title: PTEN-proficient hSS1 primary tumor #2

description:
11361X2
11361R.txt


title: rs4409764_locus_DLD

status: Public on Nov 03 2016

type: SRA

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

country: Netherlands

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

description:
Fw_primer: ACACGACGCTCTTCCGATCTGTTTGTCGATGGTCTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAGAATTCGTAACCAGCAG

library_source: genomic

data_processing:
Library strategy: 4C-seq
he raw sequencing reads were de-multiplexed based on viewpoint specific primer sequences. Reads were then trimmed to 16 bases and mapped to an in silico generated library of fragends (fragment ends) neighboring all DpnII sites in human genome (NCBI37/hg19), using the custom Perl scripts. No mismatches were allowed during the mapping and the reads mapping to only one possible fragend were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: wig files contain information abut fragend sequencing coverage (0 - not covered, 1 covered)

molecule: genomic DNA

organism: Homo sapiens

source_name: DLD

growth_protocol: DLD-1 cells were cultured in RPMI-1640 with 10% FCS and standard supplements. Cells were harvested for 4C template preparation by trypsinisation at 60-80% confluence.

extract_protocol:
4C-chromatin preparation, primer design and library preparation were described previously (van de Werken, H. J. G. et al. 4C technology: protocols and data analysis. Methods in enzymology 513, (Elsevier Inc., 2012).)
10x106 cells were used per cell type. Cells were crosslinked in 2% formaldehyde. After chromatin isolation, the chromatin was digested with DpnII (NEB, # R0543L). Digestion was stopped through heat inactivation of the restriction enzyme. Samples were diluted and ligated by T4 DNA ligase. The second digestion was carried out with CviQI (NEB, #R069S) and inactivated by phenol:chloroform extraction. The chromatin was diluted, for the final T4 ligation and the chromatin was purified. The quality of digestion and ligation was assessed on agarose gels. the PCR of 4C template was performed with 600 ng - 1,6 µg of 4C template per reaction. 8 to 10 primer pairs were multiplexed in the initial PCR reaction. Primers pairs were pooled according to primer efficiency (based on intensity on gel electrophoresis signal after PCR on test template). PCR products were purified after an initial PCR reaction of 6 cycles (reaction volume = 200 µL) and divided among 8-10 PCR reactions containing single primer pairs for another 26 cycles (reaction volume = 25 µL). Thereafter, PCR products derived from the same cells were pooled in equimolar amounts and a final 6 cycle PCR reaction containing 20 ng of pooled PCR product (reaction volume = 100 µL) was performed with primers that contained sequencing adaptor sequences. All fragments >700bp were removed using size selection on a 1% agarose gel follow by gel extraction of the selected products (Qiagen, #28704).

tag: tissue

value: DLD-1 cell line


title: rs1042058_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGCCATGTGGTAAGTGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCCATGTCCATTATTAAGA


title: rs10486483_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGGTTAAGGTCACCCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTAAGTGACGGAACTCCAG


title: rs561722_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCTGCTAGAGGAGTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAGAGGCTTGGAGTAGCTTA


title: LM-MEL-101

city: Houston

first: Miles

last: Andrews

state: TX

address: 1881 East Road

department: Surgical Oncology

country: USA

institute: MD Anderson Cancer Center

library_source: transcriptomic

data_processing:
For each sample, raw read data (fastq format) was concatenated using the UNIX command line and subsequently collapsed to provide sums of reads for any sequence detected more than once, using the FASTX-Toolkit (v0.0.13) command-line tool "FASTX-collapser" using default settings and the -Q33 switch
Collapsed raw read data in fasta format was submitted to the miRanalyzer webserver pipeline, accessed at http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php and underwent genome alignment (hg18 build), microRNA quantification and classification as mature, star, hairpin, or precursor forms, with reference to miRBase v18.
Read count data for all mature microRNA sequences was extracted and compiled into a data matrix for all samples in R.
Genome_build: hg18
Supplementary_files_format_and_content: raw and RPKM count data for all mature microRNA sequences identified in at least one sample across all 57 melanoma cell lines

molecule: total RNA

source_name: melanoma

growth_protocol: Cell lines were derived from melanoma tumours of our clinical unit. Single cell suspensions were generated from biopsy samples collected fresh and subjected to manual dissociation followed by collagenase/DNAse digestion (4-12 hours). Cell suspensions were plated in RPMI1640 media supplemented with 1% penicillin/streptomycin, 1% GlutaMAX and 10% fetal bovine serum until establishment of viable cell lines.

extract_protocol:
total RNA was extracted from cell pellets lysates using the Qiagen miRNeasy Mini Kit (Cat No 217004) and RNA quality confirmed by bioanalyzer prior to library preparation
small RNA libraries were prepared according to standard Illumina protocols

tag: cell type

value: melanoma

tag: epithelial-like or mesenchymal-like

value: mesenchymal-like

tag: braf mutation

tag: tumour site

value: ascites


title: LM-MEL-100

value: epithelial-like

value: lymph node


title: rs4845604_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGTCTTCTCTGTTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTAACCCAGAGGAAAAAGG


title: LM-MEL-98

value: bone


title: rs3024505_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAGCTACCAATAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTACGCAATGAAGGTTTGT


title: LM-MEL-97

value: wt


title: rs1517352_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATAAGGACTATCTTAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGTAAACTGACCAGCTGCTA


title: rs1819333_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTTTGACTTCAGGGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGACACCTTGATTGTCAGCT


title: rs26528_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTCCCTAGGGGGAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTACCTCCAGAGCATGGTA


title: LM-MEL-77

value: brain


title: rs3197999_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTGGCTTAGATACGCTGATC
Rv primer: CAAGCAGAAGACGGCATACGATGAAACACACACCTTTGAGA


title: PTEN-deficient hSS1 primary tumor #1

city: Salt Lake City

first: Kevin

middle: B

last: Jones

state: Utah

address: 2000 Circle of Hope Drive, Room 4263

department: Department of Orthopaedics

institute: University of Utah

description:
11361X4
11361R.txt

data_processing:
Reference fasta files generated by combining mm10 chromosome sequences with splice junction sequences generated by Useq (v8.8.8) MakeTranscriptome using Ensembl transcript models (build 74)
aligned with Novoalign (v2.08.01) allowing up to 50 alignments per read.
Best alignments selected by Useq SamTranscrimptomeParser and converted coordinates of reads aligning to splices back to genomic space.
Differential gene expression was measured using USeq DefinedRegionDifferentialSeq, which counts the number of reads aligned to each gene and then call DESeq2 (v1.4.5) using default settings.
Genome_build: mm10 Ensembl build 74
Supplementary_files_format_and_content: tab-delimited files containing FPKM values, log2 Fold Changes and FDR for all tested genes

organism: Mus musculus

source_name: primary tumor from hind limb

growth_protocol: Spontaneous tumors, primary in the limb or metastatic to the lung parenchyma

extract_protocol:
Qiagen RN-easy
Illumina TruSeq
RiboZero method

tag: ss fusion type

tag: pten genotype

value: fl/fl


title: LM-MEL-75


title: rs10781499_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTATTTTCTCAGCCCCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTCACGGAGTCCTAAGATG


title: rs2930047_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTATAATTGACCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACTGTGCCTGGTTTTTAGA


title: rs2472649_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTACTCGTGGACTCAGACGATC
Rv primer: CAAGCAGAAGACGGCATACGAACAAGTGAAAAACGTCGAAT


title: rs17293632_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGATTCTCTTGTCTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCTTCTCTCATTCCCTATT


title: rs3897478_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACATCTTAATCAGGGCAGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTTCCAGATGAGGAGACTG


title: LM-MEL-73


title: rs1991866_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCATTCCTTTAAACTTGATC
Rv primer: CAAGCAGAAGACGGCATACGATGCATCAGTCACAAATAGGA


title: LM-MEL-70

value: soft tissue


title: LM-MEL-69


title: LM-MEL-64


title: rs630923_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGTTATGAGGTAGTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAATTAAACAGGTAGGGAGCCT


title: rs2155219_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTTACAAAAGTGAATGATC
Rv primer: CAAGCAGAAGACGGCATACGATAAACAAAGTGTCCAGGCTT


title: rs7282490_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACACTCCATATTCAAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGGAGATGCTCAGCTTTTA


title: LM-MEL-82


title: LM-MEL-59


title: LM-MEL-62


title: LM-MEL-60

value: primary


title: LM-MEL-50

value: bowel


title: rs12942547_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCCTAACATGCTTCGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGCCCTTCCATTTTACTTTC


title: rs10495903_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCAGAAGGCTGCAGTAGATC
Rv primer: CAAGCAGAAGACGGCATACGACAAGAGGGTAGAGAGGAGGT


title: LM-MEL-57

value: lung


title: rs917997_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCATTCCATGTCCATGATC
Rv primer: CAAGCAGAAGACGGCATACGATTCCCAGCTCACTCTAATGT


title: rs7404095_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCCTCAGTGGTCTCTGGATC
Rv primer: CAAGCAGAAGACGGCATACGACGGAGATGGAAGTAGACTCA


title: rs1734907_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGAATAAATACCTGTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTTAGGAGCATTTTCAAGC


title: rs4899554_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTTAGCAATTCTGCATGATC
Rv primer: CAAGCAGAAGACGGCATACGATTGAAATAAAGCCATCATCA


title: rs12722515_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGTTAGGTAGGCTCTGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGACAGGGGAACTTAACCAT


title: rs1456896_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTAAGGTTGAGTCTGGCGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTATGCCAGCTCTAGCAACT


title: LM-MEL-49


title: rs2790216_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCTGGAGATGTTCTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACCTTGAAAATAAACACTGCC


title: LM-MEL-71


title: LM-MEL-46

value: heart


title: rs10797432_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACTGCACGGTTCTTGCTGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGTGCTTAGGTTTTGGAAG


title: LM-MEL-47


title: LM-MEL-48


title: rs925255_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGGCCTGCAACCTGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTTTTCCTTCTTTTGCCTT


title: rs35675666_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTCTGGAAATGGCTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGATTGCTGTTACTGTCATTTGC


title: LM-MEL-44


title: LM-MEL-45


title: rs670523_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTTTGCTCAGGGCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGATGATGGAGTAAACCTGGA


title: rs7554511_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTCAAAGTAGGCCTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGAGGAAGAGGCAGACAAGTA


title: LM-MEL-53


title: LM-MEL-41


title: LM-MEL-42

value: spleen


title: rs4911259_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACTAAAAGGCACACACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTGACTCCATTCAGTGACCT


title: rs7240004_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTAGGTTGAGGGGCCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGATTTCTTTGTTCCAGGT


title: LM-MEL-40


title: LM-MEL-39


title: rs6586030_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTAAGATGTCTCTGACCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATGAAACCGTTTAGAGGGTAC


title: LM-MEL-35


title: rs2024092_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTGCTCCTCCAGCCAAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAAACGTAAGCATGGTCAG


title: LM-MEL-38


title: rs1292053_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTATCCTTTTTCTGTGGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGTTTTGGAAAGATTACCCT


title: LM-MEL-36


title: rs913678_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATATACAAACAAATGTGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCTCCTGCTTTAGAACTCAG


title: rs4256159_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTAAGAAATGGGAGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGGTAATTGTGGGGTGTAT


title: LM-MEL-34


title: rs921720_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATAACTGGCTTCCCACTGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGATTCAAAGCACCCTCAT


title: LM-MEL-33


title: LM-MEL-28


title: LM-MEL-31


title: LM-MEL-29


title: LM-MEL-27


title: LM-MEL-30


title: rs3774959_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAAGCCAGACACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTCATTTCCTGTTGCACTT


title: rs798502_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCCTGTGACATCCTTAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATGAATACTCGCCTCTGAAA


title: rs11612508_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCTTCCCTCCCCTTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACCAACCTTCTTCTTTTCC


title: LM-MEL-26


title: rs11879191_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAGGTAGAGGGCAGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAACAAGCAACAATCAGGT


title: LM-MEL-24


title: rs12946510_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTATTCTTGTCACTCTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTGGAAATTTTACCCAAT


title: rs9557195_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATACCCACAGATAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAACAATCGGTAGTTGGATG


title: rs4802307_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGGAAAAGATGGGGGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCCTCCTTTCTTGATTACCT


title: rs12994997_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCCACATTGTTGACAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAAACAGTGCATGAGCTGAG


title: LM-MEL-20


title: LM-MEL-25


title: rs6651252_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCACATCTAGGCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATATGCAGTTCCTTTTGCTTT


title: rs6017342_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGGGTTAGGAGTTCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAGTTGCTTTGCTCTGAAG


title: LM-MEL-19


title: LM-MEL-17


title: rs11742570_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCATACACACTCTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGATTTGGAGACTCATTTCTGCT


title: LM-MEL-16


title: rs2188962_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTTCCCCAGAGTCAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCTGTGGTTTATTTGCCTAG


title: LM-MEL-15


title: LM-MEL-14


title: rs1847472_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGGGTTGTGGTTAGAAAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAACTTTCATTCCATGCCTA


title: LM-MEL-12


title: rs4722672_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTATCACTTGAACCCTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAGAGTCCCAAGGATAAGG


title: LM-MEL-9


title: rs194749_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTATCCAGGTGTATTAGATC
Rv primer: CAAGCAGAAGACGGCATACGACAAGAGGCAGAGAAGACCTA


title: LM-MEL-8


title: rs7911264_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTCTCCCTGTCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTTCTACTTGGTCAGGGT


title: LM-MEL-7


title: LM-MEL-6


title: LM-MEL-5


title: rs17695092_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTCAGACTCCCTCACCTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTTTCTGGGGTGCCTGTAC


title: LM-MEL-4


title: LM-MEL-3


title: rs8005161_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGAGGGAGAAGGAAGAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATTAGAGCAATGTTTGTCACG


title: rs529866_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGAAAACTAACTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATCATGGCAGTAGCTGACTT


title: rs12654812_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTATTATGAAGCAGACATGATC
Rv primer: CAAGCAGAAGACGGCATACGATGCTGCTGAAGTTATTAGGAG


title: LM-MEL-2


title: LM-MEL-1


title: rs907611_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTATACCATGTTTCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTAAGTGTTGCTGGGTAC


title: rs6863411_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTGATGGTCTAGCAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACACCAGGTAAAGGCTATG


title: rs2284553_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGAGTTATTAGCACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAACCCAAATGCGTAAGAGATA


title: rs11168249_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTAGTCAGGGAACCTGGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAATGGACAATTGAATCCAAG


title: rs2231884_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGAATTTCCCGACTTTAGATC
Rv primer: CAAGCAGAAGACGGCATACGATCAGTTTCTGCCTCTTGATT


title: rs3091316_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAACTGCCTTGCTCAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGACAAAGAGAGGACCAGC


title: rs254560_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCCAGGGAGCTGTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTACATGCCACTACAACCA


title: ZFC3H1_total_3

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
The RNA-Seq data was quality controled and trimmed using FastQC and Trimomomatics respectively.
The data was mapped using HISAT against hg19.
Uniquely mapped and properly paired reads were used for downstream analysis.
The data was quantified using Rsubread on the human GENCODE annotation v19.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using Bedtools and bedGraphtoBigWig. The score represents strand specific per base genome coverage.

source_name: ZFC3H1 total RNA replicate 3

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol: RNA was extracted with Trizol and PureLink RNA Mini Kits (Thermo Scientific) and using on-column DNase I (PureLink DNase; Thermo Scientific) digestion according to the manufacturer’s manual. Libraries were prepared, from ribo-depleted samples, for sequencing using standard Illumina protocol.

treatment_protocol: siRNA transfections were performed targeting EGFP(control), RRP40, ZCCHC8, RBM7, PABPN1 and ZFC3H1.

value: HeLa Kyoto


title: ZFC3H1_total_1

source_name: ZFC3H1 total RNA replicate 1


title: rs10865331_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGATTCCCAGGCCCCTGATC
Rv primer: CAAGCAGAAGACGGCATACGACGTCTGTTTAGTGTGGGTCT

value: DLD-1 cell line


title: ZCCHC8_BrU_3

source_name: ZCCHC8 BrU RNA replicate 3


title: ZFC3H1_total_2

source_name: ZFC3H1 total RNA replicate 2


title: ZFC3H1_BrU_2

source_name: ZFC3H1 BrU RNA replicate 2


title: ZFC3H1_BrU_1

source_name: ZFC3H1 BrU RNA replicate 1


title: rs11150589_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCTAAAGGTAGAAACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTGGCAAGGATGATTACAAT


title: rs6088765_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATTCTGGGACAGGCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGGGAAGGTGTGTGTTTCT


title: rs6142618_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTTGGCTATCTGGGCTTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAAAGCCTGCTTCTCTGAC


title: rs1728785_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTAGCAGACTGAAAACCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAACCTCTGCTTCACCAAGTTA


title: rs2382817_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAGGACAGTGTATCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATACGCTGCTAACCAACTGT

source_name: peripheral blood monocyte

growth_protocol: Peripheral blood was collected from a healthy donors in sodium-heparin tubes. Peripheral Blood Mononuclear Cells (PBMCs) were isolated by Ficoll-Paque gradient centrifugation. PMBCs were incubated with magnetic CD14+-microbeads (Milteny, order nr. 130-050-201) according to manufacturer’s manual. Thereafter cells were magnetically separated by the AutoMACS™ Separator, negative fraction consisted of PBLs, positive fraction of monocytes.

value: peripheral blood monocyte


title: ZCCHC8_BrU_2

source_name: ZCCHC8 BrU RNA replicate 2


title: ZFC3H1_BrU_3

source_name: ZFC3H1 BrU RNA replicate 3


title: rs516246_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGTAGGAAAAGAGACAGATC
Rv primer: CAAGCAGAAGACGGCATACGATCATAGCATTAAGTCCCGTT


title: rs4899554_locus2_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAACTTTTTAGAGGGAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTCTTTATTCTCCAGCCCT


title: ZCCHC8_total_2

source_name: ZCCHC8 total RNA replicate 2


title: ZCCHC8_total_1

source_name: ZCCHC8 total RNA replicate 1


title: RRP40_BrU_3

source_name: RRP40 BrU RNA replicate 3


title: rs11230563_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTCAGGCATTCCATGGATC
Rv primer: CAAGCAGAAGACGGCATACGATCTTCCTGATATGGGCTAAA


title: rs4246215_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGAGTTTCAGTGTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGGATTGAGACTGTGGTTTA


title: RRP40_BrU_2

source_name: RRP40 BrU RNA replicate 2


title: ZCCHC8_total_3

source_name: ZCCHC8 total RNA replicate 3


title: rs2823286_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATACAAGGGCAATGAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACCAAGTCATAAGGCAGTTTT


title: RRP40_BrU_1

source_name: RRP40 BrU RNA replicate 1


title: RRP40_total_3

source_name: RRP40 total RNA replicate 3


title: rs2266959_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCCACCATGGGCTTAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCAGAGGTTGTGTGTAGGAC


title: rs1363907_locus_DLD

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGAAGCTCCAGATTGATC
Rv primer: CAAGCAGAAGACGGCATACGATTTTAGCTGCTTTGTATGCA

source_name: DLD


title: rs6545800_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAACATTCTCTCTTTTCGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCTCTTCTTTGTAGTGACG


title: ZCCHC8_BrU_1

source_name: ZCCHC8 BrU RNA replicate 1


title: rs6426833_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGGGGTCTCTGCTGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAATCTAAGGGAAGATGTGCA


title: rs12568930_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGCTTGCAACTCCCAAGATC
Rv primer: CAAGCAGAAGACGGCATACGACTACATTCAGTGTGCAATGG


title: RBM7_BrU_1

source_name: RBM7 BrU RNA replicate 1


title: RRP40_total_2

source_name: RRP40 total RNA replicate 2


title: RBM7_BrU_2

source_name: RBM7 BrU RNA replicate 2


title: RBM7_BrU_3

source_name: RBM7 BrU RNA replicate 3


title: rs12663356_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTCACTCTGCATGACCGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTTCTGGCCCCTGAGGTAC


title: RBM7_total_3

source_name: RBM7 total RNA replicate 3


title: RRP40_total_1

source_name: RRP40 total RNA replicate 1


title: RBM7_total_1

source_name: RBM7 total RNA replicate 1


title: RBM7_total_2

source_name: RBM7 total RNA replicate 2


title: rs11564258_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTTGTTTGGGTAACTAATGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGCTCAGGAAGTGTTTGTAC

source_name: peripheral blood monocyte


title: rs6920220_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCAACCTTCACTTGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAATGCACTCATTTTCTCAGCT


title: PABPN1_BrU_2

source_name: PABPN1 BrU RNA replicate 2


title: rs13204742_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCGGAGGCTCAGAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGCACACACACATACACCAC


title: rs7134599_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTCATTTTCCCCTATGATC
Rv primer: CAAGCAGAAGACGGCATACGACCACTGTTAACAATTTGGGT


title: PABPN1_BrU_3

source_name: PABPN1 BrU RNA replicate 3


title: PABPN1_total_3

source_name: PABPN1 total RNA replicate 3


title: PABPN1_total_2

source_name: PABPN1 total RNA replicate 2


title: PABPN1_BrU_1

source_name: PABPN1 BrU RNA replicate 1


title: rs6679677_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGCGAGTCCAGGTCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAGTGCTCCACTTTCTAACC


title: rs2472649_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTACTCGTGGACTCAGACGATC
Rv primer: CAAGCAGAAGACGGCATACGAACAAGTGAAAAACGTCGAAT


title: rs1042058_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGCCATGTGGTAAGTGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCCATGTCCATTATTAAGA


title: rs17085007_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGGCAACCAGGAAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAATAACAGTAGCAGCCACA


title: PABPN1_total_1

source_name: PABPN1 total RNA replicate 1


title: rs4409764_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGTTTGTCGATGGTCTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAGAATTCGTAACCAGCAG


title: EGFP_BrU_3

source_name: EGFP(control) BrU RNA replicate 3


title: EGFP_BrU_2

source_name: EGFP(control) BrU RNA replicate 2


title: rs561722_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCTGCTAGAGGAGTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAGAGGCTTGGAGTAGCTTA


title: rs2930047_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTATAATTGACCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACTGTGCCTGGTTTTTAGA


title: rs10486483_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGGTTAAGGTCACCCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTAAGTGACGGAACTCCAG


title: EGFP_total_3

source_name: EGFP(control) total RNA replicate 2


title: EGFP_total_2

source_name: EGFP(control) total RNA replicate 3


title: EGFP_BrU_1

source_name: EGFP(control) BrU RNA replicate 1


title: rs2231884_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGAATTTCCCGACTTTAGATC
Rv primer: CAAGCAGAAGACGGCATACGATCAGTTTCTGCCTCTTGATT


title: rs3897478_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACATCTTAATCAGGGCAGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTTCCAGATGAGGAGACTG


title: rs1517352_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATAAGGACTATCTTAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGTAAACTGACCAGCTGCTA


title: rs11010067_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAATTGGGGCTAATGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGAAAGAGCAAGCACCATACT


title: rs26528_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTCCCTAGGGGGAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTACCTCCAGAGCATGGTA


title: rs4845604_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGTCTTCTCTGTTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTAACCCAGAGGAAAAAGG


title: rs17293632_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGATTCTCTTGTCTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCTTCTCTCATTCCCTATT


title: EGFP_total_1

source_name: EGFP(control) total RNA replicate 1


title: rs1250546_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAATCATTTGTCTGAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATGTAATACGCATTCTTCCCT


title: rs2790216_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCTGGAGATGTTCTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACCTTGAAAATAAACACTGCC


title: rs1819333_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTTTGACTTCAGGGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGACACCTTGATTGTCAGCT


title: rs10781499_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTATTTTCTCAGCCCCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTCACGGAGTCCTAAGATG


title: rs3024505_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAGCTACCAATAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTACGCAATGAAGGTTTGT


title: rs1991866_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCATTCCTTTAAACTTGATC
Rv primer: CAAGCAGAAGACGGCATACGATGCATCAGTCACAAATAGGA


title: rs630923_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGTTATGAGGTAGTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAATTAAACAGGTAGGGAGCCT


title: rs7282490_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACACTCCATATTCAAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGGAGATGCTCAGCTTTTA


title: rs1734907_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGAATAAATACCTGTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTTAGGAGCATTTTCAAGC


title: rs10495903_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCAGAAGGCTGCAGTAGATC
Rv primer: CAAGCAGAAGACGGCATACGACAAGAGGGTAGAGAGGAGGT


title: rs925255_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGGCCTGCAACCTGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTTTTCCTTCTTTTGCCTT


title: rs917997_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCATTCCATGTCCATGATC
Rv primer: CAAGCAGAAGACGGCATACGATTCCCAGCTCACTCTAATGT


title: rs12942547_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCCTAACATGCTTCGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGCCCTTCCATTTTACTTTC


title: rs12722515_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGTTAGGTAGGCTCTGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGACAGGGGAACTTAACCAT


title: rs7404095_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCCTCAGTGGTCTCTGGATC
Rv primer: CAAGCAGAAGACGGCATACGACGGAGATGGAAGTAGACTCA


title: rs35675666_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTCTGGAAATGGCTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGATTGCTGTTACTGTCATTTGC


title: rs10797432_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACTGCACGGTTCTTGCTGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGTGCTTAGGTTTTGGAAG


title: rs1456896_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTAAGGTTGAGTCTGGCGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTATGCCAGCTCTAGCAACT


title: rs3197999_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTGGCTTAGATACGCTGATC
Rv primer: CAAGCAGAAGACGGCATACGATGAAACACACACCTTTGAGA


title: rs7554511_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTCAAAGTAGGCCTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGAGGAAGAGGCAGACAAGTA


title: rs670523_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTTTGCTCAGGGCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGATGATGGAGTAAACCTGGA


title: rs2155219_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTTACAAAAGTGAATGATC
Rv primer: CAAGCAGAAGACGGCATACGATAAACAAAGTGTCCAGGCTT


title: rs7240004_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTAGGTTGAGGGGCCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGATTTCTTTGTTCCAGGT


title: rs913678_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATATACAAACAAATGTGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCTCCTGCTTTAGAACTCAG


title: rs4911259_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACTAAAAGGCACACACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTGACTCCATTCAGTGACCT


title: rs1292053_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTATCCTTTTTCTGTGGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGTTTTGGAAAGATTACCCT


title: rs2024092_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTGCTCCTCCAGCCAAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAAACGTAAGCATGGTCAG


title: rs6586030_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTAAGATGTCTCTGACCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATGAAACCGTTTAGAGGGTAC


title: rs4256159_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTAAGAAATGGGAGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGGTAATTGTGGGGTGTAT


title: rs921720_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATAACTGGCTTCCCACTGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGATTCAAAGCACCCTCAT


title: rs11879191_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAGGTAGAGGGCAGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAACAAGCAACAATCAGGT


title: rs4802307_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGGAAAAGATGGGGGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCCTCCTTTCTTGATTACCT


title: rs4899554_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTTAGCAATTCTGCATGATC
Rv primer: CAAGCAGAAGACGGCATACGATTGAAATAAAGCCATCATCA


title: rs798502_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCCTGTGACATCCTTAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATGAATACTCGCCTCTGAAA


title: rs11612508_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCTTCCCTCCCCTTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACCAACCTTCTTCTTTTCC


title: rs3774959_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAAGCCAGACACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTCATTTCCTGTTGCACTT


title: rs12946510_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTATTCTTGTCACTCTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTGGAAATTTTACCCAAT


title: rs12994997_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCCACATTGTTGACAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAAACAGTGCATGAGCTGAG


title: rs9557195_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATACCCACAGATAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAACAATCGGTAGTTGGATG


title: rs6017342_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGGGTTAGGAGTTCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAGTTGCTTTGCTCTGAAG


title: rs6651252_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCACATCTAGGCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATATGCAGTTCCTTTTGCTTT


title: rs2188962_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTTCCCCAGAGTCAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCTGTGGTTTATTTGCCTAG


title: rs11742570_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCATACACACTCTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGATTTGGAGACTCATTTCTGCT


title: rs1847472_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGGGTTGTGGTTAGAAAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAACTTTCATTCCATGCCTA


title: rs7911264_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTCTCCCTGTCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTTCTACTTGGTCAGGGT


title: rs194749_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTATCCAGGTGTATTAGATC
Rv primer: CAAGCAGAAGACGGCATACGACAAGAGGCAGAGAAGACCTA


title: rs11168249_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTAGTCAGGGAACCTGGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAATGGACAATTGAATCCAAG


title: rs529866_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGAAAACTAACTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATCATGGCAGTAGCTGACTT


title: rs4722672_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTATCACTTGAACCCTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAGAGTCCCAAGGATAAGG


title: rs12654812_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTATTATGAAGCAGACATGATC
Rv primer: CAAGCAGAAGACGGCATACGATGCTGCTGAAGTTATTAGGAG


title: rs3091316_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAACTGCCTTGCTCAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGACAAAGAGAGGACCAGC


title: rs254560_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCCAGGGAGCTGTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTACATGCCACTACAACCA


title: rs8005161_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGAGGGAGAAGGAAGAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATTAGAGCAATGTTTGTCACG


title: rs907611_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTATACCATGTTTCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTAAGTGTTGCTGGGTAC


title: rs10865331_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGATTCCCAGGCCCCTGATC
Rv primer: CAAGCAGAAGACGGCATACGACGTCTGTTTAGTGTGGGTCT


title: rs2284553_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGAGTTATTAGCACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAACCCAAATGCGTAAGAGATA


title: rs6863411_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTGATGGTCTAGCAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACACCAGGTAAAGGCTATG


title: rs516246_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGTAGGAAAAGAGACAGATC
Rv primer: CAAGCAGAAGACGGCATACGATCATAGCATTAAGTCCCGTT


title: rs1728785_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTAGCAGACTGAAAACCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAACCTCTGCTTCACCAAGTTA


title: rs4246215_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGAGTTTCAGTGTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGGATTGAGACTGTGGTTTA

source_name: peripheral blood lymphocyte

value: peripheral blood lymphocyte


title: rs2382817_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAGGACAGTGTATCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATACGCTGCTAACCAACTGT


title: rs11150589_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCTAAAGGTAGAAACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTGGCAAGGATGATTACAAT


title: rs1363907_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGAAGCTCCAGATTGATC
Rv primer: CAAGCAGAAGACGGCATACGATTTTAGCTGCTTTGTATGCA


title: rs4899554_locus2_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAACTTTTTAGAGGGAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTCTTTATTCTCCAGCCCT


title: rs11230563_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTCAGGCATTCCATGGATC
Rv primer: CAAGCAGAAGACGGCATACGATCTTCCTGATATGGGCTAAA


title: rs6142618_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTTGGCTATCTGGGCTTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAAAGCCTGCTTCTCTGAC


title: rs6545800_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAACATTCTCTCTTTTCGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCTCTTCTTTGTAGTGACG


title: rs12568930_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGCTTGCAACTCCCAAGATC
Rv primer: CAAGCAGAAGACGGCATACGACTACATTCAGTGTGCAATGG


title: rs6426833_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGGGGTCTCTGCTGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAATCTAAGGGAAGATGTGCA


title: rs2823286_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATACAAGGGCAATGAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACCAAGTCATAAGGCAGTTTT


title: rs17695092_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTCAGACTCCCTCACCTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTTTCTGGGGTGCCTGTAC


title: rs2266959_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCCACCATGGGCTTAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCAGAGGTTGTGTGTAGGAC


title: rs6679677_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGCGAGTCCAGGTCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAGTGCTCCACTTTCTAACC


title: rs6088765_locus_Monocytes

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATTCTGGGACAGGCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGGGAAGGTGTGTGTTTCT


title: rs12663356_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTCACTCTGCATGACCGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTTCTGGCCCCTGAGGTAC


title: rs6920220_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCAACCTTCACTTGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAATGCACTCATTTTCTCAGCT


title: rs17085007_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGGCAACCAGGAAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAATAACAGTAGCAGCCACA


title: rs11564258_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTTGTTTGGGTAACTAATGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGCTCAGGAAGTGTTTGTAC


title: rs11010067_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAATTGGGGCTAATGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGAAAGAGCAAGCACCATACT


title: rs2472649_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTACTCGTGGACTCAGACGATC
Rv primer: CAAGCAGAAGACGGCATACGAACAAGTGAAAAACGTCGAAT


title: rs7134599_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTCATTTTCCCCTATGATC
Rv primer: CAAGCAGAAGACGGCATACGACCACTGTTAACAATTTGGGT


title: rs2930047_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTATAATTGACCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACTGTGCCTGGTTTTTAGA


title: rs4409764_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGTTTGTCGATGGTCTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAGAATTCGTAACCAGCAG


title: rs10486483_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGGTTAAGGTCACCCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTAAGTGACGGAACTCCAG


title: rs561722_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCTGCTAGAGGAGTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAGAGGCTTGGAGTAGCTTA


title: rs1517352_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATAAGGACTATCTTAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGTAAACTGACCAGCTGCTA


title: rs4845604_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGTCTTCTCTGTTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTAACCCAGAGGAAAAAGG


title: rs26528_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTCCCTAGGGGGAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTACCTCCAGAGCATGGTA


title: rs1991866_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCATTCCTTTAAACTTGATC
Rv primer: CAAGCAGAAGACGGCATACGATGCATCAGTCACAAATAGGA


title: rs3897478_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACATCTTAATCAGGGCAGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTTCCAGATGAGGAGACTG


title: rs3024505_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAGCTACCAATAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTACGCAATGAAGGTTTGT


title: rs17293632_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGATTCTCTTGTCTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCTTCTCTCATTCCCTATT


title: rs1819333_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTTTGACTTCAGGGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGACACCTTGATTGTCAGCT


title: rs13204742_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCGGAGGCTCAGAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGCACACACACATACACCAC


title: rs2790216_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCTGGAGATGTTCTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACCTTGAAAATAAACACTGCC


title: rs1734907_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGAATAAATACCTGTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTTAGGAGCATTTTCAAGC


title: rs2155219_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTTACAAAAGTGAATGATC
Rv primer: CAAGCAGAAGACGGCATACGATAAACAAAGTGTCCAGGCTT


title: rs925255_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGGCCTGCAACCTGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTTTTCCTTCTTTTGCCTT


title: rs7282490_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACACTCCATATTCAAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGGAGATGCTCAGCTTTTA


title: rs1042058_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGCCATGTGGTAAGTGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCCATGTCCATTATTAAGA


title: rs1250546_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAATCATTTGTCTGAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATGTAATACGCATTCTTCCCT


title: rs10495903_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCAGAAGGCTGCAGTAGATC
Rv primer: CAAGCAGAAGACGGCATACGACAAGAGGGTAGAGAGGAGGT


title: rs917997_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCATTCCATGTCCATGATC
Rv primer: CAAGCAGAAGACGGCATACGATTCCCAGCTCACTCTAATGT


title: rs12942547_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCCTAACATGCTTCGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGCCCTTCCATTTTACTTTC


title: rs7404095_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCCTCAGTGGTCTCTGGATC
Rv primer: CAAGCAGAAGACGGCATACGACGGAGATGGAAGTAGACTCA


title: rs4899554_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTTAGCAATTCTGCATGATC
Rv primer: CAAGCAGAAGACGGCATACGATTGAAATAAAGCCATCATCA


title: rs12722515_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGTTAGGTAGGCTCTGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGACAGGGGAACTTAACCAT


title: rs10797432_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACTGCACGGTTCTTGCTGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGTGCTTAGGTTTTGGAAG


title: rs1456896_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTAAGGTTGAGTCTGGCGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTATGCCAGCTCTAGCAACT


title: rs35675666_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTCTGGAAATGGCTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGATTGCTGTTACTGTCATTTGC


title: rs2231884_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGAATTTCCCGACTTTAGATC
Rv primer: CAAGCAGAAGACGGCATACGATCAGTTTCTGCCTCTTGATT


title: rs10781499_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTATTTTCTCAGCCCCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTCACGGAGTCCTAAGATG


title: rs3197999_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTGGCTTAGATACGCTGATC
Rv primer: CAAGCAGAAGACGGCATACGATGAAACACACACCTTTGAGA


title: rs670523_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTTTGCTCAGGGCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGATGATGGAGTAAACCTGGA


title: rs7554511_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTCAAAGTAGGCCTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGAGGAAGAGGCAGACAAGTA


title: rs630923_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGTTATGAGGTAGTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAATTAAACAGGTAGGGAGCCT


title: rs7240004_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTAGGTTGAGGGGCCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGATTTCTTTGTTCCAGGT


title: rs921720_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATAACTGGCTTCCCACTGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGATTCAAAGCACCCTCAT


title: rs3774959_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAAGCCAGACACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTCATTTCCTGTTGCACTT


title: rs4911259_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACTAAAAGGCACACACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTGACTCCATTCAGTGACCT


title: rs913678_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATATACAAACAAATGTGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCTCCTGCTTTAGAACTCAG


title: rs1292053_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTATCCTTTTTCTGTGGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGTTTTGGAAAGATTACCCT


title: rs4256159_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTAAGAAATGGGAGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGGTAATTGTGGGGTGTAT


title: rs2024092_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTGCTCCTCCAGCCAAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAAACGTAAGCATGGTCAG


title: rs6586030_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTAAGATGTCTCTGACCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATGAAACCGTTTAGAGGGTAC


title: rs798502_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCCTGTGACATCCTTAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATGAATACTCGCCTCTGAAA


title: rs4802307_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGGAAAAGATGGGGGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCCTCCTTTCTTGATTACCT


title: rs6651252_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCACATCTAGGCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATATGCAGTTCCTTTTGCTTT


title: rs9557195_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATACCCACAGATAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAACAATCGGTAGTTGGATG


title: rs12946510_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTATTCTTGTCACTCTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTGGAAATTTTACCCAAT


title: rs11612508_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCTTCCCTCCCCTTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACCAACCTTCTTCTTTTCC


title: rs11742570_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCATACACACTCTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGATTTGGAGACTCATTTCTGCT


title: rs12994997_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCCACATTGTTGACAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAAACAGTGCATGAGCTGAG


title: rs1847472_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGGGTTGTGGTTAGAAAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAACTTTCATTCCATGCCTA


title: rs4722672_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTATCACTTGAACCCTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAGAGTCCCAAGGATAAGG


title: rs194749_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTATCCAGGTGTATTAGATC
Rv primer: CAAGCAGAAGACGGCATACGACAAGAGGCAGAGAAGACCTA


title: rs7911264_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTCTCCCTGTCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTTCTACTTGGTCAGGGT


title: rs529866_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGAAAACTAACTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATCATGGCAGTAGCTGACTT


title: rs17695092_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTCAGACTCCCTCACCTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTTTCTGGGGTGCCTGTAC


title: rs11879191_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAGGTAGAGGGCAGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAACAAGCAACAATCAGGT


title: rs3091316_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAACTGCCTTGCTCAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGACAAAGAGAGGACCAGC


title: rs8005161_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGAGGGAGAAGGAAGAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATTAGAGCAATGTTTGTCACG


title: rs12654812_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTATTATGAAGCAGACATGATC
Rv primer: CAAGCAGAAGACGGCATACGATGCTGCTGAAGTTATTAGGAG


title: rs254560_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCCAGGGAGCTGTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTACATGCCACTACAACCA


title: rs6017342_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGGGTTAGGAGTTCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAGTTGCTTTGCTCTGAAG


title: rs6863411_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTGATGGTCTAGCAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACACCAGGTAAAGGCTATG


title: rs2284553_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGAGTTATTAGCACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAACCCAAATGCGTAAGAGATA


title: rs1728785_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTAGCAGACTGAAAACCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAACCTCTGCTTCACCAAGTTA


title: rs907611_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTATACCATGTTTCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTAAGTGTTGCTGGGTAC


title: rs516246_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGTAGGAAAAGAGACAGATC
Rv primer: CAAGCAGAAGACGGCATACGATCATAGCATTAAGTCCCGTT


title: rs11150589_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCTAAAGGTAGAAACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTGGCAAGGATGATTACAAT


title: rs2188962_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTTCCCCAGAGTCAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCTGTGGTTTATTTGCCTAG


title: rs10865331_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGATTCCCAGGCCCCTGATC
Rv primer: CAAGCAGAAGACGGCATACGACGTCTGTTTAGTGTGGGTCT


title: rs11168249_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTAGTCAGGGAACCTGGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAATGGACAATTGAATCCAAG


title: rs2823286_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATACAAGGGCAATGAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACCAAGTCATAAGGCAGTTTT


title: rs2382817_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAGGACAGTGTATCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATACGCTGCTAACCAACTGT


title: rs2266959_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCCACCATGGGCTTAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCAGAGGTTGTGTGTAGGAC


title: rs1363907_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGAAGCTCCAGATTGATC
Rv primer: CAAGCAGAAGACGGCATACGATTTTAGCTGCTTTGTATGCA


title: rs4899554_locus2_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAACTTTTTAGAGGGAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTCTTTATTCTCCAGCCCT


title: rs11230563_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTCAGGCATTCCATGGATC
Rv primer: CAAGCAGAAGACGGCATACGATCTTCCTGATATGGGCTAAA


title: rs6426833_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGGGGTCTCTGCTGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAATCTAAGGGAAGATGTGCA


title: rs12568930_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGCTTGCAACTCCCAAGATC
Rv primer: CAAGCAGAAGACGGCATACGACTACATTCAGTGTGCAATGG


title: rs12663356_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTCACTCTGCATGACCGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTTCTGGCCCCTGAGGTAC


title: rs17085007_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGGCAACCAGGAAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAATAACAGTAGCAGCCACA


title: rs6679677_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGCGAGTCCAGGTCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAGTGCTCCACTTTCTAACC


title: rs6920220_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCAACCTTCACTTGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAATGCACTCATTTTCTCAGCT


title: rs13204742_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCGGAGGCTCAGAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGCACACACACATACACCAC


title: rs11564258_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTTGTTTGGGTAACTAATGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGCTCAGGAAGTGTTTGTAC


title: rs11010067_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAATTGGGGCTAATGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGAAAGAGCAAGCACCATACT


title: rs2472649_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTACTCGTGGACTCAGACGATC
Rv primer: CAAGCAGAAGACGGCATACGAACAAGTGAAAAACGTCGAAT


title: rs6088765_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATTCTGGGACAGGCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGGGAAGGTGTGTGTTTCT


title: rs6142618_locus_Lymphocytes2

description:
Fw_primer: ACACGACGCTCTTCCGATCTTGGCTATCTGGGCTTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAAAGCCTGCTTCTCTGAC


title: rs4246215_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGAGTTTCAGTGTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGGATTGAGACTGTGGTTTA


title: rs1042058_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGCCATGTGGTAAGTGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCCATGTCCATTATTAAGA


title: rs4409764_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGTTTGTCGATGGTCTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAGAATTCGTAACCAGCAG


title: rs2930047_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTATAATTGACCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACTGTGCCTGGTTTTTAGA


title: rs1517352_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATAAGGACTATCTTAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGTAAACTGACCAGCTGCTA


title: rs561722_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCTGCTAGAGGAGTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACAGAGGCTTGGAGTAGCTTA


title: rs3897478_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACATCTTAATCAGGGCAGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTTCCAGATGAGGAGACTG


title: rs10486483_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGGTTAAGGTCACCCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTAAGTGACGGAACTCCAG


title: rs1250546_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAATCATTTGTCTGAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATGTAATACGCATTCTTCCCT


title: rs2231884_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGAATTTCCCGACTTTAGATC
Rv primer: CAAGCAGAAGACGGCATACGATCAGTTTCTGCCTCTTGATT


title: rs3024505_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAGCTACCAATAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTACGCAATGAAGGTTTGT


title: rs6545800_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAACATTCTCTCTTTTCGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCTCTTCTTTGTAGTGACG


title: rs4845604_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGTCTTCTCTGTTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTAACCCAGAGGAAAAAGG


title: rs1819333_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTTTGACTTCAGGGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGACACCTTGATTGTCAGCT


title: rs3197999_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTGGCTTAGATACGCTGATC
Rv primer: CAAGCAGAAGACGGCATACGATGAAACACACACCTTTGAGA


title: rs1991866_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCATTCCTTTAAACTTGATC
Rv primer: CAAGCAGAAGACGGCATACGATGCATCAGTCACAAATAGGA


title: rs26528_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTCCCTAGGGGGAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTACCTCCAGAGCATGGTA


title: rs7134599_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTCATTTTCCCCTATGATC
Rv primer: CAAGCAGAAGACGGCATACGACCACTGTTAACAATTTGGGT


title: rs10781499_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTATTTTCTCAGCCCCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTCACGGAGTCCTAAGATG


title: rs17293632_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGATTCTCTTGTCTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGACCCTTCTCTCATTCCCTATT


title: rs2155219_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTTACAAAAGTGAATGATC
Rv primer: CAAGCAGAAGACGGCATACGATAAACAAAGTGTCCAGGCTT


title: rs630923_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTATGTTATGAGGTAGTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAATTAAACAGGTAGGGAGCCT


title: rs1734907_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGAATAAATACCTGTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTTTAGGAGCATTTTCAAGC


title: rs925255_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGGCCTGCAACCTGGATC
Rv primer: CAAGCAGAAGACGGCATACGAACTTTTCCTTCTTTTGCCTT


title: rs7282490_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACACTCCATATTCAAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGGAGATGCTCAGCTTTTA


title: rs2790216_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCTGGAGATGTTCTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGACCTTGAAAATAAACACTGCC


title: rs10495903_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCAGAAGGCTGCAGTAGATC
Rv primer: CAAGCAGAAGACGGCATACGACAAGAGGGTAGAGAGGAGGT


title: rs917997_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCATTCCATGTCCATGATC
Rv primer: CAAGCAGAAGACGGCATACGATTCCCAGCTCACTCTAATGT


title: rs12942547_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCCTAACATGCTTCGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGCCCTTCCATTTTACTTTC


title: rs4899554_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTTAGCAATTCTGCATGATC
Rv primer: CAAGCAGAAGACGGCATACGATTGAAATAAAGCCATCATCA


title: rs7404095_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCCTCAGTGGTCTCTGGATC
Rv primer: CAAGCAGAAGACGGCATACGACGGAGATGGAAGTAGACTCA


title: rs12722515_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGTTAGGTAGGCTCTGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGACAGGGGAACTTAACCAT


title: rs1456896_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTAAGGTTGAGTCTGGCGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTATGCCAGCTCTAGCAACT


title: rs10797432_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACTGCACGGTTCTTGCTGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGTGCTTAGGTTTTGGAAG


title: rs670523_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTTTGCTCAGGGCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGATGATGGAGTAAACCTGGA


title: rs7554511_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGCTCAAAGTAGGCCTTGATC
Rv primer: CAAGCAGAAGACGGCATACGAGAGGAAGAGGCAGACAAGTA


title: rs35675666_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTTTCTGGAAATGGCTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGATTGCTGTTACTGTCATTTGC


title: rs7240004_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTAGGTTGAGGGGCCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGATTTCTTTGTTCCAGGT


title: rs4911259_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACTAAAAGGCACACACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTGACTCCATTCAGTGACCT


title: rs6586030_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTAAGATGTCTCTGACCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATGAAACCGTTTAGAGGGTAC


title: rs2024092_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTGCTCCTCCAGCCAAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAAACGTAAGCATGGTCAG


title: rs1292053_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTATCCTTTTTCTGTGGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGGTTTTGGAAAGATTACCCT


title: rs913678_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATATACAAACAAATGTGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCTCCTGCTTTAGAACTCAG


title: rs3774959_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAAAGCCAGACACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTCATTTCCTGTTGCACTT


title: rs4256159_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTAAGAAATGGGAGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGACTGGTAATTGTGGGGTGTAT


title: rs11879191_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGACAGGTAGAGGGCAGAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAACAAGCAACAATCAGGT


title: rs921720_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATAACTGGCTTCCCACTGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGATTCAAAGCACCCTCAT


title: rs798502_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCCTGTGACATCCTTAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATGAATACTCGCCTCTGAAA


title: rs11612508_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCTTCCCTCCCCTTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACCAACCTTCTTCTTTTCC


title: rs4802307_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGGAAAAGATGGGGGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCCTCCTTTCTTGATTACCT


title: rs12994997_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTTCCACATTGTTGACAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAAACAGTGCATGAGCTGAG


title: sba1_control_chip

city: Urbana

first: Brian

middle: Christopher

last: Freeman

state: Illinois

address: 601 South Goodwin Avenue

department: Department of Cell and Developmental Biology

institute: University of Illinois at Urbana-Champaign

data_processing:
The libraries for ChIP-seq were sequenced on 1 lane for 100 cycles with an Illumina HiSeq2000 and TruSeq SBS sequencing kits version 3. Basecalls were performed with Casava1.8 (pipeline 1.9).
Raw sequencing reads were first mapped to the yeast genome (sacCer3) from UCSC Genome Browser using Bowtie  version 0.12.7 (command: bowtie -p 4 -t --sam --best -v 1 -m 1 ).
ChIP-seq peaks were identified using CisGenome (version 2.0) with options  -b 25 -w 5 -e 200. Only peaks with FDR < 0.1 were used for downstream analysis.
Genome_build: sacCer3

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: Yeast were grown in YPD at 30˚C to OD (595) = 1.

extract_protocol:
The cells were crosslinked to 1% formaldehyde for 15 min, after which 2.5 M glycine was added and the cells were incubated for additional 5 min.
The cells were lysed with glass beads for 37 min, lysate was clarified, sonicated, clarified and incubated with an antibody specific for Sba1 (Freeman et al., 2000) or normal rabbit serum (Control).

tag: strain

tag: genotype/variation

value: wild type

tag: chip antibody

value: normal rabbit serum


title: rs12946510_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTATTCTTGTCACTCTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTGGAAATTTTACCCAAT


title: rs9557195_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATACCCACAGATAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAACAATCGGTAGTTGGATG


title: sba1_chip

value: Sba1 (Freeman et al., 2000)


title: rs6017342_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGGGTTAGGAGTTCAGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAGTTGCTTTGCTCTGAAG


title: Hsp82D15

data_processing:
Quality control: fastQC (0.10.1)
Aligning the reads to the reference genome: bowtie (1.0.0), command: -m 1 -v 2 --sam ~/indexes/SacCer3. Only uniquely mapped reads were retained for further analyses.
DNase peak detection: Hotspot (v4), fdr 0.01
Footprint detector/Footprint finder (Chen and Noble, 2008), fdr 0.1
Genome_build: sacCer3
Supplementary_files_format_and_content: *mapped.hot.bed.gz contains identified hypersensitive sites; footrpint.wig.gz contains identified footrpints

source_name: wild type

growth_protocol: Yeast were grown in YPD medium from OD 0.25 till 0.65 at 30˚C, filtered from 30˚C media and shifted to 37˚C media for another 15 min.

extract_protocol:
Nuclei were isolated from logarithmically grown yeast and subject to limited DNaseI digestion. Short (>650bp) sequences were selected and deep sequenced.
The libraries were prepared with Illumina's 'TruSeq DNAseq Sample Prep kit' with one modification: adaptors were diluted 1:20. The libraries were quantitated by qPCR, and sequenced on two lanes for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and processed with Casava 1.8.2.

tag: strain background


title: G170DD15

source_name: Hsp90 temperature-sensitive strain with allele G170D

value: temperature sensitive mutant


title: rs11742570_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCATACACACTCTGGGATC
Rv primer: CAAGCAGAAGACGGCATACGATTTGGAGACTCATTTCTGCT


title: rs2188962_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTTCCCCAGAGTCAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAGCTGTGGTTTATTTGCCTAG


title: rs6651252_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGCACATCTAGGCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATATGCAGTTCCTTTTGCTTT


title: rs7911264_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATCTCTCCCTGTCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTTCTACTTGGTCAGGGT


title: rs1847472_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGGGTTGTGGTTAGAAAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAACTTTCATTCCATGCCTA


title: rs11168249_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTAGTCAGGGAACCTGGTGATC
Rv primer: CAAGCAGAAGACGGCATACGAAATGGACAATTGAATCCAAG


title: rs17695092_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTCAGACTCCCTCACCTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGTTTCTGGGGTGCCTGTAC


title: rs529866_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGAAAACTAACTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAATCATGGCAGTAGCTGACTT


title: rs254560_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGCCAGGGAGCTGTTTGATC
Rv primer: CAAGCAGAAGACGGCATACGACTTACATGCCACTACAACCA


title: rs12654812_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTATTATGAAGCAGACATGATC
Rv primer: CAAGCAGAAGACGGCATACGATGCTGCTGAAGTTATTAGGAG


title: rs3091316_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAACTGCCTTGCTCAAGAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGACAAAGAGAGGACCAGC


title: rs8005161_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAGAGGGAGAAGGAAGAAGATC
Rv primer: CAAGCAGAAGACGGCATACGATTAGAGCAATGTTTGTCACG


title: rs516246_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATGTAGGAAAAGAGACAGATC
Rv primer: CAAGCAGAAGACGGCATACGATCATAGCATTAAGTCCCGTT


title: rs6088765_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATTCTGGGACAGGCAGATC
Rv primer: CAAGCAGAAGACGGCATACGATAGGGAAGGTGTGTGTTTCT


title: rs6863411_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGATTGATGGTCTAGCAGGGATC
Rv primer: CAAGCAGAAGACGGCATACGAAACACCAGGTAAAGGCTATG


title: rs907611_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTATACCATGTTTCTTCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGGTAAGTGTTGCTGGGTAC


title: rs6142618_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTTGGCTATCTGGGCTTCGATC
Rv primer: CAAGCAGAAGACGGCATACGAAGAAAGCCTGCTTCTCTGAC


title: rs1728785_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTAGCAGACTGAAAACCAGATC
Rv primer: CAAGCAGAAGACGGCATACGAACCTCTGCTTCACCAAGTTA


title: rs11150589_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTCCTAAAGGTAGAAACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAGTGGCAAGGATGATTACAAT


title: rs1363907_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTAATGAAGCTCCAGATTGATC
Rv primer: CAAGCAGAAGACGGCATACGATTTTAGCTGCTTTGTATGCA


title: RNA from ap1 cal IM explant tissue replicate 1

city: Cologne

first: Peter

last: Frommolt

address: Joseph-Stelzmann-Str. 26

country: Germany

institute: CECAD

description:
ap1cal24315RNASeq1
processed data files: DRNL-GFPPlus_ap1cal-apices-IM.xlsx, DRNL-GFP_ap1cal-apices-IM.xlsx

data_processing:
Next-generation sequencing data were analysed using QuickNGS, a high-throughput next-generation sequencing analysis pipeline (Wagle et al., 2015):
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools.
Reads were mapped to the Arabidopsis reference genome (TAIR v 10; ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release) using TopHat2 (Kim et al., 2013)
Gene quantification was performed using a combination of Cufflinks (Trapnell et al., 2010) and the DEseq2 package (Anders and Huber, 2010) with genomic annotation from the TAIR10 genome release.
Genome_build: TAIR10
Supplementary_files_format_and_content: Xlsx-Format – Excel file containing Ensembl Gene ID, FoldChanges, FPKM-values, p Values

organism: Arabidopsis thaliana

source_name: ap1 cal IM explant tissue

growth_protocol: All plants were grown in a controlled greenhouse environment in long-day (16 h light: 8 h dark) conditions.

extract_protocol:
To generate material for fluorescence-activated cell sorting, we crossed the ap1 cal mutant (Nottingham Arabidopsis Stock Centre accession N6161) to the DRNL::erGFP marker line and identified transgenic DRNL::erGFP ap1 cal progeny in the F2 generation.
The TruSeq v2 RNA sample preparation kit (Ilumina) was used to prepare cDNA libraries starting from 200 ng total GFP+ or GFP- RNA. Poly(A)+ RNA was purified onto oligo-dT magnetic beads and was fragmented using divalent cations at elevated temperature; RNA fragments were reverse-transcribed using random primers, followed by second-strand cDNA synthesis with RNase H/DNA Polymerase I. After end repair and A-tailing, adapters were ligated and the indexed cDNA products were purified and amplified by PCR (15 cycles) to create the final cDNA libraries. Library quality was validated on a 2200 TapeStation (Agilent Technologies) and individual libraries were quantified on the Qubit System (Invitrogen) prior to pooling and pool quantification via the KAPA Library Quantification kit (Peqlab) and the 7900HT Sequence Detection System (Applied Biosystems). The pooled, indexed libraries were loaded and analysed on a HiSeq sequencer (Illumina) using the 2 × 100-bp v3 protocol.

tag: genetic and mutant background

value: Landsberg erecta, ap1 cal

tag: transgene

tag: name abbreviation

value: a

value: shoot apical meristem (SAM)

tag: cell/tissue subtype

value: inflorescence meristem (IM) explain tissue


title: RNA from GFP+ protoplasts replicate 4

description:
FACS24DRNLplus
processed data files: DRNL-GFPPlus_DRNL-GFP.xlsx, DRNL-GFPPlus_DRNL-GFP_FC2-P0.01.xlsx, DRNL-GFPPlus_DRNL-GFP_FC1.5-P0.01.xlsx, DRNL-GFPPlus_ap1cal-apices-IM.xlsx

source_name: GFP+ protoplasts

value: GFP+ 4

value: GFP+ protoplasts


title: RNA from ap1 cal IM explant tissue replicate 2

description:
ap1cal24315RNASeq2
processed data files: DRNL-GFPPlus_ap1cal-apices-IM.xlsx, DRNL-GFP_ap1cal-apices-IM.xlsx

value: b


title: RNA from GFP+ protoplasts replicate 3

description:
FACS23DRNLplus
processed data files: DRNL-GFPPlus_DRNL-GFP.xlsx, DRNL-GFPPlus_DRNL-GFP_FC2-P0.01.xlsx, DRNL-GFPPlus_DRNL-GFP_FC1.5-P0.01.xlsx, DRNL-GFPPlus_ap1cal-apices-IM.xlsx

value: GFP+ 3


title: U. bromivora Inf-Stem rep3

city: Vienna

first: Angelika

last: Czedik-Eysenberg

address: Dr-Bohr-Gasse 3

country: Austria

institute: Gregor-Mendel-Institute

data_processing:
Basecalling with Illumina RTA v1.17.21.3
Demultiplexing with BamIndexDecoder vV1.03-184-g590b59e-dirty
Transcript quantification with kallisto version 0.42.2.1 and default parameters, against  U. bromivora UB1 and Brachypodium distachyon Bd21 (Bdistachyon_283_v2.1) transcriptomes
Filtered count list to remove Brachypodium transcript counts
Genome_build: Ustilago bromivora UB1
Supplementary_files_format_and_content: tab delimited .txt file; read counts for each precicted bromivora transcript, samples in columns

molecule: polyA RNA

organism: Ustilago bromivora

source_name: U. bromivora infected Brachypodium hybridum Bd28 tissue

growth_protocol: To isolate RNA from axenic U. bromivora culture, U. bromivora UB1 was grown in axenic culture (21°C, 200 rpm, PD medium) in three independent biological replicates to an exponential phase (OD600nm = 0.8). For the isolation of RNA from infected B. hybridum Bd28 plants, Bd28 was inoculated with U. bromivora spore material. After incubating germinating caryopses with spore material for one week, caryopses were planted and harvested after twelve days.

extract_protocol:
RNA was isolated using the TRIzol method followed by DNAse treatment
Library was constructed using the NEB Next Ultra RNA Library Prep Kit

tag: growth condition

value: in planta

tag: live style

value: biotrophic


title: rs194749_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTCTATCCAGGTGTATTAGATC
Rv primer: CAAGCAGAAGACGGCATACGACAAGAGGCAGAGAAGACCTA

tag: tissue


title: U. bromivora Inf-Stem rep2


title: rs4722672_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTATCACTTGAACCCTGAGATC
Rv primer: CAAGCAGAAGACGGCATACGAAAAGAGTCCCAAGGATAAGG


title: rs2284553_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAAGAGTTATTAGCACAGATC
Rv primer: CAAGCAGAAGACGGCATACGAACCCAAATGCGTAAGAGATA


title: RNA from GFP- protoplasts replicate 4

description:
FACS24DRNL
processed data files: DRNL-GFPPlus_DRNL-GFP.xlsx, DRNL-GFPPlus_DRNL-GFP_FC2-P0.01.xlsx, DRNL-GFPPlus_DRNL-GFP_FC1.5-P0.01.xlsx, DRNL-GFP_ap1cal-apices-IM.xlsx

source_name: GFP- protoplasts

value: GFP- 4

value: GFP- protoplasts


title: RNA from GFP+ protoplasts replicate 1

description:
FACSDRNL+
processed data files: DRNL-GFPPlus_DRNL-GFP.xlsx, DRNL-GFPPlus_DRNL-GFP_FC2-P0.01.xlsx, DRNL-GFPPlus_DRNL-GFP_FC1.5-P0.01.xlsx, DRNL-GFPPlus_ap1cal-apices-IM.xlsx

value: GFP+ 1


title: rs10865331_locus_Lymphocytes1

description:
Fw_primer: ACACGACGCTCTTCCGATCTGAAGATTCCCAGGCCCCTGATC
Rv primer: CAAGCAGAAGACGGCATACGACGTCTGTTTAGTGTGGGTCT

value: peripheral blood lymphocyte


title: U. bromivora axenic culture rep2

source_name: U. bromivora axenic culture

value: axenic culture

value: saprophytic


title: RNA from GFP- protoplasts replicate 3

description:
FACS23DRNL
processed data files: DRNL-GFPPlus_DRNL-GFP.xlsx, DRNL-GFPPlus_DRNL-GFP_FC2-P0.01.xlsx, DRNL-GFPPlus_DRNL-GFP_FC1.5-P0.01.xlsx, DRNL-GFP_ap1cal-apices-IM.xlsx

value: GFP- 3


title: U. bromivora axenic culture rep3


title: RNA from GFP- protoplasts replicate 2

description:
FACSDRNL2
processed data files: DRNL-GFPPlus_DRNL-GFP.xlsx, DRNL-GFPPlus_DRNL-GFP_FC2-P0.01.xlsx, DRNL-GFPPlus_DRNL-GFP_FC1.5-P0.01.xlsx, DRNL-GFP_ap1cal-apices-IM.xlsx

value: Landsberg erecta, ap1 cal

value: GFP- 2


title: U. bromivora axenic culture rep1


title: Sample 5A-M1T1 SENhb

status: Public on Nov 02 2016

city: Columbus

first: Vijay

last: Pancholi

state: OH

address: 420W 12th Ave, TMRF-288

department: Pathology

institute: Ohio State University

data_processing: Primary sequencing data that produced by Illumina Hiseq 2000, called as raw reads were subjected to quality control to determine if resequencing step is needed. After QC, raw reads were filtered into clean reads which were then aligned to reference sequence Streptococcus pyogenes MGAS5005 NC_007297.1 with SOAPaligner/SOAP2 v2.20 [Li. R, Yu,C., LiY et al  Bioinformatics :Doi:10.1093/bioinformatics/btp336.  259(15)1966-1967]. the alignment data were utilized to calculate distribution of reads on reference genes and perform coverage analysis. Upon QC pass, down stream analysis including gene expression, novel transcript prediction and annotation were done. Gene ontology enrichment analysis were used for pathway enrichment analysis. In order to assess the effectiveness of selected mapping tool, the comparative analysis between SOAPAligner/SOAP2 and other popular-alignment tool BOWTIE [Langmead B. et al (2009)genome biology 10:25-34/ http://Bowtie-bio.sourceforge.net/index.shtml].  Because the SOAPaligner/SOAP2 performed better, quantification analysis of gene expression was done with SOAPaligner/SOAP2. For significance of didgital gene expression profile, algorithms as published [ Audic et al (1997) Gemome Res. 7:986-985] was employed. We used FDR< 0.001 [benjamini and Yekutieli(2001)Ann Statistics29:1165-1188] and the absolute value Log2 ratio > 1 as the threshold to judge the significance of gene expression difference. KEGG was used to perform Pathway enrichment analysis. For gene refinement, transcripts reads were assemble by using CUFFLINK software [Roberts et al Bioinformatics: doi:10.1093/bioinformatics. btr355].

organism: Streptococcus pyogenes

source_name: Late-log phase culture

growth_protocol: All cultures were grown in Todd Hewitt broth supplemented with 0.5% yeast extract. Cultures were grown at 37oC till O.D. reached at 0.8. (wt) mutant (0.65) i.e. till late log phase. The cultures were then centrifuged at 4oC  and washed once with sterile autoclaved PBS. The cells were then resuspended in PBS in the 1/50th of the starting culture volume.

extract_protocol:
Total RNA was extracted using  Norgen RNA isolation kit (canada) as described by the manufacturer's instructions.
The high quality total RNA samples were obtained by DNase treatment. The samples were then sent to BGI Americas. rRNA was removed from the total RNA samples. cDNA was then made using mRNA as template. Short fragments were made by heat treatment and were purified and resolved  with EB buffer for endrepairation and single nucleotide A ( adenine) addition. Short fragments were then connected to adapters. Subsequently, following agarose gel electrophoresis, the suitable fragments were selected for the PCR amplification. All qc steps i.e. for quantification and quality of sample library, ABI bioanalyzer and ABI StepOnePlus realtime PCR system were used. Library were sequenced using IlluminaHiseq 2000.
mRNA-seq transcriptome library was sequenced using Illumina HiSeq2000 sequencer.

treatment_protocol: The S. pyogenes mutant, M1T1SENhb was created  and derived from M1T15448 strain to prevent surface exportation of  enolase. The latter was achieved by  genetically replacing the wild type" eno" gene, M5005_Spy_0556 with a modified enolase encoding gene with 3' end 39 nucleotide sequence extension including the terminal stop codon encoding  enolase with a 12 amino acid hydrophobic tail  as previously described using pFW5 suicide vector [Boel et al (2005) Infect. Immun. 73:6237-6248; and Jin et al (2011) mBio 2:e00068-11]. The washed concentrated bacterial pellet was suspended in  Tris/HCl  buffer pH 7.4, containing 5mM MgCl2 ,phage lysin, and RNAse-free DNase.

value: SENhb mutant

tag: phenotype

value: Lacking -SP-PTP


title: sample 1A-M1T1  wild type

value: wild-type

value: Intact SP-PTP


title: U. bromivora Inf-Stem rep1


title: Sample 3B-M1T1 DSTK

data_processing: Primary sequencing data that produced by Illumina Hiseq 2000, called as raw reads were subjected to quality control to determine if resequencing step is needed. After QC, raw reads were filtered into clean reads which were then aligned to reference sequence Streptococcus pyogenes MGAS5005 NC_007297.1 with SOAPaligner/SOAP2 v2.20 [Li. R, Yu,C., LiY et al Bioinformatics :Doi:10.1093/bioinformatics/btp336. 259(15)1966-1967]. the alignment data were utilized to calculate distribution of reads on reference genes and perform coverage analysis. Upon QC pass, down stream analysis including gene expression, novel transcript prediction and annotation were done. Gene ontology enrichment analysis were used for pathway enrichment analysis. In order to assess the effectiveness of selected mapping tool, the comparative analysis between SOAPAligner/SOAP2 and other popular-alignment tool BOWTIE [Langmead B. et al (2009)genome biology 10:25-34/ http://Bowtie-bio.sourceforge.net/index.shtml]. Because the SOAPaligner/SOAP2 performed better, quantification analysis of gene expression was done with SOAPaligner/SOAP2. For significance of didgital gene expression profile, algorithms as published [ Audic et al (1997) Gemome Res. 7:986-985] was employed. We used FDR< 0.001 [benjamini and Yekutieli(2001)Ann Statistics29:1165-1188] and the absolute value Log2 ratio > 1 as the threshold to judge the significance of gene expression difference. KEGG was used to perform Pathway enrichment analysis. For gene refinement, transcripts reads were assemble by using CUFFLINK software [Roberts et al Bioinformatics: doi:10.1093/bioinformatics. btr355].

treatment_protocol: Using pFW5 vector, the S. pyogenes mutant lacking SP-STK was derived from type M1 strain M1T15448 as described JIn et al (2011) J Mol Biol. 357:1351-1372]. The washed concentrated bacterial pellet was suspended in  Tris/HCl  buffer pH 7.4 containing phage-lysin and RNase free DNAse to lyse the bacterial cells and digest DNA.

value: mutant


title: RNA from GFP+ protoplasts replicate 2

description:
FACSDRNL2+
processed data files: DRNL-GFPPlus_DRNL-GFP.xlsx, DRNL-GFPPlus_DRNL-GFP_FC2-P0.01.xlsx, DRNL-GFPPlus_DRNL-GFP_FC1.5-P0.01.xlsx, DRNL-GFPPlus_ap1cal-apices-IM.xlsx

value: GFP+ 2

value: shoot apical meristem (SAM)

value: GFP+ protoplasts


title: Sample 3A-M1T1 DSTK


title: sample 1B-M1T1 WT


title: sample 1B-M1T1  wild type


title: Rat rep 3 cortical neurons 0hr post-KCl stim

city: Boston

first: Bulent

last: Ataman

state: MA

address: 220 Longwood Ave. GB405

department: Neurobiology

institute: Harvard Medical School

data_processing:
For RNA-Seq of mouse and rat cortical cultures, strand-specific single-end reads of length 75 bp or shorter were trimmed at their 3' ends to 70 bp; those shorter than 70 bp (<0.2%) were discarded.  The remaining 70-bp reads were mapped to the mm10 (mouse) or rn6 (rat) genome using BWA (v.0.7.8) allowing up to 2 mismatches.  For mouse and rat respectively, the usual 20 and 21 chromosomal alignment targets were supplemented with their mitochondrial genomes plus ~8 and ~6 million short sequences.  The latter targets represent all possible intragenic exonic sets from their respective RefSeq annotations whose junctions are spannable by 70-bp reads.  Typically 80% of all reads in each mouse library (90% in rat) were mappable and ~50-80% of these aligned uniquely; nonuniquely mapped reads were discarded.
The exons for all transcripts assigned to a gene based on the RefSeq annotation for mouse (GRCm38/mm10; Dec. 2011) or for rat (RGSC 6.0/rn6; July 2014) were merged (unioned); along with the constructed library of exon-exon splice-junction sequences, these defined each gene's mature-RNA target region.  The total number of bases of all reads that overlapped a gene's exonic region were divided by the total length of the region to yield an average read Density (coverage).  Normalization of Densities to a standard of 10M 35-bp reads was effected by multiplying the raw Density by (10M/R)*(35/70), where R is the total number of uniquely mapped reads in a sample that did not overlap any RepeatMasker rRNA elements (RPKM units are proportional to Normalized Density units via  RPKM = Density/0.35).
Genome_build: mm10
Genome_build: rn6
Supplementary_files_format_and_content: Standard bigWig-formatted files (.bw) for both mouse and rat RNA-seq samples represent bwa-aligned trimmed 70-bp reads piled up with single-base-pair resolution and then averaged over tiles of width 20bp.  Each sample has its own pair of separate tracks for POS & NEG strands.

organism: Rattus norvegicus

source_name: Long-Evans

growth_protocol: Mouse and rat neuronal cultures from three independent dissections were grown for RNA-seq experiments as outlined in the Methods section.

extract_protocol:
The libraries for RNA-Seq were constructed using the NEBNext Ultra Directional RNA library prep kit (for Illumina).
Strand-specific and single-end for RNA-Seq.

treatment_protocol: For KCl depolarization of neurons, neuronal cultures were first silenced overnight in culture media with 1 μM Tetrodotoxin (TTX) and 100 μM D-AP5.  The following day samples were incubated for 0, 1 or 6 hours in 55 mM KCl prior to harvest.

value: Long-Evans

value: E17 cortex, cultured, DIV7

tag: time post-kcl stimulation

tag: replicate


title: sample 1A-M1T1 WT


title: Rat rep 2 cortical neurons 6hr post-KCl stim


title: Rat rep 2 cortical neurons 0hr post-KCl stim


title: Rat rep 2 cortical neurons 1hr post-KCl stim


title: Rat rep 1 cortical neurons 1hr post-KCl stim


title: Rat rep 3 cortical neurons 1hr post-KCl stim


title: Rat rep 1 cortical neurons 0hr post-KCl stim


title: Rat rep 1 cortical neurons 6hr post-KCl stim


title: Rat rep 3 cortical neurons 6hr post-KCl stim


title: tSBE(6+2-Vp64) norm biological replicate 2 technical replicate2

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University of Edinburgh

data_processing:
Library strategy: 4C-Seq
The sequencing data was processed through a Torrent 5C data transformation pipeline on Galaxy (https://main.g2.bx.psu.edu/). The data was mapped against a customized reference file with TMAP. The reference file contained a list of all possible contacts between Forward and Reverse 5C primers covering our regions.
The data was then filtered to remove low-quality reads (MAQ quality score of lower than 30), reads aligning more than two nucleotides away from the reference sequence start site, and reads which do not contain HindIII restriction sites.
5C data was normalized by dividing the number of reads of each 5C contact by the total number of reads from the corresponding sequence run multiplied by 10^3.
Genome_build: mm9
Supplementary_files_format_and_content: This analysis generates a matrix file containing the interaction frequencies

growth_protocol: GMEM+ Supplement for ESCs, N2B27 for 7 days for NPCs

extract_protocol:
10-20 million fixed cells were incubated for 15 min on ice in 200 ml of lysis buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP40, supplemented with fresh protease inhibitor cocktail).  Cells were then disrupted on ice with a dounce homogenizer (pestle B; 2 x 20 strokes), cell suspensions transferred to eppendorf tubes and centrifuged 5 min at 2000 g.  Supernatants were removed, the cell pellets washed twice with 100 ml of 1X CutSmart buffer (NEB) and the cell pellet resuspended in 100 ml of 1X CutSmart buffer, and divided into two eppendorf tubes.  1X CutSmart buffer (337 ml) was added to each tube, and the mixture was incubated 10 min at 65°C with 0.1% SDS.  44 ml of 10% Triton X-100 were added before overnight digestion with 400 Units HindIII.  The restriction enzyme was then inactivated by adding 86 ml of 10% SDS, and incubation for 30 min at 65°C.  Samples were then individually diluted into 7.62 ml of ligation mix (750 ml 10% Triton X-100, 750 ml 10X ligation buffer, 80 ml 10 mg/ml of BSA, 80 ml 100 mM ATP and 3000 Cohesive end Units of T4 DNA ligase) and incubated at 16°C for 2 hours. 3C libraries were incubated overnight at 65°C with 50 ml Proteinase K (10 mg/ml), and with an additional 50 ml Proteinase K the following day for 2 hours.  The DNA was purified by one phenol and one phenol-chloroform extraction, and precipitated with 0.1 volume (800 ml) of 3 M NaOAc pH 5.2 and 2.5 volumes of cold EtOH (20 ml).  After at least 1 h at -80°C, the DNA was centrifuged for 25 min at 20,000 g at 4°C, and the pellets washed with cold 70% EtOH. DNA was resuspended in 400 ml of TE pH 8.0, and transferred to eppendorf tubes for another phenol-chloroform extraction and precipitation with 40 ml of 3 M NaOAc pH 5.2 and 1.1 ml of cold EtOH.  DNA was recovered by centrifugation, and washed eight times with cold 70% EtOH.  Pellets were then dissolved in 100 ml TE pH 8.0, and incubated with RNAse A (1 ml at 10 mg/ml) for 15 min at 37°C.
3C libraries were denatured and annealed to 5C primers. 5C oligonucleotide were designed upstream (FORWARD) or downstream (REVERSE) HindIII restriction sites. Annealing was followed by ligation with Taq DNA ligase. Ligated 5C primers were then amplified with the A-key and P1-key primers to generate the 5C libraries. 5C libraries were then prepared for sequencing onto Ion 316™ Chips with an Ion PGM™ Sequencer following either the Ion Xpress™ Template Kit v2.0, and Ion Sequencing Kit v2.0 protocols, or the Ion PGM™ Template OT2 200 Kit, and Ion PGM™ Sequencing 200 Kit v2.0 protocols as recommended by the manufacturer’s instructions (Life TechnologiesTM). Libraries were prepared according to Ion Torrent's instructions

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 min at room temperature. Crosslinking was stopped with glycine (125 mM final concentration), and incubated for 5 min at room temperature followed by 15 min on ice. Cells were centrifuged at 400 g for 10 min at 4°C. Supernatants were removed and cell pellets were flash frozen on dry ice.

value: transfected 46c ESCs

tag: cell type

value: Stem cells


title: tSBE(6+2-Vp64) norm biological replicate 2 technical replicate1


title: RNA from GFP- protoplasts replicate 1

description:
FACSDRNL
processed data files: DRNL-GFPPlus_DRNL-GFP.xlsx, DRNL-GFPPlus_DRNL-GFP_FC2-P0.01.xlsx, DRNL-GFPPlus_DRNL-GFP_FC1.5-P0.01.xlsx, DRNL-GFP_ap1cal-apices-IM.xlsx

value: GFP- 1

value: GFP- protoplasts


title: NPC norm biological replicate 2 technical replicate1

source_name: 5C NPC

value: 46c ESCs N2B27 differentiation in NPCs for 7 days

value: Neural Progenitor cells


title: Sample 5B-M1T1 SENhb


title: NPC norm biological replicate 2 technical replicate2


title: tSBE2-Vp64 norm biological replicate 1

source_name: 5C tSBE2-Vp64


title: tSBE6-Vp64 norm biological replicate 1

source_name: 5C tSBE6-Vp64


title: tSBE(6+2-Vp64) norm biological replicate 1 technical replicate1


title: NPC norm biological replicate 1 technical replicate2


title: tSBE(6+2-Vp64) norm biological replicate 1 technical replicate2


title: NPC norm biological replicate 1 technical replicate1


title: Human rep 3 neurons H3K27ac ChIP 0hr post-KCl stim

data_processing:
ChIP-Seq reads were aligned to the human genome (GRCh37/hg19 assembly) using BWA with default parameters, keeping only uniquely mapped reads.  Aligned ChIPseq reads were extended to 300bp to match the median length of the sequenced DNA fragments.  BigWig tracks display the data normalized to 20 million reads per experimental condition.
genome build: hg19
processed data files format and content: Standard bigWig-formatted files (.bw) for both human and mouse RNA-seq samples represent bwa-aligned reads piled up with single-base-pair resolution and then averaged over tiles of width 20bp.  Each set of fragment-end (#1 or #2) reads for a sample have their own pair of tracks for POS & NEG strands, i.e., so there are 4 tracks per sample.

source_name: ScienCell

growth_protocol: Human neuronal cultures from five and two different individuals were grown for RNA-seq and ChIP-seq experiments, respectively, according to the supplier’s instructions (ScienCell).

extract_protocol:
The mini-ChIP assays were performed (as described in Adli and Bernstein, 2011) on human neuronal cells that had been cultured for around two weeks.  Cells were cross-linked, lysed, sonicated for 3.5 minutes using a Branson 250, and the fragmented chromatin was immunoprecipated overnight with 1ug of H3K27Ac (abcam Cat# ab4728) and H3K27me3 (Millipore Cat# 074490) antibodies.  After samples were incubated with Protein A-Sepharose beads for 2 hours they were collected and washed; the DNA was eluted from the beads twice at 65°C for 10 minutes; the eluted chromatin and the "input" samples were reverse cross-linked at 65°C for 5 hours, then Proteinase K digested at 37°C for 2 hours.  The ChIP DNA was recovered by standard phenol-chloroform-isoamyl alcohol extraction, then precipitated overnight with ethanol.
The ChIP DNA libraries were constructed using ChIP-Seq DNA Sample Prep Kit (Illumina) and sequenced using HiSeq 2000 (Illumina) in the Biopolymers facility at Harvard Medical School with non-strand-specific and single-end protocol for ChIP-Seq.

value: fetal brain

tag: Sex

value: male


title: ESC norm biological replicate 2

source_name: 5C ESC

value: 46c ESCs


title: ESC norm biological replicate 1


title: Human rep 2 neurons H3K27ac ChIP 0hr post-KCl stim

value: female


title: Human rep 2 neurons H3K4me3 ChIP


title: Human rep 2 neurons H3K4me1 ChIP


title: Human rep 2 neurons Input DNA for ChIP


title: Human rep 5 neurons 0hr post-KCl stim

data_processing:
For RNA-Seq of human fetal brain cultures, strand-specific paired-end 76-bp reads were mapped to the hg19 genome using BWA (v.0.6.2) allowing up to 5 mismatches; only #1 ends of fragment pairs were used in subsequent analyses.  The usual 24 chromosomal alignment targets were supplemented with ~7 million short sequences representing all possible intragenic exonic sets from the hg19 RefSeq annotation whose junctions are spannable by 76-bp reads.  Typically 75-95% of all reads in each library were mappable and ~90% of these aligned uniquely; nonuniquely mapped reads were discarded.
The exons for all transcripts assigned to a gene based on the RefSeq annotation for human 37.1 (12 March 2009) were merged (unioned); along with the constructed library of splice-junction sequences these defined each gene's mature-RNA target region.  The total number of bases of all reads that overlapped a gene's exonic region were divided by the total length of the region to yield an average read Density (coverage).  Normalization of Densities to a standard of 10M 35-bp reads was effected by multiplying the raw Density by (10M/R)*(35/76), where R is the total number of uniquely mapped reads in a sample that did not overlap any RepeatMasker rRNA elements (RPKM units proportional to Normalized Density units via  RPKM = Density/0.35).
Note:  Some of the human samples derived from distinct sequencing runs using reads of different length.  For consistency, reads longer than 76 bp (100 bp and 101 bp) were truncated to 76bp at their 3' ends before .fastq files from different runs were concatenated together.
For RNA-Seq of cultured mouse cortical cells, strand-specific 76-bp paired-end were mapped to the mm9 genome using BWA, with subsequent analyses the same as described for human but based on the RefSeq annotation for mouse 37.1 (5 July 2007).
genome build: hg19
processed data files format and content: Standard bigWig-formatted files (.bw) for both human and mouse RNA-seq samples represent bwa-aligned reads piled up with single-base-pair resolution and then averaged over tiles of width 20bp.  Each set of fragment-end (#1 or #2) reads for a sample have their own pair of tracks for POS & NEG strands, i.e., so there are 4 tracks per sample.

extract_protocol:
The mini-ChIP assays were performed (as described in Adli and Bernstein, 2011) on human neuronal cells that had been cultured for around two weeks.  Cells were cross-linked, lysed, sonicated for 3.5 minutes using a Branson 250, and the fragmented chromatin was immunoprecipated overnight with 1ug of H3K27Ac (abcam Cat# ab4728) and H3K27me3 (Millipore Cat# 074490) antibodies.  After samples were incubated with Protein A-Sepharose beads for 2 hours they were collected and washed; the DNA was eluted from the beads twice at 65°C for 10 minutes; the eluted chromatin and the "input" samples were reverse cross-linked at 65°C for 5 hours, then Proteinase K digested at 37°C for 2 hours.  The ChIP DNA was recovered by standard phenol-chloroform-isoamyl alcohol extraction, then precipitated overnight with ethanol.
The libraries for RNA-Seq were constructed using the PE RNAseq library kit (Illumina).


title: Human rep 5 neurons 6hr post-KCl stim


title: Human rep 4 neurons 6hr post-KCl stim


title: Human rep 4 neurons 1hr post-KCl stim


title: Human rep 3 neurons 6hr post-KCl stim


title: Human rep 5 neurons 1hr post-KCl stim


title: Human rep 4 neurons 0hr post-KCl stim


title: Human rep 2 neurons 1hr post-KCl stim


title: Human rep 2 neurons 6hr post-KCl stim


title: Human rep 3 neurons 1hr post-KCl stim


title: Human rep 3 neurons H3K27ac ChIP 6hr post-KCl stim


title: Human rep 2 neurons H3K27ac ChIP 6hr post-KCl stim


title: Human rep 1 neurons 0hr post-KCl stim


title: Human rep 1 neurons 6hr post-KCl stim


title: Human rep 2 neurons 0hr post-KCl stim


title: Human rep 1 neurons 1hr post-KCl stim


title: Mouse rep 3 cortical neurons 6hr post-KCl stim

value: E16.5 cortex, cultured, DIV7


title: Mouse rep 2 cortical neurons 6hr post-KCl stim


title: Mouse rep 3 cortical neurons 0hr post-KCl stim


title: Mouse rep 3 cortical neurons 1hr post-KCl stim


title: Mouse rep 2 cortical neurons 1hr post-KCl stim


title: Mouse rep 2 cortical neurons 0hr post-KCl stim


title: DOHH2 CUDC-907 2nM_12hr

city: Lexington

first: Kaiming

last: Sun

address: 4 Maguire Rd.

department: Translational Science

institute: Curis

data_processing:
mapped the sequencing reads to the  hg19) and gencode v19 using the software RNA STAR (v2.4.0j), which can align reads across splice junctions with or without gene annotations
did transcript abundance estimation with featureCounts (v1.4.6), using gene annotations from the database gencode v19. And FPKM values were calculated with R package edgeR (v3.8.5)
Most annotated genes can’t be detected in one given sample. So we removed genes whose mean FPKM values across all samples were less than 1, before the gene expression densities were plotted.
Genome_build: hg19 and gencode v19

growth_protocol: Cell lines were purchased from the German Collection of Microorganisms and Cell Cultures and were maintained as recommended by the source. Growth media was changed every 2 to 3 days and cells were maintained at a density of 2 x 10^6 to 4 x 10^6 cells/mL. Cells at exponential growth stage were used for the experiment

extract_protocol:
Cells were pelleted by centrifugation at 10,000 x g at 4°C for 10 min, and immediately lysed in buffer RLT Plus (QIAGEN). RNA was purified from lysed cells using RNeasy columns (QIAGEN) following the manufacturer instructions.
Total RNA input was used to construct RNASeq libraries using the TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer instructions.

treatment_protocol: Cells were seeded at densities of 3 x 10^5 per mL in 24-well plates with the recommended culture medium and incubated with CUDC-907 at various concentrations for 6 or 12 hours.

value: B cell lymphoma

tag: cell line

tag: treatment

value: CUDC-907 2nM 12hr


title: DOHH2 Control_12hr

value: control 12hr