title: CB.CUL4, 5pu_GABA_Pcp2 rep2

description: CB.CUL4, 5pu_GABA_Pcp2_m82_93


title: CB.CUL4, 5pu_GABA_Pcp2 rep1

status: Public on Jul 20 2018

type: SRA

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

country: USA

institute: Janelia Research Campus

description: CB.CUL4, 5pu_GABA_Pcp2_m32_24

library_source: transcriptomic

data_processing:
Illumina Casava and BCL2FASTQ1.8.3 were used for basecalling
Sequenced reads were trimmed for NuGEN and Illumina adaptor sequences using cutadapt v1.7.1 with parameters --overlap=7 --minimum-length=30. Ribosomal RNA, mitochondrial and phiX sequences were filtered using bowtie2 v2.1.0 with default parameters. Remaining reads were then mapped to mm10 genome using STAR v2.4.0i with parameters  --chimSegmentMin 15 --outFilterMismatchNmax 3.
Uniquely mapped reads were assigned to genes using HTSeq v0.6.1p1 with parameter -s no -m intersection-nonempty and using wgEncodeGencodeVM4Basic annotation downloaded from UCSC with ERCC information added.
Supplementary_files_format_and_content: tab deliminated files include raw counts for each sample
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: Cerebellum (CUL4, 5pu)

extract_protocol:
Acutely extracted brain was sliced at 300um thickness, digested with pronase for 1 hour at RT, triturated and GFP labeled cells were sorted manually. RNA was extracted using PicoPure kit (ThermoFisher, KIT0204).
Extracted RNA was amplified using Ovation RNA-Seq System V2 (NuGEN, #7102). 1~1.5 ug of the amplified material was used for library construction using Encore NGS Multiplex System (NuGEN, #0314).
adapters: solexa

tag: tissue

value: Cerebellum (CUL4, 5pu)

tag: strain

tag: region

value: CUL4, 5pu

tag: age (postnatal day)

tag: Sex

value: M

tag: weight (g)

tag: num_cells (# of sorted cells in the sample)

tag: ercc5 (10^-5 dilution of ercc in ul)

tag: ercc_mix (ercc mix used)


title: CB.CUL4, 5pu_GABA_Ntsr1.GN209 rep3

description: CB.CUL4, 5pu_GABA_Ntsr1.GN209_m219_67

extract_protocol:
Acutely extracted brain was sliced at 300um thickness, digested with pronase for 1 hour at RT, triturated and GFP labeled cells were sorted manually. RNA was extracted using PicoPure kit (ThermoFisher, KIT0204).
Extracted RNA was amplified using Ovation RNA-Seq System V2 (NuGEN, #7102). 1~1.5 ug of the amplified material was used for library construction using Encore NGS Multiplex System (NuGEN, #0314).
adapters: truseq


title: CB.CUL4, 5pu_GABA_Pcp2 rep3

description: CB.CUL4, 5pu_GABA_Pcp2_m38_95


title: CB.CUL4, 5pu_GABA_Ntsr1.GN209 rep2

description: CB.CUL4, 5pu_GABA_Ntsr1.GN209_m219_66


title: CB.CUL4, 5mo_GABA_Sla.KJ319 rep2

description: CB.CUL4, 5mo_GABA_Sla.KJ319_m43_482

source_name: Cerebellum (CUL4, 5mo)

value: Cerebellum (CUL4, 5mo)

value: CUL4, 5mo


title: CB.CUL4, 5pu_GABA_Ntsr1.GN209 rep1

description: CB.CUL4, 5pu_GABA_Ntsr1.GN209_m216_65


title: CB.CUL4, 5mo_GABA_Sla.KJ319 rep1

description: CB.CUL4, 5mo_GABA_Sla.KJ319_f50_481

value: F


title: HPF.CA1_GABA_SST23.2D2.virus rep3

source_name: Hippocampus (CA1)

value: Hippocampus (CA1)


title: CB.CUL4, 5mo_GABA_Sla.KJ303 rep1

description: CB.CUL4, 5mo_GABA_Sla.KJ303_m73_1711


title: CB.CUL4, 5mo_GABA_Sla.KJ303 rep4

description: CB.CUL4, 5mo_GABA_Sla.KJ303_f74_1714


title: CB.CUL4, 5mo_GABA_Sla.KJ303 rep2

description: CB.CUL4, 5mo_GABA_Sla.KJ303_f85_1712


title: CB.CUL4, 5mo_GABA_Sla.KJ303 rep3

description: CB.CUL4, 5mo_GABA_Sla.KJ303_f86_1713


title: CB.CUL4, 5mo_GABA_P159 rep2

description: CB.CUL4, 5mo_GABA_P159_m42_1274


title: CB.CUL4, 5mo_GABA_P159 rep1

description: CB.CUL4, 5mo_GABA_P159_f42_1273


title: CB.CUL4, 5mo_GABA_P159 rep3

description: CB.CUL4, 5mo_GABA_P159_f42_1275


title: CB.CUL4, 5gr_glu_HSD2-Cre rep2

description: CB.CUL4, 5gr_glu_HSD2-Cre_m196_1136

source_name: Cerebellum (CUL4, 5gr)

value: Cerebellum (CUL4, 5gr)

value: CUL4, 5gr


title: CB.CUL4, 5gr_glu_TCGO rep2

description: CB.CUL4, 5gr_glu_TCGO_m121_18

value: TCGO


title: Myc_WT2_RNASeq

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

data_processing:
Raw sequence reads were first subjected to trimming using Trimmomatic (version 0.32), where adapter sequences and low quality bases were removed (parameters: HEADCROP 3, TRAILING 20, MINLEN 35).
Afterwards reads were aligned to the GRCm38 mouse genome using the STAR alignment algorithm (version 2.4.0) (parameters: --runThreadN 4).
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each Sample.

growth_protocol: Conditional CXCL12 F/F  or Cmyc F/F mice were crossed with Pax8rtTA TeoOcre line to get either CXCL12 or Cmyc F/F Pax8rtTA (control) and CXCL12 or C-myc F/F Pax8rtTA TetOcre mice as tubule sp. KO mice

extract_protocol:
kidneys were removed and snap frozen in liquid nitrogen and stored at -80°C. RNA was extracted using RNeasy Mini kit from Qiagen Cat. No. 74106
GATC (Konstanz, Germany) proprietary library preparation protocol

treatment_protocol: bilateral ischemia reperfusion renal injury: ischemia for 22.5 minutes followed by reperfusion for 12 hours

tag: strain background

tag: genotype/variation

value: Myc Control

value: kidney

tag: replicate

value: Replicate 2


title: Myc_WT1_RNASeq

value: Replicate 1


title: Myc_WT5_RNASeq

value: Replicate 5


title: CB.CUL4, 5gr_glu_TCGO rep3

description: CB.CUL4, 5gr_glu_TCGO_m122_90


title: CB.CUL4, 5gr_glu_HSD2-Cre rep1

description: CB.CUL4, 5gr_glu_HSD2-Cre_m196_1135


title: Myc_WT4_RNASeq

value: Replicate 4


title: Myc_KO3_RNASeq

value: Myc KO

value: Replicate 3


title: Myc_KO2_RNASeq


title: CB.CUL4, 5pu_GABA_PBAP rep1

description: CB.CUL4, 5pu_GABA_PBAP_m66_112

value: Cerebellum (CUL4, 5pu)

value: PBAP

value: CUL4, 5pu


title: Myc_KO5_RNASeq


title: @pancreas__P170 rep3

source_name: pancreas

value: pancreas

value: M


title: CB.CUL4, 5gr_GABA_Cdhr1.KG66 rep1

description: CB.CUL4, 5gr_GABA_Cdhr1.KG66_f132_1755

value: F


title: Myc_KO1_RNASeq


title: @pancreas__P170 rep2


title: Cxcl12_WT3_RNASeq

value: Cxcl12 Control


title: @pancreas__P170 rep1


title: @pancreas__Ins1-EGFP rep3


title: @pancreas__Ins1-EGFP rep4


title: CB.CUL4, 5gr_glu_TCGO rep1

description: CB.CUL4, 5gr_glu_TCGO_m122_17

value: Cerebellum (CUL4, 5gr)

value: CUL4, 5gr


title: Cxcl12_KO5_RNASeq

value: Cxcl12 KO


title: Myc_WT3_RNASeq

value: Myc Control

value: kidney


title: Cxcl12_WT1_RNASeq

value: Replicate 1


title: @pancreas__Ins1-EGFP rep2


title: @pancreas__Ins1-EGFP rep1


title: CB.CUL4, 5gr_GABA_Cdhr1.KG76 rep1

description: CB.CUL4, 5gr_GABA_Cdhr1.KG76_f72_1754


title: Cxcl12_KO3_RNASeq


title: Myc_KO4_RNASeq


title: @myofiber__Pvalb-Cre rep2

source_name: myofiber

value: myofiber


title: Cxcl12_KO4_RNASeq

value: Replicate 4


title: @myofiber__Pvalb-Cre rep1


title: Cxcl12_KO2_RNASeq

value: Replicate 2


title: @myofiber__PR26 rep4


title: Cxcl12_KO1_RNASeq


title: @myofiber__PR26 rep3


title: @myofiber__PR26 rep1


title: @myofiber__PR26 rep5


title: Cxcl12_WT2_RNASeq


title: mTEChi_KO_Rep3

city: Montreal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

department: Institute for Research in Immunology and Cancer

country: Canada

institute: Montreal University

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were trimmed for adaptor sequence and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2.  Gene counts were computed using HTSeq version 0.5.4p1.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes RPKM values for cTEC, mTEClo and mTEChi. Columns are: Chromosome, Start location, Stop location, Gene, RPKM.

source_name: medullar thymic epithelial cell, MHC II high

extract_protocol:
Thymi from fourteen 7-days old C57BL/6 mice were isolated and stromal cell enrichment was performed. Thymic stromal cells were stained with biotinylated Ulex Europaeus Lectin 1 (UEA1; Vector Laboratories), PE-Texas Red conjugated streptavidin (BD Biosciences) and the following antibodies from BD Biosciences: Alexa700 anti-CD45, APC-Cy7 anti-EpCAM and Alexa647 anti-Ly51. Both cTEC (CD45 EpCAM+Ly51+UEA1 ) and mTEC (CD45 EpCAM+Ly51 UEA1+) populations were sorted on a three laser FACSAria (BD Biosciences). Total RNA was isolated using Trizol reagent as recommended by the manifacturer (Invitrogen), and the further purified using RNeasy columns (Qiagen).
Transcriptome libraries were generated from at least 10ng of total RNA using the TruSeq RNA Sample Prep Kit (v2) (Illumina). RNA libraries were prepared for sequencing following recommended Illumina protocols.

value: C57BL/6-derived BAC

tag: genotype

value: Thymus

tag: age

value: 6-8 weeks_old


title: mTEChi_WT_Rep2


title: mTEChi_KO_Rep2


title: @ependyma__TCLU rep2

source_name: ependyma

value: ependyma

value: TCLU


title: @ependyma__TCLU rep1


title: @ependyma__TCLU rep3


title: mTEClo_WT_Rep3

source_name: medullar thymic epithelial cell, MHC II low


title: @ependyma__Pvalb-Cre rep3


title: @ependyma__Pvalb-Cre rep2


title: mTEClo_WT_Rep1


title: mTEClo_WT_Rep2


title: mTEClo_KO_Rep2


title: mTEChi_WT_Rep3


title: @ependyma__Pvalb-Cre rep1


title: @bloodvessel__TCLU rep1

source_name: bloodvessel

value: bloodvessel

value: M


title: cTEC_WT_Rep2

source_name: cortical thymic epithelial cell


title: @bloodvessel__TCLU rep3


title: @bloodvessel__TCLU rep2


title: mTEClo_KO_Rep1


title: @T1.DRG_glu_TrpV1-Cre rep1

source_name: Spinal Cord [T1]

value: Spinal Cord [T1]

value: DRG


title: @myofiber__PR26 rep2


title: mTEChi_WT_Rep1


title: cTEC_KO_Rep2


title: @T1.DRG_glu_TrpV1-Cre rep2


title: cTEC_WT_Rep1


title: mTEChi_KO_Rep1


title: @T1.DRG_glu_Pvalb-Cre rep3

value: F


title: cTEC_KO_Rep1


title: @T1.DRG_glu_Pvalb-Cre rep1


title: mTEClo_KO_Rep3


title: @Sp.L_GABA_Sla.KJ319 rep1

source_name: Spinal Cord  (L)

value: Spinal Cord  (L)

value: L


title: @Sp.L_GABA_Sla.KJ319 rep2


title: @Sp.L_GABA_Sla.KJ319 rep3


title: @T1.DRG_glu_Pvalb-Cre rep2


title: @Sp.L_GABA_Sla.KJ319 rep4


title: Input DNA 2

city: Bethesda

first: Megan

middle: Leigh

last: Sampley

state: MD

address: 6 Center Drive

department: Program on Genomics of Differentiation

institute: NICHD

library_source: genomic

data_processing:
Sequence reads were aligned to the mouse genome version mm9 using bowtie version 1.0.0 (Langmead et al. 2009). A valid alignment could have a maximum of two mismatches and if a read aligned equally well to multiple places in the genome, the best scoring alignment was output using the --best parameter. If multiple reads mapped to the same genomic location, only one was kept to avoid amplification bias.
Peak-calling was performed using SICER v1.1 (Zang et al. 2009) with window size = 200 bp, fragment size = 150 bp, effective genome size = 0.74, gap size = 600 bp and FDR = 0.1.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated by SICER v1.1. Redundant reads were removed and interval size was 200 bp. Scores represent total read count within corresponding genomic interval.
Supplementary_files_format_and_content: Peak files were generated using WaveSeqR. Each row represents one peak with the following information in four columns: chromosome, start, end, score.

molecule: genomic DNA

source_name: myocytes

growth_protocol: Wild type and mutant myoblasts were isolated from mouse skeletal muscle at post-natal day 4, purified into a pure myoblast culture, and cultured in cosmic calf serum supplemented with fetal growth factor. Cells were differentiated into myotubes by withdrawing fetal growth factors from culturing conditions. After 24 hours, cells were harvested for ChIP analysis.

extract_protocol:
Approximately 2X10^6 cells were harvested and processed for ChIP according to the Millipore Magna ChIP (Catalog #17-610) protocol. ChIP DNA was purifired with an antibody against Histone H3 Lysine 36 tri-methylation (Abcam Catalog #ab9050)
Ovation Ultralow Library System (NuGen) with 10ng DNA as starting material.

value: FVB

tag: cell type

value: myocytes

value: enhancer deletion mutant

tag: passages


title: Input DNA 1

value: wild type


title: @Sp.L.dcs_GABA_GIN rep2

source_name: Spinal Cord  (L.dcs)

value: Spinal Cord  (L.dcs)

value: GIN


title: WT_H3K36me3

description: ChIP antibody: Anti-H3K36me3 (Abcam ab9050)


title: @Sp.L.Sp_glu_Grp.KH288 rep3

source_name: Spinal Cord  (L.Sp)

value: Spinal Cord  (L.Sp)


title: @Sp.L.Sp_glu_Grp.KH288 rep2


title: P42 single cell RNA-seq

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

country: China

institute: Fudan University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
For RNA-seq data, trimmed clean reads were aligned to human reference genome (hg19) using TopHat (v 2.0.12) -pass mapping steps.
Genome_build: hg19
Supplementary_files_format_and_content: TPM.txt files include the TPM values of RefSeq genes

molecule: polyA RNA

organism: Homo sapiens

source_name: Articular cartilage cells

extract_protocol: For RNA-seq data, we constructed the sequencing libraries using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #7370L).

value: Articular cartilage

value: Chondrocyte


title: VV_H3K36me3


title: @Sp.L.Sp_glu_Grp.KH288 rep1


title: @Sp.L.Sp_GABA_Rbp4.KL100 rep1


title: @Sp.L.dcs_GABA_GIN rep3


title: P41 single cell RNA-seq


title: P39 single cell RNA-seq


title: P38 single cell RNA-seq


title: @Sp.L.Sp_GABA_Rbp4.KL100 rep2


title: P40 single cell RNA-seq


title: @Sp.L.Sp_GABA_GIN rep3


title: P37 single cell RNA-seq


title: @Sp.L.Sp_GABA_GIN rep2


title: P35 single cell RNA-seq


title: P36 single cell RNA-seq


title: @Re.RGC_glu_wt.beads rep4

source_name: Retina (RGC)

value: Retina (RGC)

value: RGC


title: @Sp.L.Sp_GABA_GIN rep1

value: M


title: P34 single cell RNA-seq


title: @Re.RGC_glu_wt.beads rep2


title: P33 single cell RNA-seq


title: @Sp.L.dcs_GABA_GIN rep1


title: @Re.RGC_glu_wt.beads rep6


title: @Re.RGC_glu_wt.beads rep5


title: P31 single cell RNA-seq


title: @Re.RGC_glu_wt.beads rep3


title: P30 single cell RNA-seq


title: P29 single cell RNA-seq


title: @Re.RGC_glu_Np219Amig01 rep4


title: P27 single cell RNA-seq


title: @Re.RGC_glu_wt.beads rep1


title: @Re.RGC_glu_Np219Amig01 rep2


title: P28 single cell RNA-seq


title: @Re.RGC_glu_Np219Amig01 rep3


title: P32 single cell RNA-seq


title: P25 single cell RNA-seq


title: P26 single cell RNA-seq


title: @Re.RGC_glu_Ntsr1.GN209 rep1


title: P22 single cell RNA-seq


title: P24 single cell RNA-seq


title: P23 single cell RNA-seq


title: @Re.RGC_glu_Gad2.33.7 rep3


title: @Re.RGC_glu_Np219Amig01 rep1


title: @Pituitary__Pomc-GFP rep1

source_name: Pituitary

value: Pituitary

value: Pomc-GFP


title: P21 single cell RNA-seq


title: @Pituitary__Pomc-GFP rep3


title: P20 single cell RNA-seq


title: P19 single cell RNA-seq


title: P18 single cell RNA-seq


title: @OE__TCLC rep2

source_name: Olfactory Epithelium

value: Olfactory Epithelium

value: TCLC

value: OE


title: @Pituitary__Pomc-GFP rep2


title: @OE.VNO_glu_TCLC rep2

source_name: Olfactory Epithelium (VNO)

value: Olfactory Epithelium (VNO)

value: VNO


title: @OE__TCLC rep1

value: F


title: @OE.VNO_glu_TCLC rep1


title: @Re.RGC_glu_Gad2.33.7 rep1


title: P14 single cell RNA-seq


title: P13 single cell RNA-seq


title: P12 single cell RNA-seq


title: @OE.VNO_glu_TCLC rep3


title: P9 single cell RNA-seq


title: @OE.MOE_glu_TCLC rep1

source_name: Olfactory Epithelium (MOE)

value: Olfactory Epithelium (MOE)

value: MOE


title: P10 single cell RNA-seq


title: @Re.RGC_glu_Gad2.33.7 rep2


title: @OE.MOE_glu_Rbp4.KL100 rep1


title: @OE.MOE_glu_Rbp4.KL100 rep2


title: @OE.MOE_glu_Rbp4.KL100 rep3


title: @OE.MOE_glu_Rbp4.KL100 rep4


title: 5GY-IGG

city: Suzhou

first: shuyu

last: zhang

state: Jiangsu

address: 199 Ren'ai Road

institute: Soochow University

data_processing:
Basecalls performed using CASAVA version 1.8
RIP-seq reads were adaptor-trimmed and mapped to human genome (hg19) by bowtie2 software with default parameters.
Peak calling was performed with MACS software (v1.4.3). Differentially enriched regions were identified by diffReps software (v1.55.4).
Genome_build: hg19
Supplementary_files_format_and_content: bed

source_name: WS1 cell

growth_protocol: WS1 cell was cultured with DMEM (10%FBS)

extract_protocol:
RNA extraction protocol: total RNA was extracted from the RIP assay products using Trizol (Invitrogen,USA). All samples passed the control analysis
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded Total RNA Library Prep Kit (Illumina,USA)

treatment_protocol: 24h after a single dose of 5 Gy X-ray irradiation,cells were harvested

tag: tissue origin

value: skin

tag: cell line

value: fibroblast cell

tag: treated with

value: single dose of 5 Gy X-ray irradiation

tag: time point

value: 24h after irradiation

tag: rip antibody

value: IgG (abcam, lot:ab172730)


title: @Jugular_glu_TrpV1-GFP rep2

source_name: Jugular ganglion

tag: tissue

value: Jugular ganglion

tag: strain

tag: region

value: Jugular

tag: age (postnatal day)

tag: Sex


title: 0GY-IGG

value: none (0 Gy)


title: 0GY-RIP

value: ELAVL1 (abcam, lot:ab136542)


title: P17 single cell RNA-seq

value: Articular cartilage

value: Chondrocyte


title: @Jugular_glu_TrpV1-GFP rep1

tag: weight (g)

tag: num_cells (# of sorted cells in the sample)

tag: ercc5 (10^-5 dilution of ercc in ul)

tag: ercc_mix (ercc mix used)


title: @Jugular_glu_TrpV1-GFP rep3


title: treatment 1 (5 Gy)

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to mouse genome by hisat2 software.
Cuffdiff software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: excel format; LncRNA and mRNA FPKM

extract_protocol:
RNA extraction protocol: total RNA was extracted using Trizol(Invitrogen,USA). All samples passed the control analysis
Libraries were prepared according to Illumina's instructions accompanying TruSeq Stranded Total RNA Library Prep Kit（Illumina, USA)
lncRNA-seq and mRNA-seq


title: P16 single cell RNA-seq


title: P15 single cell RNA-seq


title: @OE.MOE_glu_TCLC rep2

value: TCLC


title: @Jugular_glu_TrpV1-Cre rep4

value: M


title: control (0 Gy)


title: @Jugular_glu_TrpV1-Cre rep3


title: @Jugular_glu_TrpV1-Cre rep1


title: P11 single cell RNA-seq


title: @BAT__56L rep1

source_name: Brown adipose tissue

value: Brown adipose tissue

value: BAT


title: @BAT__56L rep3

value: F


title: @Jugular_glu_TrpV1-Cre rep2


title: @BAT__56L rep2


title: 5GY-RIP


title: iRx_Ldb1_noDox_ChIPseq

status: Public on Jul 19 2018

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

data_processing:
Quality of reads was verified using FASTQC analysis
The Illumina reads were aligned to the mouse genome using Bowtie2
Reads that were uniquely aligned to chromosomal positions were retained and duplicate reads were removed from the aligned data using Picard tools.
The filtered aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools and then converted to big wig file using "wigToBigWig" function
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: un-induced Ldb1 ChIPseq

extract_protocol:
Cells were harvested and washed with PBS before a 2-step crosslinking procedure. First, proteins were crosslinked by incubating cells for 45min at RT in PBS supplemented with 0.83 mg/ml Di(N-succinimidyl) glutarate (DSG, Sigma). Cells were then washed 4 times with PBS, prior to formaldehyde crosslinking of proteins and DNA for 10min at RT using 1% formaldehyde (Pierce) in IMDM with 10% FCS. Formaldehyde was quenched by adding 1/10th volume 2M glycine and crosslinked cells were washed twice in ice-cold PBS. For samples to be used for histone modification ChIP, single crosslinking with 1% formaldehyde was performed. Nuclei were prepared essentially as described in Lefevre et al 2003, sonicated using a Bioruptor water bath in immunoprecipitation buffer I (25 mM Tris 1 M pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% TritonX-100 and 0.25% SDS) {Lefevre, 2003 #45}. After centrifugation the sheared 0.5-2 kb chromatin fragments (1-2 x 106 cells) were diluted with 2 volumes immunoprecipitation buffer II (25 mM Tris pH 8.0, 150mM NaCl, 2 mM EDTA pH 8.0, 1% TritonX-100, 7.5% glycerol). Immunoprecipitation was carried out for 2-4 hours at 4°C using 2 μg antibody coupled to 15 μl Protein-G dynabeads (Invitrogen), with the exception of the H3K79me2 and the H4K5Ac antibodies where immunoprecipitation was carried out overnight. Following IP, the beads were washed with low salt, high salt, LiCl and Na/TE buffers before crosslinks were reversed overnight. DNA was extracted using Ampure beads (Beckman Coulter) and qPCRs were performed to validate ChIP quality.
ChIP-seq libraries were prepared using the Kapa Hyper Prep kit for Illumina platforms according to manufacturer’s instructions

value: haemogenic endothelium (HE) cells

tag: genotype

value: un-induced

tag: antibodies

value: Ldb1, Abcam ab96799


title: iRx_FLI1_noDoxJQ1_ChIPseq

source_name: un-induced  plus JQ1 treated FLI1 ChIPseq

tag: cell type

value: un-induced and JQ1 treated

value: FLI1, Santa Cruz sc356


title: iRx_HA_RUNX1_plusDox_ChIPseq

source_name: induced HA RUNX1 ChIPseq

value: induced

value: HA (for RUNX1), Sigma H6908


title: iRx_FLI1_plusDox_ChIPseq

source_name: induced  FLI1 ChIPseq


title: iRx_Ldb1_plusDox_ChIPseq

source_name: induced Ldb1 ChIPseq


title: iRx_HA_RUNX1_plusDoxJQ1_ChIPseq

source_name: un-induced plus JQ1 treated HA RUNX1 ChIPseq

value: induced and JQ1 treated


title: iRx_HA_RUNX1_noDox_ChIPseq

source_name: un-induced HA RUNX1 ChIPseq


title: iRx_H3K79me2_plusDox_ChIPseq

source_name: induced H3K79me2 ChIPseq

value: H3K79me2, Abcam ab3594


title: iRx_H4K5Ac_noDox_ChIPseq

source_name: un-induced H4K5Ac ChIPseq

value: H4K5Ac, Millipore 07-327


title: iRx_H3K79me2_noDox_ChIPseq

source_name: un-induced H3K79me2 ChIPseq


title: iRx_BRD4_plusDox_ChIPseq

source_name: induced  BRD4 ChIPseq

value: BRD4, Bethyl Labs A301-985A-100


title: iRx_H4K5Ac_plusDox_ChIPseq

source_name: induced H4K5Ac ChIPseq


title: iRx_CDK9_plusDoxJQ1_ChIPseq

source_name: un-induced plus JQ1 treated CDK9 ChIPseq

value: CDK9, Santa Cruz sc8338X


title: iRx_CDK9_plusDox_ChIPseq

source_name: induced CDK9 ChIPseq


title: iRx_FLI1_plusDoxJQ1_ChIPseq

source_name: induced  plus JQ1 treated FLI1 ChIPseq


title: iRx_FLI1_noDox_ChIPseq

source_name: un-induced  FLI1 ChIPseq


title: iRx_CDK9_noDox_ChIPseq

source_name: un-induced CDK9 ChIPseq


title: @BAT__56L rep4

source_name: Brown adipose tissue


title: iRx_plusDox_RNAseq_rep3

data_processing:
Quality of reads was verified using FASTQC analysis
RNA-Seq reads were aligned to the mm10 mouse genome build using STAR.
Separate density files for the positive and negative strand were generated for RNA-seq data and uploaded to the UCSC genome browser
Fragments per Kilobase of transcript per Million mapped reads (FPKM) values for each gene were extracted using Cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: induced RNA-seq

extract_protocol:
RNA was extracted from cells using TRIzol (Invitrogen) according to manufacturer’s instructions. First-strand cDNA synthesis was carried out using Superscript II (Invitrogen) and Oligo dT (Invitrogen) according to manufacturer’s instructions. RNA was DNase treated using Turbo DNase (Ambion) and a further clean-up step was performed using the RNA Nucleospin kit (Macherey-Nagel) according to manufacturer’s instructions. Real-time PCR was carried out using Applied Biosystems SYBR green master mix (Thermo Fisher) with 5 μl of diluted cDNA and 0.25 μM forward and reverse primers per 10 μl reaction on an ABI 7900HT machine. Analysis was carried out on samples measured in duplicate.
RNA-seq libraries were prepared using the Tru-seq Stranded Total RNA kit (Illumina), according to manufacturer’s instructions. Libraries were sequenced in a pool of 12 indexed libraries using a NextSeq® 500/550 High Output Kit v2 (150 cycles) for paired end sequencing (Illumina, FC-404-2002) at the Genomics Birmingham sequencing facility.

tag: mouse strain


title: iRx_BRD4_noDox_ChIPseq

source_name: un-induced  BRD4 ChIPseq


title: iRx_plusDox_RNAseq_rep2


title: iRx_plusDoxJQ1_RNAseq_rep3

source_name: induced plus JQ1 treated RNA-seq

value: induced plus JQ1 treated


title: iRx_plusDox_RNAseq_rep1


title: iRx_H3K79me2_plusDoxJQ1_ChIPseq

source_name: induced plus JQ1 treated H3K79me2 ChIPseq


title: iRx_plusDoxJQ1_RNAseq_rep2


title: iRx_noDox_RNAseq_rep4

source_name: un-induced RNA-seq


title: iRx_noDox_RNAseq_rep3


title: iRx_noDox_RNAseq_rep2


title: iRx_noDoxJQ1_RNAseq_rep1

source_name: un-induced plus JQ1 treated RNA-seq

value: un-induced plus JQ1 treated


title: drug group [7-2]

city: adelaide

first: qi

last: liang

address: north terrace

country: Australia

institute: university of adelaide

data_processing:
RNA amplification was performed according to SMARTer Ultra Low Input RNA for Illumina Kit.Quantity and quality of amplified cDNAs were measured with Qubit and Agilent Bioanalyzer 2100.
RNA sequencing was performed using Illumina Hiseq 2500.
Adaptors and low quality sequences from raw reads were filtered using Trim_galore with the following parameter: --stringency 6. Trimmed reads were mapped to the mouse reference genome (mm10) using STARv2.5 with the following parameters: --out Filter Mismatch Nover L max 0.05 –seed Search Start L max 30
Raw counts of mouse refSeq genes were acquired with R package “Genomic Alignments”.
Genome_build: mm10
Supplementary_files_format_and_content: Tab deliminated text file including raw counts for mm10 reference genes acorss all samples

source_name: embryo_loaded with glucose_treated with ZGW rat serum

extract_protocol:
Zygotes from three groups were cultured in vitro to 2-cell stage, and three zygotes were randomly selected as a sample from each group and stored in liquid nitrogen. Each group was replicated three times for biological replication. Zygotes were resuspended in freshly prepared lysis buffer, each zygote was lysed with a micropipette to yield more than 7µl of lysate and the lysate stored at – 80C.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: embryo

tag: Stage

value: 2-cell stage

tag: sample group

value: loaded with high glucose and treated with ZGW rat serum


title: iRx_noDoxJQ1_RNAseq_rep2

value: haemogenic endothelium (HE) cells


title: iRx_plusDox_RNAseq_rep4


title: drug group [7-3]


title: control group [1-1]


title: 437_E

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

data_processing:
Aligned to mm10 using STAR spliced read aligner
Count read using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation (FPKM) and differential expression analysis using edgeR and limma voom.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values

extract_protocol:
Total RNA was extracted using RNeazy kit (Qiagen) accordance with the prescribed protocol provided with the kit.
Libraries prepared using the Illumina TruSeq RNA Library Prep Kit v2 and sequenced on an Illumina HiSeq4000 sequencer using strand-specific

value: Rbfox1loxP/loxP; UBC-Cre+/- + Tamoxifen

tag: background strain

tag: treatment

value: Tamoxifen


title: control group [1-3]

tag: tissue


title: drug group [7-1]

tag: strain


title: control group [1-2]


title: model group [4-1]

source_name: embryo_loaded with glucose

value: loaded with high glucose


title: 441_C

source_name: Control


title: 415_E


title: model group [4-2]


title: 418_C


title: iRx_plusDoxJQ1_RNAseq_rep1


title: B16F1-CXCL5_1

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
RNA-seq processing:
RNA-seq data were analysed with the nextpresso pipeline (http://bioinfo.cnio.es/nextpresso/) as follows:
Fastq files were randomly down-sampled with Seqtk (https://github.com/lh3/seqtk), to generate datasets with similar number of reads in all the samples. Sequencing quality was checked with FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the human genome (GRCm38/mm10) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.1.9, allowing two mismatches and five multihits.
Transcripts quantification and differential expression were calculated with Cufflinks 2.2.1, using the human GRCm38/mm10 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tabulated text file with gene FPKM values

source_name: Primary tumor

growth_protocol: Melanoma cells were grown intradermally in the flank skin of C57BL/6 J mice

extract_protocol:
RNA was isolated with Quiagen RNAeasy mini kit according to the manufacturer´s protocol.
1 µg of total RNA from the samples was used. Sample RNA Integrity Numbers were in the range 8.7 to 9.5, median 9.4 (Agilent 2100 Bioanalyzer). The poly(A)+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). The adapter-ligated library was completed by PCR with Illumina PE primers (eight cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2000 by following manufacturer's protocols.

treatment_protocol: Primary tumors were excised and snap frozen

value: CXCL5 overexpressing B16F1 murine melanoma cells

value: no treatment


title: B16F1_1

value: B16F1 murine melanoma cells


title: 398_E


title: 393_C


title: B16F1_2


title: J-Th17_CH223191

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

description: Th17+CH223191 sample J

data_processing:
Reads were trimmed to remove adapter content using Trimmomatic v0.36 with trimming steps ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Trimmed reads were aligned to GRCh38 using HISAT2 v2.0.4
Aligned reads were sorted and indexed using samtools 1.3.1
Differential expression analysis was performed using DESeq2 version 1.14.1
All data processing steps are fully documented in the pipeline.sh file
Genome_build: GRCh38 Ensembl release 84
Supplementary_files_format_and_content: raw_counts.csv is a comma separated value file containing raw read counts per sample per gene
normalized_counts.csv is a comma separated value file containing counts per gene after normalization by the estimateSizeFactors function in the Bioconductor package DESeq

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from human buffy coat (Zen-Bio, Inc., Research Triangle Park, NC) by density gradient centrifugation. Naïve CD4 T cells were purified using a commercially available kit (StemCell Technologies, Vancouver, BC, Canada).  Following purification, cells were resuspended in RPMI with serum replacement factor 3 (Sigma-Aldrich, St. Louis, MO), anti-CD28 clone CD28.2 (2ug/mL; Biolegend, San Diego, CA), L-glutamine and penicillin-streptomycin.  Cells were enumerated using trypan blue exclusion, and 0.5-1.0x106 were seeded in 24 well plates pre-coated the day before with anti-human CD3 clone OKT3 (10ug/mL; Biolegend).  Cell purity ranging from 90-98 percent was verified by flow cytometry.

extract_protocol:
Total RNA was purified from T cell cultures on day 3 using TRIzol reagent (Ambion).
RNA-seq libraries were prepared from 1 μg of total RNA per sample using the Illumina TruSeq stranded mRNA kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: To induce Th17 differentiation, naïve CD4 T cells were cultured with IL-6 (30ng/mL), TGF-b (2ng/mL), IL-1b (10ng/mL) and IL-23 (10ng/mL).  Additional treatments in experimental cultures included FICZ (200nM; Sigma-Adrich), CH223191 (4uM; Sigma-Aldrich) and Ogerin (10uM; Tocris Bioscience).

tag: individual

value: donor J

value: Peripheral Blood Mononuclear Cells


title: J-Th17_FICZ

description: Th17+FICZ sample J

source_name: PBMCs, Th17_FICZ

value: Th17 + FICZ


title: model group [4-3]


title: J-Th17

description: Th17 sample J

source_name: PBMCs, Th17


title: I-Th17_FICZ

description: Th17+FICZ sample I

value: donor I


title: J-Media

description: Control sample J

source_name: PBMCs, Media

value: Control


title: B16F1-CXCL5_2


title: I-Th17

description: Th17 sample I


title: I-Th17_CH223191

description: Th17+CH223191 sample I


title: H-Th17

description: Th17 sample H

value: donor H


title: H-Th17_FICZ

description: Th17+FICZ sample H


title: H-Media

description: Control sample H


title: iRx_noDox_RNAseq_rep1

value: un-induced


title: I-Media

description: Control sample I


title: B16F1_3


title: H-Th17_CH223191

description: Th17+CH223191 sample H


title: G-Media

description: Control sample G

value: donor G


title: G-Th17

description: Th17 sample G


title: C-Th17

description: Th17 sample C

value: donor C


title: C-Th17_CH223191

description: Th17+CH223191 sample C


title: A-Th17_FICZ

description: Th17+FICZ sample A

value: donor A


title: G-Th17_CH223191

description: Th17+CH223191 sample G


title: G-Th17_FICZ

description: Th17+FICZ sample G


title: C-Th17_FICZ

description: Th17+FICZ sample C


title: A-Th17_CH223191

description: Th17+CH223191 sample A


title: A-Media

description: Control sample A


title: A-Th17

description: Th17 sample A


title: Co100-C2

status: Public on Jul 18 2018

city: Amsterdam

first: Louis

last: Vermeulen

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine

country: Netherlands

institute: Academic Medical Center

data_processing:
preprocess: Trimmomatic 0.36 (ILLUMINACLIP:TruSeq3-SE_RA.fa:3:15:8 LEADING:15 TRAILING:15 SLIDINGWINDOW:4:20 MINLEN:36)
alignment: HISAT2 2.0.4 (--trim3 6 --dta -t) and samtools 1.3.1
assembly: stringtie 1.2.4
quantification: subread featureCounts 1.5.0-p1 (gene_id)
normalization, differential expression: DESeq2 1.10.1 (lfcThreshold = log2(1.2), altHyp=greaterAbs, ref = C, design = formula(~ Celline + Location)
Genome_build: GRCh38.85
Supplementary_files_format_and_content: read counts normalized with DESeq2 (Location edge (E) vs. centre (C)), gene annotation from org.Hs.eg.db 3.2.3

source_name: Co100 centre

growth_protocol: Human primary colon cancer cultures ( CO147, Co100) were established as described previously (Todaro et al. Cell stem cell 2007) and cultured as spheroids in polyHEMA coated flasks. Primary cell culture medium contains advanced DMEM/F12, supplemented with N-2, L-glutamine, glucose, HEPES, heparin, insulin, epidermal growth factor and basic fibroblast growth factor. Caco-2 cells were cultured in DMEM supplemented with 10% FCS. To generate in vivo tumours, 50,000 human primary colon cancer cells in medium were mixed at an 1:1 ratio with Matrigel (Corning) and injected subcutaneously into both flanks of nude or NSG mice.

extract_protocol:
Proteinase K at 56°C for 30 min, incubation at 80°C for 15 min, on ice for 3 min, centrifugation at 20000g for 15 min, supernatants treated with DNaseI for 15min at RT, RNeasy FFPE columns (Qiagen).
mRNA Library Prep Kit (Illumina)

treatment_protocol: Tumours were fixed using 4%-paraformaldehyde immediately after isolation. Frozen tumour sections were manually dissected into edge and centre fractions.

tag: tumor location

value: centre

tag: cell line


title: Co100-E1

source_name: Co100 edge

value: edge


title: CC09-E2

source_name: Co147 edge


title: Co100-E2


title: Co100-C1


title: CC09-E1


title: CC09-C2

source_name: Co147 centre


title: CC09-C1


title: HCT-15-E2

source_name: HCT-15 edge


title: HCT-15-C2

source_name: HCT-15 centre


title: Nrf1-CKO rep2

city: Houston

first: Chai-An

last: Mao

state: Texas

address: 6431 Fannin Street, MSB7.242

department: Ophthalmology And Visual Scien

institute: University of Texas McGovern Medical School

data_processing:
Align the paired-end sequences to mouse genome (mm10) via TopHat 2.7.2
Perform QC and sum counts (reads) for each gene using Htseq
The count data were normalized using a variance stabilizing transformation (VST) method that is implemmented in an R Bioconductor package "DESeq".
"GetVarianceStabiliedData" function was used to transform the data. The transformation is scaled such that for large counts, it becomes asymptotically (for large values) equal to the logarithm to base 2.
The log2 transformed data was applied to significant analysis using LIMMA package.
Genome_build: mm10
Supplementary_files_format_and_content: Text file describing the raw and normalized counts

source_name: E13.5 retinas

extract_protocol:
Retinas were removed from E13.5 embryos, and total RNA was harvested using Trizol reagent. 1 ug of total RNA were used to prepare the libraries. This was done at the "Sequencing and Microarray Facility" at UTMDACC.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

value: C57BL/6 129 mixed

tag: age


title: HCT-15-E1


title: C-Media

description: Control sample C


title: Nrf1-CKO rep1


title: WT rep2

value: wild type


title: WT rep1


title: WT_DR_WA_rep2

city: Glasgow

first: Manikhandan

middle: A V

last: Mudaliar

state: Scotland

address: Room B528, Sir Graeme Davies Building, 120 University Place

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

data_processing:
The raw data was analysed using Torrent Suite (version 4.0.2)
The single end reads generated with Ion Proton sequencer were pre-processed with cutadapt (version 1.5) tool to remove 3’ end adapters and sickle (version 0.940) to remove 3’ end sequence stretches with quality value lower than 10 and to filter out reads shorter than 54 bp (flags “–q 10 –l 54”). The remaining reads were then mapped to the Ensembl mouse genome version GRCm38 using BBmap software (version 34.90). In order to maximize the number of unique alignments the initial alignment was followed by ten additional alignment iterations. At each iteration the unmapped reads were subjected to the process where 75 base pairs were excised from the original full length reads at positions i-1*18+1 (where i is the iteration number) and subjected to alignment using the BBmap aligner. Thus the 75 bp aligned sequence stretches were excised at position 1, 19, 37, 55, 73, 92, 109, 127, 145 and 163 for each of the ten iterations, respectively, from the original full-length reads. The iterative alignment strategy applied here increased the percentage of aligned reads from 77.1% to 97.1% and percentage of uniquely aligned reads from 68.1% to 84.2% on average over 43 samples.
Differential expression analysis was performed using cuffdiff (version 2.2.1) applying --multi-read-correct and --compatible-hits-norm options. A false discovery rate of 5% was allowed and the minimum number of aligned reads in a locus needed to conduct significance testing was kept at 8. The libraries prepared from each sample were normalised using the geometric mean across the samples and the dispersion between the replicates were estimated for each condition.
Genome_build: Ensembl mouse genome version GRCm38
Supplementary_files_format_and_content: Matrix table - genes.fpkm_tracking - an output from Cuffdiff; Tab delimited FPKM per condition.

source_name: White adipose tissue

growth_protocol: Genotyping of insulin receptor substrate 1 (IRS1) global knockout (KO) mice followed previously described protocols. Mice were housed in single-sex groups from weaning. Initially mice had ad libitum (AL) access to water and standard chow (D12450B, Research Diets Inc., New Brunswick, NJ, USA; protein 20 kcal%, carbohydrate 70 kcal%, fat 10 kcal%) and kept on a 12L/12D cycle (lights on 0700–1900 h) at a housing temperature of 22 ± 2°C. At 10 weeks of age, groups of male and female wildtype (WT; Irs1+/+) and KO (Irs1-/-) mice were either kept on the AL diet or placed on a dietary restricted (DR) diet to generate 4 experimental groups- WTAL, WTDR, KOAL and KODR.

extract_protocol:
mRNA was isolated from brain, skeletal muscle, liver and white adipose tissue from WTAL (n=2), WTDR (n=3), KOAL (n=3) and KODR (n=3) female mice at 15 months of age (12 months of 30% DR) using Tri-Reagent (Life Technologies, Paisley, UK) and Qiagen RNeasy Mini Kit (Sussex, UK), following manufacturer’s protocols. RNA was re-suspended in ultra-pure water, RNA concentration and purity was determined by spectrophotometry (NanoDrop, Fisher Scientific).
The extracted RNAs were prepared using a Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher Scientific Inc.) to perform the poly A selection followed by an Ion Total RNA-Seq Kit v2 to prepare the library from the poly A selected RNAs. The constructed libraries were sequenced on an Ion Proton™ System (Thermo Fisher Scientific Inc.) using P1 chip (version P1.1.17) according to the manufacturer’s protocol.

treatment_protocol: DR mice underwent a step-down protocol, with 10% introduced at 10 weeks of age, 20% the following week and maintained at 30% of the food intake of appropriate AL controls until the completion of the study. Food intake of AL mice was determined weekly and 30% DR was calculated from the average AL mice intake over the preceding week. DR mice were fed daily between 1630 and 1730 hrs.

value: Wild type

tag: diet allowance

value: dietary restricted

value: White adipose tissue


title: WT_DR_SM_rep2

source_name: Skeletal muscle

value: Skeletal muscle


title: WT_DR_WA_rep1


title: WT_DR_SM_rep3


title: WT_DR_SM_rep1


title: WT_DR_LI_rep2

source_name: Liver

value: Liver


title: WT_DR_LI_rep3


title: potato degradome 2

city: Seoul

first: Chanseok

last: Shin

address: 1, Gwanak-ro, Gwanak-gu

department: Agricultural Biotechnology

country: South Korea

institute: Seoul National University

description: two technical replicates

data_processing:
Adaptors were removed and the qualified reads in size 15-26 nucleotides were obtained.
Structural RNAs such as rRNAs, tRNAs, snRNAs and snoRNAs were removed using BLASTN against Rfam.
Repeats and transposons were also removed using the repeat database.
The remaining reads were mapped to transcript sequences by Bowtie.
Because UTR sequences have not been identified in pepper, tomato and potato, transcripts were defined to coding sequence and ±1kb flanking sequences.
Target genes of microRNAs were identified by CleaveLand4 pipeline (cutoff: p-value ≤ 0.05 or score ≤ 4)
Genome_build: Pepper.v.1.55, ITAG v.2.3, JGI v.4.03
Supplementary_files_format_and_content: counts/# reads

organism: Solanum tuberosum

source_name: whole tissue

extract_protocol:
Total RNAs were extracted from whole tissue of pepper, tomato and potato using Ambion™ TRIzol™ Reagent, according to the manufacturer's protocol.
Degradome libraries were constructed as previously described (Addo-Quaye et al., Current Biology, 2008).

value: whole tissue

tag: cultivar

value: phureja


title: WT_DR_LI_rep1


title: potato degradome 1

description: two technical replicates


title: WT_DR_BR_rep2

source_name: Brain

value: Brain


title: WT_AL_SM_rep2

value: ad libitum


title: WT_AL_LI_rep1


title: HCT-15-C1


title: WT_AL_SM_rep1


title: WT_AL_LI_rep2


title: WT_AL_BR_rep1


title: WT_AL_WA_rep2


title: WT_AL_WA_rep1


title: KO_DR_WA_rep3


title: KO_DR_SM_rep2


title: KO_DR_WA_rep1


title: KO_DR_SM_rep1


title: KO_DR_SM_rep3


title: KO_DR_WA_rep2


title: WT_DR_BR_rep1


title: KO_DR_LI_rep3


title: WT_DR_BR_rep3


title: KO_DR_BR_rep3


title: KO_DR_LI_rep1


title: KO_DR_BR_rep2


title: KO_DR_BR_rep1


title: KO_AL_WA_rep3


title: KO_AL_WA_rep1


title: KO_AL_SM_rep3


title: KO_AL_WA_rep2


title: KO_AL_LI_rep3


title: KO_AL_SM_rep1


title: KO_AL_SM_rep2


title: WT_AL_BR_rep2


title: pepper degradome 2

description: two technical replicates

organism: Capsicum annuum


title: tomato degradome 1

description: two technical replicates

organism: Solanum lycopersicum

value: Heinz


title: KO_AL_LI_rep2


title: KO_AL_BR_rep1


title: KO_AL_BR_rep3


title: KO_AL_LI_rep1


title: KO_AL_BR_rep2


title: pepper degradome 1

description: two technical replicates


title: 19_2_Male

city: Barcelona

first: Luca

last: Cozzuto

state: Barcelona

address: Carrer Dr. Aiguader 88

department: CRG core facilities

institute: Centre for genomic regulation (CRG)

description:
all_rep_fpkm Jan 2017.txt: X19_Male_1
19_2_Male_6068_ACGT

data_processing:
tophat (version v2.0.8b)  was used for aligning with unstranded library type and options -M and -G
we used the gene annotation from iGenomes
cuffdiff (version v2.1.1) was used to estimate the FPKM  with options -b and -u and again for unstranded library
Genome_build: NCBIM37 (from iGenomes)
Supplementary_files_format_and_content: .txt file with FPKM for each replicate

source_name: Basal hair follilcle stem cells (CD49f High CD34+)

extract_protocol:
Total RNA was isolated from HFSC from adult mouse skin at indicated chronological ages using an RNA-easy Plus micro RNA extraction kit (Qiagen).
HiSeq Sequencing Kit Trueseq v3

value: Skin

tag: chronological age

value: 19 months

value: HFSC


title: 24_3_Male

description:
all_rep_fpkm Jan 2017.txt: X24_Male_1
24_3_Male_6071_CTTT

value: 24 months


title: 19_3_Male

description:
all_rep_fpkm Jan 2017.txt: X19_Male_2
19_3_Male_6069_CAGT


title: 24_4_Male

description:
all_rep_fpkm Jan 2017.txt: X24_Male_2
24_4_Male_6072_GAAT


title: 3_1_Male

description:
all_rep_fpkm Jan 2017.txt: X3_Male_0
3_1_Male_6058_AACT

value: 3 months


title: 3_2_Male

description:
all_rep_fpkm Jan 2017.txt: X3_Male_1
3_2_Male_6059_TTGT


title: KO_DR_LI_rep2

tag: genotype


title: wt_t30_rep3

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

data_processing:
Library strategy: 5P-Seq
Read demultiplexed using Illumina BaseSpace servers. Illumina BaseSpace FASTQ Generation. Version: 1.0.0
For each read we trimmed the first 8 nt (UMI, unique molecular identifier) and align the rest to S. cerevisiae genome (version R64-1-1) using Hisat2 with default parameters (except limiting the maximum intron size to 2kb). Reads with the same 5’mapping site and UMI were considered PCR duplicates and omitted from the analysis.
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Bedgraph files for UMI collapsed reads por positive and negative strand

organism: Saccharomyces cerevisiae

growth_protocol: Saccharomyces cerevisiae  cells were grown at 30°C till mid-log phase (OD600 0.4-0.5) in synthetic medium supplemented with appropriate amino acids and 2% glucose as the carbon source.

extract_protocol:
Cells were harvested and pellets were frozen in liquid nitrogen and kept at -80°C until further processing. Total RNA was extracted from yeast cells using phenol:chloroform extraction.
5PSeq methods was performed as previously described (PMID: 26820793) with minor modifications. 6µg of total RNA was used as input. After single-stranded RNA ligation, partial rRNA depletion was performed using Ribo-Zero Magnetic Gold Kit (Epicentre). 5PSeq libraries were PRC amplified (19 cycles), pooled and size selected (300-500nt). Samples were sequenced using a NextSeq500 producing single-end 75 reads.

treatment_protocol: To induce osmotic stress, KCl was added to the culture at 0.6M final concentration for 30 minutes.

value: BY4741 (MATa his3delta_1 leu2delta_0 met15delta_0 ura3delta_0)

tag: time


title: pat1_t30_rep2

value: pat1  (BY4741; MATa; ura3delta_0; leu2delta_0; his3delta_1; met15delta_0; YCR077c::kanMX4)


title: pat1_t30_rep1


title: wt_t0_rep2


title: tomato degradome 2

description: two technical replicates


title: wt_t0_rep1


title: pat1_t30_rep3


title: pat1_t0_rep3


title: pat1_t0_rep2


title: 24_2_Male

description:
all_rep_fpkm Jan 2017.txt: X24_Male_0
24_2_Male_6070_ATAT

tag: cell type


title: pat1_t0_rep1


title: lsm1_t30_rep2

value: lsm1  (BY4741; MATa; ura3delta_0; leu2delta_0; his3delta_1; met15delta_0; YJL124c::kanMX4)


title: lsm1_t0_rep2


title: lsm1_t30_rep1


title: lsm1_t0_rep1


title: lsm1_t0_rep3


title: wt_t30_rep2


title: wt_t0_rep3


title: DL2573 stationary phase biological repeat 2

city: Edinburgh

first: Benura

last: Azeroglu

address: Alexander Crum Brown Road

institute: University of Edinburgh

data_processing:
Library strategy: Marker Frequency Analysis [MFA]
Alignment: reads were aligned to an in house generated draft sequence of strain DL2573 (DL2573_draft_genome_sequence.fasta (available on the series record)) using the Burrows-Wheels Alignment software BWA-MEM and the number of reads mapped to each bp of the genome quantified using SAMtools (mpileup)
Raw Counts: The data from each of the multiple (three or four) sequencing runs  was consolidated by merging BAM files using the merge function of SAMtools and the number of reads mapped to each bp of the genome quantified using the mpileup function of SAMtools (with parameters -BQ0 -d10000000).  Genomic positions lacking any coverage were given an arbitrary value of 0.1 reads
Normalization: the number of mapped reads for each position in the reference genome was divided by the sum of the number of mapped reads at every position across the genome
Genome_build: DL2573_draft_genome_sequence.fasta (available on the series record)
Supplementary_files_format_and_content: Each CSV file contains a headerless matrix with position on the reference genome in column 1 and the associated raw or normalized read count in column 2.  Each matrix has a row for every corresponding genomic position. Values were saved with a maximum precision of 9 significant figures.

organism: Escherichia coli K-12

source_name: Bacterial Cell Lysates

growth_protocol: Cells were grown in LB media supplemented with 0.2% arabinose at 37°C to and OD600nm of 0.2-0.25

extract_protocol:
To further eliminate potential RNA, 3 units of RiboshredderTM were added per sample. Samples were purified by phenol/chloroform extraction and ethanol precipitation.
Construction of libraries using the Illumina TruSeq DNA Sample Prep kit and DNA sequencing was carried out on an Illumina HiSeq 2000 platform by Edinburgh Genomics

treatment_protocol: DNA was isolated from cultures after 1 hour induction of sbcDC expression using the Promega Wizard® Genomic DNA purification kit.

value: BW27784 PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZchi-


title: DL3391 exponential growth biological repeat 2

value: BW27784 delta_recD PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZchi-


title: DL2573 stationary phase biological repeat 1


title: DL3743 exponential growth biological repeat 2

value: BW27784 delta_recD PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZchi-


title: DL3743 exponential growth biological repeat 1


title: 3_3_Male

description:
all_rep_fpkm Jan 2017.txt: X3_Male_2
3_3_Male_6060_ACGT


title: DL2573 exponential growth biological repeat 2


title: DL3391 exponential growth biological repeat 1


title: DL2573 exponential growth biological repeat 1


title: 19_1_Male

description:
all_rep_fpkm Jan 2017.txt: X19_Male_0
19_1_Male_6067_TTGT


title: DL2006 exponential growth biological repeat 2

value: BW27784 PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZchi-


title: lsm1_t30_rep3


title: DL5699 biological repeat 2 RecA ChIP

data_processing:
Alignment: reads were mapped to bespoke reference sequence (DL4201_in_lab_reference_genome (available on series record)) using the default parameters of software Bowtie 2 (Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods, 9, 357-359).
Raw counts of mapped reads per reference base pair were then calculated using SAMtools software (with parameter –d set to 10^6).
Normalisation: Counts were normalised by applying a single, sample-specific scaling factor.  To calculate this scaling factor, we implemented the median of ratios normalisation of DESeq software (Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol, 11, R106) using R.
Genome_build: DL4201_in_lab_reference_genome (available on series record)
Supplementary_files_format_and_content: txt files of a matrix containing genome position in column 1 and number of depth of mapped reads in column 2. Also, in a CSV file of a matrix containing genome position in column 1 and subsequent coloumns with normalised number of depth of mapped reads (column names have the strain number). CSV file is on the series record.

extract_protocol:
Cells were collected by centrifugation and washed three times in ice-cold 1X PBS. The pellet was then re-suspended in 250 μl ChIP buffer (200 mM Tris-HCl (pH 8.0), 600 mM NaCl 4% Triton X, Complete protease inhibitor cocktail EDTA-free (Roche)). Sonication of crosslinked samples was performed using the Diagenode Bioruptor® at 30s intervals for 10 min at high amplitude. After sonication, 350 μl of ChIP buffer was added to each sample, the samples were mixed by gentle pipetting and 100 μl of each lysate was removed and stored as ‘input’. Immunoprecipitation was performed overnight at 4°C using 1/100 anti-RecA antibody (Abcam, ab63797). IP samples were then incubated with Protein G Dynabeads® (Life Technologies) for 2 h at room temperature. All samples were washed 3 times with 1 X PBS + 0.02% Tween-20 before re-suspending the Protein G dynabeads in 200 μl of TE buffer (10 mM Tris (pH 7.4), 1 mM EDTA) + 1% SDS. 100 μl of TE buffer was added to the input samples and all samples were then incubated at 65°C for 10 h to reverse formaldehyde crosslinks. DNA was isolated using the MinElute PCR purification kit (Qiagen). DNA was eluted in 50 μl of TE buffer using a 2-step elution. Samples were stored at -20°C.
All samples were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit.

treatment_protocol: Protein DNA interactions were crosslinked for 10 min at 22.5C with 1% formaldehyde and quenched using glycine to a final concentration of 0.5M

value: induced DNA double strand break

value: BW27784 delta_recD lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX-


title: DL4201 biological repeat 1 RecA ChIP

value: BW27784 lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZX-


title: DL4201 biological repeat 2 RecA ChIP_reanalyzed


title: DL4184 biological repeat 2 RecA ChIP_reanalyzed

value: BW27784 lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX-


title: DL2006 exponential growth biological repeat 1


title: WT ov MUNC GM rep2

city: Charlottesville

first: Anindya

last: Dutta

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

data_processing:
Illumina software was used for basecalling to generate the .bcl files which were converted to fastq file using a software named bcl2fastq
RNA-seq reads were aligned to the mm10 transcriptome using kallisto with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include transcript level estimated count and TPM values for each sample derived from kallisto

source_name: C2C12_WT ov MUNC GM

extract_protocol:
RNAeasy mini kit (Qiagen)
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB)
Sequencing was run using a NextSeq 150 cycle V2 kit with HighOutput. A paired-end (R1_75 & R2_75) run with indexing (6 cycles) were included in the workflow.

tag: strain background

value: post natal day 21

tag: tissue source

value: skeletal muscle

tag: genotype/variation

value: wild type

value: proliferating cells

tag: transfected with

value: vector coding for MUNC spliced  (ovMUNC)

tag: molecule subtype

value: polyA enriched RNA


title: MYOD-/- ov MUNC DM rep1

source_name: C2C12_MYOD-/- ov MUNC DM

value: MYOD-/-

value: differentiating cells


title: MYOD-/- EV DM rep1

source_name: C2C12_MYOD-/- EV DM

value: control vector (EV)


title: WT ov MUNC DM rep1

source_name: C2C12_WT ov MUNC DM


title: MYOD-/- EV GM rep1

source_name: C2C12_MYOD-/- EV GM


title: WT ov MUNC GM rep1


title: wt_t30_rep1

value: BY4741 (MATa his3delta_1 leu2delta_0 met15delta_0 ura3delta_0)


title: MYOD-/- EV DM rep2


title: WT EV DM rep1

source_name: C2C12_WT EV DM


title: WT EV DM rep2


title: MYOD-/- EV GM rep2


title: DL6204 biological repeat 2 RecA ChIP

tag: treatment

tag: background strain

value: BW27784 delta_recD lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZX-


title: DL6204 biological repeat 1 RecA ChIP

tag: strain


title: WT ov MUNC DM rep2


title: MYOD-/- ov MUNC GM rep2

source_name: C2C12_MYOD-/- ov MUNC GM


title: WT EV GM rep1

source_name: C2C12_WT EV GM


title: MYOD-/- ov MUNC GM rep1


title: MYOD-/- ov MUNC DM rep2


title: DgWRKY5

city: Chengdu

first: Zhenyu

last: Bai

address: 211 Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step,clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Supplementary_files_format_and_content: FPKM

organism: Chrysanthemum x morifolium

source_name: leaves

extract_protocol:
Chrysanthemum leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Jinba

tag: tissue

value: leaves

tag: name

value: Dendranthema grandiflorum


title: CK


title: DL5699 biological repeat 1 RecA ChIP

value: induced DNA double strand break

value: BW27784 delta_recD lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX-


title: WT EV GM rep2

tag: cell line

tag: age


title: DL4184 biological repeat 1 RecA ChIP

value: BW27784 lacZ::XXX mhpR::XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX-


title: S. cerevisiae Spp1_PHD_SPM_t240 ChIP-seq experiment

status: Public on Jul 17 2018

city: Debrecen

first: Halasz

last: Laszlo

address: Egyetem tér 1

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

description:
Spp1-myc PHDΔ strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4 hrs) for ChIP analysis.
Spp1_PHD_SPM_t240

data_processing:
[Alignment] Reads were aligned to the S. cerevisiae reference genome (sacCer3; SGD) with the default parameters of bwa mem algorithm.
[Filtering] Low mapping quality (MAPQ < 10) and PCR-duplicated reads were omitted from downstream analysis.
[Peak calling] BayesPeak (Spyrou et al. 2009) was used with default parameters to identify ChIP enriched regions of the genome compared to input control.
[Normalized abundance measurements] We used deepTools2 (Ramirez et al. 2014) bamCoverage to create RPKM (Reads Per Kilobase per Million mapped reads) normalized bedgraph files (--skipNonCoveredRegions --binSize 25 --smoothLength 125 --normalizeUsingRPKM --extendReads 350).
Genome_build: sacCer3
Supplementary_files_format_and_content: ChIP-seq and competition ChIP peak predictions are in bed format and their corresponding coverage files are bedgraphs.

source_name: Whole cell extracts

growth_protocol: For sporulation, cells were grown in rich medium (YPD) for 24 hours, then transferred to pre-sporulation medium (SPS) and grown overnight to a density of ~4x10^7 cells/ml. Cultures were harvested by centrifugation, washed with one volume of pre-warmed 1% potassium acetate and resuspended in sporulation medium (SPM; 1% potassium acetate supplemented with amino acids and nucleotides according to auxotrophic requirements, and 0.0001 % of polypropylene glycol 2000 as an anti-clumping agent) at a density of 2x107 cells/ml, at 30 °C. Meiotic progression and sporulation efficiency was monitored by FACS and fluorescent microscopy of DAPI-stained nuclei. Aberrantly slow or asynchronous sporulation time courses were excluded from further experiments. Spore viability was assessed by tetrad dissection and it was greater equal than 90% for all the strains involved in this study

extract_protocol:
50 mL of meiotic cells (4x10^7 cells/mL) were collected at the indicated time points and crosslinked with 1% formaldehyde for 20 min at room temperature. Formaldehyde was quenched with 125 mM glycine for 5 min at room temperature, and cells were washed three times with ice-cold 1x TBS at pH 7.5 (20 mM Tris HCL at pH 7.5, 150 mM NaCl). Cells were resuspended in 500  µL of lysis buffer (50 mM Hepes KOH at pH 7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 tablet of complete inhibitor cocktail (from Roche) in 50 mL solution) and lysed with acid-washed glass beads for 10 min in a FastPrep bead beater machine. Chromatin samples was fragmented to an average size of 300 bp by sonication (Bioruptor, Diagenode). To obtain whole-cell extract (WCE), a 50-µL pre-IP sample was removed and centrifuged at full speed for 10 sec to pellet the cell debris (supernatant = WCE). The rest of the samples were also centrifuged at 12,000 rpm (4 °C) for 20 sec to pellet the cell debris. IP was performed by adding the 450-µL extract to a pellet of magnetic protein G dynabeads (Dynal), corresponding to 50 µL or 2 x 10^7 beads, which were preincubated with the 9E11 (monoclonal mouse anti-myc, ab290, Abcam) or anti-GFP (polyclonal rabbit, ab56, Abcam) antibodies overnight at 4 °C. IP samples were washed twice with lysis buffer, twice with lysis buffer plus 360 mM NaCl, twice with washing buffer (10 mM Tris HCl at pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA), and finally once with 1x TE at pH 7.5, using the magnetic device supplied by Dynal. After reversal of cross-linking by heating in TE-1% SDS overnight at 65 °C, the proteins were digested with proteinase K (12 µL of 20mg/mLstock) for 3h at 65 °C. Nucleic acids were PCR clean up kit purified and RNA digestion (10 µg RNase) was carried out for 1 h at 37°C. The DNA was finally resuspended in 50 µL nucl
Sequencing libraries were prepared according to the Illuminas TruSeq ChIP Sample Preparation protocol. Briefly, the enriched ChIP DNA was end-repaired and indexed adapters were ligated to the inserts. Purified ligation products were then amplified by PCR. Amplified libraries were prepared in the Genomic Medicine and Bioinformatics Core Facility of the University of Debrecen, Hungary. The libraries were sequenced using 50 single end reads with Illumina HiScan SQ (Genomic Medicine and Bioinformatics Core Facility of the University of Debrecen); or with Illumina HiSeq 2500 (EMBL Genomics Core Facility, Heidelberg, Germany

tag: background

value: Mata/alpha, spp1PHD{delta}-13xmyc-KanMX4/spp1PHD{delta}-13xmyc-KanMX4, leu2/LEU2, HIS4/his4, trp1/trp1, ura3/ura3

tag: timepoint

value: 4 hr

tag: chip antibody

value: Anti-myc (Abcam, ab56)


title: S. cerevisiae Spp1_CXXC_SPM_t240 ChIP-seq experiment

description:
Spp1-myc CXXCΔ strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4 hrs) for ChIP analysis.
Spp1_CXXC_SPM_t240

tag: genotype

value: Mata/alpha, spp1CXXC{delta}-13xmyc-NatMX4/spp1CXXC{delta}-13xmyc-NatMX4, leu2/LEU2, HIS4/his4, trp1/trp1, ura3/ura3


title: S. cerevisiae Spp1_CXXC_SPM_t0 ChIP-seq experiment

description:
Spp1-myc CXXCΔ strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_CXXC_SPM_t0

value: 0 hr


title: S. cerevisiae Spp1_CXXC_SPS ChIP-seq experiment

description:
Spp1-myc CXXCΔ strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_CXXC_SPS


title: S. cerevisiae Spp1_PHD_SPS ChIP-seq experiment

description:
Spp1-myc PHDΔ strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_PHD_SPS


title: S. cerevisiae Spp1_PHD_SPM_t0 ChIP-seq experiment

description:
Spp1-myc PHDΔ strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_PHD_SPM_t0


title: S. cerevisiae Bre2_SPM_t360 ChIP-seq experiment

description:
Bre2-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
Bre2_SPM_t360

value: Mata/alpha, BRE2-13xmyc-NatMX4/BRE2-13xmyc-NatMX4, leu2/LEU2, HIS4/his4, trp1/trp1, ura3/ura3

value: 6 hr


title: S. cerevisiae Bre2_SPM_t240 ChIP-seq experiment

description:
Bre2-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4 hrs) for ChIP analysis.
Bre2_SPM_t240


title: S. cerevisiae Spp1_wildtype_SPM_t360 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
Spp1_wildtype_SPM_t360

value: Mata/alpha, SPP1-13xmyc-KanMX4/SPP1-13xmyc-KanMX4, leu2/LEU2, HIS4/his4, trp1/trp1, ura3/ura3


title: S. cerevisiae Spp1_wildtype_SPM_t120 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 2 hrs) for ChIP analysis.
Spp1_wildtype_SPM_t120

value: 2 hr


title: S. cerevisiae Spp1_wildtype_SPM_t240 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4 hrs) for ChIP analysis.
Spp1_wildtype_SPM_t240


title: S. cerevisiae Spp1_wildtype_SPM_t0 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_wildtype_SPM_t0


title: S. cerevisiae Bre2_SPM_t0 ChIP-seq experiment

description:
Bre2-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Bre2_SPM_t0


title: LNCaP control 1

city: Vienna

first: Olaf

last: Merkel

address: Waehringer Guertel 18-20

department: Clinical Institute of Pathology

country: Austria

institute: Medical University of Vienna

description: Lymph node derived PCa cells with an empty vector biological replicate 1     Empty control for pReceiver-M72 Vector;  GeneCopoeia; Cat #EX-NEG-M72 (Empty control)

data_processing:
Data acquisition performed with HiSeq Control Software (HCS)  2.2.38
Basecalling performed with Illumina Real-Time Analysis (RTA) software 1.18.61.0
BCL to BAM file conversion and demultiplexing was performed with Illumina2bam tools 1.17
RNA-seq alignment performed with Tophat 2.1.1 and Bowtie 2.2.9
Transcriptome assembly with Cufflinks 2.2.1
Transcriptome assembly merge and differential expression calling with Cuffmerge, Cuffcompare and Cuffdiff of the Cufflinks 2.2.1 package
Post-processing of Cuffdiff results with the Bioconductor cummeRbund 2.12.1 package and custom R scripts
Genome_build: UCSC hg19 based on GRCh37
Supplementary_files_format_and_content: tab separated value of FPKM per gene

source_name: Prostate cancer

growth_protocol: Metastatic Prostate cancer cell line LNCaP was maintained in medium RPMI containing 10 % FCS and 1 % penicillin/streptomycin in a humidified chamber at 37 °C.

extract_protocol:
Total RNA was isolated with TRizol reagent followed by determination of purity and concentration.
Library prepration was performed according to the Illumina TruSeq stranded mRNA LT protocol.
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 50 bp single-read chemistry.

treatment_protocol: Transfections were performed using the Lipofectamine 2000 reagent (Invitrogen) in RPMI medium containing 10 % FCS for 48 hours according to manufacturer protocol. The amounts of lipofectamine 2000 used were 12 µL for 2500 ng plasmid in 70-80% confluent cells plated onto 6-well plates.

tag: cell type

value: Prostate; derived from metastatic site:left supraclavicular lymph node

tag: passage no

value: LNCaP

tag: transfection

value: empty vector


title: LNCaP CRYM 2

description: Lymph node derived PCa cells with a CRYM vector biological replicate 2 CRYM orf expression Clone; GeneCopoeia; Cat #EX-I0311-M72 (CRYM expression vector)

value: CRYM


title: LNCaP CRYM 1

description: Lymph node derived PCa cells with a CRYM vector biological replicate 1     CRYM orf expression Clone; GeneCopoeia; Cat #EX-I0311-M72 (CRYM expression vector)


title: S. cerevisiae cSpp1_NoTag ChIP & competition ChIP  Experiment

description:
Spp1-GFP strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) and used as control for ChIP analysis.
cSpp1_NoTag

value: Mata/alpha, leu2/leu2, his4/his4, trp1/trp1, ura3/ura3, pRS426 (URA3, GFP-NLS)

value: Anti-GFP (Abcam, ab290)


title: S. cerevisiae Spp1_PHD_SPM_t120 ChIP-seq experiment

description:
Spp1-myc PHDΔ strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 2 hrs) for ChIP analysis.
Spp1_PHD_SPM_t120


title: LNCaP control 2

description: Lymph node derived PCa cells with an empty vector biological replicate 2 Empty control for pReceiver-M72 Vector;  GeneCopoeia; Cat #EX-NEG-M72 (Empty control)


title: S. cerevisiae Spp1_CXXC_SPM_t120 ChIP-seq experiment

description:
Spp1-myc CXXCΔ strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 2 hrs) for ChIP analysis.
Spp1_CXXC_SPM_t120


title: S. cerevisiae Bre2_SPM_t120 ChIP-seq experiment

description:
Bre2-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 2 hrs) for ChIP analysis.
Bre2_SPM_t120


title: S. cerevisiae cSpp1_MYC_t390_rep2 competition ChIP experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6.5 hrs) for ChIP analysis.
cSpp1_MYC_t390_rep2


title: S. cerevisiae cSpp1_Input ChIP & competition ChIP  Experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) and used as input for ChIP analysis.
cSpp1_Input


title: S. cerevisiae cSpp1_MYC_t360_rep2 competition ChIP experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
cSpp1_MYC_t360_rep2


title: S. cerevisiae Spp1_PHD_SPM_t360 ChIP-seq experiment

description:
Spp1-myc PHDΔ strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
Spp1_PHD_SPM_t360


title: S. cerevisiae Spp1_CXXC_SPM_t360 ChIP-seq experiment

description:
Spp1-myc CXXCΔ strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
Spp1_CXXC_SPM_t360


title: S. cerevisiae Spp1_wildtype_SPS ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_wildtype_SPS


title: S. cerevisiae cSpp1_MYC_t330_rep2 competition ChIP experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 5.5 hrs) for ChIP analysis.
cSpp1_MYC_t330_rep2


title: S. cerevisiae cSpp1_MYC_t270_rep2 competition ChIP experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4.5 hrs) for ChIP analysis.
cSpp1_MYC_t270_rep2


title: S. cerevisiae cSpp1_MYC_t390_rep1 competition ChIP experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6.5 hrs) for ChIP analysis.
cSpp1_MYC_t390_rep1


title: S. cerevisiae cSpp1_MYC_t330_rep1 competition ChIP experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 5.5 hrs) for ChIP analysis.
cSpp1_MYC_t330_rep1


title: S. cerevisiae cSpp1_MYC_t300_rep2 competition ChIP experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 5 hrs) for ChIP analysis.
cSpp1_MYC_t300_rep2

value: 5 hr


title: S. cerevisiae Bre2_SPS ChIP-seq experiment

description:
Bre2-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Bre2_SPS


title: S. cerevisiae cSpp1_MYC_t360_rep1 competition ChIP experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
cSpp1_MYC_t360_rep1


title: S. cerevisiae cSpp1_GFP_t300_rep1 competition ChIP experiment

description:
Spp1-GFP strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 5 hrs) for ChIP analysis.
cSpp1_GFP_t300_rep1

value: Mata/alpha, SPP1-13xmyc-KanMX4/NatMX4-pCUP1-1-yGFP-SPP1, leu2/LEU2, HIS4/his4, trp1/trp1, ura3/ura3


title: S. cerevisiae cSpp1_GFP_t360_rep1 competition ChIP experiment

description:
Spp1-GFP strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
cSpp1_GFP_t360_rep1


title: S. cerevisiae cSpp1_GFP_t330_rep1 competition ChIP experiment

description:
Spp1-GFP strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 5.5 hrs) for ChIP analysis.
cSpp1_GFP_t330_rep1


title: S. cerevisiae cSpp1_GFP_t270_rep2 competition ChIP experiment

description:
Spp1-GFP strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4.5 hrs) for ChIP analysis.
cSpp1_GFP_t270_rep2


title: S. cerevisiae cSpp1_GFP_t390_rep1 competition ChIP experiment

description:
Spp1-GFP strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6.5 hrs) for ChIP analysis.
cSpp1_GFP_t390_rep1


title: S. cerevisiae cSpp1_MYC_t300_rep1 competition ChIP experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 5 hrs) for ChIP analysis.
cSpp1_MYC_t300_rep1


title: S. cerevisiae cSpp1_GFP_t330_rep2 competition ChIP experiment

description:
Spp1-GFP strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 5.5 hrs) for ChIP analysis.
cSpp1_GFP_t330_rep2


title: S. cerevisiae cSpp1_GFP_t300_rep2 competition ChIP experiment

description:
Spp1-GFP strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 5 hrs) for ChIP analysis.
cSpp1_GFP_t300_rep2


title: S. cerevisiae Spp1_H3R2A_SPM_t360_rep2 ChIP-seq experiment

description:
Spp1-myc H3R2A strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
Spp1_H3R2A_SPM_t360_rep2

value: Mata/alpha, lys2/lys2, ho::LYS2/ho::LYS2, trp1-1/trp1-1, ura3/ura3, leu2/LEU2, HIS4/his4, hht1{delta}::HphMX/hht1{delta}::HphMX, hht2{delta}::KanMX4/hht1{delta}::HphMX, SPP1-3xHA::KanMX4/SPP1-3xHA::KanMX4, pCEN-ARS(HHT2R2A,HHF2,TRP1)

value: Anti-HA (Sigma)


title: S. cerevisiae cSpp1_GFP_t270_rep1 competition ChIP experiment

description:
Spp1-GFP strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4.5 hrs) for ChIP analysis.
cSpp1_GFP_t270_rep1


title: S. cerevisiae Spp1_H3R2A_SPM_t0_rep1 ChIP-seq experiment

description:
Spp1-myc H3R2A strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_H3R2A_SPM_t0_rep1


title: S. cerevisiae Spp1_H3R2A_SPM_t0_rep2 ChIP-seq experiment

description:
Spp1-myc H3R2A strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_H3R2A_SPM_t0_rep2


title: S. cerevisiae Spp1_H3R2A_SPM_t120_rep2 ChIP-seq experiment

description:
Spp1-myc H3R2A strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 2 hrs) for ChIP analysis.
Spp1_H3R2A_SPM_t120_rep2


title: S. cerevisiae cSpp1_MYC_t270_rep1 competition ChIP experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4.5 hrs) for ChIP analysis.
cSpp1_MYC_t270_rep1

value: Anti-myc (Abcam, ab56)


title: S. cerevisiae Spp1_H3R2A_SPM_t240_rep1 ChIP-seq experiment

description:
Spp1-myc H3R2A strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4 hrs) for ChIP analysis.
Spp1_H3R2A_SPM_t240_rep1

value: 4 hr


title: FigS6_Scc1PK_wapldel_K404E_WCE

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description: GAL-SIC1 arrest of scc3K404E wapl deletion cells (K26281)

data_processing:
Library sequencing was carried out on the Ion Torrent Proton
The quality of the raw sequence data was examined using FastQC (Galaxy tool version 1.0.0) and trimming of reads was carried out using “trim sequences” (Galaxy tool version 1.0.0)
Any reads smaller than 50bp were removed using ‘Filter FASTQ’
The final reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, SGD) or Candida glabrata genome (CBS138, genolevures) using Bowtie2 (Galaxy tool version 0.2) with the default (--sensitive) parameters
To generate an alignment in which all the sequences exclusively align to the Saccharomyces cerevisiae genome, the whole reads were first aligned to Candida glabrata genome and the unaligned reads were retrieved as a separate Fastq file. Subsequently, these unaligned reads were re-aligned to Saccharomyces cerevisiae genome and the resulting aligned BAM file therefore contained reads that were unique to Saccharomyces cerevisiae. A same strategy was used to generate alignments unique to Candida glabrata.
Genome_build: SacCer3 or Candida glabrata (ASM254v2)
Supplementary_files_format_and_content: fastq files contain reads from both organisms (S. cerevisiae and C. glabrata) but the BigWig files are S. cerevisiae only

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

growth_protocol: Yeast cells were grown in YPD to reach a density of 0.3-0.6 OD600.

extract_protocol:
To crosslink cells, 45ml of yeast culture was mixed with 4.2ml of fixation solution (50mM Tris-HCl pH 8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 30% Formaldehyde) and incubated at 18°C for 30 minutes. The crosslinking reaction was quenched by incubating with 2ml of 2.5M Glycine for 5 min. Fixed cells were harvested, washed with ice-cold PBS and re-suspended in 1ml of ChIP lysis buffer (50mM Hepes-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, Roche protease inhibitor). For each ChIP, 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells were pelleted and re-suspended in 0.3ml of ChIP lysis buffer. Cells were mixed with glass beads and disrupted by FastPrep®-24 (MP Biomedicals, USA). The entire lysis was collected and sonicated at 4°C for 40 minutes using a Bioruptor (Diagenode, Belgium). The cell debris were removed by centrifugation and supernatants containing sheared chromatin with a size range from 100-800bp were adjusted to a final volume of 1ml with ChIP lysis buffer. Extracts were pre-cleared for 1 hour at 4°C with 30µl of Protein G Dynabeads (Invitrogen). 80µl of supernatant was taken as whole cell extract (W) and stored at -80°C. Five µg of anti-PK antibody (Bio-Rad) and 50 µl of Protein G Dynal beads (Invitrogen) was used for immunoprecipitation (6 hours-overnight, rotation at 4°C). The beads were subsequently washed for 5 minutes with the following buffers: 2Ã—ChIP lysis buffer; 3x ChIP high-salt lysis buffer (50mM Hepes-KOH pH 8.0, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF); 2Ã—ChIP wash buffer (10mM Tris-HCl pH 8.0, 0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA, 1mM PMSF) and 1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). The immunoprecipitated chromatin was eluted by incubation of beads with 120µl of TES buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 1% SDS) at 65°C for 15 minutes. The supernatants were collected and termed the IP sample. The whole cell extract sample (W) was mixed with 40µl of TES3 buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 3% SDS). Both samples were de-crosslinked at 65°C overnight. RNA was degraded by incubating with 2-µl of RNAse A (10mg/ml, Roche) at 37°C for 1 hour and protein was subsequently removed by incubation with 10µl of Proteinase K (18mg/ml, Roche) at 65°C for 2 hours. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
NEBNext Fast DNA Library Prep set for Ion Torrent, E6270

tag: sac_cer strain

tag: can_gla strain

tag: antibody

value: none (input)


title: FigS6_Scc1PK_K404E_WCE

description: GAL-SIC1 arrest of scc3K404E cells (K26286)

source_name: 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells


title: FigS6_Scc1PK_K404E_IP

value: 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells

value: anti-PK antibody (Bio-Rad)


title: S. cerevisiae Spp1_H3R2A_SPM_t240_rep2 ChIP-seq experiment

description:
Spp1-myc H3R2A strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4 hrs) for ChIP analysis.
Spp1_H3R2A_SPM_t240_rep2


title: FigS5H_Scc1PK_scc4m35_NOC_WCE

description: exponentially growing scc4m35 strain with nocodazole (K24745)


title: S. cerevisiae Spp1_H3R2A_SPM_t120_rep1 ChIP-seq experiment

description:
Spp1-myc H3R2A strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 2 hrs) for ChIP analysis.
Spp1_H3R2A_SPM_t120_rep1


title: S. cerevisiae Spp1_H3K4R_SPM_t360_rep2 ChIP-seq experiment

description:
Spp1-myc H3K4R strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
Spp1_H3K4R_SPM_t360_rep2

value: Mata/alpha, lys2/lys2, ho::LYS2/ho::LYS2, trp1-1/trp1-1, ura3/ura3, leu2/LEU2, HIS4/his4, hht1{delta}::HphMX/hht1{delta}::HphMX, hht2{delta}::KanMX4/hht1{delta}::HphMX, SPP1-3xHA::KanMX4/SPP1-3xHA::KanMX4, pCEN-ARS(HHT2K4R,HHF2,TRP1)

value: 6 hr


title: S. cerevisiae Spp1_H3R2A_SPM_t360_rep1 ChIP-seq experiment

description:
Spp1-myc H3R2A strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
Spp1_H3R2A_SPM_t360_rep1


title: S. cerevisiae Spp1_H3K4R_SPM_t120_rep2 ChIP-seq experiment

description:
Spp1-myc H3K4R strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 2 hrs) for ChIP analysis.
Spp1_H3K4R_SPM_t120_rep2

value: 2 hr


title: S. cerevisiae Spp1_H3K4R_SPM_t0_rep2 ChIP-seq experiment

description:
Spp1-myc H3K4R strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_H3K4R_SPM_t0_rep2

value: 0 hr


title: FigS5H_Scc1PK_scc4m35_WCE

description: exponentially growing scc4m35 strain (K24745)


title: FigS5H_Scc1PK_scc4m35_NOC_IP


title: S. cerevisiae Spp1_H3K4R_SPM_t240_rep2 ChIP-seq experiment

description:
Spp1-myc H3K4R strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4 hrs) for ChIP analysis.
Spp1_H3K4R_SPM_t240_rep2


title: S. cerevisiae Spp1_H3K4R_SPM_t360_rep1 ChIP-seq experiment

description:
Spp1-myc H3K4R strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
Spp1_H3K4R_SPM_t360_rep1


title: FigS5H_Scc1PK_scc4m35_IP


title: S. cerevisiae Spp1_H3K4R_SPM_t0_rep1 ChIP-seq experiment

description:
Spp1-myc H3K4R strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_H3K4R_SPM_t0_rep1


title: S. cerevisiae Spp1_H3K4R_SPM_t120_rep1 ChIP-seq experiment

description:
Spp1-myc H3K4R strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 2 hrs) for ChIP analysis.
Spp1_H3K4R_SPM_t120_rep1


title: FigS5G_Scc1PK_WT_WCE

description: WT strain 60 min after release from G1 (K22005)


title: S. cerevisiae Spp1_H3_wildtype_SPM_t360_rep2 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
Spp1_H3_wildtype_SPM_t360_rep2

value: Mata/alpha, lys2/lys2, ho::LYS2/ho::LYS2,trp1-1/trp1-1, ura3/ura3,leu2/LEU2,HIS4/his4, hht1{delta}::HphMX/hht1{delta}::HphMX, hht2{delta}::KanMX4/hht1{delta}::HphMX, SPP1-3xHA::KanMX4/SPP1-3xHA::KanMX4, pCEN-ARS(HHT2,HHF2,TRP1)


title: S. cerevisiae Spp1_H3_wildtype_SPM_t240_rep2 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4 hrs) for ChIP analysis.
Spp1_H3_wildtype_SPM_t240_rep2


title: S. cerevisiae Spp1_H3K4R_SPM_t240_rep1 ChIP-seq experiment

description:
Spp1-myc H3K4R strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4 hrs) for ChIP analysis.
Spp1_H3K4R_SPM_t240_rep1


title: S. cerevisiae Spp1_H3_wildtype_SPM_t240_rep1 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 4 hrs) for ChIP analysis.
Spp1_H3_wildtype_SPM_t240_rep1


title: S. cerevisiae Spp1_H3_wildtype_SPM_t120_rep2 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 2 hrs) for ChIP analysis.
Spp1_H3_wildtype_SPM_t120_rep2


title: S. cerevisiae Spp1_H3_wildtype_SPM_t0_rep2 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_H3_wildtype_SPM_t0_rep2


title: S. cerevisiae Spp1_H3_wildtype_SPM_t120_rep1 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 2 hrs) for ChIP analysis.
Spp1_H3_wildtype_SPM_t120_rep1


title: FigS6_Scc1PK_wapldel_K404E_IP

description: GAL-SIC1 arrest of scc3K404E wapl deletion cells (K26281)


title: FigS5E_Scc1PK_EKLF_scc4del_NOC_WCE

description: exponentially growing scc2E822K L937F, scc4 deletion strain with nocodazole (K24745)


title: FigS5G_Scc1PK_scc4m35_WCE

description: scc4m35 strain 60 min after release from G1 (K25049)


title: FigS5G_Scc1PK_scc4m35_IP


title: FigS5E_Scc1PK_EKLF_scc4del_NOC_IP


title: S. cerevisiae Spp1_H3_wildtype_SPM_t0_rep1 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 0 hrs) for ChIP analysis.
Spp1_H3_wildtype_SPM_t0_rep1


title: S. cerevisiae Spp1_H3_wildtype_SPM_t360_rep1 ChIP-seq experiment

description:
Spp1-myc strains were sporulated and 50 ml sample were taken from the meiotic time course (at t 6 hrs) for ChIP analysis.
Spp1_H3_wildtype_SPM_t360_rep1


title: FigS5E_Scc1PK_EKLF_scc4del_chl4del_NOC_WCE

description: exponentially growing scc2E822K L937F, scc4 and chl4 deletion strain with nocodazole(K24745)


title: FigS5E_Scc1PK_EKLF_scc4del_chl4del_WCE

description: exponentially growing scc2E822K L937F, scc4 and chl4 deletion strain (K24745)


title: FigS5E_Scc1PK_EKLF_scc4del_chl4del_IP


title: Fig6BS5D_Scc1PK_WT_WCE

description: WT strain 75 min after release from G1 in nocodazole (K22005)


title: FigS5E_Scc1PK_EKLF_scc4del_WCE

description: exponentially growing scc2E822K L937F, scc4 deletion strain (K24745)


title: FigS5D_Scc1PK_EKLF_scc4del_WCE

description: scc2E822K L937F scc1 deletion strain 75 min after release from G1 in nocodazole (K24745)


title: Fig6BS5D_Scc1PK_WT_IP


title: FigS5E_Scc1PK_EKLF_scc4del_IP


title: Fig6BS5D_Scc1PK_EKLF_WCE

description: scc2E822K L937F strain 75 min after release from G1 in nocodazole (K24687)


title: FigS3GH_Scc1_G2_WCE

description: G2/M arrest of Scc1-PK cells with nocodazole (K25625)


title: Fig6BS5D_Scc1PK_EKLF_IP


title: FigS3EF_Scc1_G1_WCE

description: GAL-SIC1 arrest of Scc1-PK cells (K25625)


title: FigS3GH_Pds5_G2_WCE

description: G2/M arrest of Pds5-PK cells with nocodazole (K25448)


title: FigS3EF_Scc1_G1_IP


title: FigS5G_Scc1PK_WT_IP

description: WT strain 60 min after release from G1 (K22005)


title: FigS3GH_Scc1_G2_IP


title: FigS5E_Scc1PK_EKLF_scc4del_chl4del_NOC_IP


title: FigS3EF_Pds5_G1_WCE

description: GAL-SIC1 arrest of Pds5-PK cells (K25448)


title: FigS5D_Scc1PK_EKLF_scc4del_IP


title: FigS3GH_Pds5_G2_IP


title: FigS3B_Scc1PK_Smc1EQ_WCE

description: exponentially growing smc1E1158Q strain (K25640)


title: FigS3C_Scc3PK_Smc1WT_IP

description: exponentially growing WT strain (K17438)


title: FigS3C_Scc3PK_Smc1EQ_WCE

description: exponentially growing smc1E1158Q strain (K25637)


title: FigS3D_Pds5PK_Smc1EQ_WCE

description: exponentially growing smc1E1158Q strain (K25652)


title: FigS3A_Scc2PK_Smc1EQ_WCE

description: exponentially growing smc1E1158Q strain (K25644)


title: FigS3C_Scc3PK_Smc1WT_WCE


title: FigS2JS6_Scc1PK_wapldel_WCE

description: GAL-SIC1 arrest of wapl deletion cells (K20891)


title: FigS3C_Scc3PK_Smc1EQ_IP


title: FigS3A_Scc2PK_Smc1EQ_IP


title: FigS2JS6_Scc1PK_WT_IP

description: GAL-SIC1 arrest of WT cells (K22388)


title: FigS2JS6_Scc1PK_WT_WCE

description: GAL-SIC1 arrest of WT cells (K22388)


title: FigS7F_Scc1HA_WT_WCE

description: G2 arrest after addition of 5mM auxin 30 min prior to release from pheromone without depletion of Pds5 (K26277)


title: FigS2JS6_Scc1PK_wapldel_IP


title: FigS7F_Scc1HA_WT_IP

value: anti-HA antibody (Roche)


title: FigS7F_Scc1HA_Pds5AID_WCE

description: G2 arrest after addition of 5mM auxin 30 min prior to release from pheromone to deplete Pds5 (K26270)


title: FigS7F_Scc1HA_Pds5AID_IP


title: FigS7E_Untagged_WCE

description: MET-Scc1Untagged strain 60 min after release from G1 in the presence of methionine (K25222)


title: FigS3EF_Pds5_G1_IP


title: FigS7E_Untagged_IP


title: FigS7E_METScc1V137K_WCE

description: MET-Scc1V137K strain 60 min after release from G1 in the presence of methionine (K26251)


title: FigS7A_Scc1HA_WT_WCE

description: exponentially growing strain expressing WT Scc1 (K17184)


title: FigS7A_Untagged_WCE

description: exponentially growing strain expressing untagged WT Scc1 (K699)


title: FigS7E_METScc1WT_IP

description: MET-Scc1WT strain 60 min after release from G1 in the presence of methionine (K26248)


title: FigS3B_Scc1PK_Smc1EQ_IP


title: FigS7E_METScc1V137K_IP


title: FigS7A_Scc1HA_207256_IP

description: exponentially growing strain expressing Scc1 with residues 207-256 deleted (K25997)


title: FigS7A_Scc1HA_152206_WCE

description: exponentially growing strain expressing Scc1 with residues 152-206 deleted (K25995)


title: FigS3D_Pds5PK_Smc1EQ_IP


title: FigS7A_Scc1HA_WT_IP


title: FigS7A_Scc1HA_152206_244251_WCE

description: exponentially growing strain expressing Scc1 with residues 152-206 and 244-251 deleted (K26362)


title: FigS7A_Scc1HA_152206_IP


title: FigS7A_Scc1HA_152256_IP

description: exponentially growing strain expressing Scc1 with residues 152-256 deleted (K25896)


title: Fig6D_Scc2HA_WT_WCE

description: GAL-SIC1 arrest after addition of 5mM auxin 30 min prior to release from pheromone with WT Pds5 (K26274)


title: Fig6D_Scc2HA_WT_IP


title: FigS7A_Scc1HA_152206_244251_IP


title: Fig6D_Scc2HA_Pds5AID_WCE

description: GAL-SIC1 arrest after addition of 5mM auxin 30 min prior to release from pheromone to deplete Pds5 (K26273)


title: FigS7A_Untagged_IP


title: Fig6C_Scc1PK_WT_WCE

description: WT strain in GAL-SIC1 arrest (K26292)


title: Fig6D_Scc2HA_Pds5AID_IP


title: Fig6D_Scc1HA_WT_IP

description: GAL-SIC1 arrest after addition of 5mM auxin 30 min prior to release from pheromone with WT Pds5 (K26277)


title: Fig6D_Scc1HA_Pds5AID_IP

description: GAL-SIC1 arrest after addition of 5mM auxin 30 min prior to release from pheromone to deplete Pds5 (K26270)


title: Fig6D_Scc1HA_WT_WCE


title: Fig6C_Scc1PK_EKLF_WCE

description: scc2E822K L937F strain in GAL-SIC1 arrest (K26244)


title: Fig6B_Scc1PK_EKLF_IP


title: FigS7A_Scc1HA_207256_WCE


title: FigS7E_METScc1WT_WCE


title: FigS7A_Scc1HA_152256_WCE


title: Fig6AB_Scc2HA_WT_WCE

description: exponentially growing WT strain (K25054)


title: Fig6C_Pds5PK_WT_IP

description: WT strain in GAL-SIC1 arrest (K25999)


title: Fig6C_Pds5PK_EKLF_WCE

description: scc2E822K L937F strain in GAL-SIC1 arrest (K25988)


title: Fig6A_Scc2HA_Untagged_WCE

description: exponentially growing untagged strain (K699)


title: Fig6C_Pds5PK_EKLF_IP


title: Fig6AB_Scc2HA_EKLF_WCE

description: exponentially growing scc2E822K L937F strain (K25053)


title: Fig6A_Scc2HA_EKLF_scc4del_WCE

description: exponentially growing scc2E822K L937F scc4del strain (K25418)


title: Fig6D_Scc1HA_Pds5AID_WCE


title: Fig6A_Scc2HA_EKLF_scc4del_IP


title: Fig6AB_Scc2HA_EKLF_IP


title: Fig6AB_Scc2HA_WT_IP


title: Fig6C_Scc1PK_WT_IP

description: WT strain in GAL-SIC1 arrest (K26292)


title: Fig5AB_Scc1PK_EKLF_scc4ts_IP

description: scc2E822K L937F scc4ts strain 75 min after release from G1 at 37°C (K24744)


title: Fig5AB_Scc1PK_scc4ts_WCE

description: scc4ts strain 75 min after release from G1 at 37°C (K22001)


title: Fig5AB_Scc1PK_EKLF_scc4ts_WCE


title: Fig5AB_Scc1PK_scc4ts_IP


title: Fig4D_Scc2PK_WT_WCE

description: exponentially growing strain with a WT ectopic copy of Scc2 (K25185)


title: Fig4D_Scc2PK_WT_IP


title: Fig5AB_Scc1PK_WT_WCE

description: WT strain 75 min after release from G1 at 37°C (K22005)


title: Fig4D_Scc2PK_KHEE_WCE

description: exponentially growing strain with an ectopic copy of scc2K788E H789E (K25186)


title: Fig5AB_Scc1PK_EKLF_IP

description: scc2E822K L937F strain 75 min after release from G1 at 37°C (K24687)


title: Fig4D_Scc2PK_KHEE_IP


title: Fig4BC_Scc1PK_Scc2WT_IP

description: strain containing ts scc2 with a WT ectopic copy 75 min after release from G1 at 37°C (K24185)


title: Fig4BC_Scc1PK_Scc2WT_WCE


title: Fig4BC_Scc1PK_Scc2KHEE_WCE

description: strain containing ts scc2 with an ectopic copy containing mutations K788E H789E 75 min after release from G1at 37°C at 37°C (K24188)


title: Fig6C_Pds5PK_WT_WCE

description: WT strain in GAL-SIC1 arrest (K25999)


title: Fig4BC_Scc1PK_NoScc2_WCE

description: strain containing ts scc2 with no ectopic copy 75 min after release from G1 at 37°C (K22390)


title: Fig4BC_Scc1PK_Scc2KHEE_IP

description: strain containing ts scc2 with an ectopic copy containing mutations K788E H789E 75 min after release from G1 at 37°C (K24188)


title: Fig6A_Scc2HA_Untagged_IP


title: Fig3DS3D_Pds5PK_Smc3WT_IP

description: exponentially growing wild type strain (K19012)


title: Fig3DS3D_Pds5PK_Smc3WT_WCE


title: Fig4BC_Scc1PK_NoScc2_IP


title: Fig5AB_Scc1PK_EKLF_WCE


title: Fig3C_Scc3PK_Smc3EQ_WCE

description: exponentially growing smc3E1155Q strain (K25373)


title: Fig3C_Scc3PK_Smc3EQ_IP


title: Fig3C_Scc3PK_Smc3WT_WCE

description: exponentially growing wild type strain (K17438)


title: Fig3BS3B_Scc1PK_Smc3WT_IP

description: exponentially growing wild type strain (K22005)


title: Fig3C_Scc3PK_Smc3WT_IP


title: Fig3B_Scc1PK_Smc3EQ_IP

description: exponentially growing smc3E1155Q strain (K25370)


title: Fig3B_Scc1PK_Smc3EQ_WCE


title: Fig3A_Scc2PK_Smc3EQ_WCE

description: exponentially growing smc3E1155Q strain (K25467)


title: Fig3BS3B_Scc1PK_Smc3WT_WCE


title: Fig3AS3A_Scc2PK_Smc3WT_WCE

description: exponentially growing wild type strain (K21388)


title: Fig3A_Scc2PK_Smc3EQ_IP


title: Fig3AS3A_Scc2PK_Smc3WT_IP


title: Fig2B_Scc2PK_METScc1_Cycling_WCE

description: exponentially growing MET-Scc1 strain in the absence of methionine (K25222)


title: Fig2B_Scc2PK_METScc1_60min_WCE

description: MET-Scc1 strain 60 min after release from G1 in the presence of methionine (K25222)


title: Fig2B_Scc2PK_METScc1_60min_IP


title: Fig2B_Scc2PK_METScc1_Cycling_IP


title: Fig3D_Pds5PK_Smc3EQ_WCE

description: exponentially growing smc3E1155Q strain (K25376)


title: Fig2B_Scc2PK_METScc1_45min_WCE

description: MET-Scc1 strain 45 min after release from G1 in the presence of methionine (K25222)


title: Fig3D_Pds5PK_Smc3EQ_IP