to generate the S. pyogenes genome index and to align paired-end RNA-seq data using “very-sensitive-local” settings.
The aligned files were sorted, converted to BAM format and indexed using Samtools.
The locations of genes and tRNAs were determined by aligning corresponding FASTA files to the S. pyogenes genome and converting the aligned sequences into BED format.
Percentage of unambiguously mapped reads was determined with CLC Genomics Workbench (Qiagen).
Reads coverage depth of each base on the chromosome was computed with BEDTools using the “genomeCoverageBed” function [8]. The base reads were log2 transformed to reduce in-gene variation. To calculate the expression level of a particular sequence, the log-transformed base reads in that sequence were added, averaged, and exponentially transformed.
Genome_build: ASM1812v1
Supplementary_files_format_and_content: comma-separated values files include read depth of each base on the genome.

organism: Streptococcus pyogenes

source_name: NZ131 RNase Y mutant (∆rny)

growth_protocol: S. pyogenes NZ131 wild-type and RNase Y mutant (∆rny) were grown in C medium (0.5% proteose peptone #3; 1.5% yeast extract; 10 mM K2HPO4; 0.4 mM MgSO4; 17 mM NaCl) at 37°C without aeration.

extract_protocol:
Total RNA was harvested using Trizol reagent and was treated twice with Turbo DNase (Invitrogen) to remove chromosomal DNA . Ribosomal RNAs were removed from the total RNA by using a bacteria specific rRNA-depletion kit (Ribo-Zero, Illumina).
RNA samples were sent to the Oklahoma Medical Research Foundation (OMRF, Oklahoma City, OK) for cDNA library construction using TruSeq RNA Sample Preparation v2 Protocol (Illumina) and DNA sequencing (100bp paired-end) on Illumina HiSeq 2000.

treatment_protocol: Cells were harvested via centrifugation when they reached the mid exponential phase.

tag: strain background

tag: genotype/variation

value: RNase Y mutant (delta rny)


title: rny2


title: 11D_30_E

tag: FISH id

value: male

tag: developmental stage

tag: timepoint in minutes


title: wt2

source_name: NZ131 wild type (WT)

value: wild type


title: Gal_A


title: Gal_B


title: wt1


title: GP/M-2

status: Public on Jun 01 2017

city: SALT LAKE CITY

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah School of Medicine

data_processing:
base-calling by Illumina HiSeq 50 Cycle Single Read Sequencing v4
RNA-seq reads were aligned to the dm3 genome build with Ensembl transcript splice alignments using novoalign
Converted splice coordinates to genome coordinates with SamTranscriptomeParser
Generated ReadCoverage USeq file
Ran DefinedRegionDifferentialSeq using Ensembl transcripts and default settings
Data was corrected for batch effects between experimental replicates
Genome_build: dm3
Supplementary_files_format_and_content: xlsx file containing analyzed output from DESeq including counts of reads overlapping gene of interest, Variance corrected per gene in log space from DESeq, and FPKM

source_name: Whole fly lysate

extract_protocol:
Flies were flash frozen in liquid nitrogen and RNA isolated using Trizol reagent. RNA was then further purified using the Qiagen RNeasy clean-up procedure.
Libraries were prepared using Illumina TruSeq Standard mRNA Library Preparation Kit polyA selection

tag: genetic background

value: Canton S

tag: age

value: 10-11 day old adults

tag: genotype

value: wild-type

tag: grandparental obesity

value: Grandpaternal parent

tag: parental heterozygosity

value: Maternal


title: GP/M-1


title: dper_AC_f_r1

tag: strain (strain name or flybase id or drosophila species stock center id)

value: adult

tag: tissue

tag: age post eclosion (days)

tag: fly culture temperature (oc)

tag: replicate

tag: illumina barcode

value: ATTCAGAA-GGCTCTGA

value: without ERCC


title: dper_AC_f_r2

tag: flybase species id

value: abdomen without digestive or reproductive system

tag: Sex

value: CTGAAGCT-GGCTCTGA

tag: plate and well id

tag: ercc infomation


title: GP/M-3


title: Dmel female TW rep1

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

description: Academia Sinica, Taiwan

data_processing:
100-bp paired-end sequencing reads were mapped to the Drosophila melanogaster genome (FlyBase r5.48) with TopHat 2.0.6 (Trapnell et al. 2009).  We allowed two mismatches in read mapping to the reference genome.
The normalized expression levels of genes were measured in Fragments Per Kilobase of exon per Million fragments mapped (FPKMs) by Cufflinks 2.0.0 with bias correction (“--multi-read-correct” and “--frag-bias-correct”) (Trapnell, et al. 2010).
Genome_build: FlyBase D. melanogaster r5.48
Supplementary_files_format_and_content: *.fpkm_tracking: FPKM Tracking format, outputed from the Cufflinks suite. FPKM tracking files use a generic format to output estimated expression values.
Genome Build:
Adu_Dmel_Fem_AS_R1_clout.fpkm_tracking: FlyBase D. melanogaster r5.48

source_name: Dmel female TW

growth_protocol: Tuson, #14021-0248-25 flies were raised in standard cornmeal yeast extract media at 25°C. Egg laying was performed on plates with standard vinegar medium and yeast. Embryos were collected in 0.03% Triton-X100, 0.4% NaCl 16-18 hr after egg laying.

extract_protocol:
About 300-700 pairs of fly antennae of each sex from each species were collected for total RNA isolation.  The antennae resected each day were preserved in ~ 50-100 ul Trizol (Life Technology) and stored at -80 °C before further processing.  Right before the RNA isolation, we spun down antennae preserved in Trizol at the max speed for 3 min at 4 °C and put each sample into one MagNA Lyser Green Beads tube (Roche).
The RNA isolation protocol we developed combined steps from conventional Trizol extraction and RNeasy Micro Elute Kit (QIAGEN, Inc.) with some modifications to obtain high yield and quality of total RNA.  Fly antennae were disrupted with MagNA Lyser (Roche) at 7000 rpm for 15 seconds each time and repeated for 4-5 times until the tissue was almost invisible.  After 15 sec, we cooled down the lysate on ice for 10 sec to prevent RNA degradation.  Tissue lysate was transferred to a new RNase free Eppendorf tube.  We used about 400 ul Trizol to rinse the beads of each sample and combine this 400 ul Trizol with the tissue lysate for the RNA isolation.  Based on the suggestion of the Trizol standard protocol, 200 microliters of chloroform per microliter of tissue lysate were added to the lysate and mixed well by shaking vigorously for 15 sec and set 2-3 min at room temperature.  The aqueous phase was separated by centrifuging the lysate at the maximum speed at 4 °C for 15 min and carefully transferred to a new Eppendorf tube after centrifuging. We added 1 volume of 5 µl Carrier RNA (QIAGEN, Inc.) and one microliter of 70% EtOH to the aqueous phase and mixed well by inverting the tubes carefully.  To obtain greater amount of RNA, we kept the samples at -80 °C for overnight to aid in RNA precipitation.  RNA isolation followed manufacturer’s protocol of the RNeasy Micro Elute Kit with increased volumes (700 ul) of RPE buffer and 80% ethanol to wash RNA.  Genomic DNA was removed by applying on-column DNase I treatment at room temperature for 15 min.
For paired-end mRNA-seq library preparation, we used Illumina TrueSeq kits.  A total of 10 µg total RNA was used for mRNA enrichment by oligo-dT beads followed by cation-catalyzed fragmentation for 4 minutes at 94˚C.  The mRNA fragments were then converted into double stranded cDNA by random priming followed by end repair.  The fragmented cDNAs from each sex of each species were then ligated to the barcoded paired-end adaptors and subjected to 15 cycles of PCR amplification and purified by Ampure beads (Beckman Agencourt). The absolute concentrations of the libraries were determined by Qubit fluorometry (Invitrogen) and BioAnalyzer High Sensitivity DNA Kit (Agilent).  We combined barcoded cDNA from 6 samples and loaded them in 3 sequencing lanes of flow cell, and paired-end 2*100nt sequencing was conducted on Illumina HiSeq2000.

tag: gender

value: female

value: antenna

tag: developmental stage

value: Adult

value: within 1hr of eclosion

tag: strain

value: Canton-S


title: Dmel male TW rep1

description: Academia Sinica, Taiwan

data_processing:
100-bp paired-end sequencing reads were mapped to the Drosophila melanogaster genome (FlyBase r5.48) with TopHat 2.0.6 (Trapnell et al. 2009).  We allowed two mismatches in read mapping to the reference genome.
The normalized expression levels of genes were measured in Fragments Per Kilobase of exon per Million fragments mapped (FPKMs) by Cufflinks 2.0.0 with bias correction (“--multi-read-correct” and “--frag-bias-correct”) (Trapnell, et al. 2010).
Genome_build: FlyBase D. melanogaster r5.48
Supplementary_files_format_and_content: *.fpkm_tracking: FPKM Tracking format, outputed from the Cufflinks suite. FPKM tracking files use a generic format to output estimated expression values.
Genome Build:
Adu_Dmel_Mal_AS_R1_clout.fpkm_tracking: FlyBase D. melanogaster r5.48

source_name: Dmel male TW

value: male

tag: age


title: GP/P-3

tag: genetic background

tag: genotype

value: Paternal


title: GP/P-1

value: Canton S

tag: grandparental obesity

tag: parental heterozygosity


title: WT-3 (2)

value: 10-11 day old adults


title: GP/P-2

value: wild-type


title: WT-2 (2)


title: Maternal-3

description: Sample name: 12314X12

data_processing:
base-calling by Illumina HiSeq 50 Cycle Single Read Sequencing v4
RNA-seq reads were aligned to the dm3 genome build with Ensembl transcript splice alignments using novoalign
Converted splice coordinates to genome coordinates with SamTranscriptomeParser
Generated ReadCoverage USeq file
Ran DefinedRegionDifferentialSeq using Ensembl transcripts and default settings
Genome_build: dm3
Supplementary_files_format_and_content: xlsx file containing analyzed output from DESeq including counts of reads overlapping gene of interest, Variance corrected per gene in log space from DESeq, and FPKM

tag: tissue

value: whole fly

value: AKHR +/-

tag: parental obesity

value: Maternal parent


title: Maternal-1

description: Sample name: 12314X10


title: Maternal-2

description: Sample name: 12314X11


title: WT-1 (2)


title: Paternal-3

description: Sample name: 12314X9

value: Paternal parent


title: Paternal-2

description: Sample name: 12314X8


title: Paternal-1

description: Sample name: 12314X7


title: 10T_120_C

tag: FISH id

value: adult

tag: timepoint in minutes

tag: sample group

value: Control

value: Telencephalon


title: Het-1

description: Sample name: 12314X4


title: Wildtype-3

description: Sample name: 12314X3


title: Het-2

description: Sample name: 12314X5


title: 10D_120_C

value: Diencephalon


title: Het-3

description: Sample name: 12314X6


title: Wildtype-2

description: Sample name: 12314X2


title: Wildtype-1

description: Sample name: 12314X1


title: experiment-1, RNAseq data from ethanol exposed rats' nucleus accumbens, rep3

city: Gothenburg

first: Julia

last: Morud

address: Beroendemedicin, Box 410

country: Sweden

institute: University of Gothenburg

description: Transcriptome data from rat nucleus accumbens

data_processing:
Bcl to Fastq conversion was performed using bcl2Fastq v1.8 from the CASAVA software suite. The quality scale is Sanger / phred33 / Illumina 1.8+.
Sequenced reads were trimmed for low-quality sequences, then mapped to Rnor_6.0 whole genome using tophat2 v2.0.13 with parameters -p 8 -r 100
Number of reads mapping to each feacher (from SAM file) were calculated using htseq-count v0.5.3p3.
Differential expression analysis was done using DESeq2 package v1.6.2 form R/Bioconductor with the htseq-count result as an input.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The raw counts were generated from the aligned bam files (aligned with Tophat2) using htseq_count version 0.6.0.

organism: Rattus norvegicus

source_name: Nucleus accumbens tissue from ethanol exposed rats_experiment1

extract_protocol:
Qiagen RNeasy Lipid tissue mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Brain

tag: tissue compartment

value: Nucleus accumbens

tag: breed

value: Wistar


title: experiment-1, RNAseq data from ethanol exposed rats' nucleus accumbens, rep4

tag: Sex


title: ceh/eds 1

city: Botanical Garden

first: Marta

last: Bjornson

state: Zurich

address: Zollikerstrasse 107

country: Switzerland

institute: University of Zurich (UZH, Switzerland)

data_processing:
Basecalling by Illumina software (HiSeq2000)
reads trimmed and aligned using TopHat2 in Galaxy, default parameters
Counts normalized for analysis by DeSeq2
Genome_build: TAIR 10
Supplementary_files_format_and_content: Normalized counts by gene (rows) and genotype (columns)

organism: Arabidopsis thaliana

source_name: 3 week old soil-grown rosettes

growth_protocol: sunshine mix soil, watered 3x weekly, 16hr light/8hr dark, 23-25C, 3 weeks old

extract_protocol: HTR (Kumar et al Frontiers in Plant Science 2012)

value: rosette

value: 3 weeks-old


title: eds 3


title: ceh/eds 3


title: ceh/eds 2


title: experiment-1, RNAseq data from ethanol exposed rats' nucleus accumbens, rep5

value: male


title: experiment-1, RNAseq data from ethanol exposed rats' nucleus accumbens, rep2


title: eds 1


title: ceh 2


title: experiment-1, RNAseq data from water exposed rats' nucleus accumbens, rep5

source_name: Nucleus accumbens tissue from water exposed rats_experiment1


title: experiment-1, RNAseq data from ethanol exposed rats' nucleus accumbens, rep1


title: parent 3

value: wild type Col-0


title: ceh 3


title: parent 2


title: experiment-1, RNAseq data from water exposed rats' nucleus accumbens, rep2


title: eds 2


title: experiment-1, RNAseq data from water exposed rats' nucleus accumbens, rep1


title: parent 1


title: experiment-1, RNAseq data from water exposed rats' nucleus accumbens, rep4


title: RPE1 cell siRNA SAFA 48h  RNA-seq library

city: Edinburgh

first: nick

last: gilbert

address: Crewe Rd

department: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

description: RNA-seq library prepared from total RNA extracted from RPE1 cell transfected with Lipofectamine RNAi MAX and SAF-A siRNA at 48h post transfection time point.

data_processing:
Unpaired reads where aligned using Tophat (v2.0.10) calling bowtie2 (v2.1.0) using default parameters.
The output file from Tophat was an accepted_hits.bam file for each condition.
Cufflinks (v2.2.1) was run on outputted accepted_hits.bam files for each of the four conditions using -g option to align file to an Hg19 GTF file. This generated "genes_fpkm_tracking.txt" file and a transcripts.gtf file for each condition (q1- q4).
The Cuffmerge function of Cufflinks was run to create a master assembly file for the experiment combining each of the transcripts.gtf files outputted from the four Tophat alignments. Cuffmerge default parameters where used along with -g option to align to a Hg19 GTF file and -s to specific an Hg19 fasta file.
The Cuffdiff function of cufflinks was run to identify significant changes in gene expression between control and SAF-A knockdown samples at 24h and 48h. The output of Cuffmerge was used as the transcript annotation file argument along with all the Tophat outputted accepted_hits.bam file for each condition, default parameters where used along with the -u option.
The R package CummbeRbund was used for further data QC, visualisation and plotting of the output data from Cuffdiff.
Genome_build: Hg19
Supplementary_files_format_and_content: Gene expression values along with fold change and significance call for the differential gene expression analysis (0.0005 p-value cut off) from Cuffdiff are displayed as a table "RPE1_diff_expression_WT_SAFA.xlsx".

source_name: RPE1 cells

growth_protocol: RPE1 cells (ATCC CRL-4000) were cultured in DMEM-F12 supplemented with, 3 mM glutamine, 15 mM HEPES, 0.34% sodium bicarbonate, 10% FBS, penicillin (100 U ml−1), streptomycin (100 μg ml−1) and phenol red (8.1 mg l−1).

extract_protocol:
Total RNA was extracted from the cells transfected with either siRNA at 24h and 48h time points and were prepared with RNeasy Mini kit (Qiagen) and treated with ribo-Zero kit (illumina) to remove ribosomal RNA. A single replicate was performed per condition.
RNA-seq libraries were prepared with a NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB), according to manufacturer’s instructions and sample uniquely barcoded using NEBNext Multiplex oligo for Illumina (NEB). Samples were quantified using a BioAnalyzer 2100 with a High Sensitivity DNA Kit (Agilent). RNA-seq libraries were analysed by Edinburgh Genomics at the University of Edinburgh, UK, who performed quality control and sequencing using an Illumina HiSeq2500, 50 base single-end reads. Samples were indexed as follows: q1_RPE1_siRNA_con_24h NebNext illumina index2, q2_RPE1_siRNA_SAFA_24h NebNext illumina index4, q3_RPE1_siRNA_con_48h NebNext illumina index5 and q4_RPE1_siRNA_SAFA_48h NebNext illumina index6.

treatment_protocol: For the siRNA treatment RPE1 cells at 10–20% confluency were transfected with 10 nM Stealth RNA (Invitrogen) using Lipofectamine RNAi MAX (Invitrogen) following the manufacturer protocol, at 24h and 48h time points using either control or SAF-A siRNA. The transfected Stealth RNA sequences for SAF-A was CCUGGGAAUCGTGGCGGATATAATA identifier HSS104917, while the negative control RNA used was the Stealth RNAi™ siRNA Negative Control (Invitrogen).

tag: cell line

tag: sirna

value: SAF-A


title: Control2_ChIP-seq

city: Kansas City

first: Jennifer

last: Gerton

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Reads from ChIP-seq experiments were aligned to the human genome UCSC hg19 using Bowtie2 aligner 2.1.0, allowing uniquely mapped reads only up to two mismatches.
Peak calling was performed using MACS 2.0.10 to determine statistical enrichment.
The average coverage was binned in 25-bp intervals.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using Bedtools

source_name: HEK293 cells

growth_protocol: HEK293 cells were cultured and specific SET1 siRNA was used to knock down SET1 in the cells. After verifying knockdown by western blotting, ChIP-seq experiments were performed

extract_protocol:
Lysates were obtained from sonicated nuclei and chromatin was isolated with NCPAH2 antibody.
ChIP-seq libraries were prepared with Illumina's TruSeq DNA sample preparation kit.

tag: cell type

value: human embryonic kidney cells

tag: passages

value: 10-13 passages

tag: chip antibody

value: NCAPH2 (Bethyl:A302-275A)


title: SET1KD2_ChIP-seq


title: experiment-1, RNAseq data from water exposed rats' nucleus accumbens, rep3

tag: developmental stage


title: Control1_ChIP-seq


title: SET1KD1_ChIP-seq


title: ceh 1

tag: age

tag: genotype


title: RPE1 cell siRNA Control 24h RNA-seq library

description: RNA-seq library prepared from total RNA extracted from RPE1 cell transfected with Lipofectamine RNAi MAX and negative control siRNA at 24h post transfection time point.

value: control


title: RPE1 cell siRNA SAFA 24h  RNA-seq library

description: RNA-seq library prepared from total RNA extracted from RPE1 cell transfected with Lipofectamine RNAi MAX and SAF-A siRNA at 24h post transfection time point.


title: hiPSC derived NPC_SCZD patient_RNA-seq 2

city: Buffalo

first: Michal

last: Stachowiak

state: NY

address: 3435 Main Street

department: Pathology and Anathomical Sciences

institute: State University of New York at Buffalo

data_processing:
Aligned to genome using Tophat2
Cufflinks was used to get expression profile
Cuffdiff was used for differntial expression
Genome_build: hg19
Supplementary_files_format_and_content: text file, genes expression levels in FPKM

source_name: hiPSC derived NPC_SCZD patient

growth_protocol: hiPSC derived NPC were treated with neuronal media for 2 days (DMEM/F12, 1x N2, 1x B27-RA, 20 ng/ml BDNF, 20 ng/ml GDNF, 1mM dibuyryl -cyclic AMP, and 200nM ascorbic acid)

extract_protocol:
RNA was extracted using Qiagen Rneasy kit per manufacturor protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: source subject status

value: SCHIZOPHRENIA; SCZD

value: iPSC derived NPC

tag: treated with

value: neuronal media for 2 days


title: hiPSC derived NPC_SCZD patient_RNA-seq 4


title: hiPSC derived NPC_control_miRNA-seq 2

data_processing:
CLC genomic workbench was utilized to align, and generate raw counts of microRNA
Alignment was done to miRNA database version 21
Genome_build: miRNA datavase version 21
Supplementary_files_format_and_content: Raw counts

source_name: hiPSC derived NPC_control

extract_protocol:
RNA was extracted using Qiagen Rneasy kit per manufacturor protocol
smallRNA libraries were prepared for sequencing using standard Illumina protocols

value: control; healthy


title: hiPSC derived NPC_SCZD patient_RNA-seq 3


title: hiPSC derived NPC_control_RNA-seq 2


title: RPE1cell siRNA Control 48h RNA-seq library

description: RNA-seq library prepared from total RNA extracted from RPE1 cell transfected with Lipofectamine RNAi MAX and negative control siRNA at 48h post transfection time point.


title: hiPSC derived NPC_SCZD patient_RNA-seq 1


title: hiPSC derived NPC_control_RNA-seq 1


title: Patient 3_input

data_processing:
Aligned using Bowtie2 to hg19 genome
peaks were called using MACS2 q=0.01
Genome_build: hg19
Supplementary_files_format_and_content: bed format contain peak locations

extract_protocol:
lysate was sonicated and protein-genomic DNA complex were isolated with antibody
Libraries were prepared according to standard Illumina protocols


title: Control 4_input


title: hiPSC derived NPC_SCZD patient_miRNA-seq 2


title: hiPSC derived NPC_SCZD patient_miRNA-seq 1


title: Control 4_FGFR1_ChIP-seq

value: FGFR1 (Abcam, ab10646)


title: Patient 3_FGFR1_ChIP-seq


title: hiPSC derived NPC_SCZD patient_miRNA-seq 3


title: KSHV96-3

first: Yuqing

last: Li

address: North campus of Sun Yat-sen University, No.74 of Zhongshan 2nd road, Yuexiu Distinct, Guangzhou, Guangdong

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 and CQ994935.1 using bowtie software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with HTSeq v0.6.0.
Genome_build: hg19 and CQ994935.1
Supplementary_files_format_and_content: txt

source_name: Mesenchymal stem cell

growth_protocol: Human peridontal ligament stem cells (PDLSC) were cultured in alpha-MEM (containing 10% FBS and 1% anti-biotics).

extract_protocol:
After infection of KSHV for 48h and 96h, dicarded the supernatant, and total RNA from uninfected PDLSC, KSHV-48 and KSHV-96 were collected in triple, with Trizol reagent.
Library was constructed as following: Total RNA were enriched with beads binded with Oligo(DT), then broken into short fragments through fragmentation buffer. Broken RNA were used as template to synthetize the first- and second-strand of cDNA. Fragments in target size were recovered by Agarose gel electrophoresis, and amplified by PCR.

treatment_protocol: PDLSCs between passage 2 and 6 were infected with KSHV in MOI=50.

value: peridontal ligament cell

tag: passage

tag: tissue

value: peridontal ligament

tag: stress

value: KSHV-infected

tag: time point

value: 96 hr


title: KSHV96-1


title: KSHV96-2


title: KSHV48-3

value: 48 hr


title: KSHV48-1


title: KSHV48-2


title: Uninfected-2

value: uninfected


title: Uninfected-3