title: NTH8 - small RNAseq

description: Patient #8 – Normal Thyroid tissue (NTH). Small RNAseq data

data_processing:
small RNAseq. STEP: Preprocessing. Illumina Small-RNA Adapter sequences were removed from raw reads using cutadapt software (v1.2.1), retrieving reads with lenghts from 17nt to 34 nt.
small RNAseq. STEP: Alignment. Remaining reads were aligned against human genome (hg19) using Bowtie algorithm (v.0.12.7; parameters: -n 0 -l 17 –best).
STEP: Counting tags. Counts of mapped reads in genomic locations (microRNA/exons respectively) were obtained using Htseq-count software (v0.5.4; intersection-nonempty mode; hg19 and miRBase v20)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each microRNA/gene for (Htseq-count output).


title: IR

status: Public on Aug 24 2015

type: SRA

city: Nanning

first: Ying

last: Hu

address: Daxue

country: China

institute: Guangxi University

library_source: transcriptomic

data_processing:
assembling: Trinity software(version: v2012-10-05)
annotation: NCBI blast 2.2.28+, Blast2GO v2.5
expression analysis: RSEM software
Genome_build: The unigene.fasta file containing all assembled sequences is linked as a supplementary file on the Series record.
Supplementary_files_format_and_content: Read counts

molecule: total RNA

organism: Pinus massoniana

source_name: insect-resistant

growth_protocol: Tender leaves, tender stems, old leaves and old stems

extract_protocol:
libraries were prepared according to a version of Illumina HiSeq2000's mRNA-Seq protocol adapted for small sample inputs
The sequence data were assembled using Trinity software (version: v2012-10-05; parameter settings: min_kmer_cov was set to 2; other parameters used the default values)

treatment_protocol: strain insect-resistant and poor insect resistance Pinus massoniana

tag: insect resistance

value: resistant

tag: tissue


title: NTH6 - RNAseq

city: Heidelberg

first: Javier

last: Perales-Paton

state: Baden-Württemberg

address: Im Neuenheimer Feld 267

department: Faculty of Medicine

country: Germany

institute: Heidelberg University

description: Patient #6 – Normal Thyroid tissue (NTH). RNAseq data

data_processing:
RNAseq. STEP: Alignment. Reads were aligned against human genome (hg19) using TopHat algorithm (v.2.0.4; parameters: --bowtie --segment-length 20 --genome-read-mismatches 2 –read-mismatches 2 --segment-mismatches 1 --max-multihits 5 --library-type fr-firststrand )
STEP: Counting tags. Counts of mapped reads in genomic locations (microRNA/exons respectively) were obtained using Htseq-count software (v0.5.4; intersection-nonempty mode; hg19 and miRBase v20)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each microRNA/gene for (Htseq-count output).

organism: Homo sapiens

source_name: Normal Thyroid tissue

extract_protocol:
Surgically removed tissues were quickly frozen in liquid nitrogen until analysis. The samples were snap frozen on dry ice and stored at -80°C. Total RNA was extracted with TRIzol solution (Invitrogen), and the integrity of RNA was assessed using an Agilent BioAnalyzer 2100 (Agilent Technologies). All samples were collected with the informed consent of the patients and the experiments were approved by the Hospital Research Ethics Committee at Hospital Universitario La Paz.
Illumina® TruSeq® Small RNA & Illumina® TruSeq® Stranded mRNA

value: Normal Thyroid

tag: diagnosis

value: Papillary Thyroid Carcinoma

tag: sequenced molecule

value: mRNA


title: SmEDZ3

city: Ann Arbor

first: John

last: Schiefelbein

state: Michigan

address: 830 North University Avenue

department: Molecular, Cellular, and Developmental Biology

country: USA

institute: University of Michigan

data_processing:
Reads quality were checked by FastQC.
The first 15 bp of each read was trimmed to ensure high quality.
Reads were mapped to the mentioned reference annotation by Tophat2 with default setting.
Reads were quantified to RPKM by Cufflinks2 with default setting plus the correction for multi-read (-u)
Genome_build: see the reference that is listed in sample characteristics for each species.
Supplementary_files_format_and_content: A master tab-delimited text file (.csv)  includes RPKM values of different development zones for each gene .  There are two master sheets, one for gene expression of 3 development zones in 6 angiosperms, another for combined gene expression of elongation + differentiation zone in 7 vascular plants (6 angiosperms + selaginella).

organism: Selaginella moellendorffii

source_name: Root elongation + differentiation zone

growth_protocol: Seeds were sterilized and germinated on agarose-solidified MS media under constant light at 21C.

extract_protocol:
The growing tips of the seedling primary roots were dissected along the longitudinal axis into 3 development zones.  RNA was extracted by Qiagen RNeasy Plant Mini Kit.
RNA libraries were constructed by Illumina TrueSeq kit according to manufacturer procedures.

tag: cultivar

value: Plant Delights

tag: reference annotation used for mapping

value: Phytozome Sm91

tag: age

value: 21 days after plating, grown from bulbils

value: root

tag: root zone

value: Root elongation + differentiation zone


title: NTH7 - small RNAseq

description: Patient #7 – Normal Thyroid tissue (NTH). Small RNAseq data

value: small RNA


title: NTH6 - small RNAseq

description: Patient #6 – Normal Thyroid tissue (NTH). Small RNAseq data


title: NTH4 - small RNAseq

description: Patient #4 – Normal Thyroid tissue (NTH). Small RNAseq data


title: PTC6 - RNAseq

description: Patient #6 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data

source_name: Thyroid tumor tissue

value: Thyroid tumor


title: SmEDZ1


title: SmMZ2

source_name: Root meristematic zone

value: Root meristematic zone


title: SmMZ3


title: NTH2 - small RNAseq

description: Patient #2 – Normal Thyroid tissue (NTH). Small RNAseq data


title: PTC3 - RNAseq

description: Patient #3 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: NTH3 - small RNAseq

description: Patient #3 – Normal Thyroid tissue (NTH). Small RNAseq data


title: NTH5 - small RNAseq

description: Patient #5 – Normal Thyroid tissue (NTH). Small RNAseq data


title: PTC8 - small RNAseq

description: Patient #8 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: SmMZ1


title: PTC6 - small RNAseq


title: CsDZ1

organism: Cucumis sativus

source_name: Root differentiation zone

value: Phytozome Cs122

value: 4 days after plating

value: Root differentiation zone


title: NTH1 - small RNAseq

description: Patient #1 – Normal Thyroid tissue (NTH). Small RNAseq data


title: input_for_Olig2chip_rep1

city: Los Angeles

first: Yuichi

last: Nishi

state: CA

address: 1425 San Pablo St.

department: Eli and Edythe Broad-CIRM Center for Regenerative Medicine

institute: University of Southern California

description: Matching input DNA for sample 3

library_source: genomic

data_processing:
Basecalls performed using Illumina pipeline
The first 25bp of ChIP-seq reads were aligned to the unmasked mm9 genome using Eland allowing up to two mismatches (Samples 1-3, 507) or aligned against mm9 with Bowtie2 (version 2.2.4) to obtain SAM (Samples 4,8-13).
Unique reads were used to identify peaks using CisGenome peak caller in the 2-sample conditional binomial mode against matched input DNA data at FDR=0.01 cutoff
Heatmap comparison of rep1 and rep2 was performed by HOMER to generate _heatmap.txt output with the default settings.
Genome_build: mm9
Supplementary_files_format_and_content: bed files contain binding regions called in this analysis; heatmap.txt output file for heatmap comparision of rep1 and rep2

molecule: genomic DNA

organism: Mus musculus

source_name: Neural progenitor cells

growth_protocol: Ventral neural progenitors were routinely generated from mouse ESCs by two days of suspension culture in DFNB (25% DMEM, 25% F12, 50% Neurobasal supplemented with 1xB27 [Life Technologies]) or DFNK (10% Knockout Serum Replacement [Life Technologies] in place of B27 in DFNB) followed by additional three days in DFNB with 500nM all-trans retinoic acid and 160-800nM Smoothened agonist (SAG, Calbiochem/EMD Millipore).  To obtain dorsal characteristics in Gli3 profiling, SAG was omitted from the induction formula.

extract_protocol:
Cells were dissociated in trypsin then crosslinked in 1% formaldehyde at room-temperature for 30 minutes. Cells were lysed in lysis buffer (140mM NaCl, 0.5% NP40, 0.25% Triton-X 100, 10% glycerol, 1mM EDTA, 50mM HEPES-KOH, pH7.5) or (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) at 4˚C with agitation for 10 minutes then washed with Buffer 2 (200mM NaCl, 1mM EDTA, 0.5mM EGTA, 10mM Tris-Cl pH8.0) for 10 minutes at room-temperature. Chromatin was fragmented by sonication (Branson digital sonifier with microtip) in Buffer 3 (1mM EDTA, 0.5mM EGTA, 10mM Tris-Cl pH8.0). Lysate was cleared by centrifugation and supplemented with NaCl, NaDeoxycholate, and TritonX 100 to the final concentrations of 100mM, 0.1%, and 1%, respectively. Magnetic beads (Dynal/Invitrogen, sheep anti-mouse IgG, anti-rabbit IgG, and Protein G for mouse, rabbit, and goat antibodies, respectively) were blocked with a blocking buffer (5mg/ml BSA in PBS) then incubated with an antibody in the blocking buffer overnight. Unbound antibody was washed away by extensive wash with the blocking buffer. Beads/antibody complex was incubated with the lysate overnight at 4°C. Beads were washed 5 times with RIPA buffer (1% NP40, 0.7% NaDeoxycholate, 0.5M LiCl, 1mM EDTA, 50mM HEPES-KOH, pH7.5). DNA was eluted with elution buffer (1% SDS, 1mM EDTA, 50mM Tris-Cl, pH8.0) at 65˚C for 15 min, and the eluate was incubated further overnight at 65˚C to reverse crosslinking. DNA was purified by phenol/chloroform extraction and ethanol precipitation or by PCR purification kit (Qiagen). All buffers except RIPA buffer was supplemented with protease inhibitor cocktail mix (Roche).
Sequencing library was constructed using ChIP-Seq DNA Sample Prep Kit (Illumina IP-102-1001) according to the manufacturer's instruction. Briefly, DNA was blunted and phosphorylated with T4 and Klenow DNA polymerases and T4 PNK followed by adapter ligation with T4 DNA ligase. A range of 275-700bp was selected by gel purification and amplified with PCR primers 1.1 and 2.1 for 18 cycles.

tag: strain background

value: mixed; C57BL6/J, 129 Sv and Swiss Webster

tag: genotype/variation

tag: cell type

value: ES-derived neural progenitors (ventral)


title: CsDZ2


title: PTC7 - small RNAseq

description: Patient #7 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: PTC5 - small RNAseq

description: Patient #5 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: CsEZ3

source_name: Root elongation zone

value: Root elongation zone


title: input_for_Nkx2.2chip_rep1

description: Matching input DNA for sample 1

value: Rosa26-Gli1FLAG (YFP3.1 derivative)


title: PTC4 - small RNAseq

description: Patient #4 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data

value: Papillary Thyroid Carcinoma


title: SmEDZ2


title: CsEZ2


title: Olig2_NPC_ChIP-seq_rep1

description: Sample 3

tag: chip antibody

value: Anti-Olig-2 Antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: PTC2 - small RNAseq

description: Patient #2 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: PTC1 - small RNAseq

description: Patient #1 – Papillary Thyroid Carcinoma tissue (PTC). Small RNAseq data


title: Nkx6.1_NPC_ChIP-seq_rep1

description: Sample 2

tag: chip antibody info

value: Cocktail of DSHB (F55A10, F55A12, F64A6B4, and F65A2), RD Systems  (AF5857) and custom (from T. Jessell)


title: CsMZ3


title: Nkx2.2_NPC_ChIP-seq_rep1

description: Sample 1

value: Cocktail of DSHB (74.5A5), Sigma (HPA003468), and custom (from T. Jessell)


title: PTC3 - small RNAseq


title: input_for_Nkx6.1chip_rep1

description: Matching input DNA for sample 2


title: CsDZ3

value: root


title: CsMZ1


title: Patient 14 (PN, F, 24)

status: Public on Aug 23 2015

first: William

middle: R

last: Swindell

state: MI

address: 1500 E. Medical Center Drive

department: Dermatology

description: uninvolved normal skin from psoriasis patient

data_processing:
Illumina adaptor sequences were removed using CutAdapt (version 1.6) with a maximum error rate setting (-e) of 5% and a minimum post-processing read length (-m) of 20 base pairs
Reads were trimmed to remove bases with low PHRED quality scores (CutAdapt and Fast-X toolkit)
Filtered reads were mapped to the UCSC human genome (hg19) using Tophat2 (version 2.0.12)
Overlap between mapped reads and known human genes was tabulated using the htseq-count function from the HTSeq python library (version 0.5.4p3)
Cufflinks (version 2.2.1) was used to calculate fragments per kilobase of exon per million fragments mapped (FPKM) for each gene feature.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data includes raw read counts and FPKM values for all human genes (UCSC, hg19) and each sample (.txt files).

source_name: skin

growth_protocol: Patients discontinued systemic therapies for 2 weeks prior to biopsy collection (1 week for topical treatment).

extract_protocol:
RNA was extracted using QIAGEN RNEasy mini kits
Sequencing of fragmented complementary cDNA was performed using the Illumina Genome Analyzer Iix

treatment_protocol: Two biopsies were taken from each patient; one 6mm punch biopsy was obtained from lesional skin of each patient (PP sample) and the other from non-lesional skin (PN sample)

tag: group

value: PN

tag: patient

tag: gender

value: female


title: CsMZ2

tag: tissue


title: Patient 13 (PN, F, 42)


title: Patient 13 (PP, F, 42)

description: lesional skin from psoriasis patient

value: PP


title: Patient 14 (PP, F, 24)

description: lesional skin from psoriasis patient


title: Patient 12 (PN, F, 35)


title: Patient 11 (PP, F, 57)

description: lesional skin from psoriasis patient


title: Patient 11 (PN, F, 57)


title: Patient 10 (PP, M, 43)

description: lesional skin from psoriasis patient

value: male


title: Patient 12 (PP, F, 35)

description: lesional skin from psoriasis patient


title: CsEZ1

value: Phytozome Cs122


title: Patient 10 (PN, M, 43)


title: Patient 9 (PN, M, 71)


title: Patient 8 (PP, M, 52)

description: lesional skin from psoriasis patient


title: Patient 7 (PN, M, 62)


title: Patient 7 (PP, M, 62)

description: lesional skin from psoriasis patient


title: Patient 6 (PN, F, 56)


title: Patient 6 (PP, F, 56)

description: lesional skin from psoriasis patient


title: Patient 5 (PN, M, 60)


title: Patient 5 (PP, M, 60)

description: lesional skin from psoriasis patient


title: Patient 4 (PN, F, 42)


title: Patient 3 (PP, M, 53)

description: lesional skin from psoriasis patient


title: Patient 3 (PN, M, 53)


title: Patient 1 (PN, M, 47)


title: Patient 2 (PP, M, 44)

description: lesional skin from psoriasis patient


title: Patient 2 (PN, M, 44)


title: HRas_me3_2

status: Public on Aug 22 2015

city: Boston

first: Behnam

last: Nabet

state: MA

address: 360 Longwood Ave, LC-2100

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Spry124fl/fl HRasG12V MEFs, replicate2

data_processing:
Images analysis and base calling was done using the solexa pipeline.
All ChIP-Seq datasets were aligned using Bowtie2 (version 2.2.1) to their indicated build. Alignments were performed using default parameters that preserved reads mapping uniquely to the genome without mismatches.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files: For all samples, aligned sequences allocated into 50bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown. All aligned sequences were processed through MACS 1.4.2 and fragment pileup was outputted in .wig format.

source_name: Immortalized MEF

growth_protocol: MEFs that were transduced with retrovirus were cultured in DMEM containing 10% FBS and 1% Pen/Strep and 2 μg/mL puromycin.

extract_protocol:
ChIP was performed using the ChIP Assay Kit (Millipore, #17-295) according to the manufacturer's instructions, with the following modifications. After cell lysis, extracts were subjected to sonication with a 60 Sonic Dismembrator (Fisher Scientific) at 4°C for 20 cycles, cycling ON for 20 seconds and OFF for 1 minute at power setting 5, leading to an average DNA size of 200 bp. Samples were pre-cleared using 200 μL of Protein A Agarose/Salmon Sperm DNA for 4 hrs at 4°C with rotation. Antibody immunoprecipitations were performed overnight at 4°C. To collect histone complexes of interest, 100 μL Protein A Agarose/Salmon Sperm DNA was added for 4 hrs at 4°C with rotation. Each wash step (“Low Salt Immune Complex Wash Buffer,” “High Salt Immune Complex Wash Buffer,” “LiCl Immune Complex Wash Buffer,” and “TE Buffer”) was performed twice. After reverse-crosslinking overnight, samples were treated with RNase A, and subsequently treated with Proteinase K. Immunoprecipitated chromatin was extracted using QIAquick PCR Purification Kit (Qiagen).
10 ng of input and ChIP material were used to prepare libraries. Libraries were prepared using the ChIP-seq DNA Sample Kit (Illumina).

treatment_protocol: Transduced MEFs received DMEM containing 10% FBS and 1% Pen/Strep and 2 μg/mL puromycin for 24 hrs.

tag: spry status

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

tag: stable transduction

value: pBabe Puro HRasG12V

tag: culture condition

value: DMEM + 10% FBS + 1% Pen/Strep + 2 μg/mL Puromycin

tag: treatment

value: No Additional

value: H3K4me3 (Millipore, catalog# 17-614, lot# 1974075)

tag: input note

value: Corresponding input:HRas_Input_2


title: HRas_me3

description: Spry124fl/fl HRasG12V MEFs, replicate1

value: Corresponding input:HRas_Input


title: Patient 1 (PP, M, 47)

description: lesional skin from psoriasis patient


title: HRas_me1_2B

description: Spry124fl/fl HRasG12V MEFs, replicate2

value: H3K4me1 (Active Motif, catalog# 39297, lot# 21008001)

value: Corresponding input:HRas_Input_2B


title: HRas_Input_2C

description: Spry124fl/fl HRasG12V MEFs, replicate2

value: None (input)

value: Input for HRas_Ac_2C


title: Patient 9 (PP, M, 71)

description: lesional skin from psoriasis patient


title: Patient 4 (PP, F, 42)

description: lesional skin from psoriasis patient


title: Patient 8 (PN, M, 52)


title: HRas_Input_2B

description: Spry124fl/fl HRasG12V MEFs, replicate2

value: Input for HRas_me1_2B


title: HRas_Input

description: Spry124fl/fl HRasG12V MEFs, replicate1

value: Input for HRas_me3, HRas_me1, HRas_Ac


title: HRas_Input_2

description: Spry124fl/fl HRasG12V MEFs, replicate2

value: Input for HRas_me3_2


title: HRas_Ac_2C

description: Spry124fl/fl HRasG12V MEFs, replicate2

value: H3K27ac (Active Motif, catalog# 39133, lot# 01613007)

value: Corresponding input:HRas_Input_2C


title: EV_me3_2

description: Spry124fl/fl EV MEFs, replicate2

value: pBabe Puro Empty Vector

value: Corresponding input:EV_Input_2


title: EV_Input_2

description: Spry124fl/fl EV MEFs, replicate2

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

value: Input for EV_me3_2


title: EV_Input_2B

description: Spry124fl/fl EV MEFs, replicate2

value: DMEM + 10% FBS + 1% Pen/Strep + 2 μg/mL Puromycin

value: No Additional

value: Input for EV_me1_2B


title: EV_me3

description: Spry124fl/fl EV MEFs, replicate1

value: H3K4me3 (Millipore, catalog# 17-614, lot# 1974075)

value: Corresponding input:EV_Input


title: EV_me1_2B

description: Spry124fl/fl EV MEFs, replicate2

value: H3K4me1 (Active Motif, catalog# 39297, lot# 21008001)

value: Corresponding input:EV_Input_2B


title: EV_me1

description: Spry124fl/fl EV MEFs, replicate1


title: EV_Input_2C

description: Spry124fl/fl EV MEFs, replicate2

value: None (input)

value: Input for EV_Ac_2C


title: EV_Ac_2C

description: Spry124fl/fl EV MEFs, replicate2

value: Corresponding input:EV_Input_2C


title: HRas_me1

description: Spry124fl/fl HRasG12V MEFs, replicate1

value: pBabe Puro HRasG12V

value: Corresponding input:HRas_Input


title: VEC_U2_Input_for_AC

description: Spry124fl/fl MEFs unsynchronized, replicate2

growth_protocol: Spry124fl/fl (VEC) and Spry124-/- (CRE) MEFs were cultured in DMEM containing 10% FBS and 1% Pen/Strep.

treatment_protocol: Unsynchronized (U) MEFs received DMEM containing 10% FBS and 1% Pen/Strep for 24 hrs.

value: Unsynchronized (DMEM + 10% FBS + 1% Pen/Strep)

value: Input for VEC_U2_AC


title: EV_Ac

description: Spry124fl/fl EV MEFs, replicate1

value: pBabe Puro Empty Vector

value: H3K27ac (Active Motif, catalog# 39133, lot# 01613007)


title: VEC_U2_AC

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

value: H3K27ac (Active Motif, catalog# 39133, lot# 21311004)

value: Corresponding input:VEC_U2_Input_for_AC


title: HRas_Ac

description: Spry124fl/fl HRasG12V MEFs, replicate1

value: DMEM + 10% FBS + 1% Pen/Strep + 2 μg/mL Puromycin

value: No Additional


title: VEC_S2_Input_for_AC

description: Spry124fl/fl MEFs starve, replicate2

treatment_protocol: Starved (S) MEFs received DMEM containing 0.1% FBS and 1% Pen/Strep for 24 hrs.

value: Serum Starved (DMEM + 0.1% FBS + 1% Pen/Strep)

value: Input for VEC_S2_AC


title: VEC_S2_AC

description: Spry124fl/fl MEFs starve, replicate2

value: Corresponding input:VEC_S2_Input_for_AC


title: VEC_U_AC

description: Spry124fl/fl MEFs unsynchronized, replicate1

value: Corresponding input:VEC_U_Input_for_AC


title: VEC_S_Input_for_AC

description: Spry124fl/fl MEFs starve, replicate1

value: None (input)

value: Input for VEC_S_AC


title: VEC_F2_AC

description: Spry124fl/fl MEFs FGF, replicate2

treatment_protocol: FGF (F) treated MEFs received DMEM containing 0.1% FBS and 1% Pen/Strep for 20 hrs and were subsequently treated with 10 ng/mL FGF, which was added directly to the media for an additional 4 hrs.

value: 10ng/mL FGF for 4hrs

value: Corresponding input:VEC_F2_Input_for_AC


title: VEC_F2_Input_for_AC

description: Spry124fl/fl MEFs FGF, replicate2

value: Input for VEC_F2_AC


title: VEC_S_AC

description: Spry124fl/fl MEFs starve, replicate1

value: Corresponding input:VEC_S_Input_for_AC


title: CRE_U2_AC

description: Spry124-/- MEFs unsynchronized, replicate2

value: No Spry expression (Spry1,2,4 are excised)

value: Unsynchronized (DMEM + 10% FBS + 1% Pen/Strep)

value: Corresponding input:CRE_U2_Input_for_AC


title: VEC_F_Input_for_AC

description: Spry124fl/fl MEFs FGF, replicate1

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

value: Input for VEC_F_AC


title: CRE_U2_Input_for_AC

value: Input for CRE_U2_AC


title: VEC_F_AC

description: Spry124fl/fl MEFs FGF, replicate1

value: H3K27ac (Active Motif, catalog# 39133, lot# 21311004)

value: Corresponding input:VEC_F_Input_for_AC


title: CRE_S_Input_for_AC

description: Spry124-/- MEFs starve, replicate1

value: Serum Starved (DMEM + 0.1% FBS + 1% Pen/Strep)

value: No Additional

value: Input for CRE_S_AC


title: EV_Input

description: Spry124fl/fl EV MEFs, replicate1

value: pBabe Puro Empty Vector

value: DMEM + 10% FBS + 1% Pen/Strep + 2 μg/mL Puromycin

value: None (input)

value: Input for EV_me3, EV_me1, EV_Ac


title: CRE_S2_AC

description: Spry124-/- MEFs starve, replicate2

value: Corresponding input:CRE_S2_Input_for_AC


title: CRE_S2_Input_for_AC

description: Spry124-/- MEFs starve, replicate2

value: Input for CRE_S2_AC


title: CRE_U_AC

description: Spry124-/- MEFs unsynchronized, replicate1

value: No Spry expression (Spry1,2,4 are excised)

value: Corresponding input:CRE_U_Input_for_AC


title: CRE_F_Input_for_AC

description: Spry124-/- MEFs FGF, replicate1

value: 10ng/mL FGF for 4hrs

value: Input for CRE_F_AC


title: CRE_F2_Input_for_AC

description: Spry124-/- MEFs FGF, replicate2

value: Input for CRE_F2_AC


title: VEC_U2_me3

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

value: Unsynchronized (DMEM + 10% FBS + 1% Pen/Strep)

value: H3K4me3 (Millipore, catalog# 17-614, lot# 1974075)

value: Corresponding input:VEC_U2_Input


title: CRE_F2_AC

description: Spry124-/- MEFs FGF, replicate2

value: Serum Starved (DMEM + 0.1% FBS + 1% Pen/Strep)

value: H3K27ac (Active Motif, catalog# 39133, lot# 21311004)

value: Corresponding input:CRE_F2_Input_for_AC


title: CRE_F_AC

description: Spry124-/- MEFs FGF, replicate1

value: Corresponding input:CRE_F_Input_for_AC


title: VEC_U2_me1

value: No Additional

value: H3K4me1 (Active Motif, catalog# 39297, lot# 21008001)


title: VEC_U2_Input

value: None (input)

value: Input for VEC_U2_me1 and VEC_U2_me3


title: VEC_U_Input_for_AC

value: Input for VEC_U_AC


title: VEC_U_me1

value: Corresponding input:VEC_U_Input


title: VEC_U_Input

value: Input for VEC_U_me1 and VEC_U_me3


title: CRE_U_Input_for_AC

value: No Spry expression (Spry1,2,4 are excised)

value: Input for CRE_U_AC


title: VEC_S2_me3

description: Spry124fl/fl MEFs starve, replicate2

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

value: Corresponding input:VEC_S2_Input


title: VEC_S2_Input

description: Spry124fl/fl MEFs starve, replicate2

value: Input for VEC_S2_me1 and VEC_S2_me3


title: VEC_S_me1

description: Spry124fl/fl MEFs starve, replicate1

value: Corresponding input:VEC_S_Input2


title: VEC_S_me3

description: Spry124fl/fl MEFs starve, replicate1

value: Serum Starved (DMEM + 0.1% FBS + 1% Pen/Strep)

value: H3K4me3 (Millipore, catalog# 17-614, lot# 1974075)

value: Corresponding input:VEC_S_Input


title: VEC_S_Input

description: Spry124fl/fl MEFs starve, replicate1

value: Input for VEC_S_me3


title: VEC_S_Input2

description: Spry124fl/fl MEFs starve, replicate1

value: No Additional

value: Input for VEC_S_me1


title: VEC_F2_me3

description: Spry124fl/fl MEFs FGF, replicate2

value: 10ng/mL FGF for 4hrs

value: Corresponding input:VEC_F2_Input


title: VEC_F2_me1

description: Spry124fl/fl MEFs FGF, replicate2

value: H3K4me1 (Active Motif, catalog# 39297, lot# 21008001)


title: VEC_F_me3

description: Spry124fl/fl MEFs FGF, replicate1

value: Corresponding input:VEC_F_Input


title: VEC_F_Input

description: Spry124fl/fl MEFs FGF, replicate1

value: None (input)

value: Input for VEC_F_me1 and VEC_F_me3


title: CRE_U2_me1

value: No Spry expression (Spry1,2,4 are excised)

value: Unsynchronized (DMEM + 10% FBS + 1% Pen/Strep)

value: Corresponding input:CRE_U2_Input


title: CRE_U_me3

value: Corresponding input:CRE_U_Input


title: CRE_U2_me3


title: CRE_U2_Input

value: Input for CRE_U2_me1 and CRE_U2_me3


title: CRE_S2_me1

description: Spry124-/- MEFs starve, replicate2

value: Serum Starved (DMEM + 0.1% FBS + 1% Pen/Strep)

value: Corresponding input:CRE_S2_Input


title: CRE_U_me1


title: CRE_S_me3

description: Spry124-/- MEFs starve, replicate1

value: H3K4me3 (Millipore, catalog# 17-614, lot# 1974075)

value: Corresponding input:CRE_S_Input


title: CRE_U_Input

value: No Additional

value: Input for CRE_U_me1 and CRE_U_me3


title: CRE_S2_Input

description: Spry124-/- MEFs starve, replicate2

value: Input for CRE_S2_me1 and CRE_S2_me3


title: CRE_S2_me3

description: Spry124-/- MEFs starve, replicate2


title: CRE_S_Input2

description: Spry124-/- MEFs starve, replicate1

value: Input for CRE_S_me1


title: CRE_S_me1

description: Spry124-/- MEFs starve, replicate1

value: H3K4me1 (Active Motif, catalog# 39297, lot# 21008001)

value: Corresponding input:CRE_S_Input2


title: CRE_S_AC

description: Spry124-/- MEFs starve, replicate1

value: H3K27ac (Active Motif, catalog# 39133, lot# 21311004)

value: Corresponding input:CRE_S_Input_for_AC


title: CRE_F2_me1

description: Spry124-/- MEFs FGF, replicate2

value: No Spry expression (Spry1,2,4 are excised)

value: 10ng/mL FGF for 4hrs

value: Corresponding input:Sample_CRE_F2_Input


title: CRE_F2_me3

description: Spry124-/- MEFs FGF, replicate2


title: CRE_F2_Input

description: Spry124-/- MEFs FGF, replicate2

value: None (input)

value: Input for CRE_F2_me1 and CRE_F2_me3


title: VEC_S2_me1

description: Spry124fl/fl MEFs starve, replicate2

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

value: Serum Starved (DMEM + 0.1% FBS + 1% Pen/Strep)

value: Corresponding input:VEC_S2_Input


title: CRE_F_me3

description: Spry124-/- MEFs FGF, replicate1

value: H3K4me3 (Millipore, catalog# 17-614, lot# 1974075)

value: Corresponding input:CRE_F_Input


title: CRE_EV_3

description:
Spry124-/- EV MEFs, replicate3
processed data file: Oncogene_AllCounts.csv

data_processing:
Raw fastq files were first QC-processed to remove any reads which failed Illumina's purity filter, and were then trimmed using the Sickle tool with a sliding window quality score cutoff of 20 and a minimum final read length of 20 bases.
Reads were  aligned to the mm9 genome using gsnap.
Assignment of reads to genes was performed by htseq-count. The algorithm was used in 'union' mode with the minimum quality score set to 10.
Raw counts of aligned reads were normalized based on both effective library size scaling and variance stabilizing normalization.
Genome_build: mm9
Supplementary_files_format_and_content: The .csv file contains read counts for each gene in each sample. The ensemble ID for each gene is indicated.

growth_protocol: Spry124fl/fl (VEC) and Spry124-/- (CRE) MEFs were cultured in DMEM containing 10% FBS and 1% Pen/Strep. MEFs that were transduced with retrovirus were cultured in DMEM containing 10% FBS and 1% Pen/Strep and 2 μg/mL puromycin.

extract_protocol:
MEFs were lysed, homogenized using Qiashredder columns (Qiagen), and RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: pBabe Puro Empty Vector (EV)

value: DMEM + 10% FBS + 1% Pen/Strep + 2 μg/mL Puromycin

value: No Additional


title: BRaf_3

description:
Spry124fl/fl BRafV600E MEFs, replicate3
processed data file: Oncogene_AllCounts.csv

value: pBabe Puro BRafV600E


title: KRas_3

description:
Spry124fl/fl KRasG12V MEFs, replicate3
processed data file: Oncogene_AllCounts.csv

value: pBabe Puro KRasG12V


title: CRE_F_Input

description: Spry124-/- MEFs FGF, replicate1

value: Input for CRE_F_me1 and CRE_F_me3


title: HRas_3

description:
Spry124fl/fl HRasG12V MEFs, replicate3
processed data file: Oncogene_AllCounts.csv

value: pBabe Puro HRasG12V


title: VEC_EV_3

description:
Spry124fl/fl EV MEFs, replicate3
processed data file: Oncogene_AllCounts.csv


title: CRE_F_me1

description: Spry124-/- MEFs FGF, replicate1

value: No Spry expression (Spry1,2,4 are excised)

value: H3K4me1 (Active Motif, catalog# 39297, lot# 21008001)


title: CRE_EV_2

description:
Spry124-/- EV MEFs, replicate2
processed data file: Oncogene_AllCounts.csv


title: HRas_2

description:
Spry124fl/fl HRasG12V MEFs, replicate2
processed data file: Oncogene_AllCounts.csv


title: VEC_EV_2

description:
Spry124fl/fl EV MEFs, replicate2
processed data file: Oncogene_AllCounts.csv


title: CRE_EV_1

description:
Spry124-/- EV MEFs, replicate1
processed data file: Oncogene_AllCounts.csv


title: BRaf_1

description:
Spry124fl/fl BRafV600E MEFs, replicate1
processed data file: Oncogene_AllCounts.csv


title: BRaf_2

description:
Spry124fl/fl BRafV600E MEFs, replicate2
processed data file: Oncogene_AllCounts.csv


title: CRE_S_Input

description: Spry124-/- MEFs starve, replicate1

value: Input for CRE_S_me3


title: KRas_2

description:
Spry124fl/fl KRasG12V MEFs, replicate2
processed data file: Oncogene_AllCounts.csv


title: CRE_S_3

description:
Spry124-/- MEFs starve, replicate3
processed data file: VEC_CRE_AllCounts.csv


title: VEC_EV_1

description:
Spry124fl/fl EV MEFs, replicate1
processed data file: Oncogene_AllCounts.csv


title: KRas_1

description:
Spry124fl/fl KRasG12V MEFs, replicate1
processed data file: Oncogene_AllCounts.csv


title: CRE_U_3

description:
Spry124-/- MEFs unsynchronized, replicate3
processed data file: VEC_CRE_AllCounts.csv

value: Unsynchronized (DMEM + 10% FBS + 1% Pen/Strep)


title: CRE_F_3

description:
Spry124-/- MEFs FGF, replicate3
processed data file: VEC_CRE_AllCounts.csv

value: 10 ng/mL FGF for 4hrs


title: VEC_S_3

description:
Spry124fl/fl MEFs starve, replicate3
processed data file: VEC_CRE_AllCounts.csv

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)


title: VEC_F_3

description:
Spry124fl/fl MEFs FGF, replicate3
processed data file: VEC_CRE_AllCounts.csv

value: Serum Starved (DMEM + 0.1% FBS + 1% Pen/Strep)


title: VEC_U_3

description:
Spry124fl/fl MEFs unsynchronized, replicate3
processed data file: VEC_CRE_AllCounts.csv


title: CRE_F_2

description:
Spry124-/- MEFs FGF, replicate2
processed data file: VEC_CRE_AllCounts.csv


title: CRE_S_2

description:
Spry124-/- MEFs starve, replicate2
processed data file: VEC_CRE_AllCounts.csv


title: CRE_U_2

description:
Spry124-/- MEFs unsynchronized, replicate2
processed data file: VEC_CRE_AllCounts.csv


title: CRE_S_1

description:
Spry124-/- MEFs starve, replicate1
processed data file: VEC_CRE_AllCounts.csv


title: CRE_U_1

description:
Spry124-/- MEFs unsynchronized, replicate1
processed data file: VEC_CRE_AllCounts.csv


title: CRE_F_1

description:
Spry124-/- MEFs FGF, replicate1
processed data file: VEC_CRE_AllCounts.csv


title: VEC_U_2

description:
Spry124fl/fl MEFs unsynchronized, replicate2
processed data file: VEC_CRE_AllCounts.csv


title: VEC_S_2

description:
Spry124fl/fl MEFs starve, replicate2
processed data file: VEC_CRE_AllCounts.csv


title: HRas_1

description:
Spry124fl/fl HRasG12V MEFs, replicate1
processed data file: Oncogene_AllCounts.csv


title: VEC_S_1

description:
Spry124fl/fl MEFs starve, replicate1
processed data file: VEC_CRE_AllCounts.csv


title: Du5hr-2

city: Beijing

first: Guanghua

last: Huang

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology

data_processing:
Software Illumina OLB_1.9.4 was used for basecalling.
Dirty raw reads were filtered by removing reads with adaptors and low quality, and the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads) according to Mortazavi, et a., Nature Methods, 2008, and the formula is shown as follows: RPKM=106C/(NL/103). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene .
Genome_build: Candida albicans SC5314 genome (ASM18296v1)
Supplementary_files_format_and_content: text files include RPKM values for each Sample

organism: Candida albicans

source_name: Sorbitol treatment, 5h

growth_protocol: Candida albicans wild type strain SC5314 cells were grown to stationary phase in liquid YPD medium at 30°C.

extract_protocol:
Total RNA were extracted using the GeneJET RNA Purification kits according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were collected by centrifugation and washed three times with ddH2O. 6 x 107 cells per ml were treated in 2% sorbitol, 2% glucose, and 2% GlcNAc media at 30°C with shaking for 5 hours.

tag: strain

tag: genotype

value: wild type


title: Du5hr-4

source_name: GlcNAc treatment, 5h


title: VEC_U_1

description:
Spry124fl/fl MEFs unsynchronized, replicate1
processed data file: VEC_CRE_AllCounts.csv


title: RFX3_ChIPSeq

city: Geneva

first: Walter

last: Reith

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

data_processing:
Basecalls performed using CASAVA
ChIP-seq read sequences were aligned to the mm9 genome assembly using bowtie with the following parameters: -v 2 -k 1 -m 1 -r
mapped positions of read 5' ends were shifted to the estimated center-positions of DNA fragments ('centered') using chipcenter (http://sourceforge.net/projects/chip-seq/)
peaks were called using chippeak (http://sourceforge.net/projects/chip-seq/) with the following parameters: -r -f feature_name -w 200 -v 400 and a Peak Threshold value -t adapted to the average density of the mapped reads
Genome_build: mm9

source_name: mouse pancreatic beta cell line MIN6

growth_protocol: classical cell culture conditions

extract_protocol:
Chromatin immunprecipitation and DNA purification were performed as described in       Masternak K,   Peyraud N,   Krawczyk M,   Barras E,   Reith W    : Chromatin remodeling and extragenic transcription at the MHC class II locus control region. Nat Immunol 2003;4:132–137
ChIP-seq Sample Preparation Kit (Illumina)

treatment_protocol: Cells were fixed with formaldehyde and cross linked chromatin was purified as described in       Masternak K,   Peyraud N,   Krawczyk M,   Barras E,   Reith W    : Chromatin remodeling and extragenic transcription at the MHC class II locus control region. Nat Immunol 2003;4:132–137

value: mouse beta cell line


title: Du24h-4

source_name: GlcNAc treatment, 24h

treatment_protocol: Cells were collected by centrifugation and washed three times with ddH2O. 6 x 107 cells per ml were treated in 2% sorbitol, 2% glucose, and 2% GlcNAc media at 30°C with shaking for 24 hours.


title: Du24h-2

source_name: Sorbitol treatment, 24h


title: VEC_U_me3

description: Spry124fl/fl MEFs unsynchronized, replicate1

value: H3K4me3 (Millipore, catalog# 17-614, lot# 1974075)

value: Corresponding input:VEC_U_Input


title: Du24h-3

source_name: Glucose treatment, 24h


title: Ino4_input

status: Public on Aug 21 2015

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Reads were mapped to the S. cerevisiae sacCer2 genome assembly using BWA mem (version 0.7.5a-r405) to generate coverage maps for each data set.
Genome_build: The SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: Text files of coverage maps

organism: Saccharomyces cerevisiae

source_name: meiotic culture

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 13.5–14 hr at 30ºC, harvested, resuspended in 2% potassium acetate, and sporulated at 30ºC.

extract_protocol:
ChIP was performed as described (Murakami et al., 2014). Cells were sporulated and 50 mL of meiotic culture (2 x 109 cells) was collected at 4h and crosslinked with 1% formaldehyde for 30 min at room temperature. Crosslinking was terminated by 5 min incubation with 131 mM glycine. Cells were washed twice with ice-cold TBS, flash frozen with liquid nitrogen and stored at -80°C. Cells were suspended in 1 mL of Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 mM PMSF, 7 ug/mL aprotinin, 1% protease inhibitor cocktail (Sigma), 1x Complete Protease Inhibitor Cocktail (Roche)) with ca. 900 uL of 0.5 mm zirconia/silica beads (BioSpec Products) in 2 mL screw-cap tubes. Cells were disrupted by vigorous shaking 3 min x 6 times in Mini-beadbeater-16 (BioSpec Products) or at 6.5 m/s for 1 min x 8 times in FastPrep24 (MP Biomedicals). 1 mL of Lysis buffer was added after cell disruption. Subsequently, chromatin in the whole cell extracts (WCE) was sheared by sonication with "M" intensity, 30 sec ON/ 30 sec OFF for 15 min x 2 times in Bioruptor Sonication System UCD200 (Diagenode) in 15 mL polystyrene conical tubes. Insoluble fraction (cell debris) was removed by centrifugation at 21,130 g, 5 min, 4°C. WCE was further sonicated with the same conditions 1-3 times to yield average DNA size less than 500 bp. WCE was flash frozen and stored at -80°C.
The ChIPseq library was prepared following Illumina standard protocol. We used Trueseq DNA sample prep kit.

tag: epitope tag

value: anti-Myc antibody (9E10) [made in-house at MSKCC]

tag: time

value: 4 hr in meiosis


title: Ino4_ChIP

tag: chip antibody


title: VEC_F_2

description:
Spry124fl/fl MEFs FGF, replicate2
processed data file: VEC_CRE_AllCounts.csv


title: 2-3h zld- Dl ChIP-seq rep2 input

first: Christine

last: Rushlow

address: 100 Washington Sq. E. Room 1001

department: Biology

institute: NYU

data_processing:
All sequencing reads were aligned to the Drosophila melanogaster genome (dm3, BDGP Release 5) using Bowtie (v0.12.7), allowing a maximum of 2 mismatches and including only uniquely aligned reads.
Aligned reads were then extended to the average insert size of the library estimated by Bioanalyzer for ChIP-seq, or extended to the corresponding paired-end tag for MNase-seq.
MACS (v1.4) was used to call peaks with the default setting and the “call-subpeaks” function.
DESeq (R package) was used to analyze differential Dl binding between wt and zld- embryos, or differential Zld binding between wt and gd7 embryos
The tag density of MNase-Seq and Pol II ChIP-Seq was calculated by custermized scripts and saved into bIgWig files.
Genome_build: dm3
Supplementary_files_format_and_content: bigWig files contain tag density. DESeq files contain 8 columns, each of which contains chromosome, start of region, end of region, average normalized reads in both genotypes, average normalized reads in wt, average normalized reads in mutant, fold change between two genotypes, log2 fold change between two genotypes, p value of the fold change, and FDR of the fold change, respectively.

organism: Drosophila melanogaster

source_name: embryos

extract_protocol:
Nuclei were collected from homogenized embryos and sonicated. Protein-DNA complexes, which are in the supernatant after sonication and centrifugation, were isolated with antibodies corresponding to each ChIP experiment.
Libraries were prepared from ChIP and input DNA using the NEBNext® DNA Library Prep Master Mix Set for Illumina® kit (#E6040) either following the manufacturer’s instructions, or with a modified protocol using biotin-labeled dATP (Chen et al., 2013).

tag: developmental stage (after egg laying)

value: zld-

tag: embryos hand-sorted or not

value: sorted


title: 2-3h wt Pol II ChIP-seq rep2

value: wt

value: 8WG16 (Covance #MMS-126R)


title: VEC_F_1

description:
Spry124fl/fl MEFs FGF, replicate1
processed data file: VEC_CRE_AllCounts.csv


title: 2-3h zld- Dl ChIP-seq rep2

value: Dl


title: 2-3h wt Dl ChIP-seq rep2 input


title: ino4_1

description: Spo11-associated DNA oligonucleotides

data_processing:
Base calls perfomed using HiSeq Control Software v.1.5.15.1 for samples sequenced on Illumina HiSeq 2000, and HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled and analyzed in R (v. 2.15.3)
Genome_build: The SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: wig files include RPM (reads per million mapped) for each sample at each non-zero base position in the genome

extract_protocol:
Based on Pan et al. 2011 Cell 144:719-731. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-protein A fusion with IgG sepharose beads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell 144:719-731. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors

tag: genotype/variation

value: ino4 null


title: 2-3h wt Dl ChIP-seq rep2


title: ino4_2

description: Spo11-associated DNA oligonucleotides


title: ino4_3

description: Spo11-associated DNA oligonucleotides


title: Du5hr-3

source_name: Glucose treatment, 5h


title: Bas1_ChIP


title: bas1_4

description: Spo11-associated DNA oligonucleotides

value: bas1 null


title: 2-3h zld- Pol II ChIP-seq rep2 input


title: 2-3h wt Pol II ChIP-seq rep2 input


title: RFX1_ChIPSeq

tag: cell type


title: 2-3h zld- Dl ChIP-seq rep1 input


title: WT_1

description: Spo11-associated DNA oligonucleotides


title: 2-3h wt Dl ChIP-seq rep1 input


title: bas1_3

description: Spo11-associated DNA oligonucleotides


title: bas1_1

description: Spo11-associated DNA oligonucleotides


title: WT_2

description: Spo11-associated DNA oligonucleotides


title: ino4_H3_2

description: ChIP-seq

data_processing:
Reads were mapped to the sacCer2 genome assembly using bwa mem (version 0.7.5a-r405).
The midpoint position of each paired-end read was extracted.
Genome_build: The SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: Text files include read midpoints for each sample at each non-zero base position in the genome

extract_protocol:
Approximately 250 OD units of cells were collected for each sample. Cells were crosslinked with 1% formaldehyde for 15 minutes and quenched with 125 mM glycine for 5 minutes at room temperature. Cells were collected and disrupted by bead beating in 200 µl lysis buffer (50 mM HEPES-NaOH, pH 7.5, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate). Chromatin was prepared and washed with MNase reaction buffer (10 mM Tris-HCl, pH 7.5, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 1 mM β-mercaptoethanol, 0.1% Igepal) and digested to predominantly mono-nucleosomes with 2 units MNase at 37°C for 30 minutes.
The ChIPseq library was prepared following Illumina standard protocol. We used Trueseq DNA sample prep kit.

value: Histone H3, Abcam, ab1791


title: bas1_H3_1

description: ChIP-seq


title: ino4_H3_1

description: ChIP-seq


title: 2-3h wt Dl ChIP-seq rep1


title: 2-3h gd7 Zld ChIP-seq rep2 input


title: bas1_H3_2

description: ChIP-seq


title: WT_H3_2

description: ChIP-seq


title: Bas1_input


title: bas1_2

description: Spo11-associated DNA oligonucleotides


title: ino4_H3K4me3_2

description: ChIP-seq

value: Histone H3 (tri methyl K4), Abcam, ab8580


title: WT_H3_1

description: ChIP-seq


title: bas1_H3K4me3_2

description: ChIP-seq


title: 2-3h zld- Dl ChIP-seq rep1


title: bas1_H3K4me3_1

description: ChIP-seq


title: 2-3h wt Zld ChIP-seq rep2 input


title: ino4_H3K4me3_1

description: ChIP-seq


title: 2-3h wt Zld ChIP-seq rep2

value: Zld


title: WT_H3K4me3_1

description: ChIP-seq


title: WT_H3K4me3_2

description: ChIP-seq


title: VEC_F_me1

description: Spry124fl/fl MEFs FGF, replicate1

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

value: Serum Starved (DMEM + 0.1% FBS + 1% Pen/Strep)

value: 10ng/mL FGF for 4hrs

value: H3K4me1 (Active Motif, catalog# 39297, lot# 21008001)

value: Corresponding input:VEC_F_Input


title: 2-3h zld- Pol II ChIP-seq rep2


title: Oct6_Brn1_control

city: Singapore

first: Arun George

last: Devasia

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Basecalls and ChIPSeq read alignments were done using illumina GA pipeline 1.3.4
peaks were called using MACS version 1.3.7 with the default parameters
Genome_build: mm8
Supplementary_files_format_and_content: peak files in WIG format

source_name: ES-derived NS5 cells_control

growth_protocol: Undifferentiated NS5 cells were maintained as described in Conti et al (2005) PLoS Biol 3:e283

extract_protocol:
Chromatin was sonicated and immunoprecipitated with respective antibodies
Illumina Genome Analyzer library prep

treatment_protocol: NS5 cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde to cross-link chromatin

value: neural stem cell line

value: rabbit polyclonals

tag: chip antibody vendor

value: Dies Meijer' lab, Edinburgh

tag: chip antibody cat. #


title: Brn2_control

value: Brn-2 Antibody (C-20); goat polyclonal

value: Santa Cruz Biotechnology


title: Sox2_control

value: Sox-2 Antibody (Y-17); goat polyclonal


title: R1_dZn4_GFPpos_d4

first: Teresita

last: Arenzana

state: California

address: 675 Charles E. Young Dr. S., MRL 6-535

department: Microbiology, Immunology, and Molecular Genetics

institute: UCLA

data_processing:
Base calling was performed using HCS 1.3.8, RTA 1.10.36, Recipe Fragments 1.3.1/HiScanSQ 1.1.1 software bundle.
Reads were aligned to the mouse genome (mm9) using Tophat with the following parameters:-p 8 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-stranded- --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
Per base report of genome coverage (BedGraph) was obtained using the Bedtools suite.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph file values represent per base coverage of the genome, and was imported to UCSC Genome Browser to provide a visual representation of genome coverage

molecule: polyA RNA

source_name: ICNpos T cell d4

extract_protocol:
Single cell suspensions were prepared, stained with appropriate antibodies, and sorted on a FACSAriaII cell sorter. Total RNA was purified from Tri-Reagent LS using Qiagen RNEasy MinElute columns according to manufacturer protocol.
Illumina RNA TruSeq Sample Prep

tag: age

value: 4 week

tag: Sex

value: Female

tag: tissue

value: Thymus

tag: culture conditions

value: Lin- thymic cells co-cultured with OP9-DL1 cells


title: Brn2_ChIPSeq

source_name: ES-derived NS5 cells_ChIP


title: R2_dZn4_GFPpos_d2

source_name: ICNpos T cell d2


title: R1_dZn4_GFPpos_d7

source_name: ICNpos T cell d7


title: R1_dZn4_GFPpos_d2


title: 2-3h gd7 Zld ChIP-seq rep2

value: sorted


title: R2_dZn4_GFPneg_d7

source_name: ICNneg T cell d7


title: R1_dZn4_GFPneg_d7


title: R2_dZn4_GFPneg_d4

source_name: ICNneg T cell d4


title: R1_dZn4_GFPneg_d4


title: Oct6_ChIPSeq


title: R1_dZn4_GFPneg_d2

source_name: ICNneg T cell d2


title: R2_dZn4_GFPneg_d2


title: Sox2_ChIPSeq


title: R1_dZn4_d0

source_name: T cell d0


title: R2_dZn4_d0


title: R2_dZn4_GFPpos_d4


title: R1_WT_GFPpos_d7

value: WT


title: R2_dZn4_GFPpos_d7


title: R2_WT_GFPpos_d7


title: 7d LNA 51

city: Oxford

first: Laurynas

last: Pliuskys

address: Windmill Rd

department: NDORMS

country: United Kingdom

institute: University of Oxford

description: 7 day treatment with LNA against the same demethylases as targetted by GSK-J4

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2
The quality of the reads was assessed with FastQC v0.9.2. Reads below quality scores of 25 (Illumina 1.5 ecoding) and any adapter or universal primer sequences were trimmed and only reads longer than 24bp were retained.
Reads were aligned with bowtie v2.1.0 using the “--sensitive” parameter.
Peaks were called using MACS v2.0.10.20131028 by pre-estimating the parameter “-extsize” with predictd and then defining the latter value as well as additional parameters “--keep-dup auto --nomodel”.
Differential enrichment was assessed with MACS2 bdgdiff by normalizing with sequencing depth and providing the additional parameters “-g 60 -l 120”.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: multiple myeloma

growth_protocol: JJN-3 cells were maintained in 1:1 IMDM (Iscoves Modified Dulbeccos Medium, Lonza): DMEM (Dulbeccos Modified Eagle’s Medium, Sigma) with 20% FCS (foetal calf serum, Sigma) and 2 mM L-glutamine (Sigma). Cultured at 37oC in humidified cabinet at 5% CO2 (Heraeus Function Line).

extract_protocol:
Cells were fixed in 1% formaldehyde solution for 8 min followed by quenching of the reaction with glycine (125 mM) for 5 min. Cell were lysed in ChIP Lysis Buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) and sonicated using Bioruptor Pico (Diagenode). Sonication was performed at 4°C using 5 sets of 10 cycles (each consisting of 30s sonication, 30s refraction). Protein A Sepharose beads (Sigma, P9424) were washed and pre-blocked in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167mM NaCl, 16.7 mM Tris-HCl pH 8.1) with 5mg/ml BSA and 0.2mg/ml yeast tRNA (Sigma, R5636) for 2 hours at 4°C.  Once sonication was complete, samples were diluted 10 times with ChIP dilution buffer and incubated with pre-blocked beads for 1 hour. Beads were then removed and the pre-cleared samples were incubated overnight with 2µg/sample of anti-H3K4me3 (Millipore, 07-473) at 4°C. Beads were washed twice with ChIP Low Salt Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl pH 8.1), once with ChIP High Salt Buffer (0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH 8.1), once with ChIP LiCl Buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl pH 8.1) and twice with TE buffer (1mM EDTA, 10mM Tris-HCl pH 8.0). Chromatin was eluted with ChIP Elution buffer (1% SDS, 100mM NaHCO3, 250mM NaCl) and de-cross-linked at 65°C for at least 4 hours. Protein was digested by adding 0.7mg/ml Proteinase K and heating at 55°C for at least 1 hour. DNA was isolated using 1.8 volumes of AMPureXP beads (Beckman Coulter, A63881).
DNA libraries for Next-Generation Sequencing (NGS) were prepared using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, E7370S) and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB, E7335S). Samples were 4-plexed on each lane and 50 bp single-ended reads were obtained.

treatment_protocol: Cells were seeded the day before treatment. The final DMSO concentration for compound treatments and controls was 0.1 %. 5µM GSK-J4 or 5µM LNA was used for treatment. Compound treatments were carried out for 6h or 48h. LNA treatments were carried out for 7 days.

tag: cell line

value: myeloma cell line JJN-3

tag: treatment

value: 7 day

value: anti-H3K4me3 (Millipore, catalog# 07-473, lot# 2207275)


title: 48h J4

description: 48h treatment with GSK-J4


title: R2_WT_GFPpos_d4

tag: strain


title: 48h DMSO

description: 48h negative control sample

value: DMSO (negative control)


title: 6h J4

description: 6h treatment with GSK-J4


title: Brn1_ChIPSeq


title: 6h DMSO

description: 6h negative control sample


title: R2_WT_GFPneg_d4

tag: genotype


title: R1_WT_GFPpos_d2


title: R1_WT_GFPneg_d4


title: R2_WT_GFPneg_d7


title: R2_WT_GFPpos_d2


title: R1_WT_GFPneg_d7


title: 7d LNA Scr

description: 7 day treatment with Scrambled LNA (negative control)

value: LNA Scrambled (negative control)


title: R1_WT_GFPpos_d4


title: 0h

description: starting material - culture that has not been treating with anything


title: input

description: Input Control

value: Input Control


title: R2_WT_GFPneg_d2


title: R2_dZn4_DN2

source_name: DN2 thymocytes

value: HSC co-cultured with OP9-DL1 cells


title: R1_WT_d0


title: R2_WT_DN4

source_name: DN4 thymocyte


title: R2_WT_d0


title: R2_dZn4_ETP

source_name: ETP thymocytes


title: R2_dZn4_DN4


title: R1_WT_GFPneg_d2


title: R1_dZn4_DN3

source_name: DN3 thymocytes


title: R1_WT_DN4


title: R2_dZn4_DN3


title: R1_dZn4_DN4


title: R1_dZn4_DN2


title: R1_WT_DN3


title: R2_WT_DN3


title: R2_WT_DN2


title: R2_WT_ETP


title: VEC_F2_Input

description: Spry124fl/fl MEFs FGF, replicate2

source_name: Immortalized MEF

tag: spry status

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

tag: stable transduction

tag: culture condition

value: Serum Starved (DMEM + 0.1% FBS + 1% Pen/Strep)

value: 10ng/mL FGF for 4hrs

value: None (input)

tag: input note

value: Input for VEC_F2_me1 and VEC_F2_me3


title: R1_WT_ETP

value: 4 week

value: Female


title: 2-3h zld- Pol II ChIP-seq rep1

source_name: embryos

tag: developmental stage (after egg laying)

value: zld-

tag: embryos hand-sorted or not

tag: chip antibody

value: 8WG16 (Covance #MMS-126R)


title: 2-3h wt Pol II ChIP-seq rep1

value: wt

value: sorted


title: 2-3h wt Pol II ChIP-seq rep1 input


title: 2-4h wt MNase-seq rep2

extract_protocol:
Nuclei were collected from homogenized embryos, then digested with an MNase (Worthington Biochemical Corporation #LS004798) concentration gradient of 10U, 5U, 5/2U, 5/4U, and 0U (negative control) at 37°C for 30min. Mono-nucleosome sized DNA was extracted from the lane containing 5/2U MNase digested sample on a 1.7% agarose gel.
Libraries were prepared using the NEBNext® DNA Library Prep Master Mix Set for Illumina® kit (#E6040) following the manufacturer’s instructions.

value: unsorted


title: 2-3h gd7 Zld ChIP-seq rep1

value: Zld


title: R1_WT_DN2

value: WT

value: Thymus


title: 2-3h gd7 Zld ChIP-seq rep1 input


title: 2-4h wt MNase-seq rep1


title: 2-3h zld- Pol II ChIP-seq rep1 input


title: 2-3h wt MNase-seq rep2

extract_protocol:
Nuclei were collected from homogenized embryos, then digested with an MNase (Worthington Biochemical Corporation #LS004798) concentration gradient of 20U, 10U, 5U, 5/2U, 5/4U, 5/8U, 5/16U, 5/32U, and 0U (negative control) at 37°C for 30min. Mono-nucleosome sized DNA was extracted from lanes containing 20U and 10U MNase digested samples on a 1.7% agarose gel, when the di-nucleosome sized DNA band just disappeared.
Libraries were prepared using the NEBNext® DNA Library Prep Master Mix Set for Illumina® kit (#E6040) with a modified protocol using biotin-labeled dATP (Chen et al., 2013). After PCR, mono-nucleosome sized DNA libraries (250-300bp) were extracted from a 1.5% agarose gel.


title: 2-3h wt Zld ChIP-seq rep1 input


title: 2-3h wt Zld ChIP-seq rep1


title: H3K23ac ChIP-Seq WT Q 2

status: Public on Aug 20 2015

city: Eugene

middle: N

last: McKnight

state: OR

address: 1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2 on very sensitive mode
Genome_build: Saccharomyces_cerevisia.EF4.65

growth_protocol: log cells were grown to OD600 0.4 to 0.6; DS cells were harvested 2 hours after glucose exhaustion; Q cells were purified from 7-day stationary phase cultures with a Percoll gradient; thiolutin (3 ug/mL final) or rapamycin (100 nM) was added to log cells for 1 hour at OD600=0.6 prior to crosslinking and ChIP

extract_protocol:
Cells were disrupted with glass beads then crosslinked DNA was sonicated to generate ~300 bp fragments.
Libraries were constructed using NuGEN Ovation UltraLow Library systems

treatment_protocol: Cells were fixed with 1% formaldehyde for 20 minutes

tag: strain background

tag: genotype/variation

value: wild-type

tag: isolate number

value: isolate 2

tag: conditions of harvest

value: quiescent cells

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat #

tag: chip antibody lot #


title: TFIIB ChIP-Seq WT Q 2

value: TFIIB

value: Steve Hahn Lab


title: 2-3h zld- MNase-seq rep2


title: CO1

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

description: control plant

data_processing:
RNA-seq: the cDNA library with a fragment length range of 200 bp (±25 bp) was consturcted and the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2000).
Filtering: the trimming adapter sequences were removed and low-quality reads (less than 13 bp or reads with unknown nucleotides larger than 5%) were filtered with the software
Gene annotation: For annotating the unigenes of the two transcriptomes from a bioinformatics approach, the unigenes assembled were each searched against into seven public databases, including the Swiss-Prot protein database, Gene Ontology (GO) database, NCBI non-redundant protein sequences (NR) database, NCBI nucleotide sequences (NT) database, KEGG ortholog (KO) database, eukaryotic ortholog groups (KOG) database, and protein family (PFAM) database.
Gene expression analysis: Gene expression levels were measured in the RNA-Seq analysis as expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM). The DEseq software was used to identify differentially expressed genes. DESeq analysis was performed by fitting normalized count data with a generalized linear model (GLM) estimating a negative binomial distribution to the calculated mean values of the two biologically independent samples. For each gene, fold changes and P values (pval) as well as P values adjusted (padj) for multiple testing with the Benjamini-Hochberg procedure, were used to control false discovery rate (FDR). The Sequence with a padj of less than 0.05 was deemed to be significantly differentially expressed genes (DEGs)
Supplementary_files_format_and_content: the excel file contain the gene name, sample name, read count, and FPKM value

organism: Boehmeria nivea

source_name: Qingyezhuma

extract_protocol:
After twenty days the ramie suffering from Cd stress, two CO and two CdS plants were sampled as two CO and CdS replicates for Illumina sequencing. The whole plant’s tissues for each plant, including root, stem, leaves and shoot, were sampled as one replicate. The sampled tissues were immediately frozen in liquid nitrogen and stored at -80° until use. Total RNA of each sample was extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, USA) according to the manufacturer’s protocol.
RNA of four samples were separately used to construct the cDNA library with a fragment length range of 200 bp (±25 bp). Then, the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2000) according to the manufacturer’s instructions (Illumina, San Diego, CA).

treatment_protocol: The four potted 40-day-old plants were used for experiment. Two potted ramie were set as  treatment group (CdS) treated by Cd stress with a CdCl2∙H2O solution (Cd), which made the soil concentration of Cd in every pot 100 mg/kg; whereas the other two potted plant were set as control (CO). The CO and CdS contained two replicates which were named as CO1, CO2 and CdS1 and CdS2, respectively. After twenty days the ramie suffering from Cd stress, two CO and two CdS plants were sampled as two CO and CdS replicates for Illumina sequencing.

tag: tissue

value: All tissues of the whole plant

tag: developmental stage


title: CO2

description: control plant


title: HvS_GCAC

city: Havana

first: Camilo

last: Ayra-Pardo

country: Cuba

institute: CIGB

description: Digital gene expression tag profiling

data_processing:
Base-calling software: Bustard and GERALD with default setting
Short read were taken with Phread quality score > 20 using Biopython
Tag extraction was conducted using a homemade perl script
Supplementary_files_format_and_content: File “Hv_Vip-Sel_GCCT” is a TXT file that contains raw counts of sequencing reads for Tags with the index code GCCT from a HT-SuperSAGE library of Heliothis virescens Vip-Sel strain.
Supplementary_files_format_and_content: File “Hv_Vip-Unsel_GCAC” is a TXT file that contains raw counts of sequencing reads for Tags with the index code GCAC from a HT-SuperSAGE library of Heliothis virescens Vip-Unsel strain.

organism: Heliothis virescens

source_name: Midgut tissue

growth_protocol: The Heliothis virescens Vip-Sel and Vip-Unsel subpopulations, resistant and susceptible to the Vip3A protoxin respectively, were obtained and maintained for generations in the Imperial College London facilities at Silwood Park campus. Insects were reared at 25 ± 2 ºC, 75 ± 5% RH with 16:8 (light:dark) cycle on artificial diet.

extract_protocol:
The gut tissue was dissected from ice-anesthetized third-instar larvae of Vip-Sel and Vip-Unsel subpopulations (25 larvae each) by cutting off the hindbody between the last two pairs of prolegs. Total RNA was extracted from gut samples (pools of five guts) using the total RNA isolation system (Promega, Madison, WI) according to manufacturer's instructions. RNA concentration was determined at 260 nm in a GeneQuant (Amersham Pharmacia, Amersham, UK) while the RNA quality was assessed by determining the 260 of 280 and 260 of 230 ratios.
RNA pools of Vip-Sel and Vip-Unsel samples (five RNA preparations each) were prepared and used for the construction of SuperSAGE libraries HvR_GCCT and HvS_GCAC, respectively, according to the procedure described by Matsumura et al. [PLoS ONE (2010) vol 5: e12010).

tag: strain

tag: subpopulation

value: third-instar larvae

value: Midgut tissue

tag: index

value: GCAC


title: TFIIB ChIP-Seq WT DS 2

source_name: W303 DS

value: diauxic shift cells


title: 2-4h gd7 MNase-seq rep1

tag: genotype


title: Rpb3 ChIP-Seq WT Q 2

value: BioLegend


title: H3K23ac ChIP-Seq WT log 1

source_name: W303 log

value: isolate 1

value: log cells


title: 2-3h zld- MNase-seq rep1

value: zld-

value: sorted


title: CdS1

description: cadmium-stressed plant


title: Input DNA (for RPB3 and TFIIB) WT DS 2


title: Rpb3 ChIP-Seq WT DS 2


title: TFIIB ChIP-Seq WT log 2


title: Input DNA (for RPB3 and TFIIB) WT Q 1


title: Input DNA (for RPB3 and TFIIB) WT Q 2


title: Rpb3 ChIP-Seq WT log 2


title: Rpb3 ChIP-Seq WT Q 1


title: HvR_GCCT

description: Digital gene expression tag profiling

value: GCCT


title: Rpb3 ChIP-Seq WT DS 1

value: wild-type


title: Input DNA (for RPB3 and TFIIB) WT DS 1


title: TFIIB ChIP-Seq WT Q 1


title: Rpb3 ChIP-Seq WT log 1


title: Input DNA Rpd3-Myc thio 2

source_name: RPD3-MYC log

value: isolate 2

value: thiolutin-treated log cells


title: Rpd3-Myc ChIP-Seq Rpd3-Myc thio 2

value: c-Myc

value: Covance

value: 9E10 Ascites


title: TFIIB ChIP-Seq WT DS 1

value: TFIIB

value: Steve Hahn Lab


title: Input DNA Rpd3-Myc rap 2

value: rapamycin-treated log cells


title: Rpd3-Myc ChIP-Seq Rpd3-Myc rap 2


title: Input DNA (for RPB3 and TFIIB) WT log 2


title: Rpd3-Myc ChIP-Seq Rpd3-Myc Q 2

source_name: RPD3-MYC Q

value: quiescent cells


title: Input DNA Rpd3-Myc Q 2


title: Rpd3-Myc ChIP-Seq Rpd3-Myc thio 1


title: Input DNA Rpd3-Myc DS 2

source_name: RPD3-MYC DS

value: diauxic shift cells


title: Rpd3-Myc ChIP-Seq Rpd3-Myc DS 2


title: TFIIB ChIP-Seq WT log 1


title: 2-4h gd7 MNase-seq rep2

value: unsorted


title: Input DNA Rpd3-Myc log 2


title: Input DNA Rpd3-Myc thio 1

value: isolate 1


title: Rpd3-Myc ChIP-Seq Rpd3-Myc rap 1


title: Input DNA  Rpd3-Myc Q 1


title: Input DNA Rpd3-Myc rap 1


title: Rpd3-Myc ChIP-Seq Rpd3-Myc Q 1


title: Rpd3-Myc ChIP-Seq Rpd3-Myc log 1

value: log cells


title: Input DNA Rpd3-Myc log 1


title: Input DNA (for RPB3 and TFIIB) WT log 1


title: Input DNA Drpd3 Q 2

source_name: Δrpd3 Q


title: H4ac (Penta) ChIP-Seq Drpd3 Q 2

value: Hyperacetylated H4 (Penta)

value: Millipore


title: Input DNA Drpd3 log 2

source_name: Δrpd3 log


title: H4ac (Penta) ChIP-Seq Drpd3 log 2


title: Rpd3-Myc ChIP-Seq Rpd3-Myc log 2


title: H4ac (Penta) ChIP-Seq Drpd3 Q 1


title: H3 ChIP-Seq Drpd3 log 2

value: Active Motif


title: Input DNA Drpd3 Q 1


title: CdS2

description: cadmium-stressed plant

value: All tissues of the whole plant


title: H3 ChIP-Seq Drpd3 Q 1


title: H4ac (Penta) ChIP-Seq Drpd3 log 1


title: H3 ChIP-Seq WT Q 2

value: wild-type

value: isolate 2


title: Input DNA Drpd3 log 1


title: H3 ChIP-Seq Drpd3 Q 2


title: Input DNA WT log 2


title: H3 ChIP-Seq Drpd3 log 1


title: H4ac (Penta) ChIP-Seq WT Q 2


title: Input DNA WT DS 2


title: 2-3h wt MNase-seq rep1

value: wt

value: sorted


title: H3 ChIP-Seq WT log 2


title: H4ac (Penta) ChIP-Seq WT DS 2


title: H4ac (Penta) ChIP-Seq WT Q 1


title: Input DNA WT log 1


title: H3 ChIP-Seq WT DS 2


title: H4ac (Penta) ChIP-Seq WT log 1


title: Input DNA WT Q 1


title: RNA-Seq of rpd3 Q cells-2

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) appended with ERCC Spike-in Control reads (https://tools.lifetechnologies.com/content/sfs/manuals/ERCC92.zip) using TopHat2
Mapped reads were filtered using SAMtools flags -f 3 -F 256
Differential transcript analysis was performed using CuffDiff (cufflinks 2.2.1) with a maskfile for rRNA and tRNA
Data were normalized such that ERCC control transcript abundance was equal across samples
Data were scaled to reflect RNA content per cell with scaling factors of: 1.0 for WT Q, 2.5 for WT DS, 5.0 for WT Log, 3.0 for rpd3 Q, 3.5 for rpd3 DS, 5.0 for rpd3 Log
Independent isolates were merged
Genome_build: Saccharomyces_cerevisiae.EF4.65
Supplementary_files_format_and_content: Normalized FPKM Values Correcting for External Spike-in Control and RNA per Cell

source_name: Δrpd3 Q cells

growth_protocol: log cells were grown to OD600 0.4 to 0.6; DS cells were harvested 2 hours after glucose exhaustion; Q cells were purified from 7-day stationary phase cultures with a Percoll gradient

extract_protocol:
RNA was extracted with hot acid phenol, treated with Dnase I, combined with ERCC Spike-in control and depleted of rRNA
Strand-specific libraries were prepared according to dUTP method and TruSeq (Illumina) Sample Prep Kit

treatment_protocol: Cells were subject to grinding with glass beads under liquid nitrogen

tag: conditions at harvest

tag: equivalents of ercc spike


title: H3 ChIP-Seq WT log 1


title: R1_dZn4_ETP

tag: age

value: 4 week

tag: Sex

value: Female

value: Thymus

tag: culture conditions

value: HSC co-cultured with OP9-DL1 cells


title: H4ac (Penta) ChIP-Seq WT log 2

tag: strain background

tag: genotype/variation

tag: chip antibody


title: H3 ChIP-Seq WT Q 1

tag: isolate number

tag: conditions of harvest

value: quiescent cells

tag: chip antibody vendor


title: RNA-Seq of rpd3 DS cells-2

source_name: Δrpd3 DS cells

value: diauxic shift cells


title: RNA-Seq of rpd3 log cells-1

source_name: Δrpd3 log cells


title: RNA-Seq of rpd3 DS cells-1


title: RNA-Seq of wild type DS cells-2

source_name: W303 DS cells


title: RNA-Seq of rpd3 log cells-2


title: Input DNA WT Q 2


title: RNA-Seq of wild type Q cells-2

source_name: W303 Q cells


title: RNA-Seq of wild type log cells-2b

source_name: W303 log cells


title: RNA-Seq of wild type log cells-1a


title: RNA-Seq of wild type log cells-1b


title: RNA-Seq of wild type DS cells-1


title: RNA-Seq of wild type log cells-2a


title: MNase-Seq Q 50%

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Tophat2
Mapped reads were filtered using SAMtools flags -f 3 -F 256
Dyads were calculated by taking the midpoint of paired-end reads from fragments between 100 and 200 bp
Data were normalized such that average value at a genomic position was 1.0
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized dyad counts; coverage file (chr, position, count)

growth_protocol: log cells were grown to OD600 0.4 to 0.6; Q cells were purified from 7-day stationary phase cultures with a Percoll gradient

extract_protocol:
DNA was purified by phenol/chloroform and mononucleosome size fragments were purified from an agarose gel for library construction
TruSeq protocol (Illumina) was followed

treatment_protocol: cells were treated with zymolyase and spheroplasts were treated with MNase and ExoIII to produce nucleosome ladders of desired digetsion extents

tag: percent mononucleosomes

value: 50% mononucleosomes

value: quiescent cells (7d stationary phase culture)


title: MNase-Seq log 80%

value: 80% mononucleosomes


title: MNase-Seq Q 80%


title: RNA-Seq of rpd3 Q cells-1

value: isolate 1


title: PIN_RNB_Bead_E_PR3

city: Warszawa

first: Andrzej

last: Dziembowski

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

description: RNA Pol II ChIP

data_processing:
Reads were mapped to the human reference genome hg19 (GRCh37) using the short read aligner program Bowtie2.
Quality control, duplicate read removal, filtering, extending and counting reads and visualization was perfrormed using custom scripts implementing elements of the SAMtools (version 0.1.19 and 1.2.1), BEDTools (version 2.23.0) and RseQC (version 2.6) packages.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Count table (tab seperated)

source_name: PIN_RNB DIS3 cells Mock control replicate 3

extract_protocol:
ChIP experiments for RNA polymerase II were performed with MNase treatment and anti-RNA Polymerase II antibody (clone 8WG16, BioLegend).
KAPA Hyper Prep Kit (Kapa Biosystems)

tag: cell type

value: PIN RNB mutant DIS3


title: PIN_RNB_Bead_PR1

description: RNA Pol II ChIP

source_name: PIN_RNB DIS3 cells Mock control replicate 1


title: PIN_RNB_IP_E_PR3

description: RNA Pol II ChIP

source_name: PIN_RNB DIS3 cells RNA Pol II CHIP replicate 3


title: PIN_RNB_IP_C_PR2

description: RNA Pol II ChIP

source_name: PIN_RNB DIS3 cells RNA Pol II CHIP replicate 2


title: WT_Bead_PR1

description: RNA Pol II ChIP

source_name: WT DIS3 cells Mock control replicate 1

value: WT DIS3


title: WT_IP_E_PR3

description: RNA Pol II ChIP

source_name: WT DIS3 cells RNA Pol II CHIP replicate 3


title: PIN_RNB_IP_PR1

description: RNA Pol II ChIP

source_name: PIN_RNB DIS3 cells RNA Pol II CHIP replicate 1


title: WT_IP_C_PR2

description: RNA Pol II ChIP

source_name: WT DIS3 cells RNA Pol II CHIP replicate 2


title: WT_Bead_C_PR2

description: RNA Pol II ChIP

source_name: WT DIS3 cells Mock control replicate 2


title: WT_IP_PR1

description: RNA Pol II ChIP

source_name: WT DIS3 cells RNA Pol II CHIP replicate 1


title: WT_Bead_E_PR3

description: RNA Pol II ChIP

source_name: WT DIS3 cells Mock control replicate 3


title: MM1uni

city: St Andrews,

first: Darren

middle: James

last: Parker

state: Fife

address: Dyers Brae House

department: Centre for Biological Diversity

institute: University of St. Andrews

data_processing:
Reads were quality trimmed (bases with a phred score of <20 or two consecutive bases with a phred score <32 were trimmed) and screened for adaptor sequences using trimmomatic (v. 0.30)
Bowtie2 was used to map and assign reads from each sample to the reference assembly (default parameters)
Read counts from scaffolds identified as having with overlapping regions as by SOAPdenovo-trans were combined together using RSEM (RNA-seq by Expectation Maximization) to produce estimated read counts
Genome_build: The Transcriptome Shotgun Assembly reads are mapped to has been deposited at DDBJ/EMBL/GenBank under the accession GDKQ00000000. The version used here is the first version, GDKQ01000000.
Supplementary_files_format_and_content: Data files contain 4 columns: Col1: scaffolds reads are mapped to, Col2: name fore grouped scaffolds identified by SOAPdenovo (LOCUS), Col3: Top Blast Hit Accession number for each contig, Col4: Mapped read counts from RSEM

organism: Nicrophorus vespilloides

source_name: Pooled brains (10)

extract_protocol:
Brains from the head were dissected within six minutes of decapitation and placed in 50 μl of Ambion RNAlater and stored at -20°C prior to RNA extraction. RNA was extracted from each sample using the TRIzol Plus RNA Purification Kit (Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 21 days post eclosion

tag: parenting stage

value: Control

tag: parenting type

value: uniparental

value: male

tag: origin

value: Devichoys Wood, Cornwall, U.K.


title: RNA-Seq of wild type Q cells-1

value: wild-type


title: MF1uni

value: Female


title: MM2uni


title: MF2uni


title: CM2uni

value: Parenting


title: PCM1uni

value: Post-parenting


title: MNase-Seq log 50%

tag: strain


title: PCF1uni


title: PCF2uni


title: PIN_RNB_Bead_C_PR2

description: RNA Pol II ChIP

source_name: PIN_RNB DIS3 cells Mock control replicate 2

tag: genotype


title: PCM2uni


title: CF1uni


title: MM1bi

value: biparental


title: MM2bi


title: PCM1bi


title: MF1bi


title: CF2bi


title: PCF1bi


title: GM12878_H3K4me3_1.3

city: Stanford

first: Fabian

last: Grubert

address: 300 Pasteur Drive

institute: Stanford University

description: FG.cell_H3K4Me3_GM78_std_0.0.interactions.fdr-2.bedpe

data_processing:
Personal genomes were created by adding the SNPs of each individual into hg19. SNPs were obtained from the 1000 Genomes Project or imputed using shapeIt and IMPUTE2
For ChIP-seq, ChIP-seq reads were aligned to personal genomes with BWA 0.6.1 (options -q 20, -t 4 and the rest set to defaults)
For ChIP-seq, peaks were called using MACS2 on merged replicates, subsampled to 50 million single reads. Genome-wide signal tracks (bigWig) were generated using wiggler, also on the subsampled data.
For HiC, we aligned reads using HICUP, which aligns reads to an in-silico HindIII digested genome in the hg19 assembly. Our HiC-interaction analysis is based on restriction-fragment level resolution. We  obtained the interaction count for each pair of fragments. To estimate the proximity between two restriction fragments A and B we calculated their co-variance as the fraction of fragments that interact with both A and B, normalized by the number of fragments interacting only with A or only with B. The processed data file contains unique interactions, specified with the following entries: i=id of first interaction fragment, j=id of second interaction fragment, x=number of shared interaction partners between fragment i and j, cor=proportion of interaction partners of i and j that are shared between i and j, pos_i=midpoint of fragment i, pos_j=midpoint of fragment j, pair_id=unique identifier for the interaction. The file contains only interactions with an entry for cor > 0.2
For ChIA-PET, data analysis was carried out using software developed in-house, Mango (paper submitted). PETs were trimmed to remove linker sequences.  In addition, only PETs that have the same linker sequences at both ends are kept for further processing.  The resulting reads were aligned to the genome using the Bowtie software suite(Ben Langmead et al., 2009). Duplicate reads were removed that may be due to PCR duplication. MACS2 was used to call binding peaks, which are subsequently used as anchor regions for the detection of interactions in the next step(Zhang et al., 2008). The probability of observing a PET linking any two peaks was modeled as a function of both genomic distance and the read depth of each peak.  Using this model statistical confidence estimates are assigned to interactions. The resulting P-values are corrected to account for multiple hypothesis testing using the Benjamini-Hochberg method and filtered to a user defined false discovery rate (FDR). The processed files are in bedpe format and contain the following entries: chrom1: chromosome of anchor 1, start1:  start position of anchor 1, end1:  end position of anchor 1, chrom2: chromosome of anchor 2, start2: start position of anchor 2, end2: end position of anchor 1, name: unique ID for each interaction, peak1: # of mid range PETs in anchor1, peak2: # of mid range PETs in anchor2, PETs:  # of PETs linking anchor 1 to anchor 2, distance: # the distance in between anchor 1 to anchor 2, P_IAB_distance:  The probability of observing a PET with the distance that these two anchors are separated by. P_combos_distance: The probability of observing two anchors separated by the distance that these two anchors are separated by. P_IAB_depth:  The probability of observing a PET linking two anchors with the same read depths as these two anchors, P_combos_depth: The probability of observing a pair of loci with the same read depths as these two anchors,  p_binom:  # The binomial probability of observing a single PET linking these two loci, P:  # The actual P-value of the interaction (calculated using the binomial distribution), Q: # The P-value after Benjamini-Hochberg correction (for all possible pairs of loci not just once linked by >= 1 PET).
Genome_build: hg19
Supplementary_files_format_and_content: Peaks are in the narrowPeak format. bigWig files were generated using wiggler.

source_name: Lymphoblastoid Cell Line

growth_protocol: LCLs were grown to a density of 0.6-0.8 x 10^6/mL in RPMI1640 with 15% fetal bovine serum and 1% PenStrep.

extract_protocol:
Cells for GM12878 were crosslinked and chromatin prepared for immunoprecipitation with antibodies against Rad21 and H3K4me3, respectively. Immuno-complexes were pulled down with Protein-G dynabeads, marked with biotin and proximity ligated. Biotinylated fragments were pulled down with Streptavidin Dynabeads and libraries prepared for Illumina sequencing.
For ChIP-Seq, nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 x 30-s intervals). Clarified lysates corresponding to 20 million cells were treated with 1-5ug of antibody coupled to Protein G Dynabeads (Invitrogen #10003D, New York). The protein-DNA complexes were washed with RIPA buffer and eluted in 1% SDS TE at 65°C.
ChIP DNA sequencing libraries were generated according to Illumina DNA Tru-Seq DNA Sample Preparation Kit Instructions (Illumina Part # FC-121-2001, San Diego, CA).

treatment_protocol: Cross linking was performed in 1% formaldehyde for 10 minutes at room temperature. Followed by quenching with Glycin with a final concentration of 125mM

tag: cell line

tag: antibody


title: GM12878_H3K4me3_2.2


title: MF2bi

tag: age

tag: Sex


title: CM2bi


title: CM1bi


title: GM12878_H3K4me3_1.2


title: GM12878_Rad21_2.1

description: FG.cell_RAD21_GM78_std_0.0.interactions.fdr-2.bedpe


title: GM12878_Rad21_2.2


title: PCF2bi


title: GM12878_Rad21_1.1


title: CF1bi


title: GM12878_Rad21_1.2


title: GM12878_HIC_5

description:
HiC.GM12878.correlations.txt.gz
library strategy: HiC

extract_protocol:
25 million cells for GM12878 were cross linked and chromatin digested with HindIII. DNA overhangs were biotinylated and proximity ligated under dilute conditions to favor ligation of fragments in three-dimensional proximity. DNA was then sheared, biotinylated fragments were enriched with streptavidin beads and prepared for Illumina sequencing
For ChIP-Seq, nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 x 30-s intervals). Clarified lysates corresponding to 20 million cells were treated with 1-5ug of antibody coupled to Protein G Dynabeads (Invitrogen #10003D, New York). The protein-DNA complexes were washed with RIPA buffer and eluted in 1% SDS TE at 65°C.
ChIP DNA sequencing libraries were generated according to Illumina DNA Tru-Seq DNA Sample Preparation Kit Instructions (Illumina Part # FC-121-2001, San Diego, CA).


title: GM12878_HIC_7


title: CM1uni


title: GM12878_HIC_4


title: PCM2bi


title: GM12878_HIC_3


title: CF2uni


title: GM12878_H3K4me3_2.1


title: GM12878_HIC_2


title: GM19210_H3K27AC

data_processing:
Personal genomes were created by adding the SNPs of each individual into hg19. SNPs were obtained from the 1000 Genomes Project or imputed using shapeIt and IMPUTE2
ChIP-seq reads were aligned to personal genomes with BWA 0.6.1 (options -q 20, -t 4 and the rest set to defaults)
Peaks were called using MACS2 on merged replicates, subsampled to 50 million single reads. Genome-wide signal tracks (bigWig) were generated using wiggler, also on the subsampled data.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks are in the narrowPeak format. bigWig files were generated using wiggler.

extract_protocol:
For ChIP-Seq, nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 x 30-s intervals). Clarified lysates corresponding to 20 million cells were treated with 1-5ug of antibody coupled to Protein G Dynabeads (Invitrogen #10003D, New York). The protein-DNA complexes were washed with RIPA buffer and eluted in 1% SDS TE at 65°C.
ChIP DNA sequencing libraries were generated according to Illumina DNA Tru-Seq DNA Sample Preparation Kit Instructions (Illumina Part # FC-121-2001, San Diego, CA).


title: GM19143_H3K27AC


title: GM19144_H3K27AC


title: GM19159_H3K27AC


title: GM12878_HIC_6


title: GM19159_H3K4ME1


title: GM19159_H3K4ME3


title: GM19210_H3K4ME3


title: GM19153_H3K4ME3


title: GM19210_H3K4ME1


title: GM12878_HIC_1


title: GM19153_H3K4ME1


title: GM19144_H3K4ME3


title: GM19143_H3K4ME1


title: GM19201_H3K27AC


title: GM19143_H3K4ME3


title: GM19153_H3K27AC


title: GM18871_H3K27AC


title: GM19201_H3K4ME3


title: GM18871_H3K4ME1


title: GM18858_H3K27AC


title: GM18907_H3K27AC


title: GM18871_H3K4ME3


title: GM18501_H3K4ME1


title: GM19099_H3K27AC


title: GM18858_H3K4ME3


title: GM19223_H3K27AC


title: GM19131_H3K27AC


title: GM19144_H3K4ME1


title: GM18501_H3K4ME3


title: GM18858_H3K4ME1


title: GM18856_H3K27AC


title: GM18498-2_H3K27AC


title: GM18502-2_H3K27AC


title: GM19201_H3K4ME1


title: GM19172_H3K4ME1


title: GM18498_H3K27AC


title: GM18522_H3K4ME1


title: GM18916_H3K27AC


title: GM18522_H3K4ME3


title: GM19223_H3K4ME1


title: GM19207_H3K4ME1


title: GM19207_H3K4ME3


title: GM18508_H3K4ME1


title: GM18510_H3K27AC


title: GM18489_H3K27AC


title: GM19152_H3K4ME3


title: GM18502-2_H3K4ME3


title: GM19152_H3K4ME1


title: GM18505_H3K4ME1


title: GM19116_H3K4ME1


title: GM18505_H3K4ME3


title: GM19138_H3K27AC


title: GM19093_H3K27AC


title: GM19108_H3K4ME3


title: GM19138_H3K4ME3


title: GM19147_H3K4ME1


title: GM19172_H3K4ME3


title: GM19138_H3K4ME1


title: GM18909_H3K4ME1


title: GM18909_H3K4ME3


title: GM19160_H3K4ME1


title: GM18909_H3K27AC


title: GM19223_H3K4ME3


title: GM19204_H3K4ME1


title: GM19204_H3K4ME3


title: GM18508_H3K27AC


title: GM19257_H3K4ME3


title: GM19116_H3K4ME3


title: GM19257_H3K4ME1


title: GM18498-2_H3K4ME1


title: GM19147-2_H3K27AC


title: GM18499-2_H3K4ME1


title: GM18499-2_H3K4ME3


title: GM19130_H3K27AC


title: GM19222_H3K27AC


title: GM19130_H3K4ME1


title: GM19130_H3K4ME3


title: GM18489-2_H3K4ME3


title: GM19172_H3K27AC


title: GM19222_H3K4ME1


title: GM19099_H3K4ME1


title: GM18853_H3K4ME1


title: GM19147-1_H3K4ME3


title: GM19099_H3K4ME3


title: GM18853_H3K4ME3


title: GM18508_H3K4ME3


title: GM18519_H3K4ME1


title: GM19225_H3K4ME3


title: GM18489-2_H3K4ME1


title: GM18511_H3K27AC


title: GM19204_H3K27AC


title: GM19200_H3K27AC


title: GM18489-2_H3K27AC


title: GM18498-2_H3K4ME3


title: GM18502_H3K27AC


title: GM19098_H3K27AC


title: GM18522_H3K27AC


title: GM18507_H3K4ME3


title: GM19108_H3K4ME1


title: GM19114_H3K4ME1


title: GM19114_H3K4ME3


title: GM18499_H3K4ME1


title: GM19225_H3K4ME1


title: GM18507_H3K4ME1


title: GM18501_H3K27AC


title: GM18489_H3K4ME3


title: GM18504_H3K27AC


title: GM18861_H3K27AC


title: GM18502_H3K4ME3


title: GM18499-2_H3K27AC


title: GM18502_H3K4ME1


title: GM18870_H3K27AC


title: GM18861_H3K4ME3


title: GM18489_H3K4ME1


title: GM19137_H3K4ME1


title: GM18916_H3K4ME3


title: GM19171_H3K27AC


title: GM19108_H3K27AC


title: GM19137_H3K4ME3


title: GM18510_H3K4ME1


title: GM19093_H3K4ME3


title: GM18916_H3K4ME1


title: GM19093_H3K4ME1


title: GM19160_H3K4ME3


title: GM18519_H3K4ME3


title: GM19119_H3K27AC


title: GM18510_H3K4ME3


title: GM18502-2_H3K4ME1


title: GM18517_H3K27AC


title: GM19119_H3K4ME1


title: GM18499_H3K4ME3


title: GM19209_H3K27AC


title: GM19119_H3K4ME3


title: GM19209_H3K4ME1


title: GM19098_H3K4ME1


title: GM19200_H3K4ME1


title: GM18912_H3K4ME1


title: GM19114_H3K27AC


title: GM19200_H3K4ME3


title: GM19147-1_H3K27AC


title: GM18523_H3K4ME1


title: GM18912_H3K27AC


title: GM18907_H3K4ME3


title: GM18523_H3K27AC


title: GM19098_H3K4ME3


title: GM18907_H3K4ME1


title: GM18912_H3K4ME3


title: GM19222_H3K4ME3


title: GM18499_H3K27AC


title: GM18520_H3K27AC


title: GM19160_H3K27AC


title: GM18523_H3K4ME3


title: GM19152_H3K27AC


title: GM19190_H3K27AC


title: GM19171_H3K4ME3


title: GM18520_H3K4ME1


title: GM19137_H3K27AC


title: GM18861_H3K4ME1


title: GM19171_H3K4ME1


title: GM19131_H3K4ME1


title: GM19209_H3K4ME3


title: GM18520_H3K4ME3


title: GM19190_H3K4ME3


title: GM18507_H3K27AC


title: GM18853_H3K27AC


title: GM18498_H3K4ME3


title: GM19131_H3K4ME3


title: GM18517_H3K4ME1


title: GM18498_H3K4ME1


title: GM18501-2_H3K27AC


title: GM19207_H3K27AC


title: GM19102_H3K27AC


title: GM18856_H3K4ME1


title: GM18504_H3K4ME1


title: GM18856_H3K4ME3


title: GM19116_H3K27AC


title: GM18511_H3K4ME3


title: GM18511_H3K4ME1


title: GM19102_H3K4ME1


title: GM19147-2_H3K4ME3


title: GM19190_H3K4ME1


title: GM18516_H3K4ME1


title: GM18516_H3K27AC


title: GM19225_H3K27AC


title: GM18504_H3K4ME3


title: GM18501-2_H3K4ME3


title: GM18516_H3K4ME3


title: GM18501-2_H3K4ME1


title: GM18519_H3K27AC


title: RRP6_KD_2

city: Stockholm

first: Neus

last: Visa

address: Svante Arrhenius väg 20c

department: Molecular Biosciences, The Wenner-Gren Institute (MBW)

country: Sweden

institute: Stockholm University

description: Drosophila S2 cells grown in Schneider medium

data_processing:
High quality reads were mapped with TopHat/2.0.4 to the D. melanogaster reference genome dm3 (BDGP6).
BAM alignments were indexed with SAMtools.
Read counts per gene were generated using HTSeq-count on bam files.
Differential expression analysis was carried out using Limma package in R.
Reads that appeared more than twice at the same position on the same strand were discarded to remove PCR duplication.
Genome_build: dm3
Supplementary_files_format_and_content: For RNA-seq data: HTSeq output files containing read counts per gene. For ChIP-seq data: tab-delimited text files (in Microsoft Excel format) with RRP6 enrichment peaks and their corresponding genomic coordinates.

growth_protocol: S2 cells were cultured at 28 °C according to the instructions of the Drosophila Expression System manual from Invitrogen.

extract_protocol:
RNA was extracted from cultured cells with RNAquous Kit (Ambion).
Random primed cDNA libraries where constructed by GATC Biotech from rRNA depleted total RNA samples. Libraries were sequenced on a HiSeq2500 sequencer

treatment_protocol: S2 cells were treated with dsRNA to knock down RRP6. Control cells were treated in parallel with dsRNA that was complementary to GFP

tag: cell line background


title: GFP2

tag: genotype/variation

value: GFP-KD (control)


title: GM18517_H3K4ME3


title: GM18870_H3K4ME1


title: GFP1


title: RRP6_KD_1


title: GM19102_H3K4ME3


title: GM18870_H3K4ME3


title: GM18862_H3K4ME1


title: GM19203_H3K4ME1


title: GM19203_H3K4ME3


title: ChIP_RRP6_Su(var)3-9-KD_Input

data_processing:
RRP6 ChIP-Seq reads were aligned to the D. melanogaster reference genome dm3 by Bowtie with at most 2 mismatches.
Reads that appeared more than twice at the same position on the same strand were discarded to remove PCR duplication.
BIGWIG files were generated from the coverage for visualization purposes.
MACS2 v2.1.0.20140616 was used to identify RRP6-rich regions at q-value cutoff 0.01 using broad peak setting.
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited text files with RRP6 enrichment peaks and their corresponding genomic coordinates.

source_name: Drosophila S2-RRP6-V5 cells grown in Schneider medium

extract_protocol:
Input DNA was isolated with the ChIP cleanup and concentrator Kit (Zymo Research)
DNA libraries were prepared by Zymo Research Epigenetics Services and were sequenced on a HiSeq2500 sequencer

treatment_protocol: RRP6-V5 cells were treated with dsRNA for either GFP (controls) or Su(Var)3-9, and used for ChIP-seq with anti-V5 antibody.

tag: dsrna target


title: ChIP_RRP6_WT_IP

extract_protocol:
Immunoprecipitated DNA was isolated with the ChIP cleanup and concentrator Kit (Zymo Research)
DNA libraries were prepared by Zymo Research Epigenetics Services and were sequenced on a HiSeq2500 sequencer

tag: chip antibody

value: Anti-V5 antibody (Abcam; ab9116)

value: GFP


title: GM18862_H3K4ME3


title: ChIP_RRP6_Su(var)3-9-KD_IP


title: ChIP_RRP6_WT_Input


title: GM19206_H3K4ME3


title: Whole funiculus 3

city: Winnipeg

first: Michael

middle: G.

last: Becker

state: Manitoba

address: 66 Chancellors Circle

department: Biological Sciences

country: Canada

institute: University of Manitoba

data_processing:
Alignments performed using TopHat2 (v2.0.13)
Transcript abundances were calculated as Fragments Per Killobase of transcript per Million mapped reads (FPKMs) using the Cufflinks pipeline (v2.2.1)
DESeq (differential expression of RNA-seq data at the gene level, version 1.16.0) was used to determine the relationships between biological replicates and tissue types.
Of the transcripts uniquely present in individual tissue systems (i.e. detected in any epidermis, cortex, and/or vasculature, but not in the WF, a tissue specificity index (I) was calculated according to the following formula modified from Tong et al. (2013) and Yanai et al. (2005):
The lists of Arabidopsis genes were inputted into the online program AgriGO version 1.2 (http://bioinfo.cau.edu.cn/agriGO/) to identify enriched gene ontology (GO) terms against the Arabidopsis genome. A GO term was considered enriched if the log10 p value ≤ -3 (i.e. p ≤ 0.001).
Genome_build: Brassica napus v4.1
Supplementary_files_format_and_content: Fastq files represent raw sequencing data. Cufflinks file contain normalized counts in FPKMs.

organism: Brassica napus

source_name: Whole funiculus

growth_protocol: Plants were grown in Sunshine Mix #1 (Sun Gro Horticulture, Agawam, MA, USA) under long day conditions (16 h light, –100-150 µmol photons  m–2  s–1) at 22ºC with 50-70% relative humidity. Open flowers were pollinated and siliques allowed to develop for 7 days; this corresponds to the globular stage of seed development.

extract_protocol:
RNA was extracted from LMD-collected tissues using the Ambion RNA Aqueous microkit (Life Technologies, Carlsbad, CA, USA) according to manufacturer's instructions
cDNA was amplified with the Ovation RNA-seq V2 kit (NuGEN, San Carlos, CA, USA). The cDNA libraries were then further refined using the Illumina TruSeqTM RNA Sample Preparation v2 kit (Illumina, San Diego, CA, USA) using the low-throughput protocol according to manufacturer’s instructions

tag: cultivar

value: Topaz

tag: line

tag: tissue

value: Whole funiculus


title: GM18505_H3K27AC


title: GM19257_H3K27AC


title: Funiculus Vasculature 3

source_name: Funiculus Vasculature

value: Vasculature


title: GM19206_H3K4ME1


title: Funiculus Vasculature 2


title: GM19203_H3K27AC


title: GM18862_H3K27AC


title: GM19141_H3K27AC


title: GM19127_H3K4ME1


title: GM18852_H3K4ME1


title: Funiculus Vasculature 1


title: GM18852_H3K4ME3


title: Funiculus Cortex 1

source_name: Funiculus Cortex

value: Cortex


title: Funiculus Epidermis 3

source_name: Funiculus Epidermis

value: Epidermis


title: GM19141_H3K4ME3


title: Funiculus Epidermis 2


title: GM19141_H3K4ME1


title: Funiculus Cortex 2


title: GM18855_H3K4ME1


title: GM18855_H3K4ME3


title: GM19127_H3K27AC


title: GM18913_H3K4ME1


title: Whole funiculus 2


title: JB

first: Kemal

middle: Marc

last: Akat

address: 1230 York Avenue

institute: The Rockefeller University

description:
barcode: TTGGT
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TTGGTTCGTATGCCGTCTTCTGCTTG
Library 2

data_processing:
Base calling was done using CASAVA versions 1.6 - 1.8.2.
The data was processed as described in Brown et al. (2013, Front Genet, 4:145) using a curated miRNA (Farazi et al. 2011, 71:4443) and other non-coding and coding RNA transcriptomes.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: The processed data files contain raw, i.e. not-normalized or transformed, miRNA counts based on unique miRNA sequences, or based on precursor clusters and sequence families.

source_name: normal skin

extract_protocol:
Total RNA was isolated using the miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion.  The amount of RNA was assessed by NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE).  The quality of extracted RNA was examined using Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).
The small RNA libraries for the solid tissue samples were prepared using the protocol described in Hafner et al. (2008, 44:3, 2012, 58:164). The libraries for for the serum and plasma samples had the following modifications: 1) the amount of the 10 spiked-in synthetic calibrator oligoribonucleotides was reduced from 0.5 fmol each per 2 µg total RNA input to 0.005 fmol each, 2) the synthetic P32-labeled 19-nt and 24-/35-nt ssRNAs used for size selection were not spiked-into the samples. Note: no calibrator oligoribonucleotides were spiked-in to library 8. The sequences of the 10 used calibrator oligoribonucleotides can be obtained from Hafner et al. 2012 (Methods, 58:164).

treatment_protocol: placebo or diphencyprone (DPCP) gel application

tag: sample id

value: JB

tag: gender

value: Male

tag: race

value: Caucasian

value: Skin


title: GM18859_H3K27AC


title: GM19128_H3K27AC


title: 16 fuRx

description:
barcode: TAACG
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TAACGTCGTATGCCGTCTTCTGCTTG
Library 2

source_name: further resolving DTH reaction (4 months after challenge)

value: African American


title: GM19092_H3K27AC


title: TM

description:
barcode: TTACA
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TTACATCGTATGCCGTCTTCTGCTTG
Library 2

value: TM

value: Female


title: 15 fuRx

description:
barcode: TTAAG
common adapter: TCGTATGCCGTCTTCTGCTTG
complete adapter: TTAAGTCGTATGCCGTCTTCTGCTTG
Library 2


title: GM19101_H3K4ME3


title: GM19101_H3K4ME1