title: sRMycNod3

city: Castanet Tolosan

first: Erika

last: Sallet

address: 24 Chemin de Borde Rouge, CS 52627

department: Plant Health and the Environment

country: France

institute: INRA/CNRS

description: small RNA fraction

data_processing:
Raw reads of smRNA sequencing were filtered by the LeARN Pipeline adapted for plant smRNAs. In brief, reads were cleaned (adaptors suppression, 18-25nt size filtering, reads containing ‘N’ suppression and suppression of tRNA and rRNA), the redundancy was counted and removed.
Supplementary_files_format_and_content: Multifasta file of cleaned smRNA. The fasta headers give the number of times each sequence is present in each library

organism: Medicago truncatula

source_name: Root, Factor Myc/Nod control roots

growth_protocol: Plants from the reference sequenced line Jemalong A17 or from the sunn-sickle hypernodulating double mutant (Jemalong A17 genetic background, of the barrel medic (Medicago truncatula L.)) were grown in different way depending on the interaction of interest. For the interaction with Rhizophagus irregularis (DAOM197198), plants from the A17 line were grown in a greenhouse (16-hour light/8-hour dark cycle) for 7 weeks in a soil substrate inoculated with 1000 spores/liters. The substrate was hydrated with a Long-Ashton solution with a phosphate concentration of 7.5 µM. The well-established mycorrhization was controlled by the grid intersection method. For the interaction with Sinorhizobium meliloti plants from the sunn-sickle hypernodulating double mutant were grown in an aeroponic chamber at 23 °C and 75 % of humidity during five days (16-hour light/8-hour dark cycle) in a nitrogen-less liquid Fahraeus medium nebulization inoculated with bacteria . For the induction by both Myc-LCO and Nod factors, the A17 plants were obtained in the same way but with Fahraeus medium adjusted at 7.5 µM of phosphate. After five days, the plants were transferred in a 10-8 M Myc-LCO or Nod factors solution during 4 h and 24 h before being pooled dependently to the induction. For comparison between roots, root tips (1 cm long), plants of the Jemalong A17 genotype were cultivated in a hydroponic culture system on N-containing Fahräeus medium during 10 days at 23°C and 75% humidity (16-hour light/8-hour dark cycle). For the interaction with root pathogens, seedlings from the Jemalong A17  genotype, known to be susceptible to Ralstonia solanacearum GMI1000 strain and resistant to Verticillium albo-atrum V31.2 strain, were grown in an hydroponic culture system on N-containing Farhäeus medium in a growth chamber with 16 h light (170 µmol m–2 s–1) at 25 °C and 8 h dark at 23 °C. Inoculation with V. albo-atrum was performed as described in paper Ben C. Journal of experimental botany 2013. Inoculated plants were then transferred back to the nutritive solution and incubated in a growth chamber at 20 °C with 16 h photoperiod. For inoculation with R. solanacearum, cut roots were immersed for 30 min in a bacterial solution of the GMI1000 strain at a concentration of 108CFU/ml. Inoculated plants and controls treated with water were then placed in a phytotron with 12 h light (170 µmol m–2 s–1) at 28 °C and 12 h dark at 26 °C. For each condition of inoculation, samples were obtained as pools of roots of five to fifty  plants harvested every day from one day to one week after inoculation.

extract_protocol:
Plant roots were harvested and crushed with liquid nitrogen. For the Myc-LCO and Nod factor libraries and their corresponding controls, total RNA were isolated from 100 mg of powder with the mirVana miRNA isolation kit (Ambion) according to the manufacturer’s instructions. For the other libraries, total RNAs were extracted using 1 mL of Trizol per 50-100 mg of powder. Phenol-Chloroform separation, isopropanol precipitation, ethanol wash and RNA solubilization were performed according to the TRI REAGENT manufacturer’s instructions. RNA integrity and quality have been checked thanks to the Agilent Bioanalyzer 2100.
The smRNA libraries were obtained thanks to the Small RNA Sample Prep kit from Illumina according to the “Preparing Samples for Small RNA sequencing using the Alternative v1.5” protocol. libraries were sequenced using HiSeq Solexa sequencer from Illumina.

treatment_protocol: For the induction by both Myc-LCO and Nod factors, the A17 plants were obtained in the same way but with Fahraeus medium adjusted at 7.5 µM of phosphate. After five days, the plants were transferred in a 10-8 M Myc-LCO or Nod factors solution during 4 h and 24 h before being pooled dependently to the induction. For comparison between roots, root tips (1 cm long), plants of the Jemalong A17 genotype were cultivated in a hydroponic culture system on N-containing Fahräeus medium during 10 days at 23°C and 75% humidity (16-hour light/8-hour dark cycle). For the interaction with root pathogens, seedlings from the Jemalong A17  genotype, known to be susceptible to Ralstonia solanacearum GMI1000 strain and resistant to Verticillium albo-atrum V31.2 strain , were grown in an hydroponic culture system on N-containing Farhäeus medium in a growth chamber with 16 h light (170 µmol m–2 s–1) at 25 °C and 8 h dark at 23 °C. Inoculation with V. albo-atrum was performed as described in  Ben C. Journal of experimental botany 2013. Inoculated plants were then transferred back to the nutritive solution and incubated in a growth chamber at 20 °C with 16 h photoperiod. For inoculation with R. solanacearum, cut roots were immersed for 30 min in a bacterial solution of the GMI1000 strain at a concentration of 108CFU/ml. Inoculated plants and controls treated with water were then placed in a phytotron with 12 h light (170 µmol m–2 s–1) at 28 °C and 12 h dark at 26 °C. For each condition of inoculation, samples were obtained as pools of roots of five to fifty  plants harvested every day from one day to one week after inoculation.For the interaction with Rhizophagus irregularis  (DAOM197198), plants from the A17 line were grown in a greenhouse (16-hour light/8-hour dark cycle) for 7 weeks in a soil substrate inoculated with 1000 spores/liters. The substrate was hydrated with a Long-Ashton solution with a phosphate concentration of 7.5 µM. The well-established mycorrhization was controlled by the grid intersection method. For the interaction with Sinorhizobium meliloti  plants from the sunn-sickle  hypernodulating double mutant  were grown in an aeroponic chamber at 23 °C and 75 % of humidity during five days (16-hour light/8-hour dark cycle) in a nitrogen-less liquid Fahraeus medium nebulization inoculated with bacteria .

value: Root


title: sRMycNod1

status: Public on Aug 15 2014

type: SRA

description: small RNA fraction

library_source: transcriptomic

molecule: total RNA

tag: tissue


title: sRNod2

description: small RNA fraction

source_name: Root, treated with NOD factor


title: Microglia1

city: Dallas

first: kenian

last: chen

state: TX

address: 5323 Harry Hines Boulevard

department: Population and Data Science

country: USA

institute: UTsouthwestern

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Reads were mapped to reference genome (version mm9) using Tophat (version 1.3.3) which uses the Bowtie (version 0.12.7)read mapper, Tophat was fed with the option of“–no-novel-juncs”and  option "–G" which supplies Tophat with known transcript GTF file (download from cufflinks website)
Mapped reads were assembled into RNA transcripts using the Cufflinks software (version 1.3.0). Cufflinks was run using the annotation file (downloaded from Cufflinks web site) of known genes and the mapped reads produced by Tophat. FPKM values (Fragments Per Kilobase of exon model per Million mapped fragments, a normalized gene expression value that are comparable between different samples and genes) together with confidence intervals were estimated for each replicate.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: cerebral cortex

extract_protocol:
Total RNA was extracted using the miRNeasy kit (Qiagen) under manufactor’s protocols. The quality was accessed by BioanalyzerTM. Samples with high RNA integrity number (RIN) (>8) were used for library construction. 100ng total RNAs were used for each sequencing library.
RNA samples were polyA selected and paired-end sequencing libraries were constructed using TruSeq RNA Sample Prep Kit as described in the TruSeq RNA Sample Preparation V2 Guide (Illumina).

tag: strain

value: FVN/Swiss

value: cerebral cortex

tag: cell type

value: microglia


title: Microglia2


title: MO2

value: myelinating oligodendrocytes


title: MO1


title: sRNod1

description: small RNA fraction


title: sRNod3

description: small RNA fraction


title: sRMyc3

description: small RNA fraction

source_name: Root, treated with Myc-LCO factor


title: NFO2

value: newly formed oligodendrocytes


title: WC3

source_name: whole cortex


title: NFO1


title: OPC2

value: oligodendrocyte precursor cells


title: sRMycNod2

description: small RNA fraction


title: sRMyc2

description: small RNA fraction


title: Neuron1

value: neuron


title: Neuron2


title: sR4

description: small RNA fraction

source_name: Root, untreated

value: Root tips


title: sRMyc1

description: small RNA fraction


title: OPC1


title: Astrocyte1

value: Astrocyte


title: sRNoGi

description: small RNA fraction


title: sRGI

description: small RNA fraction

source_name: Root, Rhizophagus irregularis-infected


title: sSNRSm

description: small RNA fraction

source_name: Supernodulator Root, Sinorhizobium meliloti Sm2011-infected


title: sRS

description: small RNA fraction

source_name: Root, treated by Salt (NaCl 100mM)


title: sR

description: small RNA fraction


title: 078265N

city: Beijing

first: Tao

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute Of Biological Sciences, Beijing (NIBS)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to hg19 whole genome using Tophat v2.0.4 with parameters -i 10 -I 80000 --solexa1.3-quals --min-coverage-intron 20 --max-coverage-intron 11000 --min-segment-intron 10 --max-segment-intron 81000 --segment-length 20 -G genes.gtf -g 10 -p 15
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.2) with the provision of a GTF annotation file (hg19).
Gene expression differences were assessed by Cuffdiff, with false discovery rate correction for multiple testing.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Homo sapiens

source_name: liver tissue

extract_protocol:
trizal reagent to prepare total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: tumor and paratumoral tissue were resected and RNAlater reagents treated immediately for overnight, followed by -80 freezer storage before use

value: paratumoral liver tissue


title: sRRs

description: small RNA fraction

source_name: Root, Ralstonia solanacearum GMI1000-infected


title: sRNoRs

description: small RNA fraction


title: Vir

description: small RNA fraction

source_name: Leaves, untreated

value: Leaves


title: sRVaa

description: small RNA fraction

source_name: Root, Verticillium albo-atrum-infected


title: sSNR

description: small RNA fraction

source_name: Supernodulator Root, untreated


title: 078265T

value: HCC


title: sR2

description: small RNA fraction


title: 078222T


title: 078222N


title: 082552T


title: sRS2

description: small RNA fraction

source_name: Root, treated by Salt


title: 082552N


title: Astrocyte2


title: 070830T


title: 070830N


title: inp_Suz12_mixed_2

status: Public on Aug 14 2014

city: Boston

first: Ruslan

last: Sadreyev

state: Massachusetts

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

library_source: genomic

data_processing:
OLB 1.9.0 / RTA 1.13 used for base-calling
CHIPseq reads aligned to dm3 using BWA, allowing up to 1 mismatch and otherwise default settings
Data were filtered for reads aligning to multiple positions, pcr duplicates, and inferred fragment size <100 or >800.
Genome_build: dm3
Supplementary_files_format_and_content: Wig files generated using SPP's "smoothed.density" function, following default guidelines estimating peak separation distance and removing low quality and anomalous tags.

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Eggs were harvested 5-13h after laying, nuclei extracted and marked parasegment-specific nuclei sorted by FACS

extract_protocol:
Nuclei were sonicated and ChIP performed using the appropriate antibody.
Libraries were prepared as described in Bowman et al., 2013.

value: embryo

tag: age

tag: tissue subtype

value: whole embryo


title: inp_Suz12_PS7_2

value: parasegment 7


title: inp_Pc_PS7_2


title: inp_Pol2_PS7_1


title: inp_CTCF_mixed_1


title: inp_Suz12_Pol2_mixed_1


title: Suz12_mixed_2

tag: chip antibody

tag: chip antibody ref.

value: Müller et al 2002


title: Suz12_PS7_2


title: Suz12_mixed_1


title: Pol2_PS7_1

value: anti-RNA Pol II phospho-S5

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#


title: Pol2_mixed_1


title: Control Input

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

description: Input DNA

data_processing:
Sequenced 36-bp reads were aligned to the reference genome (mouse mm9 assembly) using Bowtie algorithm. Those reads that mapped to unique genomic locations with at most two mismatches were retained for further analysis
Peaks were called using SISSRS  [PMID: 18684996]
Genome_build: mm9
Supplementary_files_format_and_content: TEXT files containing the list of binding sites as defined by SISSRs [PMID: 18684996]

source_name: E14Tg2a ES Cells

growth_protocol: Mouse ES cells were routinely maintained on gelatin-coated plates in the ESGRO complete plus clonal grade medium (Millipore). For ChIP experiments, passage 20-35 cells were cultured in M15 medium: DMEM (Invitrogen) supplemented with 15% FBS (vol/vol), 10 mM 2-mercaptoethanol, 0.1 mM nonessential amino acids (Invitrogen), 1× EmbryoMax nucleosides (Millipore), and 1U per ml of ESGRO mLIF (Millipore)

extract_protocol:
Input and ChIP DNA were size-selected (~200-500nt).
Libraries were prepared from size-selected Input and ChIP DNA according to the standard Illumina library preparation protocol

treatment_protocol: ES cells in culture dishes were cross-linked with 1% formaldehyde for 10 minutes, processed for chromatin lysate preparation and chromatin immunoprecipitation (ChIP). Chromatin lysate was sonicated with a Bioruptor system (Diagenode) to yield a DNA smear averaging ~200-500 bp. Sonicated chromatin lysate from 5 million ES cells was used for each ChIP with 2 µg antibody.

value: Embryonic stem cells


title: KO4 [RNA-seq]

city: Cleveland

first: Xiaodong

last: Bai

address: 10900 Euclid Avenue

department: Center for RNA Molecular Biology

institute: Case Western Reserve University

description: isolated retinal mRNA

data_processing:
Base-calling was performed using the Illumina pipeline software ELAND v1.7
Data were processed and aligned with the University of California-Santa Cruz (UCSC) mouse genome assembly and transcript annotation (mm9) using Genomic Short-read Nucleotide Alignment Program (GSNAP),.
The raw read counts for mouse RefSeq genes were extracted using HTSeq-count program and used for calculations of reads per kilobase per million mapped reads (RPKM) values
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample

source_name: cKO retina

extract_protocol:
Mice were euthanized by cervical dislocation. Eyes were enucleated and retinas were dissected and immediately placed in RNAlater stabilization reagent (Qiagen, Valencia, CA, USA) to preserve RNA content and integrity.
Two mouse retinas were homogenized at once and passed through a QIAShredder column (Qiagen) as per manufacturer’s directions to further homogenize the  tissues. Total RNA was then purified by using the RNeasy Mini Kit (Qiagen) with on column DNase treatment (Qiagen) as per manufacturer’s directions. Poly(A) RNA was isolated with the Oligotex kit (Qiagen) as per the manufacturer’s instructions. Pooled total RNA samples of 4 mice 4 weeks of age were used for each retina library preparation.  For first strand cDNA synthesis, instructions from the SuperScript III kit protocol (Invitrogen) were followed. About 400-450 ng of isolated poly(A) RNA was mixed with 50 ng of random primers and 1 mM deoxyribonucleotide triphosphate (dNTP), incubated at 65°C for 5 min and then placed on ice for 5 min. A reaction mixture comprising 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT, and 200 U SuperScript III reverse transcriptase was added to the initial mix to achieve a total volume of 20 µL. The mixture was incubated at 25°C for 10 min, followed by 50 min at 50°C. The reaction was terminated at 85°C for 5 min and then chilled on ice for 10 min. At this point, 2 U RNase H was added and the mix was incubated at 37°C for 20 min. The first strand cDNA synthesis reaction was immediately used for second strand synthesis. To the first strand product, 300 µM dNTP, E. coli DNA polymerase I buffer, and water was added to obtain a total volume of 95 µL and allowed to incubate on ice for 10 min. Then, 0.05 U E. coli DNA polymerase I (New England Biolabs, Beverly, MA, USA) was added and the mixture was incubated at 16°C for 2.5 h. The resulting double stranded cDNA was purified with the Wizard SV Gel and PCR Clean-up System (Promega, Madison, WI, USA) and eluted in 100 µL nuclease-free water and then fragmented by the Covaris S2 instrument (Woburn, MA, USA) to generate ~200 bp fragments as follows: 10% duty cycle, intensity of 5, 100 cycles per burst, with a bath temperature of 7.7°C and an acoustic power of 24 W.   The Illumina library was prepared according to the manufacturer’s instructions and purified using the Wizard SV Gel and PCR Clean-up System (Promega). Overhangs were converted into blunt ends with T4 DNA polymerase and Klenow DNA polymerase by incubating the mixed sample at 20°C for 30 min. cDNA was purified and eluted in 32 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The purified sample was then mixed with Klenow fragment (3’ to 5’ exo minus) and incubated at 37°C for 30 min to add an ‘A’ base to the 3’ end of the blunt phosphorylated DNA fragments. The cDNA was then purified and eluted in 23 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). Eluted DNA was mixed with Illumina Adapter Oligo mix and T4 DNA ligase and incubated at room temperature for 15 min to ligate adapters to the ends of the DNA fragments to prepare them for hybridization to the flow cell. cDNA then was purified and eluted in 10 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). cDNAtemplates were purified by running samples on a 1% agarose gel at 120 V for 60 min and excising the region of the gel in the 200 bp range. The 200 bp cDNA enriched fragments were purified and eluted in 30 µL of nuclease free water with the Wizard PlusMinipreps DNA purification system (Promega). cDNA in the library was then amplified by a 15 cycle PCR with two primers that annealed to the ends of the adapters. The amplified cDNA was purified and eluted in 30 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The size, purity and concentration of the final library was checked with the Bio-Rad Experion DNA specific chip. Each library was sequenced as one lane on an Illumina HiScan instrument.

tag: strain background

value: Mixed C57BL/6J - SJL

tag: genotype/variation

value: Dicerfl/fl, iCre75+

value: 4 Weeks

value: Retina


title: ChIP-Seq NF-YA

description: ChIP DNA

value: NFYA:Santa-cruz, NF-YA (G-2)X, sc-17753X, Mouse monoclonal IgG2a


title: WT1 [RNA-seq]

description: isolated retinal mRNA

source_name: control retina

value: Dicerfl/fl, iCre75-


title: ChIP-Seq NF-YB

description: ChIP DNA

value: NFYB:Santa-cruz, NF-YB (FL-207)X, sc-13045X, Rabbit polyclonal


title: WT2 [RNA-seq]

description: isolated retinal mRNA


title: WT3 [RNA-seq]

description: isolated retinal mRNA


title: KO3 [RNA-seq]

description: isolated retinal mRNA


title: KO2 [RNA-seq]

description: isolated retinal mRNA


title: ChIP-Seq NF-YC

description: ChIP DNA

value: NFYC:Santa-cruz, NF-YC (N-19)X, sc-7715X, Rabbit polyclonal


title: inp_Suz12_PS7_1


title: inp_Pol2_mixed_2


title: inp_Pc_PS7_1


title: Pc_mixed_2

value: anti-Pc

value: Schuettengruber et al 2009


title: inp_Pc_mixed_1

value: embryo


title: inp_Pc_mixed_2

value: whole embryo


title: Pc_PS7_1

value: parasegment 7


title: IgG_1

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

data_processing:
The 3'-adapter sequence was first removed (using fastx_clipper -a TGGAATT), and reads with a length of <15 nts were discarded.
Reads were mapped to the human genome (hg19) using Bowtie2 (local mode) with parameters "--local -5 4 -3 4". Reads with a mapping quality score (MAPQ) of ≥10 were selected for further analysis.
mRNA abundance was measured using reads per kilobase per million reads (RPKM) based on exonic regions of RefSeq sequences.
Genome_build: hg19
Supplementary_files_format_and_content: uniquely mapped reads, the 5th column in bed file represents read number

source_name: Human embryonic kidney (HEK) 293T cells

growth_protocol: HEK293T cells (24 x 107/3 x 150-mm dishes) were incubated in 200 nM okadaic acid for three hours.

extract_protocol:
Cellular RNAs bound by p-UPF1 were immunoprecipitated using anti-p-UPF1(S1116) (Millipore, anti-phospho-Upf1(Ser1127)) and Dynabeads protein A magnetic beads (Life Technologies). The RNA in bead-bound RNA p-UPF1(S1116) complexes was digested to primarily  100 nts by incubation for 30 min at 4°C with RNase I (1U/l; Life Technologies); for RNA size estimations after RNase I digestion, ~200 ng of RNA were radio-labeled using  32P-ATP (Perkin Elmer) and T4 polynucleotide kinase (New England Biolabs) and subsequently visualized using a Typhoon 9410 Variable Mode Imager (GE Healthcare) after electrophoresis in 6M urea 15% polyacrylamide. After extensive washing, bound complexes were eluted using IP elution buffer (Kurosaki and Maquat 2013), and RNA fragments were purified using TRIzol Reagent and then separated in 6M urea 15% polyacrylamide in parallel with a DynaMarker Prestain Marker for Small RNA (BioDynamics Laboratory). Small-range RNAs (~25-40 nts) were excised from 6M urea 15% polyacrylamide and agitated overnight at 25°C in RNA extraction buffer (20 mM Tris, 300mM sodium acetate, 2 mM EDTA, 0.2 % v/v SDS). RNAs were eluted from 6M urea 15% polyacrylamide gel using a Coaster Spin-X column (Corning) and further purified using TRIzol Reagent followed by ethanol precipitation. In parallel, control IPs using rabbit IgG were performed. Additional control samples were prepared without IP.
Purified 25-40-nt RNA fragments were treated with recombinant shrimp alkaline phosphatase (New England Biolabs) to remove 3'-phosphates and subsequently phosphorylated at 5'-hydroxyl groups using T4 polynucleotide kinase (New England Biolabs). Phosphorylated RNA fragments were purified with RNeasy Mini Columns (Qiagen). A 3'-adenylated adapter was ligated to the phosphorylated RNA fragments using truncated T4 RNA ligase (New England Biolabs). An RT primer was annealed to the adapted RNAs to prevent adapter self-ligation, followed by 5' RNA adapter ligation using T4 RNA ligase (New England Biolabs). After RT of adapter-ligated RNAs, cDNAs were amplified using 15 PCR cycles. Amplified cDNAs were purified in 8% polyacrylamide, and the quality and quantity of cDNAs were assessed using an Agilent Bioanalyzer and qPCR. cDNAs were then sequenced using the Illumina HiSeq 2500 platform.

tag: cell line

value: Human embryonic kidney

tag: ip antibody

value: rabbit IgG


title: inp_Pol2_PS7_2


title: Pol2_mixed_2

value: anti-RNA Pol II phospho-S5

value: Abcam


title: Pol2_PS7_2


title: Pc_PS7_2


title: CTCF_mixed_1

value: anti-CTCF

value: Smith et al., Developmental Biology 2009


title: inp_H3K27ac_PS7_1

description: nuclei from embryo 5-13h

data_processing:
OLB 1.9.0 / RTA 1.13 used for base-calling
CHIPseq reads aligned to dm3 using BWA, allowing up to 1 mismatch and otherwise default settings
Data were filtered for reads aligning to multiple positions, pcr duplicates, and inferred fragment size <100 or >800.
Genome_build: dm3; GCA_000001215.2
Supplementary_files_format_and_content: Wig files generated using SPP's "smoothed.density" function, following default guidelines estimating peak separation distance and removing low quality and anomalous tags.

extract_protocol:
Nuclei were digested with MNase, solubilized and ChIP performed using the appropriate antibody.
Libraries were prepared as described in Bowman et al., 2013.


title: inp_H3K27ac_PS7_2

description: nuclei from embryo 5-13h


title: inp_Ph_PS7_1

description: nuclei from embryo 5-13h


title: inp_H3K4me3_PS7_2

description: nuclei from embryo 5-13h


title: inp_Ph_mixed_1

description: nuclei from embryo 5-13h


title: inp_H3K4me3_PS7_1

description: nuclei from embryo 5-13h


title: inp_CTCF_PS7_2

description: nuclei from embryo 5-13h


title: inp_H3K4me3_mixed_1

description: nuclei from embryo 5-13h


title: inp_H3K27ac_mixed_2

description: nuclei from embryo 5-13h


title: inp_CTCF_mixed_2

description: nuclei from embryo 5-13h


title: inp_H3K27me3_PS7_2

description: nuclei from embryo 5-13h


title: inp_CTCF_PS7_1

description: nuclei from embryo 5-13h


title: inp_H3K27ac_mixed_1

description: nuclei from embryo 5-13h


title: inp_H3K27me3_PS5_2

description: nuclei from embryo 5-13h

value: parasegment 5


title: inp_H3K27me3_PS5_1

description: nuclei from embryo 5-13h


title: inp_H3K27me3_PS6_1

description: nuclei from embryo 4-10h

value: parasegment 6


title: inp_H3K27me3_PS6_2

description: nuclei from embryo 4-10h


title: inp_Ph_PS7_2

description: nuclei from embryo 5-13h


title: Mut2 [small RNA-seq]

description: cKO replicate 2; isolated retinal small RNAs

data_processing:
Base-calling was performed using the Illumina pipeline software ELAND v1.7
Reads were processed to remove Illumina adapter sequences and associated with samples based on the multiplex identifier. Identical reads were grouped into clusters before being mapped to mouse miRNA sequences from miRBASE (50) using the bowtie program (51)
Identical reads were grouped into clusters before being mapped to mouse miRNA sequences from miRBASE using the bowtie program
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

extract_protocol:
Mice were euthanized by cervical dislocation. Eyes were enucleated and retinas were dissected and immediately placed in RNAlater stabilization reagent (Qiagen, Valencia, CA, USA) to preserve RNA content and integrity.
Total RNA was isolated from a pool of 6 retinas per library. After removal of RNALater, Qiazol (Qiagen, Germantown, MD) was added and the tissue was disrupted using a Tissuelyser II bead mill. RNA was purified from the Qiazol homogenate using the Zymo Direct-zol (Zymo Research, Irvine, CA) protocol with on-column DNase I digestion. Libraries were made from 1 µg of total RNA utilizing the Illumina (San Diego, CA) Truseq Small RNA Sample Preparation kit, amplified with 11 rounds of PCR, and size selected for micro-RNA size inserts by gel purification. Each library was prepared to incorporate a unique index sequence which permitted multiplexing of all six libraries for sequencing. Final libraries were analyzed and quantified using the Bioanalzyer and pooled in equimolar proportions. The pooled libraries were sequenced as one 50 bp single-end run on an Illumina HiSeq 2500 instrument using a rapid-run flowcell.

value: Mixed C57BL/6J - SJL

value: Dicerfl/fl, iCre75+

value: 4 Weeks

value: Retina

tag: molecule subtype

value: Small RNAs/miRNA


title: inp_H3K27me3_PS4_1

description: nuclei from embryo 5-13h

value: parasegment 4


title: inp_H3K27me3_PS7_1

description: nuclei from embryo 5-13h

value: embryo


title: inp_H3K27me3_mixed_1

description: nuclei from embryo 5-13h

value: whole embryo


title: inp_H3K27me3_mixed_2

description: nuclei from embryo 5-13h


title: Mut1 [small RNA-seq]

description: cKO replicate 1; isolated retinal small RNAs


title: inp_H3K4me3_mixed_2

description: nuclei from embryo 5-13h


title: inp_H3K27me3_PS4_2

description: nuclei from embryo 5-13h


title: WT3 [small RNA-seq]

description: Control replicate 3; isolated retinal small RNAs

value: Dicerfl/fl, iCre75-


title: Pc_mixed_1

value: anti-Pc

value: Schuettengruber et al 2009


title: WT1 [small RNA-seq]

description: Control replicate 1; isolated retinal small RNAs


title: Ph_PS7_1

description: nuclei from embryo 5-13h

value: parasegment 7

value: anti-Ph (residues 772-984)

value: Oktaba et al., 2008


title: WT2 [small RNA-seq]

description: Control replicate 2; isolated retinal small RNAs


title: Ph_PS7_2

description: nuclei from embryo 5-13h


title: cKO.2_RNAseq

city: Gifu

first: Takashi

last: MaruYama

address: 1-1 Yanagido

country: Japan

institute: Gifu University

data_processing:
Basecalls performed using CASAVA version 1.8.
38bp reads aligned to genome using bowtie program with default settings on TopHat 2.0, filtered with low Phred score(< 25), converted to BED files using SamTools, filtered rRNAs and tRNAs annotations using IntersectBed command in BEDtools.
Gene annotations were found using RegionMiner on Genomatix Genome Analyzer, inputting BED files, processed across 2 replicates for identification of differentially expressed genes between cKO and Ctrl
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include NE values for each Sample. A normalized expression value (NE-value) calculated based on the following formula: NE =10^7 * the number of reads in transcripts / the number of total reads mapped * length of the transcripts.

source_name: Splenic B cells

growth_protocol: Purified splenic B cells cultured under LPS (20 mg/ml) stimulation for 72 h in RPMI 1640 medium supplemented with 10% heat-inactivated FCS, 100 U/mL penicillin, 100 mg/mL streptomycin, 2 mM L-glutamine, 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, and 50 mM 2-mercaptoethanol at 37degree in 5% CO2.

extract_protocol:
Total RNA was extracted by using RNeasy (Qiagen)
NEBNext Ultra RNA Library Prep Kit for Illumina

value: LPS stimulated B cells

value: cKO

tag: passage


title: Mut3 [small RNA-seq]

description: cKO replicate 3; isolated retinal small RNAs


title: H3K4me3_PS7_2

description: nuclei from embryo 5-13h

value: Millipore

tag: chip antibody cat. #


title: Control.2_RNAseq

value: control


title: Control.1_RNAseq


title: cKO.1_RNAseq


title: Ph_mixed_2

description: nuclei from embryo 5-13h


title: REC1_Washout_3

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

data_processing:
Sequence reads were aligned to the hg19 genome using TopHat
Gene expression levels were called using Cufflinks
Differential expressed genes were called using CuffDiff
Genome_build: hg19
Supplementary_files_format_and_content: FPKM expression level table

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% FBS and 2mM L-glutamine.  Cells were passaged every 3 days.  CUTTL cells >20 passages were discarded

extract_protocol:
Cells were collected and the pellets lysed in Trizol solution.  Extraction was performed using a Qiagen RNA preparation kit per standard protocol
Libraries were constructed using purified total RNA as above.  Polyadenylated mRNA was purified, and the library for RNAseq was constructed using the Truseq v2 kit (Illumina).  Quality control was assessed by BioA analysis (Agilent Technologies) prior to library construction and again prior to sequencing

treatment_protocol: Cells were treated with 1uM GSI (or DMSO vehicle) for 24 hours (HCC1599) or 72 hours (CUTLL and REC1), washed extensively in growth media without GSI/DMSO, then replated back into growth media with or without GSI. "Control" cells were grown in DMSO and replated into DMSO.  "GSI" cells were grown in GSI and replated into GSI.  "Washout" cells were grown in GSI and replated into DMSO.  Cyclohexamide was not used in any of the experiments.

value: Mantle cell lymphoma cell line containing an activating Notch1 mutation

tag: treatment

value: GSI 72 hrs, wash out 4 hrs


title: H3K4me3_mixed_1

description: nuclei from embryo 5-13h

tag: tissue


title: H3K4me3_mixed_2

description: nuclei from embryo 5-13h


title: H3K27ac_PS7_1

description: nuclei from embryo 5-13h

value: Active Motif


title: REC1_GSI_2

value: GSI 72 hrs


title: H3K27ac_PS7_2

description: nuclei from embryo 5-13h


title: H3K27ac_mixed_2

description: nuclei from embryo 5-13h


title: REC1_Washout_2


title: REC1_Control_2

value: vehicle


title: CTCF_PS7_2

description: nuclei from embryo 5-13h

value: embryo

value: anti-CTCF

value: Smith et al., Developmental Biology 2009


title: REC1_Washout_1


title: CTCF_PS7_1

description: nuclei from embryo 5-13h


title: REC1_GSI_1


title: Ph_mixed_1

description: nuclei from embryo 5-13h

value: whole embryo


title: H3K27me3_PS7_2

description: nuclei from embryo 5-13h


title: REC1_GSI_3


title: CTCF_mixed_2

description: nuclei from embryo 5-13h


title: REC1_Control_1


title: HCC1599_GSI_3

value: Triple negative breast cancer cell line containing an activating Notch1 mutation, grown in suspension


title: H3K27me3_PS6_2

description: nuclei from embryo 4-10h

value: parasegment 6


title: HCC1599_Control_3


title: H3K27me3_PS6_1

description: nuclei from embryo 4-10h


title: HCC1599_Washout_2


title: HCC1599_GSI_2


title: HCC1599_Control_2


title: H3K27me3_PS4_2

description: nuclei from embryo 5-13h

value: parasegment 4


title: H3K27me3_PS5_1

description: nuclei from embryo 5-13h

value: parasegment 5


title: H3K27me3_PS4_1

description: nuclei from embryo 5-13h


title: HCC1599_GSI_1


title: HCC1599_Control_1


title: H3K27me3_mixed_2

description: nuclei from embryo 5-13h


title: CUTLL_Washout_3

value: T-ALL cell line containing a t(7;9) rearrangement and aberrant NOTCH1 activation


title: HCC1599_Washout_1


title: H3K27me3_mixed_1

description: nuclei from embryo 5-13h


title: HCC1599_Washout_3


title: CUTLL_Washout_2


title: H3K27me3_PS7_1

description: nuclei from embryo 5-13h

value: parasegment 7


title: med27 RNAi central brain pupal neuroblasts 2 (Tech. Rep. 2)

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

data_processing:
Basecalls performed using RTA v1.13.48.0
The strand specific paired-end reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq). Non matching reads were considerd downstream.
The rRNA subtracted paired-end reads were aligned with TopHat (v1.4.1) against the Drosophila melanogaster genome (FlyBase r5.44) and a maxiumum of 6 missmatches.  Introns between 20-150000 bp are allowed which is based on FlyBase statistics. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (FlyBase r5.44).
Aligned reads in valid pairs are subjected to FPKM estimation with Cufflinks (v1.3.0). In this step bias detection and correction was performed. Furthermore, only those fragments compatible with FlyBase annotation (r5.44) were allowed and counted towards the number of mapped hits used in the FPKM denominator.  snRNA, rRNA, tRNA, snoRNA and pseudogenes are masked.
The aligned reads were counted with HTSeq. Counts for technical replicates are summed up. The polyA containing transcripts were subjected to differential expression analysis with DESeq (v1.8.3). DESeq parameters were chosen to match the DESeq publication (Anders S, Huber W., 2010).
Genome_build: FlyBase dmel_r5.44
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (Standard output cufflinks); tab-delimited text file with differentially expressed genes for the whole analysis (standard output DESeq).

source_name: pupal brain

growth_protocol: Flies expressing UAS-CD8::GFP in background containing empty Landing site VIE-260B (VDRC TID:60100) or UAS-CD8::GFP and med27 RNAi (VDRC TID:106703) under inscuteable-Gal4 were flipped on fresh food, left to lay for 24 h, flipped into fresh vials and then kept at 29oC degree for five or 6 days respectively, before dissection of late 3rd instar larval or 0-2hrs pupal brains.

extract_protocol: Central brain neuroblasts (large cells, high GFP expression) were FACS sorted from wild type (TID:60100) or med27 RNAi and RNA was isolated using Trizol reagent. Total RNA(~1µg) was enriched for polyA mRNA, fragmented and first strand and second strand (dUTP, instead dTTP was used) was generated. Library preparation was done using a modified protocol from Illumina with NEBNext DNA sample Prep Reagent kits (NEB), and UGDase treatment was done to confer strand specificity.

value: Neuroblasts

tag: Stage

value: 0-2hr after pupa formation

tag: marker

value: cells express membrane-bound GFP marker (UAS-CD8::GFP)

value: med27 RNAi


title: med27 RNAi central brain pupal neuroblasts 2 (Tech. Rep. 1)

tag: cell type


title: CUTLL_Washout_1

value: GSI 72 hrs, wash out 4 hrs


title: CUTLL_GSI_3

value: GSI 72 hrs


title: med27 RNAi central brain pupal neuroblasts 1 (Tech. Rep. 2)


title: med27 RNAi central brain pupal neuroblasts 1 (Tech. Rep. 1)


title: CUTLL_GSI_2


title: H3K27me3_PS5_2

description: nuclei from embryo 5-13h

tag: age

tag: tissue subtype

value: Active Motif


title: CUTLL_GSI_1


title: wild-type central brain pupal neuroblasts 2 (tech. Rep. 2)


title: wild-type central brain pupal neuroblasts 2 (tech. Rep. 1)


title: CUTLL_Control_3

value: vehicle


title: CUTLL_Control_2


title: WT Treg 1032

city: New York

first: Aaron

last: Arvey

state: NY

institute: Memorial Sloan-Kettering Cancer Center

description: WT Treg

data_processing:
Reads were aligned using STAR and BWA.
Raw counts were normalized by edgeR
Differential expression was computed using edgeR
Genome_build: mm9

source_name: Treg

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions
SMARTer amplification was followed by the standard Proton preparation protocol

tag: cell source

value: Primary Mouse T cells isolated ex-vivo and sorted


title: wild-type central brain pupal neuroblasts 1 (tech. Rep. 2)


title: CNS2KO Treg 407

description: CNS2KO Treg


title: CNS2KO Treg 408

description: CNS2KO Treg


title: wild-type central brain pupal neuroblasts 1 (tech. Rep. 1)


title: WT Treg 405

description: WT Treg


title: CNS2KO Treg 399

description: CNS2KO Treg


title: CUTLL_Control_1


title: wild type central brain larval neuroblasts 2

source_name: larval brain

value: late third instar larva


title: WT Treg 407

description: WT Treg


title: WT Treg 402

description: WT Treg


title: sRS4

description: small RNA fraction

value: Root tips


title: Suz12_PS7_1

value: embryo

tag: chip antibody

tag: chip antibody ref.

value: Müller et al 2002


title: WT Treg 398

description: WT Treg


title: aFLe2_mRNAseq

city: Basel

first: Patrick

last: Tschopp

address: Vesalgasse 1

department: Department of Environmental Sciences

country: Switzerland

institute: University of Basel

data_processing:
base calling using standard Illumina software
Adaptor sequences were trimmed using FASTX_trimmer (Hannon lab)
Reads were mapped to genome builds mm9 (Mus musculus; using UCSC mm9 refseq annotation) and Anocar2.0 (Anolis carolinensis; using ASU_Acar version 2.1 annotation) using RNA-Seq unified mapper (RUM) verison 1.11 (Grant et al., 2011)
To account for species-specific differences in non-uniquely mapping (NU) reads, we redistributed NU reads based on the number of uniquely mapping (U) reads mapping to the respective loci, following the logic outlined in Brawand et al, 2011
Only orthologous genes found in both species were used for further analyses
Genome_build: mm9, Anocar2.0
Supplementary_files_format_and_content: tab-delimited text files including total read counts for all samples of the same species

organism: Anolis carolinensis

source_name: embryonic tissue

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Life Technologies) and enriched for mRNA fraction using MPG mRNA Purification Kit (PureBiotech)
Multiplexed RNA-seq libraries were produced using the SPIA cDNA synthesis kit and the Ovation Ultralow DR Multiplex system (NuGen)

tag: tissue type

value: forelimb bud

value: stage 3


title: aFLe1_mRNAseq


title: aTBe2_mRNAseq

value: tailbud


title: tjGAL4>RnpS1 RNAi

first: Colin

middle: Dean

last: Malone

address: NYUMC, Skirball Institute, 540 1st Ave, 4-10

department: Skirball Institute - Developmental Genetics

institute: NYU Medical Center

description: Test case 4

data_processing:
Illumina Genome Analyzer II, GPL13304
Illumina reads were stripped of the 3’ linker (CTGTAGGCACCATCAATC) and then 5nts at both the 5' and 3' ends were trimmed, due to the addition of 5 randomized nucleotides on each small RNA adapter to limit cloning biases. The resulting small RNA sequences were mapped to the Release 5 genome excluding the Uextra portion. Only reads matching the fly genome 100% were used for further analysis. For annotation, we used Flybase for protein coding genes, UCSC for non-coding RNAs and transposons/repeats (repeat masker tracks) and the most recent miRNA catalog. To control for sequencing depth, small RNA counts were normalized to the same total number after subtracting those matching abundant cellular RNAs such as rRNAs and tRNAs. For the piRNA analysis, we selected small RNAs, which exceeded 22 nt in length and were not annotated as miRNA, tRNA, rRNA, snoRNA, snRNA or smRNA. All small RNAs were converted into DNA for sequencing, therefore U's are represented as T's.
Genome_build: Dm3
Supplementary_files_format_and_content: csv format with MAPNUM = the number of times a read maps to the Dm3 genome assembly.

source_name: knockdown

growth_protocol: 25 degree C, aged for 3-5 days with added yeast

extract_protocol:
Trizol
Small RNA library production as previously described (Brennecke, et al, 2007, Cell)

treatment_protocol: Trizol/Phenol Chloroform extraction

tag: strain background

value: 3-5 days old

tag: genotype/variation

value: tjGAL4>RnpS1 RNAi

value: ovary

value: 19-28nt from total RNA


title: tjGAL4>mago nashi RNAi

description: Test case 3

value: tjGAL4>mago nashi RNAi


title: WT Treg 1037

description: WT Treg


title: tjGAL4>CyO control

description: Soma control

source_name: control

value: tjGAL4>CyO control


title: MDCK control

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

data_processing:
Illumina Casava1.7 software used for basecalling
Read mapping: Two reference sequences were prepared based on the canfam3 dog reference
The alignment was performed using the bowtie alignment software version  0.12.8
Methylation calls files for C's in the bowtie alignment files were generated using Bismark software.
Genome_build: canfam3
Supplementary_files_format_and_content: methylation calls files [column  header names : Chromosome, position, Methylated C's, Unmethylated C's]

organism: Canis lupus familiaris

source_name: normal kidney cells

growth_protocol: Cells were cultured in DMEM at 10% FBS, 5% CO2. Control cells were maintained in culture during 30 days, in parallel with the TGFbeta-treated cells.

extract_protocol:
DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)
BS-seq library constructing, 10ug genomic DNA was fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and methylated-adaptor ligation. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size were excised from the same lane of a 2% TAE agarose gel. Normally, three bands are excised corresponding to DNA insert sizes of 80-100 bp, 100-120 bp to 120-150bp. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. PCR was carried out in a final reaction volume of 50ul consisting of 20ul purified DNA, 4ul 2.5 mM dNTP, 5 ul 10X buffer, 0.5 ul JumpStart Taq DNA polymerase, 2ul 10uM PCR primers and 37.5 ul ÎœltraPure TM Water and the following thermal cycling program: 94C 30 s, 10 cycles of 94C 30 s, 60C 30 s, 72C 30 s then prolong with 1 min at 72C. PCR products were sequenced with an Illumina genome analyzer. The reads generated by Illumina sequencing were aligned to the reference genome using SOAPaligner2. The alignment and methylation estimation was performed as described before (Li, Y. et al. PLoS Biol 8, e1000533 (2010)).
100 bases Pair-end reads.

treatment_protocol: Treatment with TGFbeta at 5 ng/ml (RD Systems)

tag: cell line

value: MDCK

tag: agent

value: untreated

tag: cell phenotype

value: epithelial


title: MDCK TGFb

value: TGF-beta treated

value: mesenchymal


title: UAS-Dcr2;NGT>RnpS1 RNAi

description: Test case 2

value: UAS-Dcr2;NGT>RnpS1 RNAi

tag: molecule subtype


title: aTBe1_mRNAseq


title: UAS-Dcr2;NGT>mago nashi RNAi

description: Test case 1

value: UAS-Dcr2;NGT>mago nashi RNAi


title: wild type central brain larval neuroblasts 1

value: Neuroblasts

value: late third instar larva

value: cells express membrane-bound GFP marker (UAS-CD8::GFP)


title: aHPl1_mRNAseq

value: hemipenis

value: stage 9


title: mFLe1_mRNAseq

value: forelimb bud

tag: strain


title: mFLe2_mRNAseq


title: aHPl2_mRNAseq


title: mTBe2_mRNAseq

value: tailbud


title: mTBe1_mRNAseq


title: aHPe2_mRNAseq

value: stage 5


title: aHPe1_mRNAseq


title: aLBl2_mRNAseq

value: hindlimb bud


title: mGBl2_mRNAseq

value: genital tubercle


title: mGBl1_mRNAseq


title: mGBe2_mRNAseq


title: mLBl2_mRNAseq


title: aLBl1_mRNAseq


title: mLBe2_mRNAseq


title: mGBe1_mRNAseq


title: aLBe2_mRNAseq

value: stage 3


title: mLBl1_mRNAseq


title: E12.5_Pol2_rep2

status: Public on Aug 13 2014

first: Fei

last: Gu

state: MA

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

description:
E12.5
ChIP_DNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the UCSC mm9 genome assembly using tophat version 1.4, reads were count using htseq-count version 0.5.3
ChIP-seq reads were aligned to the UCSC mm9 genome assembly using bwa 0.5.9, peaks were called using MACS 1.4
Genome_build: UCSC mm9
Supplementary_files_format_and_content: bigwig files report ChIP-seq peaks

source_name: Heart

growth_protocol: All animal procedures were approved by the Institutional Animal Care and Use Committee of Boston Children’s Hospital.

extract_protocol:
Fragments 150-300 bp were size-selected by 2% agarose gel electrophoresis. Recovered DNA was amplified using Phusion DNA polysome (NEB), multiplexing PCR primer 1.0, and one indexed primer. The amplified libraries were purified with Agencourt AMPure XP beads (Beckman Coulter). The libraries were quantitated using the Quant-iT DNA quantitation kit (Invitrogen). The DNA size distribution of the library was measured by an Agilent Bioanalyzer.
RNA-seq and ChIP-seq library preparation were performed according to the instruction of NEB NEXT-generation library preparation kit.
2 µg of pooled RNA were used for two rounds of poly(A) mRNA purification by Dynabeads Oligo(dT)25 (Invitrogen). RNA was reverse transcribed by SuperScript III (Invitrogen) and random hexamer primers. After RNaseH treatment and PolI catalyzed 2nd-strand cDNA synthesis, DNA end repair was achieved by End-it kit (Epicnetre). DNA was then A-tailed with Exo- Klenow (NEB), and adaptors were ligated using Quick T4 DNA Ligase (NEB).

treatment_protocol: Gata4fbio, Rosa26BirA, cTNTcre, and Gata4flox alleles were described previously(He, et al. G&D 2012; Circ Res 2012).

tag: tissue

value: primary heart tissues

tag: chip antibody details

tag: input


title: H3K4me3_PS7_1

description: nuclei from embryo 5-13h

value: embryo

value: parasegment 7

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: UAS-Dcr2;NGT>CyO control

description: Germline control

tag: age

value: 3-5 days old

value: UAS-Dcr2;NGT>CyO control

value: ovary

value: 19-28nt from total RNA


title: E12.5_H3K27ac_rep2

description:
E12.5
ChIP_DNA


title: Adult_Pol2_rep2

description:
Adult
ChIP_DNA

value: Adult


title: E12.5_H3K27ac_Gata4KO_rep1

description:
E12.5
ChIP_DNA

value: Gata4 KO


title: E12.5_histone_input_rep2

description:
E12.5
Total_DNA

value: none (input)


title: E12.5_H3K4me1_rep2

description:
E12.5
ChIP_DNA


title: E12.5_H3K27ac_Gata4KO_rep2

description:
E12.5
ChIP_DNA


title: mLBe1_mRNAseq

tag: Stage


title: E12.5_H3K4me3_rep2

description:
E12.5
ChIP_DNA

tag: chip antibody

value: Active Motif:39159, lot832164


title: Adult_H3K27ac_rep2

description:
Adult
ChIP_DNA


title: Adult_H3K4me3_rep2

description:
Adult
ChIP_DNA


title: Sham_RNAseq

description:
Sham
mRNA

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-seq reads were aligned to the UCSC mm9 genome assembly using tophat version 1.4, reads were count using htseq-count version 0.5.3
ChIP-seq reads were aligned to the UCSC mm9 genome assembly using bwa 0.5.9, peaks were called using MACS 1.4
Genome_build: UCSC mm9
Supplementary_files_format_and_content: bigwig files report ChIP-seq peaks, txt files report RNA-seq counts.

tag: stress

value: Sham


title: Banding_Sham_Gata4_input

description:
Sham and banding
Total_DNA

value: Sham and banding


title: Sham_Gata4_fb

description:
Sham
Flagbio_DNA

value: none (streptavidin-coated beads used to pulldown biotinylated Gata4; 11205D, M-280 Streptavidin Invitrogen)


title: Banding_Gata4_fb

description:
Banding
Flagbio_DNA

value: Banding


title: Banding_RNAseq

description:
Banding
mRNA


title: E12.5_RNAseq_Gata4_KO

description:
E12.5_Gata4_KO
mRNA


title: E12.5_RNAseq

description:
E12.5
mRNA


title: E12.5_Pol2

description:
E12.5
ChIP_DNA


title: aLBe1_mRNAseq

tag: tissue type

value: hindlimb bud

value: stage 3


title: E12.5_histone_input

description:
E12.5
Total_DNA

value: primary heart tissues


title: E12.5_H3K27me3

description:
E12.5
ChIP_DNA

value: 17-622, Millipore


title: E12.5_H3K27ac

description:
E12.5
ChIP_DNA


title: E12.5_H3K4me3

description:
E12.5
ChIP_DNA


title: E12.5_H3K4me1

description:
E12.5
ChIP_DNA


title: E12.5_Gata4_fb1

description:
E12.5
Flagbio_DNA


title: E12.5_Gata4_fb2

description:
E12.5
Flagbio_DNA


title: E12.5_Gata4_Ab1

description:
E12.5
ChIP_DNA

value: sc-1237x, Santa Cruz


title: E12.5_Gata4_Ab2

description:
E12.5
ChIP_DNA


title: Adult_Pol2

description:
Adult
ChIP_DNA


title: Adult_histone_input

description:
Adult
Total_DNA


title: Adult_H3K27me3_rep3

description:
Adult
ChIP_DNA


title: Adult_RNAseq_rep1

description:
Adult
mRNA


title: Adult_H3K27me3_input

description:
Adult
Total_DNA


title: Adult_H3K27me3_rep1

description:
Adult
ChIP_DNA


title: Adult_H3K27me3_rep2

description:
Adult
ChIP_DNA


title: Adult_H3K27ac

description:
Adult
ChIP_DNA


title: Adult_Gata4_fb_rep1

description:
Adult
Flagbio_DNA


title: Adult_Gata4_fb_rep2

description:
Adult
Flagbio_DNA


title: E12.5_H3K27me3_input

description:
E12.5
Total_DNA


title: Adult_H3K4me3

description:
Adult
ChIP_DNA


title: Adult_Gata4_Ab_rep1

description:
Adult
ChIP_DNA


title: Adult_H3K4me1

description:
Adult
ChIP_DNA


title: Adult_Gata4_Ab_rep2

description:
Adult
ChIP_DNA


title: E12.5_Gata4_Input

description:
E12.5
Total_DNA


title: IBA-28_IBF_rep2

city: Illkirch

last: YE

address: 1 rue Laurent Fries

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Basecalls performed using CASAVA version 1.8.2
Data were processed using miRDeep2 package (2.0.0.5). The raw reads were firstly trimmed against Illumina adapters, then mapped to the AgamP3 genome assembly with the Mapper module.
The miRBase release 19, An. gambiae annotation was refined to contain both 5p and 3p mature sequences and then used for the quantification.
Genome_build: AgamP3
Supplementary_files_format_and_content: tab-delimited text files include abundance measurements  values for each sample

organism: Anopheles gambiae

source_name: whole body

growth_protocol: A. gambiae G3 strain was reared and maintained in humidified incubator at 28°C on a 12 h light and dark cycle.

extract_protocol:
Total RNA was isolated from 30-50 females using a TRI Reagent (MRC).
small RNA libraries were prepared using Illumina’s protocol (Truseq small RNA, # 15004197 Rev. C). 2mg of total RNA was used to construct small RNA libraries.

treatment_protocol: Adult female mosquitoes were collected at 3 h after regular blood feeding (samples #3-4) and P. berghei-infected blood feeding (samples #7-8), as control females fed on 10% sugar solution were used (samples #1-2). Samples #5-6 were prepared using adult female mosquitoes injected with 0.6mg of dsRNA with targeted activity against Ago1 and Ago2.

value: adult body

tag: gender

value: female

tag: protocol

value: 4-5 day old P. berghei-infected


title: Adult_RNAseq_rep2

description:
Adult
mRNA


title: IBA-25_RNAi_Ago2

value: adult  body

value: 24h post RNAi Ago2, sugar-fed


title: B140H_B

city: Minneapolis

first: David

middle: A.

last: Largaespada

state: MN

address: 2231 6th Street SE

department: Dept. of Genetics, Cell Biology and Development, Cancer Center

institute: The University of Minnesota

data_processing:
Illumina 1.5 software used for basecalling.
RNA-seq reads were mapped to mm9_canonical genome assembly and NCBI37/mm9 gtf using TopHat version 2.0.4.
FPKMs were calculated by Cuffdiff, minimum alignment count = 10, false discovery rate = 0.05
Genome_build: MGSCv37
Supplementary_files_format_and_content: The tab-delimited text files include FPKM values for each Sample.

source_name: Acute myeloid leukemia

growth_protocol: Passaged in ASM media in absence of Ara-C.

extract_protocol:
RNeasy Midi Kit (QIAGEN, Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols for RNA-seq

treatment_protocol: Exposed to increasing concentrations of Ara-C.

tag: cell line

value: AML cell line B140H

tag: ara-c ic50

value: ~60 ug/ml

tag: ara-c sensitivity

value: highly-resistant

tag: rna isolation also used for microarray analysis


title: B117H_B

tag: strain

value: AML cell line B117H


title: B117P_B

value: parental AML cell line B117P

value: sensitive


title: IBA-08_BF_rep1

tag: tissue

value: 4-5 day old blood-fed


title: IBA-27_BF_rep2


title: IBA-24_RNAi_Ago1

value: 24h post RNAi Ago1, sugar-fed


title: IBA-03_IBF_rep1


title: A-431_cytoRNA24

status: Public on Aug 12 2014

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH-Science for Life Laboratory

data_processing:
All sequences were aligned to the human genome reference hg19 with tophat version 1.1.4 and samtools version 0.1.8
Sequences aligned to the human genome were assigned to features and counted by HTSeq version 0.4.6
The R/Bioconductor package DESeq was used to call differential gene expression on counts generated by HTSeq
Reads per kilobase of exon per million mapped sequence reads (RPKM) values for features were calculated by rpkmforgenes.py
Genome_build: hg19, GRCh37.59.gtf
Supplementary_files_format_and_content: tab-delimited text files include read counts from HTSeq and rpkm values from rpkmforgenes.py

extract_protocol:
Trizol® method
RNA libraries were prepared for sequencing using standard Illumina protocols for paired end sequencing and clustered on cBot

tag: fraction type

value: cytoplasmic RNA


title: A-431_cytoRNA22


title: A-431_cytoRNA21


title: A-431_cytoRNA23


title: Adult_Gata4_input

description:
Adult
Total_DNA

value: primary heart tissues

value: Adult

value: none (input)


title: U-2 OS_cytoRNA16

source_name: U-2 OS

value: U-2 OS


title: U-251MG_cytoRNA18


title: B140P_B

value: parental AML cell line B140P


title: U-2 OS_cytoRNA15


title: U-251MG_cytoRNA17


title: U-251MG_cytoRNA20


title: U-2 OS_cytoRNA13


title: A-431_totRNA12

value: total RNA


title: U-2 OS_cytoRNA14


title: A-431_totRNA11


title: H3K27ac_mixed_1

description: nuclei from embryo 5-13h

value: embryo

tag: tissue subtype

value: whole embryo

value: Active Motif


title: A-431_totRNA10


title: IBA-26_SF_rep2

value: adult  body

value: female

value: 4-5 day old sugar-fed


title: A-431_totRNA9


title: U-251MG_totRNA6


title: IBA-01_SF_rep1


title: U-251MG_totRNA7


title: U-2 OS_totRNA2


title: U-2 OS_totRNA1


title: U-251MG_totRNA5


title: REC1_Control_3

tag: cell type

value: Mantle cell lymphoma cell line containing an activating Notch1 mutation

tag: passage

tag: treatment

value: vehicle


title: MCF7 Input CHART-seq Flavopiridol treatment, rep2

description: CHART Input DNA.

data_processing:
Library strategy: CHART-Seq
Base-calling was performed using Illumina Real Time Analysis software.
Reads were aligned using Bowtie v 0.12.5 with the following options: -m 1 -v 2 -k 1 -X 2000 --best --strata.
After alignment, reads were processed and filtered according to the SPP guidelines, where the genomic positions with a number of mapped tags above the significance threshold of z-score = 7 were identified as anomalous, and the tags mapped to such positions were discarded.
The coverage for each sample represents frequencies of the paired-end reads spanning over a given genomic position, which were corrected for library size and subsequently input normalized.
For analysis of CHART-seq and PSF paired-end ChIP-seq data from untreated MCF-7 cells, coverage was normalized by input as n_norm = [(n+1)/(ni+1)] * [Ni/N], where n, ni, N, and Ni are positional coverage in experiment and input, and total genome coverage in experiment and input, respectively. The resulting normalized coverage files are included in this dataset in bigwig format.
Input-subtracted, normalized read densities of flavopiridol, E2, and respective vehicle CHART-seq were generated using SPP with a bandwidth of 1kb and a step size of 500 bp and are included in this dataset in bigwig format.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: All processed data files are in bigwig format and represent input-normalized CHART-seq or ChIP-seq coverage.

source_name: MCF-7, Flavopiridol, CHART input

extract_protocol:
For CHART-seq, nuclei were isolated from 10^8 MCF-7 cells (ATCC HTB-22) that were crosslinked with 1% formaldehyde for 10 minutes. Nuclei were further crosslinked with 3% formaldehyde for 30 minutes. Chromatin was sheared to a fragment size between 2 kb and 10 kb. Sheared chromatin was incubated overnight with biotinylated DNA oligonucleotides with complementarity to either the NEAT1 or MALAT1 RNAs, and subsequently captured with streptavidin beads. After incubation and washing, captured materials were eluted using RNaseH and subjected to crosslink reversal. DNA was purified by ethanol precipitation and subjected to library construction.
Genomic DNA isolated by CHART enrichment, as well as input DNA, was fragmented using sonication. Sonicated DNA was then subjected to end-repair, A-tailing, ligation to universal adapters, amplification with indexed primers, and size selection using SPRI beads.

value: mammary adenocarcinoma cell line

value: Flavopiridol

tag: capture oligo

tag: antibody


title: MCF7 MALAT1 Sense CHART-seq Flavopiridol treatment, rep2

description: MALAT1 CHART enriched DNA.

source_name: MCF-7, Flavopiridol, MALAT1 CHART

value: MALAT1 Sense


title: U-2 OS_totRNA3


title: U-251MG_cytoRNA19

value: cytoplasmic RNA


title: MCF7 NEAT1 Sense CHART-seq Flavopiridol treatment, rep2

description: NEAT1 CHART enriched DNA.

source_name: MCF-7, Flavopiridol, NEAT1 CHART

value: NEAT1 Sense


title: MCF7 NEAT1 CO1 CHART-seq Flavopiridol treatment, rep2

description: NEAT1 CHART enriched DNA.

value: NEAT1 CO1


title: MCF7 NEAT1 CO2 CHART-seq Flavopiridol treatment, rep2

description: NEAT1 CHART enriched DNA.

value: NEAT1 CO2


title: MCF7 MALAT1 CO1 CHART-seq Flavopiridol treatment, rep1

description: MALAT1 CHART enriched DNA.

value: MALAT1 CO1


title: MCF7 MALAT1 Sense CHART-seq Flavopiridol treatment, rep1

description: MALAT1 CHART enriched DNA.


title: MCF7 MALAT1 CO2 CHART-seq Flavopiridol treatment, rep1

description: MALAT1 CHART enriched DNA.

value: MALAT1 CO2


title: MCF7 Input CHART-seq Flavopiridol treatment, rep1

description: CHART Input DNA.


title: MCF7 NEAT1 Sense CHART-seq Flavopiridol treatment, rep1

description: NEAT1 CHART enriched DNA.


title: MCF7 NEAT1 CO2 CHART-seq Flavopiridol treatment, rep1

description: NEAT1 CHART enriched DNA.


title: MCF7 Input CHART-seq DMSO treatment, rep2

description: CHART Input DNA.

source_name: MCF-7, DMSO vehicle, CHART input

value: DMSO vehicle


title: MCF7 NEAT1 CO1 CHART-seq Flavopiridol treatment, rep1

description: NEAT1 CHART enriched DNA.


title: U-251MG_totRNA8

value: total RNA


title: MCF7 MALAT1 Sense CHART-seq DMSO treatment, rep2

description: MALAT1 CHART enriched DNA.

source_name: MCF-7, DMSO vehicle, MALAT1 CHART


title: MCF7 MALAT1 CO1 CHART-seq DMSO treatment, rep2

description: MALAT1 CHART enriched DNA.


title: MCF7 MALAT1 CO2 CHART-seq DMSO treatment, rep2

description: MALAT1 CHART enriched DNA.


title: MCF7 MALAT1 CO1 CHART-seq Flavopiridol treatment, rep2

description: MALAT1 CHART enriched DNA.


title: MCF7 MALAT1 CO2 CHART-seq Flavopiridol treatment, rep2

description: MALAT1 CHART enriched DNA.


title: MCF7 NEAT1 Sense CHART-seq DMSO treatment, rep2

description: NEAT1 CHART enriched DNA.

source_name: MCF-7, DMSO vehicle, NEAT1 CHART


title: MCF7 NEAT1 CO2 CHART-seq DMSO treatment, rep2

description: NEAT1 CHART enriched DNA.


title: MCF7 NEAT1 CO1 CHART-seq DMSO treatment, rep2

description: NEAT1 CHART enriched DNA.


title: MCF7 Input CHART-seq DMSO treatment, rep1

description: CHART Input DNA.


title: MCF7 MALAT1 CO2 CHART-seq DMSO treatment, rep1

description: MALAT1 CHART enriched DNA.


title: MCF7 NEAT1 Sense CHART-seq DMSO treatment, rep1

description: NEAT1 CHART enriched DNA.


title: MCF7 MALAT1 Sense CHART-seq E2 treatment, rep2

description: MALAT1 CHART enriched DNA.

source_name: MCF-7, E2, MALAT1 CHART


title: MCF7 MALAT1 CO1 CHART-seq DMSO treatment, rep1

description: MALAT1 CHART enriched DNA.


title: MCF7 NEAT1 CO2 CHART-seq DMSO treatment, rep1

description: NEAT1 CHART enriched DNA.


title: MCF7 MALAT1 CO1 CHART-seq E2 treatment, rep2

description: MALAT1 CHART enriched DNA.


title: MCF7 MALAT1 CO2 CHART-seq E2 treatment, rep2

description: MALAT1 CHART enriched DNA.


title: MCF7 Input CHART-seq E2 treatment, rep1

description: CHART Input DNA.

source_name: MCF-7, E2, CHART input


title: MCF7 MALAT1 Sense CHART-seq E2 treatment, rep1

description: MALAT1 CHART enriched DNA.


title: MCF7 MALAT1 CO1 CHART-seq E2 treatment, rep1

description: MALAT1 CHART enriched DNA.


title: MCF7 NEAT1 CO2 CHART-seq E2 treatment, rep2

description: NEAT1 CHART enriched DNA.

source_name: MCF-7, E2, NEAT1 CHART


title: MCF7 NEAT1 CO1 CHART-seq E2 treatment, rep2

description: NEAT1 CHART enriched DNA.


title: MCF7 MALAT1 CO2 CHART-seq E2 treatment, rep1

description: MALAT1 CHART enriched DNA.


title: MCF7 NEAT1 Sense CHART-seq E2 treatment, rep2

description: NEAT1 CHART enriched DNA.


title: Input_histones_2

city: Heidelberg

first: Jan-Philipp

last: Mallm

address: Im Neuenheimer Feld 267

country: Germany

institute: DKFZ

description:
genomic DNA
major_consensus_DNA_H3K9me3_H3K36me3_normalized_counts

data_processing:
alignment to the mouse genome assembly mm9 with bowtie
alignment to major satellite repeat consensus sequence (GGACCTGGAATATGGCGAGAAAACTGAAAATCACGGAAAATGAGAAATACACACTTTAGG  ACGTGAAATATGGCGAGGAAAACTGAAAAAGGTGGAAAATTTAGAAATGTCCACTGTAGG  ACGTGGAATATGGCAAGAAAACTGAAAATCATGGAAAATGAGAAACATCCACTTGACGAC  TTGAAAAATGACGAAATCACTAAAAAACGTGAAAAATGAGAAATGCACACTGAA) with bowtie
read counting for annotated major satellite repeats (repeatMasker)
normalization on total read number
Genome_build: mm9
Supplementary_files_format_and_content: tag count

source_name: Neural progenitor cells

growth_protocol: mESC were depleted from LIF for four days in STEMPan medium (Pan Biotech) in suspension flasks. 5 µM retinoic acid was added for four days, then the cells were plated on matrigel in NSC medium (PAA) for four additional days.

extract_protocol:
For each sample, 1 x 106 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes, pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). For histone modifiacations,  chromatin was sheared to mononucleosomal fragments and for HP1/Suv39h1 to 200-300 bps.
Libraries were prepared according to Illumina standard protocols with external barcodes.

value: ES-derived neural progenitor cells


title: Input_histones_1


title: H3K36me3_ChIPseq_2

description:
ChIP DNA
major_consensus_DNA_H3K9me3_H3K36me3_normalized_counts

value: ab9050, abcam


title: MCF7 NEAT1 CO1 CHART-seq E2 treatment, rep1

description: NEAT1 CHART enriched DNA.


title: MCF7 MALAT1 Sense CHART-seq DMSO treatment, rep1

description: MALAT1 CHART enriched DNA.


title: MCF7 NEAT1 Sense CHART-seq E2 treatment, rep1

description: NEAT1 CHART enriched DNA.


title: MCF7 NEAT1 CO2 CHART-seq E2 treatment, rep1

description: NEAT1 CHART enriched DNA.


title: H3K9me3_ChIPseq_2

value: ab8898, abcam


title: MCF7 MALAT1 Sense CHART-seq Ethanol treatment, rep2

description: MALAT1 CHART enriched DNA.

source_name: MCF-7, ethanol vehicle, MALAT1 CHART

value: ethanol vehicle


title: H3K9me3_ChIPseq_1


title: MCF7 NEAT1 CO1 CHART-seq DMSO treatment, rep1

description: NEAT1 CHART enriched DNA.


title: MCF7 Input CHART-seq E2 treatment, rep2

description: CHART Input DNA.


title: MCF7 Input CHART-seq Ethanol treatment, rep2

description: CHART Input DNA.

source_name: MCF-7, ethanol vehicle, CHART input


title: MCF7 NEAT1 Sense CHART-seq Ethanol treatment, rep2

description: NEAT1 CHART enriched DNA.

source_name: MCF-7, ethanol vehicle, NEAT1 CHART


title: H3K36me3_ChIPseq_1


title: Input_DNA_1

description:
genomic DNA
major_consensus_DNA_HP1_Suv39h1_Suv39h2_normalized_counts


title: MCF7 MALAT1 CO2 CHART-seq Ethanol treatment, rep2

description: MALAT1 CHART enriched DNA.


title: Input_DNA_2


title: MCF7 NEAT1 CO2 CHART-seq Ethanol treatment, rep2

description: NEAT1 CHART enriched DNA.


title: Suv39h2_ChIPseq_1

description:
ChIP DNA
major_consensus_DNA_HP1_Suv39h1_Suv39h2_normalized_counts

value: ab71683, abcam


title: Suv39h1_ChIPseq_2

value: ab12405, abcam


title: Suv39h2_ChIPseq_2


title: HP1_beta_ChIPseq_2

value: 1MOD-1A9-AS, euromedex


title: MCF7 Input CHART-seq Ethanol treatment, rep1

description: CHART Input DNA.

value: mammary adenocarcinoma cell line


title: MCF7 MALAT1 CO2 CHART-seq Ethanol treatment, rep1

description: MALAT1 CHART enriched DNA.


title: MCF7 MALAT1 Sense CHART-seq Ethanol treatment, rep1

description: MALAT1 CHART enriched DNA.

value: MALAT1 Sense


title: HP1_beta_ChIPseq_1


title: MCF7 MALAT1 CO1 CHART-seq Ethanol treatment, rep1

description: MALAT1 CHART enriched DNA.


title: Suv39h1_ChIPseq_1


title: MCF7 NEAT1 Sense CHART-seq Ethanol treatment, rep1

description: NEAT1 CHART enriched DNA.


title: MCF7 NEAT1 CO2 CHART-seq Ethanol treatment, rep1

description: NEAT1 CHART enriched DNA.


title: YAP-ERMS mouse Tead ChIP-Seq

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Reads were mapped using Bowtie2 aligner on the necessary reference genome (hg19 or mm9), accepting the best match for each hit.
Aligned reads were used for a peak-calling step with the software MACS, setting a lower cutoff of fold change variation for the model building to 5 and a pvalue cutoff to 10E-08
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: Standard MACS output containing genomic locations for each peak in bed format

source_name: YAP-ERMS mouse cell line

extract_protocol:
RD cells or cells derived from YAP-driven tumors under Myf5-Cre or Pax7-CreER cells were cross-linked in 1% formaldehyde for 10 minutes at room temperature after which the reaction was stopped by addition of 0.125M glycine. Cells were lysed and harvested in ChIP buffer
Chromatin was disrupted by sonication using a Diagenode Bioruptor sonicator UCD-200 to obatin fragments of average 200-500 b in size. Suitable amounts of chromatin were incubated with specific antibodies overnight. Immunoprecipitated complexes were recovered on Protein-A/G agarose beads (Pierce) or Protein G Dynabeads (Invitrogen). After extensive washes, DNA was recovered by reverse crosslinking and purification using QIAquick PCR purification kit (Qiagen)
ChIP-Seq libraries were built using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, E7370) according to manufacturer's recommendation. Libraries for each celle lines were barcoded using NEBNext multiplex oligos for Illumina (NEB, E7335) and run on a single lane of HiSeq2000 (Illumina)


title: MCF7 MALAT1 CO1 CHART-seq Ethanol treatment, rep2

last: Sadreyev

institute: Massachusetts General Hospital

description: MALAT1 CHART enriched DNA.


title: YAP-ERMS mouse Input ChIP-Seq

value: YAP-driven tumors under Myf5-Cre or Pax7-CreER cells


title: MCF7 NEAT1 CO1 CHART-seq Ethanol treatment, rep1

description: NEAT1 CHART enriched DNA.


title: MCF7 Input single end ChIP-seq, rep2

description: ChIP Input DNA.

data_processing:
Base-calling was performed using Illumina Real Time Analysis software.
Reads were aligned using Bowtie v 0.12.5 with the following options: -m 1 -v 2 -k 1 -X 2000 --best --strata.
After alignment, reads were processed and filtered according to the SPP guidelines, where the genomic positions with a number of mapped tags above the significance threshold of z-score = 7 were identified as anomalous, and the tags mapped to such positions were discarded.
The coverage for each sample represents frequencies of the paired-end reads spanning over a given genomic position, which were corrected for library size and subsequently input normalized.
For analysis of CHART-seq and PSF paired-end ChIP-seq data from untreated MCF-7 cells, coverage was normalized by input as n_norm = [(n+1)/(ni+1)] * [Ni/N], where n, ni, N, and Ni are positional coverage in experiment and input, and total genome coverage in experiment and input, respectively. The resulting normalized coverage files are included in this dataset in bigwig format.
Input-subtracted, normalized read densities of flavopiridol, E2, and respective vehicle CHART-seq were generated using SPP with a bandwidth of 1kb and a step size of 500 bp and are included in this dataset in bigwig format.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: All processed data files are in bigwig format and represent input-normalized CHART-seq or ChIP-seq coverage.

source_name: MCF-7, untreated, ChIP input

extract_protocol:
For ChIP-seq, 10^8 MCF-7 cells (ATCC HTB-22) were crosslinked for 10 minutes with 1% formaldehyde. After nuclei isolation and sonication, sheared chromatin was incubated overnight with protein A beads bound to PSF antisera (clone 39-1; Santa Cruz Biotechnology, sc-101137, Lot # L1012). After incubation, beads were extensively washed and bound DNA was eluted through incubation with proteinase K at 55 degrees C for 1 hour. Eluted DNA was subjected to crosslink reversal overnight at 65 degrees C. DNA was purified using ethanol precipitation and subjected to library construction.
Genomic DNA isolated by ChIP enrichment, as well as input DNA, was fragmented using sonication. Sonicated DNA was then subjected to end-repair, A-tailing, ligation to universal adapters, amplification with indexed primers, and size selection using SPRI beads.


title: Group-23 Cocktail replicate 3

first: Rebecca

last: LaRue

address: 117 Pleasant St SE

department: Department of Lab medicine and Pathology

institute: University of Minnesota

data_processing:
Illumina 1.5 software used for basecalling.
RNA-seq reads were mapped to mm10_canonical genome assembly and mm10 gtf using TopHat version 2.0.9.
FPKMs were calculated by Cuffdiff v2.1.1, minimum alignment count = 10, false discovery rate = 0.05
Genome_build: mm10_canonical
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each sample

source_name: CD8 T cells

growth_protocol: Negatively selected CD8 T cells from OT-I mice were mixed 2:1 with 7 day grown BMDC coated with SIINFEKL peptide and put into T cell medium (RPMI 1640 + heat-inactivated FBS, non-essential amino acids, HEPES buffer, sodium pyruvate and 2-mercaptoethanol) with either IL-2 or a cocktail of IL-7, IL-21, 2-deoxyglucose and TWS119 and grown for 14 days being passaged once as on the first day after one week

extract_protocol:
RNA was extracted with the Arcturus PicoPure RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols for RNA-seq

treatment_protocol: Cells were sorted by immunophenotype into purified populations and then pelleted for RNA extraction

value: CD8 T cells

value: Cocktail grown

tag: immunophenotype

tag: days in vitro


title: Naïve_1 replicate 1

value: Naïve


title: MCF7 NEAT1 CO1 CHART-seq Ethanol treatment, rep2

first: Ruslan

description: NEAT1 CHART enriched DNA.

value: NEAT1 CO1


title: MCF7 Input for MALAT1 CHART-seq

description: CHART Input DNA.

source_name: MCF-7, untreated, MALAT1 CHART input


title: Group-23 Cocktail replicate 2


title: Naïve_2 replicate 2


title: Group-23 Cocktail replicate 1


title: MCF7 PSF paired end ChIP-seq, rep1

description: PSF ChIP enriched DNA.

source_name: MCF-7, untreated, PSF ChIP

value: anti-PSF


title: MCF7 Input paired end ChIP-seq, rep1

description: ChIP Input DNA.


title: Group-22 Cocktail replicate 3


title: MCF7 PSF single end ChIP-seq, rep2

description: PSF ChIP enriched DNA.


title: MCF7 Input for NEAT1 CHART-seq

description: CHART Input DNA.

source_name: MCF-7, untreated, NEAT1 CHART input


title: MCF7 NEAT1 CO1 CHART-seq

description: NEAT1 CHART enriched DNA.

source_name: MCF-7, untreated, NEAT1 CHART


title: Group-1 IL-2 replicate 3

value: IL-2 grown


title: MCF7 MALAT1 CO2 CHART-seq

description: MALAT1 CHART enriched DNA.

source_name: MCF-7, untreated, MALAT1 CHART

value: MALAT1 CO2


title: RD human IgG ChIP-Seq

source_name: RD human cell line

value: RD


title: Group-22 Cocktail replicate 1


title: Group-21 Cocktail replicate 3


title: Group-22 Cocktail replicate 2


title: Group-21 Cocktail replicate 2


title: Naïve_3 replicate 3


title: MCF7 NEAT1 CO2 CHART-seq

description: NEAT1 CHART enriched DNA.

value: NEAT1 CO2


title: 6hA replicate2

status: Public on Aug 11 2014

city: Goettingen

first: Anna

last: Sawicka

address: Am Fassberg 11

department: Dep. of Molecular Biology

institute: Max Planck Institure for Biophysical Chemistry

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 6 h treatment with anisomycin (188.5 nM) (replicate2)

data_processing:
Base callling was performed using RTA version 1.17.21.3. Demultiplexing was performed using BamIndexDecoder version V1.13-3-g8bb9b0 from the Illumina2Bam utils.
Following demultiplexing, the reds were trimmed for the barcode sequence and mapped to the mouse genome (mm9) using TopHat (version 1.4.1). Only one mismatch was allowed per 18 bp segment. Only uniquely mapped reads were retained.
We used htseq-count script (using the "union" model) to calculate the number of reads per each of 21608 mouse RefSeq genes. In cases were multiple RefSeq entries corresponded to one gene symbol, RefSeq accessions associated with the longest transcript were retained. Read numbers from htseq-count script were divided by the sum of the exon lengths of each transcript and normalized by the library size.
Genome_build: mm9
Supplementary_files_format_and_content: Tab deliminated files containing RPKM values for mouse RefSeq genes. Each file contains a header with "RefSeq"and "RPKM".

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, 6h anisomycin treated (188.5 nM)

growth_protocol: Swiss 3T3 fibroblasts were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% (vol/vol) fetal calf serum (FCS) in the presence of Penicillin and Streptomycin. The cells were serum-deprived for 72 h using DMEM containing 0.2% FCS (vol/vol).

extract_protocol:
RNA was isolated using Trizol (Invitrogen) according to manufacturer'instructures.
10 μg of total RNA was subjected to two rounds of polyA selection with Dynabeads® mRNA Purification kit (Invitrogen). mRNA was subsequently fragmented by hydrolysis (40 mM TrisOAc pH 8.2, 100 mM KOAc, 150 mM MgOAc) at 94oC for 3 min. 1st strand cDNA synthesis was performed using Superscript III Reverse Transcriptase kit (Invitrogen) with random hexamers priming (Applied Biosystems) in the presence of Actinomycin D (5 ng/ml).  Second strand cDNA was synthesized using DNA Pol I, DNA ligase (both Invitrogen) and RNase H (NEB) with random hexamers (Applied Biosystems) in the presence of dUTP. The libraries were prepared by CSF NGS unit (csf.ac.at) using NEBNext® Library Prep Reagent Set for Illumina (NEB).The following TrueSeq barcodes were used: sample 0h_1 TAGCTT, sample 0h_2 ATCACG, sample 1hA_1 GGCTAC, sample 1hA_2 CGATGT.

treatment_protocol: Serum-straved (72 h) mouse 3T3 fibroblasts we treated with 188.5 nM of anisomycin (Sigma) for 3 or 6 h, with or without 15-min pre-treatment with 10 uM of H89 inhibitor (Santa Cruz Biotechnology).

value: Swiss 3T3 fibroblasts

value: fibroblasts


title: U-2 OS_totRNA4

source_name: U-2 OS

value: U-2 OS

value: total RNA


title: 6hH89 replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 6h15min treatment with H89 (10 uM) (replicate2)

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, 6h15min H89 treated (10 uM)


title: 6hA+H89 replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 15 min pre-treatment with H89 (10 uM) and 6 h treatment with anisomycin (188.5 nM) (replicate2)

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, 6h anisomycin treated (188.5 nM), 15 min pre-treatment with H89 (10 uM)


title: Group-1 IL-2 replicate 2


title: 93N

data_processing:
Illumina Casava1.7 software used for basecalling
Read mapping: Rtwo reference sequences were prepared based on the HG19 reference genome
The alignment was performed using the bowtie alignment software version  0.12.8
methylation calls files for C's in the bowtie alignment files were generated using Bismarck software
Genome_build: HG19
Supplementary_files_format_and_content: methylation calls files. Columns are : chromosome, position, methylated, unmethylated

source_name: Normal aortic tissue

extract_protocol:
DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)
BS-seq library constructing, 10ug genomic DNA was fragmented using a Covaris sonication system (Covaris S2). Following fragmentation, libraries were constructed using the Illumina Paired-End protocol consisting of end repair, <A> base addition and methylated-adaptor ligation. Ligated DNA was bisulfite converted using the EZ DNA Methylation-Gold kit (ZYMO). Different insert size were excised from the same lane of a 2% TAE agarose gel. Normally, three bands are excised corresponding to DNA insert sizes of 80-100 bp, 100-120 bp to 120-150bp. Products were purified by using QIAquick Gel Extraction kit (Qiagen) and amplified by PCR. PCR was carried out in a final reaction volume of 50ul consisting of 20ul purified DNA, 4ul 2.5 mM dNTP, 5 ul 10X buffer, 0.5 ul JumpStart Taq DNA polymerase, 2ul 10uM PCR primers and 37.5 ul ÎœltraPure TM Water and the following thermal cycling program: 94C 30 s, 10 cycles of 94C 30 s, 60C 30 s, 72C 30 s then prolong with 1 min at 72C. PCR products were sequenced with an Illumina genome analyzer. The reads generated by Illumina sequencing were aligned to the reference genome using SOAPaligner2. The alignment and methylation estimation was performed as described before (Li, Y. et al. PLoS Biol 8, e1000533 (2010)).

treatment_protocol: Fresh frozen in RNAlater (Ambion)

tag: disease state

value: Healthy

value: carotid tissue


title: Group-1 IL-2 replicate 1


title: 93A

source_name: Atherosclerotic lesion

value: Diseased


title: 6hA replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 6 h treatment with anisomycin (188.5 nM) (replicate1)


title: 6hH89 replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 6h15min treatment with H89 (10 uM) (replicate1)


title: MCF7 MALAT1 CO1 CHART-seq

description: MALAT1 CHART enriched DNA.

value: mammary adenocarcinoma cell line

value: MALAT1 CO1


title: 1hA_replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 1h treatment with anisomycin (188.5 nM) (replicate2)

data_processing:
Base callling was performed using RTA version 1.13.48.0. Demultiplexing was performed using BamIndexDecoder 1.03 from the Illumina2Bam utils.
Following demultiplexing, the reds were trimmed for the barcode sequence and mapped to the mouse genome (mm9) using TopHat (version 1.4.1). Only one mismatch was allowed per 18 bp segment. Only uniquely mapped reads were retained.
We used htseq-count script (using the "union" model) to calculate the number of reads per each of 21608 mouse RefSeq genes. In cases were multiple RefSeq entries corresponded to one gene symbol, RefSeq accessions associated with the longest transcript were retained. Read numbers from htseq-count script were divided by the sum of the exon lengths of each transcript and normalized by the library size.
Genome_build: mm9
Supplementary_files_format_and_content: Tab deliminated file containing RPKM values for mouse RefSeq genes. Each file contains a header with "RefSeq"and "RPKM".

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2

treatment_protocol: Serum-straved (72 h) mouse 3T3 fibroblasts we treated with 188.5 nM of anisomycin (Sigma) for 1 h.

value: Swiss 3T3


title: 3hA+H89 replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 15 min pre-treatment with H89 (10 uM) and 3 h treatment with anisomycin (188.5 nM) (replicate2)

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, 3h anisomycin treated (188.5 nM), 15 min pre-treatment with H89 (10 uM)


title: scRNA_control_untreated_replicate2

description: Short-capped RNA after 72h starvation in the medium containing 0.2% FCS (replicate2)

data_processing:
Base callling was performed using RTA version 1.8.70.0 (samples scRNA_0h_1 and scRNA_1hA_1) and RTA version 1.13.48.0 (samples scRNA_0h_2 and scRNA_1hA_2).
Following adapter removal, reads derived from scRNA-seq were first trimmed to 25bp and then mapped to the mouse genome (mm9) using TopHat version 1.4.1 allowing for one mismatchin a n 18bp segment.  Only uniquely mapped reads were retained.
Duplicated reads were removed a bedgraph file (normalized to the total library size) using genomeCoverageBed -bga from BedTools was generated. Chromosome size information was downloaded from UCSC. BigWig files were generated from bedgraph files using bedGraphToBigWig.
Genome_build: mm9
Supplementary_files_format_and_content: read desity at genomic positions (bigWig format)

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2

extract_protocol:
The cells growing onto 15-cm Petri dishes were washed twice with 10 ml of ice cold PBS, harvested in 5 ml of ice cold PBS and centrifuged for 5 min 500 x g, 4oC. The cell pellet was resuspended in 10 ml of Solution I (150 mM KCl, 4 mM MgOAc, 10 mM Tris-HCl pH 7.4) and spun down for 5 min at 500 x g, 4oC. The supernatant was removed; the cells were reuspended in 10 ml of Solution II (Solution I + 0.5% NP40) and incubated on ice for 10 min. The nuclei were pelleted through a 4 ml cushion of 0.6 M sucrose at 900 x g for 10 min, 4oC. All but 200 l of supernatant was removed and 2 ml of Solution I was added. The pellet was resuspended and spun down at 900 x g for 5 min, 4oC.  Following the removal of the supernatant, 1 ml of Trizol® reagent (Invitrogen) was added and RNA was further isolated according to the manufacturer's protocol.
scRNA-seq was performed as described (Nechaev et al., Science 2010), with modifications.The following adapters and primers were used: 3’adaptor_PE: 5‘-/5Phos/rArGrATCGGAAGAGCGGTTCAGC/3ddC/ -3‘; 5’adaptor_PE: 5‘rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU-3‘; RT_Primer_PE (primer for reverse transcription):5‘- TCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT -3‘; Library amplification primers: 5‘-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’ and 5‘-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3’. Briefly, 10 μg of nuclear RNA was size selected on a 15% TBE-urea gel (Bio-Rad) and RNA molecules sized between 25 nt and 120 nt were extracted and subjected to RNA 5’Polyphosphatase treatment (1 u/μl, Epibio) for 30 min at 37oC and subsequently with Terminator 5’phosphate-Dependent Exonuclease (0.05 u/μl, Epibio) for 60 min at 30oC, what was followed by ligation of 30 pmol of 3’adapter in the presence of 0.1 u/μl of T4 ssRNA Ligase I ( NEB) and 1 mM of ATP at 20oC for 6 hours.  Then RNA was size selected on 15% TBE-urea gel (Bio-Rad), RNA molecules between 50 nt and 150 nt were excised and treated with 1 μl  of APexTM Heat-Labile Alkaline Phosphatase (Epibio) for 10 min at 37oC  followed by the treatment with 2.5 u of Tobacco Acid Pyrophosphatase (Epibio) for 1 hour at 37oC.  Subsequently, 50 pmol of 5’adapter was ligated in the presence of 0.1 u/μl of T4 ssRNA Ligase I (NEB) and 1mM of ATP at 20oC for 6 hours. Following size selection on 10% TBE-urea gel (Bio-Rad), RNA was subjected to reverse transcription using Superscript III Reverse Transcriptase kit (Invitrogen). cDNA was amplified using PhusionTM DNA Polymerase (Finnzymes), 15 cycles of amplification were performed. The library was size selected on 6% TBE gel (Rio-Rad).


title: 3hH89 replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 3h15min treatment with H89 (10 uM) (replicate2)

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, 3h15min H89 treated (10 uM)


title: Group-21 Cocktail replicate 1

source_name: CD8 T cells

value: CD8 T cells

value: Cocktail grown


title: 3hH89 replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 3h15min treatment with H89 (10 uM) (replicate1)


title: RNAPIIS2ph_control_untreated_replicate2

description: RNAPIIS2ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2

data_processing:
Basecalling with Bustard version 1.8.0 (samples H3S28ph_0h_rep1, H3S28ph_1hA_rep1,  RNAPIIS2ph_0h_rep2, H3K9ac_0h_rep1, H3K9ac_1hA_rep1) or Bustard version 1.9.4 (samples H3K9ac_0h_rep2, H3K9ac_1hA_rep2) or RTA version 1.8.70.0 (samples RNAPIIS5ph_0h_rep1, RNAPIIS5ph_1hA_rep1, RNAPIIS2ph_0h_rep1, RNAPIIS2ph_1hA_rep1, RNAPIIS5ph_0h_rep2, RNAPIIS5ph_1hA_rep2, RNAPIIS2ph_1hA_rep2, H3K4me3_0h_rep1, H3K4me3_1hA_rep1, H3S28ph_0h_rep2, H3S28ph_1hA_rep2) or RTA version 1.13.48.0 (samples input_0h, input_1hA, H3K4me3_0h_rep2, H3K4me3_1hA_rep2).
ChIP-seq reads were mapped to the mouse genome (mm9) using Bowtie version 12.5. Up to two mismatches were allowed. Reads that map to only one genomic location were retained. Reads derived from the input samples were trimmed to 36bp prior to the mapping.
Duplicated reads were removed and unique reads were extended to the length of 200 bp (average DNA fragment size of after chromatin sanitation). Then a bedgraph file (normalized to the total library size) using genomeCoverageBed -bga from BedTools was generated. Chromosome size information was downloaded from UCSC. BigWig files were generated from bedgraph files using bedGraphToBigWig.
Genome_build: mm9
Supplementary_files_format_and_content: read desity at genomic positions (bigWig format)

source_name: RNAPIIS2ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 2

extract_protocol:
Chromatin immunorecipitation was performed as described (Hauser et al., Molecular and Cellular Biology, 2002) with the following modifications: chromatin-antibody complexes were pulled down using Dynabeads® protein A or G beads (Invitrogen). The following antibodies were used in the study: H3S28ph (Sigma, cat number H9908), H3K9ac (Millipore, cat number 06-942), H3K4me3 (Millipore, cat number 07-473), RNAPIIS5ph (Bethyl, cat number A300-655A), RNAPIIS2ph (Bethyl, cat number  A300-654A).
Immunoprecipitated DNA as well as input samples were subjected to library preparation protocol using NEBNext® Library Prep Reagent Set for Illumina (NEB). The following TrueSeq barcodes were used for the input samples: sample input_0h TTAGGC, sample input_1hA  TGACCA.


title: 3hA+H89 replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 15 min pre-treatment with H89 (10 uM) and 3 h treatment with anisomycin (188.5 nM) (replicate1)


title: 3hA replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 3 h treatment with anisomycin (188.5 nM) (replicate2)

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, 3h anisomycin treated (188.5 nM)


title: RD human TEAD ChIP-Seq


title: RNAPIIS5ph_1hA_replicate2

description: RNAPIIS5ph ChIP in serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2

source_name: RNAPIIS5ph, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 2

value: RNAPIIS5ph (Bethyl, cat number A300-655A)


title: control untreated replicate2

description: Gene expression after 72h starvation in the medium containing 0.2% FCS (replicate2)

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts


title: SWI6-myc_swi4d_IP_2

city: St. Louis

last: Spivak

state: MO

address: 4444 Forest Park Avenue

institute: Washington University in St. Louis

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
swi4del SWI6-myc tag IP2

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the S288C genome assembly using novoalign-2.07.0
If a sequenced fragment did not uniquely align to the genome, it was discarded
peaks were called using MACS-1.4.0rc2 with the following options "-g 12156677 --diag  --call-subpeaks -w"
Genome_build: S288C R64-1-1
Supplementary_files_format_and_content: peaks.bed files were generated by MACS

organism: Saccharomyces cerevisiae

growth_protocol: NRG1-myc, SUT1-myc, and SWI4-myc strains were grown at 30° C in YPD rich media to exponential mid-log phase (OD600 ~ 0.8).  GCN4-myc and RTG3-myc strains were grown in YPD rich media to OD600 ~ 0.7, after which rapamycin was added to the media to a final concentration of 100 nM and the cultures were harvested after 20 minutes

extract_protocol:
Cells were lysed in a beadbeater and then sonicated.  The supernatant was collected and used for immunoprecipitation.  A sample was removed and labeled as the INPUT sample. Immunoprecipitations were performed using anti-c-myc resin. Samples were incubated overnight at 70°C to reverse cross-links.  Samples were RNAse treated and DNA was isolated by Phenol:Chlorofom extraction.
ChIP DNA was blunt ended, had addition of “A” base to 3’ end, and had sequencing adapters ligated to the ends. The fragments were size selected to 200-600 base pairs, and underwent amplification for 15 cycles. The resulting libraries were sequenced using the Illumina HiSeq-2000 as single reads extending 42 bases.

treatment_protocol: cross-linked in a final concentration of 1% formaldehyde for 15 minutes.  The reaction was quenched with 150 ml 2.5M glycine (50 mL for the 330mL cultures) and incubated at room temperature for 10 minutes.

value: W303 yeast strain Z1256

tag: chip antibody

value: anti-Myc EZiew affinity gel; Sigma E6779


title: SWI6-myc_IP_1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type SWI6-myc tag IP1


title: 1hA_replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 1h treatment with anisomycin (188.5 nM) (replicate1)

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM), replicate 1

tag: cell line


title: control_untreated_replicate2


title: scRNA_1hA_replicate2

description: Short-capped RNA after 72h starvation in the medium containing 0.2% FCS followed by 1h treatment with anisomycin (188.5 nM) (replicate2)


title: control_untreated_replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS (replicate1)

source_name: Serum-starved (72h)  Swiss 3T3 fibroblasts, replicate 1


title: 6hA+H89 replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 15 min pre-treatment with H89 (10 uM) and 6 h treatment with anisomycin (188.5 nM) (replicate1)


title: SWI4-myc_INPUT

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type SWI4-myc tag INPUT for IP


title: SWI4-myc_IP_1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type SWI4-myc tag IP


title: 3hA replicate1

description: Gene expression after 72h starvation in the medium containing 0.2% FCS followed by 3 h treatment with anisomycin (188.5 nM) (replicate1)


title: input_1hA

description: Sonicated chromatin (~200 bp fragment length) of serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM)

source_name: Input, Serum-starved (72h)  Swiss 3T3 fibroblasts, 1h anisomycin treated (188.5 nM)


title: SUT1-myc_IP_3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type SUT1-myc tag IP3


title: input_control_untreated

description: Sonicated chromatin (~200 bp fragment length) of serum-starved (72h)  Swiss 3T3 fibroblasts

source_name: Input, Serum-starved (72h)  Swiss 3T3 fibroblasts


title: SWI6-myc_swi4d_INPUT

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
swi4del SWI6-myc tag INPUT for IP


title: SUT1-myc_IP_2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type SUT1-myc tag IP2


title: SWI6-myc_swi4d_IP_1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
swi4del SWI6-myc tag IP1


title: SWI6-myc_INPUT

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type SWI6-myc tag INPUT for IP


title: SWI6-myc_IP_2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type SWI6-myc tag IP2


title: SUT1-myc_IP_1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type SUT1-myc tag IP1


title: control untreated replicate1

value: 72h starvation in the medium containing 0.2% FCS


title: SUT1-myc_nrg1d_IP_2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
nrg1del SUT1-myc tag IP2


title: SWI4-myc_swi6d_INPUT

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
swi6del SWI4-myc tag INPUT for IP


title: SWI4-myc_swi6d_IP_1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
swi6del SWI4-myc tag IP


title: SUT1-myc_nrg1d_IP_1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
nrg1del SUT1-myc tag IP1


title: NRG1-myc_IP_3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type NRG1-myc tag IP3


title: NRG1-myc_INPUT

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type NRG1-myc tag INPUT for IP


title: NRG1-myc_IP_2

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type NRG1-myc tag IP2


title: NRG1-myc_sut1d_INPUT

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
sut1del NRG1-myc tag INPUT for IP


title: SUT1-myc_nrg1d_INPUT

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
nrg1del SUT1-myc tag INPUT for IP


title: SUT1-myc_INPUT

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type SUT1-myc tag INPUT for IP


title: NRG1-myc_IP_1

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
wild-type NRG1-myc tag IP1


title: NRG1-myc_sut1d_IP_3

description:
Harbison, C.T., et al., Transcriptional regulatory code of a eukaryotic genome. Nature, 2004. 431(7004): p. 99-104.
sut1del NRG1-myc tag IP3