title: SELEX-seq of CstF64tau

status: Public on Sep 30 2013

city: Irvine

first: Yongsheng

last: Shi

address: University of California, Irvine B240, Med Sci I

institute: University of California, Irvine

data_processing:
Library strategy: SELEX-Seq
iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to build hg19 of the human genome using bowtie
iCLIP-seq reads were mapped to hg19 using Bowtie
Direct RNA sequencing: Reads were filtered and mapped to hg19 using indexDPgenomic tool in Helisphere (www.Helicosbio.com)
SELEX-seq:  Raw data were debarcoded and the adaptor sequences were removed from both sides. The remaining 20nt sequence were then used for the enrichment analysis.
For the 20nt sequences obtained from SELEX-seq, we collect all 10mers and calculate the frequency of all 10mers. And then check each 10mer's enrichment level by compute its frequency ratio in CstF64/tau to that in control, the SELEX_CstF64_and_CstF64tau_enrichment_level.txt file listed 10mers and its corresponding enrichment level of CstF64 and CstF64tau
Genome_build: hg19
Supplementary_files_format_and_content: .bed files are bed format; .txt files are tab-delimited text files

organism: synthetic construct

source_name: In vitro synthesized

growth_protocol: DMEM + 10% fetal bovine serum

extract_protocol:
In vitro synthesized RNAs bound to GST-CstF64tau-RRM were amplified by RT-PCR and sequenced on Illumina Hi-Seq
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen)

treatment_protocol: HeLa cells were transfected with shRNA construct and/or siRNAs using Lipofectamine 2000 (Invitrogen)

tag: sample type


title: rL5

status: Public on Oct 01 2013

type: SRA

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

country: Germany

institute: University of Luebeck

description: One zoo colony

library_source: transcriptomic

data_processing:
Brain and liver samples were sequenced on seven different flow cells of an Illumina Genome Analyzer I. Sequencing data was analyzed starting from Illumina 'chastity' filtered FastQ files. For these files, quality scores were converted to PHRED-scale (Ewing and Green 1998). Heart, kidney and testis samples were sequenced on ten different flow cells on the Genome Analyzer II platform, and sequences called with Ibis (Kircher, Stenzel, and Kelso 2009).
PHRED-scaled FastQ files from both platforms were filtered for adapter and chimera sequences (Kircher, Heyn, and Kelso 2011) and reads with at least 9nt of the adapter sequence (TCGTATGCCGTCTTCTGCTTG) at the read end removed. The last read base (the first adapter base) of the remaining 18nt reads was clipped off, and reads with more than 1 base below a quality score of 10 were discarded. Further, reads with sequence entropy below 0.85 were removed, as these are likely to originate from flow cell artifacts (Kircher, Heyn, and Kelso 2011).
We extended the reads by a 'CATG' restriction motif and aligned these using bowtie 0.12.4 (Langmead et al. 2009) to the following versions of the human, chimpanzee and rhesus macaque genomes: hg19/GRCh37 (excluding additional haplotypes), pantro2/CGSC 2.1 and rhemac2/MGSC Merged 1.0 (with the addition of a mitochondrial genome sequence from the Ensembl MMUL_1.54 build). Bowtie was configured to report up to 100 equally good alignments (with up to two mismatches) and to discard reads that produce more than 100 alignments (parameters -a -m 100 --best --strata).
We used the non-symmetrical UCSC liftOver chains and the command line tool liftOver in a reciprocal manner, to transfer gene start and end coordinates of the human Ensembl v59 annotation separately, and required the projected coordinates to be on the same chromosome and strand. Further, the new gene length was not permitted to change length by more than a factor of 10, or at most 100kb. The rhesus genome does not include a mitochondrial genome in the assembly version provided by UCSC. Hence, all 37 mitochondrially encoded genes were projected using a ClustalW (Thompson, Higgins, and Gibson 1994) mitochondrial genome alignment of the three species. From a total of 51,715 genes, 43,020 (83%) could be projected to chimpanzee and 33,259 (64%) to chimpanzee and rhesus macaque.
For quantifying gene expression, bowtie outputs of mapped tags were sorted by coordinates. Per-site counts were determined and sites observed fewer than three times were removed, to reduce the effect of including erroneous alignments in long transcripts.
Genome_build: hg19/GRCh37, pantro2/CGSC 2.1 and rhemac2/MGSC Merged 1.0

molecule: polyA RNA

organism: Macaca mulatta

extract_protocol:
Samples were obtained from brain (pre-frontal cortex), heart, kidney, liver, and testis tissues of male humans, chimpanzees and rhesus macaques. Samples were processed in tissue batches, randomizing species in library preparation and sequencing.
Illumina NlaIII DGE libraries for all samples were generated following the vendor protocol. Expressed 3' tags from polyA RNAs

tag: Sex

value: male

tag: age

tag: rin

tag: tissue

value: liver


title: SELEX-seq of CstF64

state: CA

country: USA

molecule: total RNA

extract_protocol:
In vitro synthesized RNAs bound to GST-CstF64-RRM were amplified by RT-PCR and sequenced on Illumina Hi-Seq
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen)


title: SELEX-seq of RNA control pool

extract_protocol:
In vitro synthesized RNAs were amplified by RT-PCR and sequenced on Illumina Hi-Seq
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen)

value: RNA control pool


title: AH_CSFemale_3

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Medicine Biomedical Sciences

institute: Florida State University

data_processing:
Basecalls performed using CASAVA version 1.3
Barcode, primer, and adapter sequences were trimmed using custom perl scripts..
Reads were aligned to the D. melanogaster genome FB5.30 (FlyBase v5.30) using Bowtie (v0.12.8; --tryhard, --best, --strata, -m1).
Unaligned reads were 3’ end quality trimmed and homopolymers (5+) were removed. Quality trimmed reads were mapped again using bowtie.
Unaligned reads were aligned to junctions estimated by Tophat.
Any remaining unaligned reads were mapped to FB5.30 genome using LAST (v193; -l 20, -Q3).
Using FlyBase annotions, overlapping exons regardless of strand were combined into the maximum exonic region.
Expression was then quantified for each exonic region using Reads Per Kilobase Per Million Mapped Reads (RPKM).
Genome_build: Flybase 5.30
Supplementary_files_format_and_content: Are in the CSV format. With the following columns: exonic region id, sample id, number of mapped reads, number of reads in the exonic region, coverage in exonic region (number of reads in exonic region / read length), exonic region length, average per nucleotide coverage, RPKM.

organism: Drosophila melanogaster

source_name: Adult Head Tissue

growth_protocol: Flies were raised on standard cornmeal food medium at 25˚C on a 12 hour light and 12 hour dark cycle.

extract_protocol:
Total RNA was extracted using TRIzol® Reagent (Invitrogen), and RNA was precipitated by addition of 250 µL 100% isopropanol and 250 µL 1.2 M NaCitrate, 0.8 M NaCl in DEPC-treated water. The Zymo Research RNA Clean & Concentrator™-25 In-Column DNase Digestion protocol and 10 units Ambion® TURBO™ DNase was used on ~25 µg total RNA. Poly(A)+ transcripts were subsequently isolated from total RNA using Ambion® MicroPoly(A)Purist™ Kit.
One hundred ng mRNA was chemically fragmented to a range of approximately 200-500 base pairs using the Ambion® RNA Fragmentation Reagent, and the reaction was cleaned using Zymo Research RNA Clean & Concentrator™-5. First strand cDNA was synthesized using SuperScript® II Reverse Transcriptase (Invitrogen™) and a combination of 3 µg random hexamers and 0.15 µg oligo(dT)20 primers. The second strand of the cDNA was synthesized using DNA polymerase I (Invitrogen™), RNase H (New England Biolabs® Inc.), dNTPs and second strand buffer (Invitrogen™). This reaction and all subsequent reactions were cleaned using Zymo Research DNA Clean & Concentrator™-5 kit. Double stranded cDNA templates were blunt ended using End-It™ Repair Kit (Epicentre®). A-overhangs were added to both ends with Klenow fragment (3'→5' exo-minus) (New England Biolabs® Inc.) and Illumina sequencing adapters were then ligated to both ends of the cDNA templates using Fast-Link™ DNA Ligation Kit (Epicentre®). cDNA templates were  amplified by performing PCR for 18 cycles, which extended the adapter and incorporated a different six base pair index into each sample. The product was then isolated by gel purification of 250-550 base pair fragments.

tag: strain

value: Canton-S

tag: genotype

value: wild type

value: Female

tag: developmental stage

value: adult

value: head


title: AH_CSFemale_2


title: wild type_48hpi reps1-3

city: Honolulu

first: Yangrae

last: Cho

state: HI

address: 3190 Maile Way, St John 317

department: Plant and Environmental Protection Sciences

institute: University of Hawaii at Manoa

description: enriched polyA RNA

data_processing:
Image analysis, base-calling, and quality checks were performed with the Illumina data analysis pipeline CASAVA v1.8.0.
The sequenced reads were mapped to the genome sequence of Al. brassicicola (version 1; http://jgi.doe.gov/Abrassicicola) and the latest genome release of Ar. thaliana (TAIR10 ) (ftp://ftp.arabidopsis.org/home/tair/Genes/) using the programs Tophat 1.3.1 (Trapnell et al., 2009) and Bowtie 0.12.7 (Langmead et al., 2009).
The program Cuffdiff version 1.0.3 (which is part of Cufflinks, (Trapnell et al., 2010)) was used to identify reads overlapping with previously predicted genes.
The expression levels of each predicted gene were determined and normalized by the mapped Fragments Per Kilobase of exon model per Million (FPKM).  Differentially expressed genes between the wild type and the mutant were determined by comparing FPKM from three biological replicates for both the wild type and the mutant.  We also applied a cutoff of at least a two-fold change in expression value for differential expression.  The bias correction method was used while running Cuffdiff (Roberts et al., 2011).
Genome_build: genome sequence of Al. brassicicola (version 1; http://jgi.doe.gov/Abrassicicola)
Genome_build: genome release of Ar. thaliana (TAIR10 )
Supplementary_files_format_and_content: Altbr1_expression_12hpi_48hpi.txt: ProteinId, A12W (normalized expression level of gene in the wild type Alternaria), A12F2 (normalized expression level of gene in the abpf2 mutant Alternaria), A48W (normalized expression level of gene in the abpf2 mutant Alternaria), A48F2 (normalized expression level of gene in the abpf2 mutant Alternaria), PFAM annotation, GO annotation, A12W -> A12F2: Up/Down, A12W -> A12F2: q value, A12W -> A12F2: >2-fold and significant difference?, A12W -> A48W: Up/Down, A12W -> A48W: q value, A12W -> A48W: >2-fold and significant difference?, , , A12F2 -> A48F2: Up/Down, A12F2 -> A48F2: q value, A12F2 -> A48F2: >2-fold and significant difference?, A48W -> A48F2: Up/Down, A48W -> A48F2: q value, A48W -> A48F2: >2-fold and significant difference?
Supplementary_files_format_and_content: Arabidopsis_expression_12hpi_48hpi.txt: ProteinId, A12W (normalized expression level of plant gene inoculated with wild type Alternaria), A12F2 (normalized expression level of plant gene inoculated with abpf2 mutant Alternaria), A48W, A48F2, PFAM annotation, GO annotation, A12W -> A12F2: Up/Down, A12W -> A12F2: q value, A12W -> A12F2: >2-fold and significant difference?, A12W -> A48W: Up/Down, A12W -> A48W: q value, A12W -> A48W: >2-fold and significant difference?, , , A12F2 -> A48F2: Up/Down, A12F2 -> A48F2: q value, A12F2 -> A48F2: >2-fold and significant difference?, A48W -> A48F2: Up/Down, A48W -> A48F2: q value, A48W -> A48F2: >2-fold and significant difference?

organism: Alternaria brassicicola

source_name: tissues containing both Arabidopsis thaliana plant leaves and Alternaria brassicicola fungal mycelia

growth_protocol: Arabidopsis thaliana (Col-0) were grown under 8/14 light and dark cycle for 5 weeks.

extract_protocol: Total RNA was extracted from mixed tissues of plant leaves and fungal mycelia.  PolyA RNA was enriched and libraries were constructed using TruSeq RNA sample prep kit (Illumina)

treatment_protocol: Arabidopsis thaliana was infected with either wild type or abpf2 deletion mutant

tag: fungal pathogen

value: Alternaria brassicicola

tag: pathogen genotype/variation

tag: infected host plant

value: Arabidopsis thaliana

value: early germination stage

tag: time


title: direct RNA sequencing (DRS) of CstF64tau-RNAi cells

data_processing:
iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to build hg19 of the human genome using bowtie
iCLIP-seq reads were mapped to hg19 using Bowtie
Direct RNA sequencing: Reads were filtered and mapped to hg19 using indexDPgenomic tool in Helisphere (www.Helicosbio.com)
SELEX-seq:  Raw data were debarcoded and the adaptor sequences were removed from both sides. The remaining 20nt sequence were then used for the enrichment analysis.
For the 20nt sequences obtained from SELEX-seq, we collect all 10mers and calculate the frequency of all 10mers. And then check each 10mer's enrichment level by compute its frequency ratio in CstF64/tau to that in control, the SELEX_CstF64_and_CstF64tau_enrichment_level.txt file listed 10mers and its corresponding enrichment level of CstF64 and CstF64tau
Genome_build: hg19
Supplementary_files_format_and_content: .bed files are bed format; .txt files are tab-delimited text files

organism: Homo sapiens

source_name: Stable HeLa cell line

extract_protocol:
RNAs were extracted from cells using Trizol reagent (Invitrogen) and directly sequenced on the Helicos platform as described in Yao et al PNAS 46): 18773-8.
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen)

tag: cell line

value: HeLa


title: AH_Male_FruM(C)_3

value: P(w+mC, UAS-Gal4)/P(w+mC, UAS-FruMC); fru P1-Gal4/+

value: Male


title: Δabpf2_48hpi reps1-3

description: enriched polyA RNA

value: abpf2 deletion mutant

value: mixed tissues of plant leaves and fungal mycelia


title: AH_CSFemale_1


title: AH_Male_FruM(C)_1


title: AH_Female_FruM(C)_3


title: AH_Male_FruM(C)_2


title: AH_Female_FruM(C)_1


title: wild type_12hpi reps1-3

description: enriched polyA RNA

data_processing:
Image analysis, base-calling, and quality checks were performed with the Illumina data analysis pipeline CASAVA v1.8.0.
The sequenced reads were mapped to the genome sequence of Al. brassicicola (version 1; http://jgi.doe.gov/Abrassicicola) and the latest genome release of Ar. thaliana (TAIR10 ) (ftp://ftp.arabidopsis.org/home/tair/Genes/) using the programs Tophat 1.3.1 (Trapnell et al., 2009) and Bowtie 0.12.7 (Langmead et al., 2009).
The program Cuffdiff version 1.0.3 (which is part of Cufflinks, (Trapnell et al., 2010)) was used to identify reads overlapping with previously predicted genes.
The expression levels of each predicted gene were determined and normalized by the mapped Fragments Per Kilobase of exon model per Million (FPKM).  Differentially expressed genes between the wild type and the mutant were determined by comparing FPKM from three biological replicates for both the wild type and the mutant.  We also applied a cutoff of at least a two-fold change in expression value for differential expression.  The bias correction method was used while running Cuffdiff (Roberts et al., 2011).
genome build: genome sequence of Al. brassicicola (version 1; http://jgi.doe.gov/Abrassicicola)
genome build: genome release of Ar. thaliana (TAIR10)

Supplementary_files_format_and_content: Altbr1_expression_12hpi_48hpi.txt: ProteinId, A12W (normalized expression level of gene in the wild type Alternaria), A12F2 (normalized expression level of gene in the abpf2 mutant Alternaria), A48W (normalized expression level of gene in the abpf2 mutant Alternaria), A48F2 (normalized expression level of gene in the abpf2 mutant Alternaria), PFAM annotation, GO annotation, A12W -> A12F2: Up/Down, A12W -> A12F2: q value, A12W -> A12F2: >2-fold and significant difference?, A12W -> A48W: Up/Down, A12W -> A48W: q value, A12W -> A48W: >2-fold and significant difference?, , , A12F2 -> A48F2: Up/Down, A12F2 -> A48F2: q value, A12F2 -> A48F2: >2-fold and significant difference?, A48W -> A48F2: Up/Down, A48W -> A48F2: q value, A48W -> A48F2: >2-fold and significant difference?
Linked as supplementary file on Series record.
Supplementary_files_format_and_content: Arabidopsis_expression_12hpi_48hpi.txt: ProteinId, A12W (normalized expression level of plant gene inoculated with wild type Alternaria), A12F2 (normalized expression level of plant gene inoculated with abpf2 mutant Alternaria), A48W, A48F2, PFAM annotation, GO annotation, A12W -> A12F2: Up/Down, A12W -> A12F2: q value, A12W -> A12F2: >2-fold and significant difference?, A12W -> A48W: Up/Down, A12W -> A48W: q value, A12W -> A48W: >2-fold and significant difference?, , , A12F2 -> A48F2: Up/Down, A12F2 -> A48F2: q value, A12F2 -> A48F2: >2-fold and significant difference?, A48W -> A48F2: Up/Down, A48W -> A48F2: q value, A48W -> A48F2: >2-fold and significant difference?
Linked as supplementary file on Series record.


title: AH_Male_FruM(B)_1

value: P(w+mC, UAS-Gal4)/P(w+mC, UAS-FruMB); fru P1-Gal4/+


title: AH_Male_FruM(B)_2


title: AH_Female_FruM(B)_2


title: AH_Male_FruM(A)_3

value: P(w+mC, UAS-Gal4)/P(w+mC, UAS-FruMA); fru P1-Gal4/+


title: AH_Female_FruM(B)_1


title: AH_Female_FruM(B)_3


title: AH_Male_FruM(A)_2


title: AH_Female_FruM(A)_2


title: AH_Male_FruM(A)_1


title: AH_Female_FruM(A)_3


title: AH_FruW12/ChaM5_2

value: unknown

value: fruw12/ Df(3R)ChaM5


title: AH_FruW12/ChaM5_3


title: AH_Female_FruM(A)_1


title: AH_FruW12/ChaM5_1


title: AH_FruW12/ChaM5_4


title: AH_FruP14/440_3


title: AH_Male_FruM(B)_3


title: Δabpf2_12hpi reps1-3

description: enriched polyA RNA


title: AH_FruP14/440_4


title: AH_FruP14/440_2


title: AH_CS_3

value: Canton-S


title: AH_FruP14/440_1


title: AH_Female_FruM(C)_2


title: AH_BerM_3

value: Berlin

value: wild type


title: AH_BerM_2

value: adult


title: AH_BerF_2

value: Female

value: head


title: AH_BerF_3


title: AH_BerF_1


title: AH_CS_1


title: AH_CS_4


title: AH_BerM_1


title: AH_CS_2


title: Input

city: Vienna

first: Meinrad

last: Busslinger

address: Dr. Bohrgasse 7

country: Austria

institute: Instutute of Molecular Pathology

library_source: genomic

data_processing:
Basecalling: RTA 1.8.70.0
alignment: bowtie 0.12.5  -S -p 10 --trim5 0 --trim3 0 -v 2 --best --strata --tryhard -m 1 --phred33-quals --chunkmbs 256
genome build: NCBI37

molecule: genomic DNA

organism: Mus musculus

source_name: Pro-B cell

growth_protocol: Rag2–/– and Pax5–/– Rag2–/– pro-B cells were cultured on OP9 cells in IL-7 containing IMDM as described (Nutt et al., 1997).

extract_protocol:
About 5x107 pro-B cells were used for  chromatin precipitation by streptavidin pulldown (Bio-ChIP) Ebert et al., 2011
The precipitated genomic DNA was quantified by real-time PCR, and at least 5 ng of ChIP-precipitated DNA were used as starting material for the generation of paired-end sequencing libraries as described by Illumina’s ChIP Sequencing sample preparation protocol followed by size selection of DNA fragments of 200–350 bp. Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS library quantification kit.

tag: cell type

value: in vitro cultured Pro-B cells (4d)


title: PAIR4-HD 10226 62M7DAAXX 6

data_processing:
Basecalling (see below)
splitting with 3 mismatches by the primer sequence
truncation os split reads at restriction enzyme site in the primer sequence
truncation of reads at 3' end to 55nt
alignment of reads using bowtie 12.5 -v 2 --best --strata --tryhard -m 1 --chunkmbs 256
Genome_build: mm9
Supplementary_files_format_and_content: bed files of alignment
Supplementary_files_format_and_content: for all 62* files (Samples 1-33), basecalling is OLB v. 1.8; for other fastq files, basecalling is RTA VN:1.12.4.2.

source_name: cultured cells

extract_protocol:
Pro-B cells isolated from the bone marrow of Rag2–/–, Eμ–/– Rag2–/–, 3’RR–/– Rag2–/–, IGCR1/CBE–/– Rag2–/– and homozygous JHT mice were expanded in vitro for 4 days on OP9 cells in the presence of IL-7. Pro-B cells from the bone marrow of Rag2–/– and Rag1Cre/+ Yy1fl/fl mice were stained with CD19-PE antibody and anti-PE MACS beads prior to MACS-sorting, resulting in a purity of 94% (Figure S6B). Total thymocytes were isolated from wild-type C57BL/6J mice by passing the thymi through cell strainers and removing the dead cells by density centrifugation (Lympholyte M, Cedarlane Lab. [CEDCL5031]).
The 4C-seq experiments were performed as previously described (Simonis et al., 2007) with the following modifications. For sequestration of SDS, 50 μl of 20% Triton-X 100 was incubated with the chromatin for 2-3 hours. The total amount of the primary restriction enzyme (HindIII, EcoRI or BglII) equaled 700 U and was added as follows: 300 U overnight, 200 U for 4 hours and finally 200 U for another 4-6 hours. In the second digestion round with the secondary restriction enzyme, the ligation products were incubated with 50 U of NlaIII (NEB, R0125S) overnight or 150 U of DpnII (NEB, R0543T), which were added sequentially (50 U) as described above. The digested chromatin was ligated overnight at 16oC followed by a 1 hr incubation at room temperature both for the first and the second ligation step. After ethanol precipitation, the final 4C template was purified twice using the Wizard® SV Gel and PCR Clean-Up System (Promega, A9282), each time with one column per sample prepared from 1x107 cells. The DNA concentration was measured using the Nanodrop spectrophotometer. Approximately 20 μg of 4C template was obtained from 1x107 pro-B cells. For each viewpoint, 16 individual PCR amplifications were performed with ~150 ng of 4C template each by using specific primers that were extended with Illumina sequencing adaptors. Thus, ~2.4 μg of 4C template corresponding to approximately 1x106 pro-B cells were analyzed for each viewpoint. The amplification consisted of 35 PCR cycles because 30 cycles resulted in too little product to be visualized. The PCR products of pooled reactions were purified using the Wizard® SV Gel and PCR Clean-Up System (Promega). After column purification, the PCR products obtained with the third Rag2–/– and Pax5–/– Rag2–/– replica 4C templates as well as the Eμ–/– Rag2–/–, 3’RR–/– Rag2–/–, IGCR1/CBE–/– Rag2–/– and Rag1Cre/+ Yy1fl/fl 4C templates were selected for a fragment size below 1 kb as follows. Ten percent of purified and pooled reactions were quantified on an agarose gel by measuring ethidium-bromide incorporation. Equal amounts of PCR products between 100 and 1000 bp, that were prepared from cells of the same genotype, were pooled and separated on a 2% agarose gel (Lonza [Nusieve GTG agarose, 50080]). After cutting out the lanes, agarose was degraded with β-agarase I enzyme (NEB, M0392L). The DNA was extracted twice with phenol and precipitated with ethanol after phenol removal with chloroform. The precipitate was dissolved in 10 mM Tris pH 8 and quantified by the Bioanalyzer instrument.

value: pro B cell

tag: primer

value: hindiii

value: dpnii

value: TGTAGTGGAACAATACTCTAAGCTT

value: CTTAGAGAGAATAAGATTTGTCTAATGT


title: PAIR4-HD 9697 62M2WAAXX 6


title: Emu-HD 9691 62M2WAAXX 5

value: wt

value: TGCCTCAGACTTCAAGCTT

value: GGGAAATAAACTGTCTAGGGAT


title: HS8-ED 10234 62M7DAAXX 6

value: ecori

value: GACACTGGCCCTCAGAAT

value: TGGAACAGTGGAGTCAGAT


title: HS3B-HD 9683 62M2WAAXX 4

value: T cells

value: CCCACCTAACTCCAAGCTT

value: CAGACATGTGGGCTGAGAT


title: Pro-B cell Yy1(ihCd2/+ ) Rag2(-/-) R26(BirA/BirA)

data_processing:
alignment: bowtie 0.12.5  -S -p 10 --trim5 0 --trim3 0 -v 2 --best --strata --tryhard -m 1 --phred33-quals --chunkmbs 256
genome build: NCBI37
processed data files format and content: bed files of alignment

extract_protocol: Pro-B cells isolated from the bone marrow of Yy1ihCd2/+ Rosa26BirA/BirA Rag2–/– mice were expanded in vitro for 4-5 days on OP9 cells in the presence of IL-7. About 5x107 pro-B cells were used for chromatin precipitation by streptavidin pulldown (Bio-ChIP), as recently described in detail (Ebert et al., 2011). The precipitated genomic DNA was quantified by real-time PCR, and at least 5 ng of ChIP-precipitated DNA were used as starting material for the generation of paired-end sequencing libraries as described by Illumina’s ChIP Sequencing sample preparation protocol followed by size selection of DNA fragments of 200–350 bp. Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS library quantification kit. Cluster generation and paired-end sequencing was carried out by using the Illumina GAIIx system according to the manufacturer’s guidelines, which yielded a read length of 76 bp for each end of a DNA fragment. Peaks were called using the MACS program version 1.3.6.1 (Zhang et al., 2008) with default parameters, a read length of 76, a genome size of 2,654,911,517 bp (mm9) and the appropriate input control sample. Peaks were filtered for p-values of < 10-10.

value: Yy1(ihCd2/+ ) Rag2(-/-) R26(BirA/BirA)

value: Pro-B cell

value: Dynabeads M-280 Streptavidin (Invitrogen)

tag: antibody


title: J558.89-HD 10230 62M7DAAXX 6

value: pro B cell

value: AAAGGCATGTTAGCTAAGCTT

value: CATTCTCCATCCATTAGGATC


title: HS3B-HD 9692 62M2WAAXX 5

value: hindiii

value: dpnii


title: Emu-HD 9682 62M2WAAXX 4

value: wt


title: PAIR8-HD 9124 628NCAAXX 8

value: TGGTATATGGAAAGGAAGC

value: GGCAGGATGGATTTTCTC


title: Emu-HD 9124 628NCAAXX 8

value: TGCCTCAGACTTCAAGCTT

value: GGGAAATAAACTGTCTAGGGAT


title: PAIR5-HD 9124 628NCAAXX 8

value: AATCAGTCAGCTACACAAGC

value: CGACACCAAACCTAATCAAG


title: PAIR4-HD 9124 628NCAAXX 8

value: TGTAGTGGAACAATACTCTAAGCTT

value: CTTAGAGAGAATAAGATTTGTCTAATGT


title: 7183.16-HD 9124 628NCAAXX 8

value: TCCCCTAGACTTCTCAAGC

value: GTTGGACCTAACATATTCAGG


title: J558.89-HD 9124 628NCAAXX 8


title: PAIR8-HD 9123 628NCAAXX 7


title: PAIR5-HD 9123 628NCAAXX 7


title: Emu-HD 9123 628NCAAXX 7


title: ESC_Control_H33B-HA

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

data_processing:
ChIP-seq reads were aligned at 36bp to the mm9 genome assembly using Bowtie.
duplicates removed using samtools
wig files made using igvtools and normalized based on read counts
peak calling using MACS
Genome_build: mm9

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA or 1.5 mM EGS followed by 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina protocol.

value: anti-HA (12CA5)


title: 7183.16-HD 9123 628NCAAXX 7

value: pro B cell


title: Emu-HD 9063 6224PAAXX 3


title: PAIR8-HD 9063 6224PAAXX 3


title: PAIR4-HD 9123 628NCAAXX 7


title: PAIR5-HD 9063 6224PAAXX 3


title: PAIR4-HD 9063 6224PAAXX 3


title: 7183.16-HD 9063 6224PAAXX 3


title: HS3B-HD 9063 6224PAAXX 3

value: CCCACCTAACTCCAAGCTT

value: CAGACATGTGGGCTGAGAT


title: Emu-HD 9062 628NCAAXX 6

value: hindiii


title: HS3B-HD 9124 628NCAAXX 8

value: dpnii


title: PALB2 sh-lane2

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

description:
Sample 11
processed data file: PALB2sh_Forward.wig
processed data file: PALB2sh_Reverse.wig

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
alignment: BOWTIE v 0.12.7 (default parameters)
tag density files: genomeCoverageBed (from BEDTools suite)
Genome_build: hg 18

source_name: MCF10A_PALB2 sh_RNA-seq strand specific

extract_protocol: ScriptSeqv2 kit along with ScriptSeq Index PCR primers (Epicentre)

value: breast epithelial cells

tag: genotype/variation

value: PALB2 knockdown (shRNAs)

value: RNA-seq strand specific

tag: molecule subtype

value: total RNA - ribosome depleted


title: PALB2 sh-lane1

description:
Sample 10
processed data file: BRCA1sh_Forward.wig
processed data file: BRCA1sh_Reverse.wig

tag: sample type


title: PAIR4-HD 9062 628NCAAXX 6


title: 7183.16-HD 9062 628NCAAXX 6


title: PAIR5-HD 9062 628NCAAXX 6


title: CTRL sh-lane1

description:
Sample 6
processed data file: CTRLsh_Forward.wig
processed data file: CTRLsh_Reverse.wig

source_name: MCF10A_CTRL sh_RNA-seq strand specific


title: CTRL sh-lane2

description:
Sample 7
processed data file: BRCA1sh_Forward.wig
processed data file: BRCA1sh_Reverse.wig


title: PolyA+ RNA - lane2

description:
Sample 5
processed data file: RNAPolyA.bedGraph

source_name: MCF10A_PolyA+ RNA-seq

extract_protocol: Epicentre (Illumina) mRNA-seq kit

value: RNA-seq

value: polyA RNA


title: BRCA1 sh-lane2

description:
Sample 9
processed data file: CTRLsh_Forward.wig
processed data file: CTRLsh_Reverse.wig

source_name: MCF10A_BRCA1 sh_RNA-seq strand specific

value: BRCA1 knockdown (shRNAs)


title: PALB2

description: Sample 2

extract_protocol: ChIP-Seq DNA Sample Prep Kit (Illumina, inc.)

value: ChIP-seq

value: immunoprecipitated DNA

tag: chip-seq antibody

value: anti-PALB2 rabbit polyclonal

tag: chip-seq antibody vendor

value: Bethyl

tag: chip-seq antibody cat. #


title: HS3B-HD 9123 628NCAAXX 7

tag: strain


title: BRCA1 sh-lane1

description:
Sample 8
processed data file: PALB2sh_Forward.wig
processed data file: PALB2sh_Reverse.wig


title: PolyA+ RNA - lane1

description:
Sample 4
processed data file: RNAPolyA.bedGraph


title: HS3B-HD 9062 628NCAAXX 6

tag: genotype


title: BRCA1

description: Sample 1

value: anti-BRCA1 rabbit polyclonal I-20

value: Santa Cruz


title: Input_HCT116_Parental

city: Kansas City

first: Joan

last: Conaway

state: MO

institute: Stowers Institute

description: Input DNA from whole cell extract

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
Peaks were called for H3K4me1 and H3K27ac using the broad domain peak detector SICER v1.1 (Zang, C. et al, 2009) at the FDR < 1e-8, window size of 200, and gap size of 600. Peak detection of the other samples was done using MACS v1.4.2 (Zhang, Y. et al, 2008) . Associated control samples were used to determine statistical enrichment at a p-value < 1e-5 and FDR < 0.05. The enrichment of MLL4 in mouse ES cells was determined at a p-value < 1e-3.
Genome_build: UCSC hg19 and UCSC mm9
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

source_name: Colon cancer cell line

growth_protocol: Parental HCT116 and Mll4∆set HCT116 cells were previously described (Guo et al., 2012) and were grown in McCoy’s 5A medium with 10% FBS (Sigma). Mouse KH2 embryonic stem cells were grown in feeder-free medium ESGRO (Millipore, SF001-500)

extract_protocol:
ChIP assays were performed as previously described (Lee et al., 2006) . Briefly, 5x10^7 cells were crosslinked with 1% paraformaldehyde (Electron microscropy science #15710) at room temperature for 10 min and sonicated to generate chromatin fragments of 200-600bp. The sheared chromatin was immunoprecipated with a specific antibody.
ChIP libraries were prepared with the TruSeq DNA Sample Kit (Illumina #FC-121-2001) according to Illumina's instructions.

value: human colon cancer cell

tag: chip antibody


title: Input_HCT116_MLL4_delta_set

description: Input DNA from whole cell extract

value: Mll4∆set HCT116

value: human colon cancer cell with MLL4∆set


title: MLL4_mES

description: Chromatin IP of MLL4

source_name: ES cell culture

value: mouse embryonic stem cell

value: (rb) α-MLL4 (#403; Ali  Shilatifard)


title: Input_mES

description: Input DNA from whole cell extract


title: ESC_H33KD1_H3K27ac

growth_protocol: ESCs (C57Bl/6J background) were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cell were harvested and crosslinked in 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina protocol.

value: anti-H3K27ac (Ab4729)


title: ESC_H33KD1_H3K4me3


title: ESC_Control_H3K27ac


title: H3K4me3_HCT116_MLL4_delta_set

description: Chromatin IP of H3K4me3

value: (rb) α-H3K4me3 (#528; Ali  Shilatifard)


title: P-Ser2

description: Sample 3

value: breast epithelial cells

value: anti-P-ser2 RNAPII  rabbit polyclonal


title: ESC_Hira_null_Catch-it

data_processing:
Library strategy: CATCH-IT
reads aligned to mm9 at 51bp using bowtie
duplicates removed using samtools
wig files made using igvtools and normalized based on read counts
Genome_build: mm9

growth_protocol: ESCs (C57Bl/6J or 129S1/Sv background) were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
Samples were prepared as previously described (Deal et al, 2010). Briefly, cells were labeled with azidohomoalanine for 30 min. MNase digested chromatin was treated with biotin alkyne, and labeled chromatin was captured using streptavidin beads. Samples were treated with urea to remove non-H3 associated DNA, and remaining DNA was purified for use in library generation.
Libraries were constructed according to the Illumina protocol.


title: ESC_Control_H3K4me3


title: H3K4me3_HCT116_Parental

description: Chromatin IP of H3K4me3


title: PAIR8-HD 9062 628NCAAXX 6

value: pro B cell

value: hindiii

value: dpnii

value: TGGTATATGGAAAGGAAGC

value: GGCAGGATGGATTTTCTC


title: ESC_Hira_WT_Catch-it


title: H3K4me2_HCT116_MLL4_delta_set

description: Chromatin IP of H3K4me2

value: (rb) α-H3K4me2 (#527; Ali  Shilatifard)


title: ESC_H33KO1_Jmjd3

value: anti-Jmjd3 (rabbit polyclonal)


title: H3K4me2_HCT116_Parental

description: Chromatin IP of H3K4me2


title: ESC_H33KO1_UTX

value: anti-UTX (Ab84190)


title: H3K4me1_HCT116_MLL4_delta_set

description: Chromatin IP of H3K4me1

value: (rb) α-H3K4me1 (#524; Ali  Shilatifard)


title: ESC_WT_Jmjd3


title: H3K4me1_HCT116_Parental

description: Chromatin IP of H3K4me1

value: human colon cancer cell


title: ESC_H33KO2_Hira

value: anti-Hira (WC15/WC119)


title: ESC_WT_UTX


title: ESC_WT_Hira


title: MLL4_HCT116_Parental

description: Chromatin IP of MLL4


title: CstF64-tau iCLIP-seq

data_processing:
Library strategy: CLIP-Seq
iCLIP-seq: 1. Raw reads were demultiplexed using the sequencing barcode unique to each replicate and an additional random trinucleotide identifying individual DNA molecules was clipped but kept as metadata; 2. Reads with quality less than 20 for 10% or more of the bases were removed.3. We mapped the remaining reads to build hg19 of the human genome using bowtie
iCLIP-seq reads were mapped to hg19 using Bowtie
Direct RNA sequencing: Reads were filtered and mapped to hg19 using indexDPgenomic tool in Helisphere (www.Helicosbio.com)
SELEX-seq:  Raw data were debarcoded and the adaptor sequences were removed from both sides. The remaining 20nt sequence were then used for the enrichment analysis.
For the 20nt sequences obtained from SELEX-seq, we collect all 10mers and calculate the frequency of all 10mers. And then check each 10mer's enrichment level by compute its frequency ratio in CstF64/tau to that in control, the SELEX_CstF64_and_CstF64tau_enrichment_level.txt file listed 10mers and its corresponding enrichment level of CstF64 and CstF64tau
Genome_build: hg19
Supplementary_files_format_and_content: .bed files are bed format; .txt files are tab-delimited text files

source_name: HeLa

extract_protocol:
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; libraray construction and sequencing were performed as described in Yao et al. PNAS 109 (46): 18773-8.
iCLIP-seq: RNAs were extracted from immunoprecipitated protein-RNA complexes; for direct RNA sequencing, RNAs were extracted from cells using Trizol reagent (Invitrogen)

value: HeLa


title: ESC_HiraM2

value: anti-Flag (M2)


title: ESC_Suz12null_H33B-HA

value: anti-HA (12CA5)


title: P300_HCT116_Parental

description: Chromatin IP of P300

value: Santa Cruz (cat. no. SC-585)


title: CTCF antibody ChIP on Rag2–/–, Pax5–/– pro-B cells

value: in vitro cultured Pro-B cells (P5R2-19)

value: Rabbit anti-Ctcf antibody (07-729, Millipore, unpurified)


title: CTCF antibody ChIP on Rag2–/– pro-B cells

value: in vitro cultured Pro-B cells (4d)


title: J5588.8-ED 10816 C0FNKACXX 6

data_processing:
Basecalling: RTA 1.12.4.2
splitting with 3 mismatches by the primer sequence
truncation os split reads at restriction enzyme site in the primer sequence
truncation of reads at 3' end to 55nt
alignment: bowtie 0.12.5  -S -p 10 --trim5 0 --trim3 0 -v 2 --best --strata --tryhard -m 1 --phred33-quals --chunkmbs 256
genome build: mm9
processed data files format and content: bed files of alignment
Library strategy: 4C-Seq

extract_protocol:
Pro-B cells isolated from the bone marrow of Rag2–/–, Eμ–/– Rag2–/–, 3’RR–/– Rag2–/–, IGCR1/CBE–/– Rag2–/– and homozygous JHT mice were expanded in vitro for 4 days on OP9 cells in the presence of IL-7. Pro-B cells from the bone marrow of Rag2–/– and Rag1Cre/+ Yy1fl/fl mice were stained with CD19-PE antibody and anti-PE MACS beads prior to MACS-sorting, resulting in a purity of 94% (Figure S6B). Total thymocytes were isolated from wild-type C57BL/6J mice by passing the thymi through cell strainers and removing the dead cells by density centrifugation (Lympholyte M, Cedarlane Lab. [CEDCL5031]).
library construction protocol: The 4C-seq experiments were performed as previously described (Simonis et al., 2007) with the following modifications. For sequestration of SDS, 50 μl of 20% Triton-X 100 was incubated with the chromatin for 2-3 hours. The total amount of the primary restriction enzyme (HindIII, EcoRI or BglII) equaled 700 U and was added as follows: 300 U overnight, 200 U for 4 hours and finally 200 U for another 4-6 hours. In the second digestion round with the secondary restriction enzyme, the ligation products were incubated with 50 U of NlaIII (NEB, R0125S) overnight or 150 U of DpnII (NEB, R0543T), which were added sequentially (50 U) as described above. The digested chromatin was ligated overnight at 16oC followed by a 1 hr incubation at room temperature both for the first and the second ligation step. After ethanol precipitation, the final 4C template was purified twice using the Wizard® SV Gel and PCR Clean-Up System (Promega, A9282), each time with one column per sample prepared from 1x107 cells. The DNA concentration was measured using the Nanodrop spectrophotometer. Approximately 20 μg of 4C template was obtained from 1x107 pro-B cells. For each viewpoint, 16 individual PCR amplifications were performed with ~150 ng of 4C template each by using specific primers that were extended with Illumina sequencing adaptors. Thus, ~2.4 μg of 4C template corresponding to approximately 1x106 pro-B cells were analyzed for each viewpoint. The amplification consisted of 35 PCR cycles because 30 cycles resulted in too little product to be visualized. The PCR products of pooled reactions were purified using the Wizard® SV Gel and PCR Clean-Up System (Promega). After column purification, the PCR products obtained with the third Rag2–/– and Pax5–/– Rag2–/– replica 4C templates as well as the Eμ–/– Rag2–/–, 3’RR–/– Rag2–/–, IGCR1/CBE–/– Rag2–/– and Rag1Cre/+ Yy1fl/fl 4C templates were selected for a fragment size below 1 kb as follows. Ten percent of purified and pooled reactions were quantified on an agarose gel by measuring ethidium-bromide incorporation. Equal amounts of PCR products between 100 and 1000 bp, that were prepared from cells of the same genotype, were pooled and separated on a 2% agarose gel (Lonza [Nusieve GTG agarose, 50080]). After cutting out the lanes, agarose was degraded with β-agarase I enzyme (NEB, M0392L). The DNA was extracted twice with phenol and precipitated with ethanol after phenol removal with chloroform. The precipitate was dissolved in 10 mM Tris pH 8 and quantified by the Bioanalyzer instrument.

value: pro B cell

value: ecori

value: TTCCAGAACCTTCCTACCT

value: ATCACATGTTAATCACTGCAG


title: J606.5-HD 11467 C11ABACXX 2

data_processing:
Basecalling (see below).
splitting with 3 mismatches by the primer sequence
truncation os split reads at restriction enzyme site in the primer sequence
truncation of reads at 3' end to 55nt
alignment of reads using bowtie 12.5 -v 2 --best --strata --tryhard -m 1 --chunkmbs 256
Genome_build: mm9
Supplementary_files_format_and_content: bed files of alignment
Supplementary_files_format_and_content: basecalling is RTA VN:1.12.4.2.

value: Yy1 (f/f) Rag1 (cre/+)

value: hindiii

value: dpnii

value: AGTTCAGGACATGTGTAAGTTAA

value: ATCCATTAATGCCATTGTTC


title: J5588.8-ED 10800 D102NACXX 1


title: HS3B-HD 12042 C11ABACXX 8

source_name: BAC

extract_protocol: The templates for random 4C-seq BAC libraries were generated using DNA mixtures of 8 to 9 C57BL/6J BAC clones (listed in Figure S4B), which contained the viewpoint of interest and covered the mouse Igh locus with every other BAC to avoid sequence overlaps (Figure S4B) that would have otherwise resulted in distortion of the sequence pattern at the junctions. BAC DNA was mixed at equimolar ratio, and 25 μg of DNA was digested with 250 U HindIII in 250 μl volume overnight at 37°C followed by ligation with 62.5 U T4 DNA ligase in a 150 μl volume. The ligated DNA was digested by 120 U Sau3AI in a 250 μl volume. To favor intramolecular ligation, the second ligation was performed in dilution by ligating the Sau3AI-digested DNA in 4 ml (at 6.3 ng/μl) with 62.5 U T4 DNA ligase. Between each step, DNA was purified by phenol-chloroform extraction followed by ethanol precipitation. After the second ligation, DNA was purified by phenol-chloroform extraction, ehanol precipitation and the Wizard® SV Gel and PCR Clean-Up System (Promega, A9282). The BAC DNA template was mixed with a mouse genomic DNA template (prepared in the same way as the BAC template) at a ratio of 1:20 and was subjected to PCR amplification with viewpoint-specific primers. PCR amplification and subsequent DNA purification were performed as described in the 4C-sequencing section.

value: wt

value: BAC

value: HindIII

value: CCCACCTAACTCCAAGCTT

value: CAGACATGTGGGCTGAGAT


title: PAIR8-HD 12039 C11ABACXX 8

value: TGGTATATGGAAAGGAAGC

value: GGCAGGATGGATTTTCTC


title: J558.89-HD 12043 C11ABACXX 8

value: AAAGGCATGTTAGCTAAGCTT

value: CATTCTCCATCCATTAGGATC


title: 7183.16-HD 12032 C11ABACXX 7

value: TCCCCTAGACTTCTCAAGC

value: GTTGGACCTAACATATTCAGG


title: J558.89-HD 12035 C11ABACXX 7


title: Emu-HD 12033 C11ABACXX 7

value: TGCCTCAGACTTCAAGCTT

value: GGGAAATAAACTGTCTAGGGAT


title: HS3B-HD 12034 C11ABACXX 7


title: PAIR4-HD 12029 C11ABACXX 7

value: TGTAGTGGAACAATACTCTAAGCTT

value: CTTAGAGAGAATAAGATTTGTCTAATGT


title: PAIR8-HD 12031 C11ABACXX 7

value: hindiii

value: dpnii


title: HS8-ED 11491 C11ABACXX 4

value: pro B cell

value: ecori

value: GACACTGGCCCTCAGAAT

value: TGGAACAGTGGAGTCAGAT


title: PAIR4-HD 11487 C11ABACXX 4


title: J558.89-HD 11485 C11ABACXX 4


title: J558.89-HD 11469 C11ABACXX 3


title: PAIR4-HD 11471 C11ABACXX 3


title: Emu-HD 11464 C11ABACXX 2


title: HS8-ED 11452 C11ABACXX 1


title: Emu-HD 12041 C11ABACXX 8

value: wt

value: BAC

value: HindIII


title: 7183.16-HD 12040 C11ABACXX 8


title: PAIR4-HD 12037 C11ABACXX 8


title: Zfp386-HD 11258 D102NACXX 5

value: GAAAAGACAAAAGTGAAAGCT

value: ATTACCTTTGTGACTTGTGGA


title: J558.89-HD 11447 C11ABACXX 1

value: AAAGGCATGTTAGCTAAGCTT

value: CATTCTCCATCCATTAGGATC


title: J606.5-HD 11256 D102NACXX 5

value: AGTTCAGGACATGTGTAAGTTAA

value: ATCCATTAATGCCATTGTTC


title: J558.70-HD 11257 D102NACXX 5

value: GGCATGCTAGCTAAGCTT

value: ATTCTCCATGCATTAGGATC


title: J606.5-HD 11239 D102NACXX 4

value: hindiii


title: HS8-ED 11153 D102NACXX 3

value: dpnii


title: Zfp386-HD 11241 D102NACXX 4

value: pro B cell


title: J558.70-HD 11240 D102NACXX 4


title: PAIR4-HD 11150 D102NACXX 3

value: TGTAGTGGAACAATACTCTAAGCTT

value: CTTAGAGAGAATAAGATTTGTCTAATGT


title: PAIR4-HD 11139 D102NACXX 2


title: HS8-ED 11143 D102NACXX 2

value: ecori

value: GACACTGGCCCTCAGAAT

value: TGGAACAGTGGAGTCAGAT


title: J558.89-HD 11136 D102NACXX 2


title: J558.89-HD 10824 D0YPUACXX 5


title: PAIR4-HD 10826 D0YPUACXX 5


title: HS8-ED 11474 C11ABACXX 3


title: HS8-BN 10823 C0FNKACXX 6

value: bglii

value: nlaiii

value: GCCTATATCCCTGTGACCAC

value: GCCAGTGTTGACTGGACAC


title: HS3A-BN 10822 C0FNKACXX 6

value: TTTAGAAATCAGGTCCAGATC

value: CTATATTGGTAACTGAACCGTG


title: IGCR1-BN 10820 C0FNKACXX 6

value: ACAGCAGCAGGGAGATCT

value: TCTGTAGATTGACTGGAGATTT


title: HS8-ED 10818 C0FNKACXX 6


title: IGCR1-ED 10817 C0FNKACXX 6

value: CACAGGTACCCAGATAGAATTC

value: GTGGTTGGAGGGTTGATC


title: J558.88-ED 10816 C0FNKACXX 6

value: NOTFOUND

value: dpnii

value: TTCCAGAACCTTCCTACCT

value: ATCACATGTTAATCACTGCAG


title: HS3B-HD 10814 C0FNKACXX 6

value: pro B cell

value: hindiii

value: CCCACCTAACTCCAAGCTT

value: CAGACATGTGGGCTGAGAT


title: Emu-HD 10815 C0FNKACXX 6

value: TGCCTCAGACTTCAAGCTT

value: GGGAAATAAACTGTCTAGGGAT


title: PAIR4-HD 10812 C0FNKACXX 6

value: TGTAGTGGAACAATACTCTAAGCTT

value: CTTAGAGAGAATAAGATTTGTCTAATGT


title: PAIR8-HD 10810 C0FNKACXX 6

value: TGGTATATGGAAAGGAAGC

value: GGCAGGATGGATTTTCTC


title: PAIR5-HD 10811 C0FNKACXX 6

value: AATCAGTCAGCTACACAAGC

value: CGACACCAAACCTAATCAAG


title: 7183.16-HD 10813 C0FNKACXX 6

value: TCCCCTAGACTTCTCAAGC

value: GTTGGACCTAACATATTCAGG


title: IGCR1-BN 10804 D102NACXX 1

value: bglii

value: nlaiii

value: ACAGCAGCAGGGAGATCT

value: TCTGTAGATTGACTGGAGATTT


title: HS8-ED 10802 D102NACXX 1

value: pro B cell

value: ecori

value: dpnii

value: GACACTGGCCCTCAGAAT

value: TGGAACAGTGGAGTCAGAT


title: HS8-BN 10807 D102NACXX 1

value: GCCTATATCCCTGTGACCAC

value: GCCAGTGTTGACTGGACAC


title: J558.89-HD 10808 C0FNKACXX 6

value: hindiii

value: AAAGGCATGTTAGCTAAGCTT

value: CATTCTCCATCCATTAGGATC


title: HS3B-HD 10798 D102NACXX 1

value: CCCACCTAACTCCAAGCTT

value: CAGACATGTGGGCTGAGAT


title: Emu-HD 10799 D102NACXX 1

value: TGCCTCAGACTTCAAGCTT

value: GGGAAATAAACTGTCTAGGGAT


title: J558.89-HD 11149 D102NACXX 3


title: J558.88-ED 10800 D102NACXX 1

value: NOTFOUND

value: TTCCAGAACCTTCCTACCT

value: ATCACATGTTAATCACTGCAG


title: 7183.16-HD 10797 D102NACXX 1

value: pro B cell

value: TCCCCTAGACTTCTCAAGC

value: GTTGGACCTAACATATTCAGG


title: HS8-ED 10830 D0YPUACXX 5

value: ecori

value: dpnii

value: GACACTGGCCCTCAGAAT


title: J558.89-HD 10792 D102NACXX 1


title: PAIR8-HD 10794 D102NACXX 1

value: TGGTATATGGAAAGGAAGC

value: GGCAGGATGGATTTTCTC


title: HS8-ED 10456 C0FUYACXX 3

value: TGGAACAGTGGAGTCAGAT


title: HS8-ED 10456 C0FUYACXX 4


title: J558.89-HD 10452 C0FUYACXX 4

value: hindiii

value: AAAGGCATGTTAGCTAAGCTT

value: CATTCTCCATCCATTAGGATC


title: HS8-ED 10456 C0FUYACXX 2


title: J558.89-HD 10452 C0FUYACXX 3


title: J558.89-HD 10452 C0FUYACXX 2


title: PAIR4-HD 10448 C0FUYACXX 4

value: TGTAGTGGAACAATACTCTAAGCTT

value: CTTAGAGAGAATAAGATTTGTCTAATGT


title: PAIR4-HD 10448 C0FUYACXX 3


title: PAIR4-HD 10448 C0FUYACXX 2


title: HS8-ED 10257 C0FUYACXX 6


title: HS3A-BN 10806 D102NACXX 1

value: bglii

value: nlaiii

value: TTTAGAAATCAGGTCCAGATC

value: CTATATTGGTAACTGAACCGTG


title: J558.89-HD 10249 C0FUYACXX 6

value: pro B cell


title: PAIR4-HD 10252 C0FUYACXX 6


title: IGCR1-ED 10801 D102NACXX 1

value: CACAGGTACCCAGATAGAATTC

value: GTGGTTGGAGGGTTGATC


title: ESC_H33KD2_RNA-seq

data_processing:
reads were aligned to mm9 using TopHat v1.4 using 25bp segment length
bed files made using BEDTools bamToBed using ' -split' option
wig files made from bed files using igvtools
Genome_build: mm9

extract_protocol:
Total RNA was extracted from embryonic stem cells using the Qiagen Rneasy kit. 4 ug of Dnase I treated RNA was used for library preparation.
Libraries were constructed according to the Illumina Tru-Seq protocol

value: embryonic stem cells

value: H3.3-depleted (KO)


title: ESC_H33KD1_Catch-it


title: ESC_Control_RNA-seq

value: wild type (control)


title: ESC_H33KD1_RNA-seq


title: ESC_H33KD1_Input

value: no antibody


title: ESC_Control_Input


title: ESC_Control_H3gen

value: anti-H3gen (Ab1791)


title: ESC_Control_Catch-it


title: ESC_Control_H3K27me3

value: anti-H3K27me3 (Millipore 07-449)


title: ESC_H33KD1_H3gen


title: U1C knockdown

city: Giessen

first: Lee-Hsueh

last: Hung

state: Hessen

address: Heinrich-Buff-Ring 58

department: Biochemistry

institute: University of Giessen

data_processing:
Sequence reads are aligned to human genome (hg19) and junction sequences using GENCODE Gene Annotation (Version 11).
Only unique aligned reads (from both genomic and junction sequences) are selected for coverage assembly.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files are created for ctr (combined ctr1.fastq and ctr2.fastq alignment result) and kn (combined kn1.fastq and kn2.fastq alignment result) samples using coverage assembly.

extract_protocol:
Total RNA was harvested using Trizol reagent, using oligo(dT) for poly(A)+ selection
RNA libraries were prepared for sequencing using non-strand-sensitive standard Illumina protocols

value: HeLa

tag: treatment

value: U1C knockdown


title: control knockdown

value: control knockdown


title: ESC_H33KD1_H3K27me3


title: K38C miRNA-Seq

status: Public on Sep 29 2013

city: shenzhen

first: JACK

last: LI

address: beishangongyequ

country: China

institute: beijing genomics insititute

description: small RNA

data_processing:
miRNA analysis was performed using RNAFold software version 1.7.1 using the following criteria:
miRNA:
1.the sequences of tags which don't include "N" was reserved, for example,"ATGTCGTNACT" was filtered.
2.the length of tags should between 18-30 nt.
3.there could not have more than 6 bases which are smaller than Q13 in a tag.
version of genome annotations used is hg19

source_name: kidney cancer tissue

extract_protocol:
Total RNA was extracted from ccRCC and normal adjacent tissues by TRIZOL reagent (Invitrogen, US) according to the manufacture¡¯s protocol. In breif, 50mg tissue was milled in liquid nitrogen and lysised in 1 ml TRIZOL reagent. Adding 0.2 ml of chloroform, vortexing, centrifuging,and transfering upper aqueous phase to a fresh tube following precipitating by isopropyl alcohol and washing with 75% ethanol.Then, tatal RNA was air-dryed and dissolved in DEPC-treated water.
5μg of total RNA was used in miRNA sequencing. In short, after ligation of both 5’adapter and 3’adapter, Reverse transcription by Superscript II was performed at 42℃ for 1 h and 70℃ for 15 min. A separate-15-cycles reaction was run using the following program: 98℃ 30 sec, followed by 15 cycles of 98℃ for 10 sec, 72℃ for 15 sec, and then 72℃ for 10 min. The PCR products were run on a 6% PAGE gel and the ~92bp DNA band was excised and purified using Spin-X filter column ethanol precipitation. Finally, miRNA libraries were sequenced on the Illumina Cluster Station and Genome Analyzer Ⅱ following the manufacturer’s protocol.

tag: tissue

value: kidney cancer

tag: tumor stage

tag: pathology

value: renal clear cell


title: K44N miRNA-Seq

description: small RNA

source_name: kidney normal tissue

value: kidney normal


title: TIGR4 RNA-Seq

city: Baltimore

first: Jerry

last: Liu

address: 801 W. Baltimore St.

institute: IGS

description: total RNA depleted of rRNA

data_processing:
Basecalls performed using Illumina Bustard 1.4
sequence reads were mapped to reference genome TIGR4 (AE005672) using ELAND aligner
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated per gene
Genome_build: AE005672
Supplementary_files_format_and_content: space-delimited text file with RPKM values
Genome_build: ASM688v1

organism: Streptococcus pneumoniae TIGR4

source_name: Streptococcus pneumoniae TIGR4 adherent to pharyngeal epithelial cells

extract_protocol:
RNA was isolated using TRIzol in a lysing matrix containing silica beads and a FastPrep Instrument.  Purification was done using i) phase separation with TRIzol and ii) column exclusion with the RNeasy Mini Kit.  Contaminating genomic DNA was removed by DNase treatment.
The library was prepared with the mRNA-Seq Sample Prep Kit. The poly-A selection step was omitted.

value: adherence to D562 human pharyngeal epithelial cells

tag: time

value: 2 hours


title: K55N miRNA-Seq

description: small RNA


title: K55C miRNA-Seq

description: small RNA


title: K44C miRNA-Seq

description: small RNA


title: ESC_H33KD2_Catch-it

tag: cell type


title: K39C miRNA-Seq

description: small RNA


title: K27C miRNA-Seq

description: small RNA


title: K27N miRNA-Seq

description: small RNA


title: K6N miRNA-Seq

description: small RNA


title: K6C miRNA-Seq

description: small RNA


title: K7N miRNA-Seq

description: small RNA


title: K38N miRNA-Seq

description: small RNA


title: K7C miRNA-Seq

description: small RNA


title: TAF7LKO-mRNA-seq-testis

city: Berkeley

first: Haiying

last: Zhou

address: 188 Li Ka Shing Center

department: MCB

institute: HHMI/UCB

data_processing:
Mapping sequencing reads to the genome: Sequenced reads were mapped to the July 2007 assembly of the mouse genome (UCSC version mm9, NCBI37) using Bowtie (Langmead et al., 2009) with the command-line options ‘-c -q -n 2 -l 48 -m 1’, thereby keeping for further analyses only reads that mapped uniquely to the genome with at most two mismatches at the first 48 bases.
Digital gene expression of mRNA-seq: The reads were then mapped to the mouse transcriptome (created using UCSC table browser, version mm9, on February 2012), using TopHat (Trapnell et al., 2009), version v1.4.0., using default parameters. We then applied cufflinks (Trapnell et al., 2010), version v1.3.0, using the default parameters except: --max-mle-iterations 1, to estimate the digital expression levels at each transcript.
Genome_build: MGSCv37 (mm9)

source_name: TAF7l KO testis expression mRNA-seq

extract_protocol:
Total RNAs were extracted individually from 3-month-old WT and Taf7l-/Y mice testis (6 of each group) by RNeasy Plus Mini Kit (Qiagen Inc., Germantown, MD).
mRNA-seq libraries preparation and deep sequencing: 6 extracted RNAs from WT and KO testes were pooled with equal amount and 8 μg of WT and KO pooled RNA samples was used to purify mRNA and subsequently converted into to mRNA-seq library using mRNA-Seq Sample Prep Kit (Illumina Inc., San Diego, CA) and sequenced on an Illumina HiSeq 2000 sequencer.qualities of the libraries were assessed by 2100 Bioanalyzer (Functional Genomics Laboratory, Berkeley,CA) and then subjected to ultra-high throughput sequencing on an Illumina HiSeq 2000 sequencer (GSL core facility, UC Berkeley, CA) as previously described (Zhou et al., 2013),  each sample yielded ∼100–200 million reads.

value: testis

tag: age

value: 3-month old

value: TAF7L knockout


title: TAF7L ChIP-seq-testis

data_processing:
Mapping sequencing reads to the genome: Sequenced reads were mapped to the July 2007 assembly of the mouse genome (UCSC version mm9, NCBI37) using Bowtie (Langmead et al., 2009) with the command-line options ‘-c -q -n 2 -l 48 -m 1’, thereby keeping for further analyses only reads that mapped uniquely to the genome with at most two mismatches at the first 48 bases.
Peak calling methods: we used MACS (Zhang et al., 2008) (version 1.4, with default settings except: --nomodel --shiftsize = 110 --pvalue=1e-2 --mfold = 10,10,000 --slocal = 2000 --llocal = 20,000), with an FDR significant threshold of 0.05 (using IgG ChIP as a control). Second, we applied the Grizzly peak fitting algorithm (Harrison et al., 2011), which uses a model-based iterative approach to accurately identify multiple binding loci at every enriched region. Peaks were then associated with the nearest TSS (using gene annotations from UCSC, version mm9), and classified as promoter peaks (up to 500 bp from an annotated start site), proximal enhancer peaks (Distance greater than 500 bp and less than 5 kb), distal enhancer peaks (less than 50 kb from TSS), or none (further away than any start site).
Genome_build: MGSCv37 (mm9)

source_name: TAF7L ChIP in testis

extract_protocol: ChIP, ChIP libraries preparation, and deep sequencing (ChIP-seq): Homogenize WT and Taf7l KO testis tissue from 10 3-month-old mice followed by fixation with 1% formaldehyde for 10 min at room temperature then use 0.125 M glycine to stop the crosslinking for an additional 5 min and collect tissue by spinning down. The chromatin obtained from WT and Taf7l KO testis tissue was fragmented to sizes ranging from 175 to 225 bp using a Covaris-S2 sonicator (Covaris, Inc., Woburn, MA) for a total processing time of 20 min (30 s on, 30 s off). 1mg of the sonicated chromatin was used in each immunoprecipitation reaction with 4ug of Pol II and TAF7L antibodies, 8ug equally mixed mouse and rabbit IgG were used as negative control.Preparation of the sequencing libraries on the DNA samples of the immunoprecipitation from antibodies and IgGs precisely followed the instructions from Illumina (Illumina Inc., San Diego, CA).

value: wild type


title: K3C miRNA-Seq

description: small RNA


title: WT-mRNA-seq-testis

source_name: WT testis expression mRNA-seq


title: K3N miRNA-Seq

description: small RNA


title: Pol II ChIP-seq-testis

source_name: Pol II ChIP in testis


title: K2N miRNA-Seq

description: small RNA


title: IgG ChIP-seq-testis

source_name: IgG IP testis samples as control


title: K39N miRNA-Seq

description: small RNA


title: K1C miRNA-Seq

description: small RNA


title: K55N

description: polyA RNA

data_processing:
gene expression analysis of sequence data was performed using custom perl scripts using the following criteria:
mRNA:
1.the sequences of tags which don't include "N" was reserved, for example,"ATGTCGTNACT" was filtered.
2.the tags which do not have insert sequence were filtered.
3.the tags including adaper sequence were filtered.
4.the tags only have one copy were filtered.
version of genome annotations used is hg19

extract_protocol:
Total RNA was extracted from ccRCC and normal adjacent tissues by TRIZOL reagent (Invitrogen, US) according to the manufacture¡¯s protocol. In breif, 50mg tissue was milled in liquid nitrogen and lysised in 1 ml TRIZOL reagent. Adding 0.2 ml of chloroform, vortexing, centrifuging,and transfering upper aqueous phase to a fresh tube following precipitating by isopropyl alcohol and washing with 75% ethanol.Then, tatal RNA was air-dryed and dissolved in DEPC-treated water.
4μg total RNA of each sample was used in DGE sequencing. In brief, after double-stranded cDNA synthesis using oligo(dT)18 beads, the cDNA was digested with NlaIII and ligated to first adapter (GEX adapter 1) which contains a recognition site for the MmeI. Following MmeI digestion were dephosphorylation with alkaline phosphatase CIAP and purification. A second adapter (GEX index adapter) containing a 2bp degenerate 3’ overhangs was then ligated. Tags flanked by both adapters were enriched by PCR using Phusion DNA polymerase and Gex PCR primers 1 and 2 following the manufacturer’s protocol. 15 cycles reaction was run using the following program: 98℃ 30 sec, followed by 15 cycles of 98℃ for 10 sec, 60℃ for 30 sec and 72℃ for 15 sec, and then 72℃ for 10 min. ~85bp DNA band of PCR products was excised by gel selection and purified using Spin-X filter column ethanol precipitation. Finally, DGE libraries were sequenced on the Illumina Cluster Station and Genome Analyzer Ⅱ following manufacturer’s protocol.


title: K55C

description: polyA RNA


title: K1N miRNA-Seq

description: small RNA


title: K44C

description: polyA RNA


title: K44N

description: polyA RNA


title: K39N

description: polyA RNA


title: K27N

description: polyA RNA


title: K38N

description: polyA RNA


title: K38C

description: polyA RNA


title: K7N

description: polyA RNA


title: K6C

description: polyA RNA


title: K39C

description: polyA RNA


title: K6N

description: polyA RNA


title: K3N

description: polyA RNA


title: K1C

description: polyA RNA


title: K2C

description: polyA RNA


title: K3C

description: polyA RNA


title: GP5dsiRAD21_REST_Rabbit

status: Public on Sep 28 2013

city: Stockholm

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: ChIP-seq experiment on cells treated with siRNA to RAD21

data_processing:
Basecalls performed using Casava 1.4
fastq files were split by barcode
reads were aligned to the human genome (hg18) using BWA
peaks were called with MACS 1.4, using the following settings: --mfold=2,6 –keep-dup=1
Genome_build: hg18
Supplementary_files_format_and_content: text files generated using MACS 1.4

growth_protocol: GP5d (ECACC cat no. 95090715) colon adenocarcinoma cells were cultured in DMEM supplemented with penicillin/streptomycin and 10% FBS under standard culture conditions.

extract_protocol: Cells were cross-linked by 1% formaldehyde, and DNA was sonicated to 200- 400 bp fragments. Antibodies (5 µg) were added and collected using protein G Sepharose (GE). Cross-links were reversed and proteins digested by incubation with proteinase K at 65 °C overnight. DNA was then purified using Qiagen PCR purification kit.

treatment_protocol: 5 μl of HiPerfect (QIAGEN) was mixed with 50 nM of siRNA oligos targeting human RAD21 (Thermo Scientific, cat no M-006832-01) or neutral control (QIAGEN, cat no 1027281) in 100 μl of Opti-MEM (Invitrogen), vortexed vigorously, transferred to a 24-well tissue culture plate and incubated for 10 min at room temperature. 80% confluent GP5d cells were trypsinized, washed with PBS and resuspended in culture medium. Cells (∼1–3 × 104) were added on top of the transfection mixture and cultured for 72 hr before harvesting. Knockdown efficiency was monitored using qPCR and western blotting.

tag: cell line

value: colon adenocarcinoma

tag: hgn

value: REST

tag: antibody

value: Abcam :ab21635

tag: control sample

tag: sirna

tag: number of peaks, fdr < 5%


title: GP5dsiRAD21_RAD21_Rabbit

value: Santa Cruz Biotechnology, Inc. :sc-98784


title: GP5dsiRAD21_SMC3_Rabbit

value: Abcam :ab9263


title: GP5dsiRAD21_RFX2_Goat

value: Santa Cruz Biotechnology, Inc. :sc-10659 X


title: K2C miRNA-Seq

description: small RNA


title: GP5dsiRAD21_JUND_Rabbit

value: JUND

value: Abcam :ab28837


title: GP5dsiRAD21_NIPBL_Rabbit

value: NIPBL

value: Bethyl Laboratories, Inc. :A301-779A


title: GP5dsiRAD21_MYC_Rabbit

value: MYC

value: Abcam :ab32


title: GP5dsiRAD21_KLF5_Rabbit

value: Santa Cruz Biotechnology, Inc. :sc-22797


title: K7C

description: polyA RNA

value: kidney cancer

value: renal clear cell


title: K27C

description: polyA RNA


title: GP5dsiRAD21_IgG_Rabbit

value: IgG

value: Santa Cruz Biotechnology, Inc. :sc-2027

value: ND


title: GP5dsiRAD21_IgG_Mouse

value: colon adenocarcinoma

value: Santa Cruz Biotechnology, Inc. :sc-2025


title: GP5dsiRAD21_HNF4A_Rabbit

value: Santa Cruz Biotechnology, Inc. :sc-8987


title: K2N

description: polyA RNA

value: kidney normal


title: K1N

description: polyA RNA


title: GP5dControl_SMC3_Rabbit

description: ChIP-seq experiment on cells treated with neutral non-targeting siRNA

value: Abcam :ab9263

value: Control


title: GP5dControl_RFX2_Goat

value: Santa Cruz Biotechnology, Inc. :sc-10659 X


title: GP5dControl_IgG_Rabbit


title: GP5dControl_MYC_Rabbit


title: GP5dControl_KLF5_Rabbit


title: GP5dControl_REST_Rabbit

value: REST

value: Abcam :ab21635


title: GP5dsiRAD21_CTCF_Goat

value: CTCF

value: Santa Cruz Biotechnology, Inc. :sc-15914 X


title: GP5dControl_JUND_Rabbit

value: JUND

value: Abcam :ab28837


title: GP5dControl_HNF4A_Rabbit


title: GP5dControl_H3K4me1_Rabbit

value: Abcam :ab1791


title: GP5dsiRAD21_IgG_Goat

value: IgG

value: Santa Cruz Biotechnology, Inc. :sc-2028


title: GP5dControl_IgG_Goat

value: ND


title: GP5dControl_CTCF_Goat

value: colon adenocarcinoma


title: GP5dControl_IgG_Mouse

value: Santa Cruz Biotechnology, Inc. :sc-2025


title: GP5dsiRAD21_H3K4me1_Rabbit


title: ros1-1_methyl-Seq

status: Public on Sep 27 2013

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

data_processing:
Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China)
A pseudo-C24 genome was generated through the replacement of SNPs in the Col-0 genome with C24 variants  (http://1001genomes.org/data/MPI/MPISchneeberger2011/releases/current//C24/Marker/C24.SNPs.TAIR9.txt)
Clean reads were mapped to the pseudo-C24 genome using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW v2.0.1
acgt-count command of BRAT-BW v2.0.1 was used to count mapped Cs and Ts at each  cytosine of forward and reverse strands of the reference
Genome_build: A pseudo-C24 genome was generated through the replacement of SNPs in the Col-0 genome (TAIR10) with C24 variants  (http://1001genomes.org/data/MPI/MPISchneeberger2011/releases/current//C24/Marker/C24.SNPs.TAIR9.txt)
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (converted_C / ( converted_C+ unconverted_C ) ).

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Plants were grown on soils under long day condition at 22 ℃

extract_protocol: The extracted was sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols

tag: genotype/variation

value: ros1 mutant

tag: background ecotype


title: siSUZ12_BiolRep1

city: Boulder

first: Chen

last: Davidovich

state: Colorado

address: 596 UCB, JSCBB, 3415 Colorado Ave

institute: CU Boulder

description: HEK293T17 cells, 48 h after treatment with siSUZ12 RNA

data_processing:
For RNA-seq data, Primary data evaluation was performed using the FastX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html).  RNA-seq reads were aligned to the human genome (hg19 build) using tophat2.0.4 (http://tophat.cbcb.umd.edu), in conjunction with bowtie2.0.0 (http://bowtie-bio.sourceforge.net). Regulated genes were called by cuffdiff, using two biological replicates for knockdown and two biological replicates for control treatments. Genes were called as ?regulated? using a false discovery rate (q-value) of 0.05, controlled by the Benjamini-Hochberg Procedure
Genome_build: hg19
excel spreadsheet include output information produced by cuffdiff, include fold change and significance for RefSeq genes.

source_name: HEK293T17 cell culture

extract_protocol: Cell culture: HEK293T/17 cells were cultured in DMEM with 10% FBS for no longer than 15 passages. ON-TARGETplus SMARTpool for human SUZ12 (Thermo Scientific, Dharmacon cat # L-006957-00-0005) was used to knockdown SUZ12 (siSUZ12) and ON-TARGETplus Non-targeting Pool (Dharmacon cat # D-001810-10-05) was used as a negative control (siCtrl). A total of 25 nM siRNA was transfected in 6-well dishes using Lipofectamine™ RNAiMAX Reagent (Life Technologies, Invitrogen) following the manufacturer’s recommendations. RNA-seq: Polyadenylated RNA was purified from 4 ug of RNA. cDNA libraries were prepared and double-stranded cDNA was fragmented using DNase I according to Illumina specifications, prior to adaptor ligation. Sequencing libraries were amplified and sequenced using an Illumina HiSeq 2000 sequencer. ChIP-seq: 30 million cells at 80% to 90% confluent culture were crosslinked in 1% v/v formaldehyde for 10 min, quenched in 150 mM glycine, washed with cold 1xPBS and harvested by scraping. Cells were lysed in Lysis Buffer (1% w/v SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1) with 1x Complete® protease inhibitors (Roche). Cells were sonicated for 10 to 15 min using a Bioruptor™ UCD-200 (Diagenode) with 30 sec pulses at maximum power. Lysates were diluted to 10 ml in IP Buffer (0.01% w/v SDS, 1.1% v/v Triton-X, 1.2 mM EDTA, 16.7 mM Tris-HCL pH 8.0, 167 mM NaCl) and 10 to 20 ng of antibodies were added and incubated overnight at 4 ⁰C with rotation. Antibodies were immunoprecipitated with 60 µl protein G Plus/protein A Agarose Suspension (Calbiochem cat # IP05) and washed sequentially with 1 ml Low Salt Wash Buffer (0.1% w/v SDS, 1% v/v Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), 1 ml High Salt Wash Buffer (0.1% w/v SDS, 1% v/v Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), 1 ml LiCl Wash Buffer (0.25 M LiCl, 1% v/v Nonidet P-40, 1% w/v deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0) and 1 ml TE buffer (Qiagen). DNA was eluted with 0.4 ml of 0.1 M NaHCO3 and 1% w/v SDS. Eluent was transferred into a new tube and NaCl was added to a final concentration of 200 mM. Crosslinks were reversed by incubation at 65 ⁰C for 2 hours. Next, proteins and RNA were digested by adding 33 µl of Digestion Reagent (0.6 M Tris-HCl pH 6.5, 152 mM EDTA, 61 ng/ml RNase A (Invitrogen cat # AM2274) and 0.61 mg/ml Proteinase K (NEB cat # P8102)) following by 1 hour incubation at 37 ⁰C. DNA was extracted by phenol:chloroform and ethanol precipitated. DNA was resuspended in Milli-Q pure water and concentration was measured using Qubit™ (Invitrogen). At least 10 ng of recovered DNA was used to synthesize sequencing libraries using the ChIP-seq Sample Preparation kit (Illumina). Between 6 and 10 pmoles were used for sequencing on the HiSeq2000 sequencer.

tag: biological replicate


title: siCtrl_BiolRep1

description: HEK293T17 cells, 48 h after treatment with siCtrl RNA


title: siCtrl_BiolRep2


title: C24_WT_methyl-Seq

description: treated with bisulfite

data_processing:
Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China)
A pseudo-C24 genome was generated through the replacement of SNPs in the Col-0 genome with C24 variants  (http://1001genomes.org/data/MPI/MPISchneeberger2011/releases/current//C24/Marker/C24.SNPs.TAIR9.txt)
Clean reads were mapped to the pseudo-C24 genome using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW v2.0.1
acgt-count command of BRAT-BW v2.0.1 was used to count mapped Cs and Ts at each  cytosine of forward and reverse strands of the reference
Genome_build: A pseudo-C24 genome was generated through the replacement of SNPs in the Col-0 genome (TAIR10) with C24 variants  (http://1001genomes.org/data/MPI/MPISchneeberger2011/releases/current//C24/Marker/C24.SNPs.TAIR9.txt)
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

value: WT


title: GP5dControl_RAD21_Rabbit

value: Santa Cruz Biotechnology, Inc. :sc-98784


title: siSUZ12_BiolRep2


title: rdm16ros1-1_methyl-Seq

description: treated with bisulfite

value: rdm16ros1 double mutant


title: nrpd1ros1-1_methyl-Seq

description: treated with bisulfite

value: nrpd1ros1 double mutant


title: EZH2_ChIP-seq

description: HEK293T17 cells, untreated

data_processing:
For ChIP-seq data, Primary data evaluation was performed using the FastX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Reads of ChIP-seq datasets were aligned to the human (build mm9) genome using bowtie, retaining only unambiguously aligned reads (option ??m 1?). No further settings were altered from default alignment specifications, except for memory increment aimed at eliminating loss of aligned reads due to memory overflow (option ?--chunkmbs 256?). ChIP-seq peaks called by MACS2.0, with FDR of 0.01. Genes were called ?associated? with a given chromatin mark only when peaks were called within -0.5 kb to +0.5 kb around TSS.
Genome_build: hg19
MACS2 output peak.bed files, include information about peaks location, Enrichment fold and significance


title: MeDIP_shGFP

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

description: Sample 1

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1  -S --sam-nohead -m 1
Data were filtered using the following specifications: duplicate reads were filtered out
Peaks were called using MACS v1.4.1 with the following setting: --gsize=mm --nolambda --bw=300
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated from mapped SAM file using MACS for peak calling using a pvalue=1E-5

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue kit (Qiagen).
Genomic DNA was sonicated for 17' pulse 30"ON/30"OFF high  with Bioruptor Twin (Diagenode). GLIB precipitation was performed using Hydroxymethyl Collector (Active Motif). Libraries were generated with ChIP-seq Sample Prep Kit (Illumina) and sequenced on Illumina HiScanSQ Platform.

value: E14 embryonic stem cells

tag: transfected with

value: shGFP

tag: enrichment method

value: Hydroxymethyl Collector (Active Motif)


title: BioDnmt3L_ESC_shGFP

description: Chromatin

data_processing:
Basecalls performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1 -S --sam-nohead -m 1.
Data were filtered using the following specifications: duplicate reads were filtered out.
Peaks were called using MACS v1.4.1 with the following setting: --gsize=mm --nolambda --bw=300.
Genome_build: MGSCv37
Supplementary_files_format_and_content: Bed files were generated from mapped SAM file using MACS software.

source_name: E14-BioDnmt3L embryonic stem cells, shGFP, Dnmt3L ChIP

extract_protocol:
Chromatin from fixed cells was extracted with 1% SDS buffer and sonicated for 20' prior to immunoprecipitation step (detailed description is in Material and Methods of manuscript).
Library were performed using ChIP-Seq Sample Prep Kit from Illumina.

value: embryonic stem cells

tag: transfection

tag: chip antibody

value: Dynabeads MyOne Streptavidin T1 (Invitrogen, #65601)


title: GP5dControl_NIPBL_Rabbit

value: NIPBL

value: Bethyl Laboratories, Inc. :A301-779A

value: Control


title: Ezh2_ESC_shDnmt3L

description: Chromatin

source_name: E14 embryonic stem cells, shDnmt3L, Ezh2 ChIP

value: Ezh2 (D2C9) (Cell Signaling, #5246)


title: Input_DNA_G18

city: Wuerzburg

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.8).
Fastq files were generated by CASAVA only considering high quality sequences (PF-cluster).
Overall sequnecing quality was checked with the FastQC script.
Reads were aligned to the genome (mm9 (NPC), hg19 (MDA-MD-231)) with BOWTIE v0.12.7.
Peak calling was performed with MACS v1.4.2 using default parameters but a p value of 1e-10 and input samples as control files.
Genome_build: GRCh37
Supplementary_files_format_and_content: MACS14 output bed file (contains peak localisation).

source_name: MDA-MD-231, input

growth_protocol: MDA-MD-231 cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (PAA) and penicillin/streptomycin (PAA). Neuronal progenitor cells (NPCs) were isolated from mouse brain at E13.5 and expanded in cell culture as neurospheres.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10' at 37°C. After cell lysis, nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Protein-A/G-Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using chloroform/phenol extraction.
Libraries were constructed following manufacturer's instructions (NEB Next ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired, A tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of an agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system and quantified using picogreen assay. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufacturer's instructions.


title: Ezh2_ESC_shGFP

description: Chromatin

source_name: E14 embryonic stem cells, shGFP, Ezh2 ChIP


title: MeDIP_shDnmt3L

description: Sample 2


title: H2Aub1 AurbKO

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Aurora B KO (Homozygous Rosa26-CreERT2/Aurkb flox) treated for 48 hours with  250 nM 4-hydroxytamoxifen

data_processing:
The reads were aligned to Mouse genome mm9 using Bowtie version 0.12.8 using '-S -n 2 -l 25 -m 1' parameters. Only reads aligned uniquely to the genome were retained for further analysis.
Reads with identical chromosomal co-ordinates and orientation (duplicates) were filtered using Picard version 1.65
To visualise the genomic coverage of samples in UCSC genome browser, the reads were extended to estimated fragment size and converted to BigWig format. The fragment size was estimated using SISSR method (Jothi et al., 2008)
Genome_build: mm9
Supplementary_files_format_and_content: BigWig

source_name: CD43 negative mouse resting B cells

growth_protocol: RPMI, 15% foetal calf serum, 0.1 U/mL penicillin, 0.1 μg/mL streptomycin, 2 mM L-Glutamine, 50 μM beta-mercaptoethanol, 6 ng/ml IL-4

extract_protocol: Cells were fixed with 1% formaldehyde and isolated nuclei were sonicated to the desired fragment size. For H2Aubq  in wild-type and Aurkb KO cells, unfixed chromatin was prepared from isolated nuclei digested with Micrococcal Nuclease to di-/mono-nucleosome. Pre-coupled antibodies-beads were used to immunoprecipitated chromatin bound proteins/histone marks. After DNA purification, a total of 10 ng immunoprecipitated input was used for the library preparation with NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)

treatment_protocol: 48 hours incubation with 4-hydroxytamoxifen for samples labeled WT or KO

tag: strain background

value: mixed

value: Aurkb KO (Cre-ERt2/Aurkb flox homozygous)

tag: developmental stage

value: adult

tag: tissue of origin

value: spleen

value: CD43 negative mouse resting B cells

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: RNAP-S5ph Ring1B KO

description: RING1B KO (Homozygous Rosa26-CreERT2/Rnf2 flox) treated for 48 hours with  250 nM 4-hydroxytamoxifen

value: Ring1B KO (Cre-ERt2/Rnf2 flox homozygous)

tag: cell type

value: Ser5ph RNA Pol II

value: Covance


title: 8WG16 AurkB KO


title: H2Aub1 WT

description: Homozygous Rosa26-CreERT2 treated for 48 hours with  250 nM 4-hydroxytamoxifen

value: wild-type (Cre-ERt2 homozygous)


title: H3K4me2/3_ChIP-seq

description: HEK293T17 cells, untreated

tag: antibody


title: H3S28ph AurkB KO

value: Aurora B KO (Cre-ERt2/Aurkb flox homozygous)

value: Abcam


title: RNAP-S5ph WT

data_processing:
The reads were aligned to Mouse genome mm9 using Bowtie version 0.12.8 using '-S -n 2 -l 25 -m 1' parameters. Only reads aligned uniquely to the genome were retained for further analysis.
Reads with identical chromosomal co-ordinates and orientation (duplicates) were filtered using Picard version 1.65.
To visualise the genomic coverage of samples in UCSC genome browser, the reads were extended to estimated fragment size and converted to BigWig format. The fragment size was estimated using SISSR method (Jothi et al., 2008)
Genome_build: mm9
Supplementary_files_format_and_content: BigWig

extract_protocol: Cells were fixed with 1% formaldehyde and isolated nuclei were sonicated to the desired fragment size. Pre-coupled antibodies-beads were used to immunoprecipitated chromatin bound proteins/histone marks. After cross-link reversal and DNA purification, a total of 10 ng immunoprecipitated input was used for the library preparation with NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)

value: Homozygous Rosa26-CreERT2

tag: tissue

tag: treated with

value: 250 nM 4-hydroxytamoxifen for 48hrs

tag: chip antibody info.

value: Ser5ph RNA Pol II (MMS-128P), Covance


title: H3S28ph WT

tag: genotype/variation


title: 8WG16 Ring1B KO

value: RING1B KO (Homozygous Rosa26-CreERT2/Rnf2 flox)

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


title: 8WG16 WT

value: mixed


title: BioDnmt3L_ESC_shSuz12

description: Chromatin

source_name: E14-BioDnmt3L embryonic stem cells, shSuz12, Dnmt3L ChIP

tag: cell line

value: embryonic stem cells

value: Dynabeads MyOne Streptavidin T1 (Invitrogen, #65601)


title: Ring1B KO

value: adult

value: spleen

value: Ring1B (D139-3), MBL


title: H3K27me3

description: Wild-type

value: wild-type

value: H3K27me3 (ab6002), Abcam


title: USP16

description: Wild-type

value: USP16 (sc-130906), Santa Cruz


title: Aurora B KO

value: Aurora B KO (Homozygous Rosa26-CreERT2/Aurkb flox)

value: Aurora B (ab2254), Abcam


title: Ring1B

description: Wild-type


title: Resting B cells Replicate 4

description: Expression profiling of Quiescent B-cells

data_processing:
RNA-seq sequencing reads were aligned to mm9 using Tophat version 1.4.1 with default parameters. Gene coordinates from Ensembl version 64 was used as known gene model
FPKM values for each sample was estimated using Cufflinks version 1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values

extract_protocol: Cell lysates were homogenized using QIAshredder spin columns (Qiagen). Total RNA was purified with RNeasy Mini Kit (Qiagen), eluted in 30 μl of DEPC-treated water and quantified on an ND-1000 spectrophotometer. mRNA-seq libraries were prepared using 2 μg of total RNA purified as previously described. A total of four libraries were prepared for four independent biological replicates. Libraries were prepared using the TruSeq RNA Sample Preparation Kits v2 (Illumina) according to the manufacturer’s protocol.

treatment_protocol: Resting B cells were isolated from the spleens of adult mice. The spleens were dissected and minced on sieves and the single-cell suspensions were centrifuged on a Ficoll-Paque cushion to remove erythrocytes and dead cells. The resulting splenocytes were resuspended at a concentration of 10^7 cells/ml in 0.1% BSA/HBSS supplemented with 5% goat serum and anti-CD16 antibody. The cells were firstly incubated with biotinylated anti-CD43 antibody and then with Dynabeads Biotin Binder beads to capture CD43+ cells. Bound CD43+ cells were removed by 4 sequential magnetic separations. The remaining population of CD43- cells was cultured at a concentration of 2-5x10^6 cells/ml.

tag: strain

value: wild type

value: Spleen

value: CD43 negative mouse resting B cells


title: Resting B cells Replicate 3


title: Aurora B

description: Wild-type

data_processing:
The reads were aligned to Mouse genome mm9 using Bowtie version 0.12.8 using '-S -n 2 -l 25 -m 1' parameters. Only reads aligned uniquely to the genome were retained for further analysis.
Reads with identical chromosomal co-ordinates and orientation (duplicates) were filtered using Picard version 1.65.
To visualise the genomic coverage of samples in UCSC genome browser, the reads were extended to estimated fragment size and converted to BigWig format. The fragment size was estimated using SISSR method (Jothi et al., 2008)
Aurkb binding regions were identified using MACS2 with default parameters (MACS2_Peaks_GEO.xlsx)
Genome_build: mm9
Supplementary_files_format_and_content: BigWig
Supplementary_files_format_and_content: 'MACS2_Peaks_GEO.xlsx' peak file


title: Cbx7

description: Wild-type

value: Cbx7 (ab31765), Abcam


title: Ezh2

description: Wild-type

value: Ezh2 (39875), Active Motif


title: Resting B cells Replicate 2


title: Resting B cells Replicate 1


title: dbl KO (clone #61, set 2)

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

description: Sequencing result of mir-141 and mir-200c double knockout cells, clone #61 (exp. set 2)

data_processing:
FASTQ sequences from the sequencer were aligned into human reference genome by Tophat2.
After the calculation of RPKM (Reads Per Kilobase of transcript per Million mapped reads) for each isoform, representative isoforms for each gene with the highest RPKM were identified.
Based on this data, reference genome was rebuilt, and RPKM was re-calculated with Tophat2.
Fold change was calculated after the quantile normalization against RPKM, and LOWESS smoothing was applied for fold change.
Genome_build: human reference genome (GRCh37.p10)
Supplementary_files_format_and_content: Log2(fold change) of transcripts in each knockout cells compared to wild type cells (parental cells for knockout) was calculated.

source_name: SK-BR-3 cells

extract_protocol:
Total RNA was extracted with TRIzol, and DNase I was treated.
mRNA was enriched from total RNA by Oligo(dT)-Dynabead. The enriched mRNA was randomly fragmented in the Magnesium ion-containing buffer. The mRNA fragments ranging 70-90nt were fractionated, ligated to adaptors at both 5' and 3' ends, and reverse-transcribed for PCR amplification. The final PCR products were sequenced by HiSeq 2000.

tag: genotype

value: mir-141 and mir-200c knockout

tag: experimental set

value: set 2


title: Miz1_ChIPseq_G18

source_name: MDA-MD-231, G18 ChIP

value: G18 (Santa Cruz, sc-5986)


title: JFY-4

city: Wuhan

first: Fangyan

last: Jin

state: Hubei

address: No.1, Shizishan Street

institute: Huazhong Agriculture University

description: Gossypium hirsutum cv. YZ1

data_processing:
Millions of raw reads with a length approximate 50bp were generated via Illumina HiSeq™ 2000
Clean reads occupied > 98% of raw reads were produced after filtering dirty raw reads
By using SOAPaligner/soap2, all clean reads were mapped to the reference sequences which were cotton unigenes collected from NCBI, supporting up to 2 bases mismatches in the alignment.
Transcription levels were calculated in RPKM (reads per kilobase of exon model per million mapped reads) which was able to get rid of the disturbance of different gene length and sequencing discrepancy on the calculation of gene expression
Genome_build: Gossypium hirsutum: UniGene Build #11
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

organism: Gossypium hirsutum

source_name: zygotic torpedo-shaped embryos

growth_protocol: The cotton plants (Gossypium hirsutum cv. YZ1), used for zygotic embryos collection, were cultivated in the field under normal farming condition during growing seasons in Wuhan, China. Tissue culture was carried out for somatic embryos collection using hypocotyls excised from germfree seedlings. The explants were cultured on MSB (MS medium plus B5 vitamins) medium supplemented with the combination of 1.0 mg/L IBA plus 0.1 mg/L kinetin. After 40 d of culture, all explants were transferred to fresh MSB medium for induction of embryogenic calli (ECs). The ECs were subcultured monthly on MSB medium, with KNO3 doubled but NH4NO3 removed, and supplemented with 3% (w/v) glucose, 0.25% (w/v) Phytagel, 0.5 mg/L IBA, 0.15 mg/L kinetin, 1.0g/L glutamine and 0.5 g/L asparagines, for embryo maturation. All media were autoclaved at 121°C for 15 min. Cultures were maintained in a room at 28 ± 2 °C under a 14-h photoperiod (irradiance of 135 μmol/m∙s). Different stages of somatic embryos were sampled.

extract_protocol:
Guanidine thiocyanate method was used to extract total RNA
Approximate 20ug of total RNA was sent to Beijing Genomics Institute (Shenzhen, China) where the tag libraries were prepared and sequenced. Before construction of library, RNA quality and quantity were determined by Agilent 2100 with rRNA ratio [28s/18s] > 1.0 and RNA Integrity Number (RIN) > 7. Then mRNA were enriched by using the oligo(dT) magnetic beads, and interrupted by adding the fragmentation buffer to short segments (about 200bp) which were used as templates to synthesize double strand cDNA tags by random hexamer-primer. After purified, washed for end repair and single nucleotide A (adenine) addition, and attached the sequencing adaptors, the library required fragments were enriched by PCR amplification. Millions of raw reads with a length approximate 50bp were generated via Illumina HiSeq™ 2000.

tag: cultivar

value: zygotic embryo

value: torpedo-shaped stage


title: JFY-6

description: Gossypium hirsutum cv. YZ1

source_name: zygotic cotyledonal embryos

value: cotyledonal stage


title: JFY-9

description: Gossypium hirsutum cv. YZ1

source_name: somatic globular-shaped embryos

value: somatic embryo

value: globular-shaped stage


title: 141 KO (clone #10, set 2)

description: Sequencing result of mir-141 knockout cells, clone #10 (exp. set 2)

value: mir-141 knockout


title: JFY-11

description: Gossypium hirsutum cv. YZ1

source_name: somatic cotyledonal embryos


title: 200c KO (clone #29, set 2)

description: Sequencing result of mir-200c knockout cells, clone #29 (exp. set 2)

value: mir-200c knockout


title: WT cells (set 2)

description: Sequencing result of wild type SK-BR-3 cells (exp. set 2)


title: RNAP-S5ph AurkB KO

value: mixed

value: Aurora B KO (Homozygous Rosa26-CreERT2/Aurkb flox)

value: adult

value: spleen

value: 250 nM 4-hydroxytamoxifen for 48hrs

value: Ser5ph RNA Pol II (MMS-128P), Covance


title: dbl KO (clone #55, set 1)

description: Sequencing result of mir-141 and mir-200c double knockout cells, clone #55 (exp. set 1)

value: set 1


title: WT cells (set 1)

description: Sequencing result of wild type SK-BR-3 cells (exp. set 1)

value: wild type


title: 200c KO (clone #11, set 1)

description: Sequencing result of mir-200c knockout cells, clone #11 (exp. set 1)


title: 141 KO (clone #23, set 1)

description: Sequencing result of mir-141 knockout cells, clone #23 (exp. set 1)


title: JFY-10

description: Gossypium hirsutum cv. YZ1

source_name: somatic torpedo-shaped embryos


title: Input DNA

city: San Francisco

first: Vera

last: Huang

address: 1450 Third Street, Helen Diller Cancer Research Building, Room 302

department: Urology

institute: UCSF

data_processing:
CASAVA_v1.8.0. was used for base-calling
alignment to human genome was performed with bowtie (version 0.12.7)
filtering: reads mapped to multiple genomic regions were removed from the analysis
peak-calling was performed with CCAT (version 3.0) using Input DNA as control (*peak.txt files)
Genome_build: Hg19

source_name: Input DNA

growth_protocol: PC3 cells grown at exponential phase

extract_protocol: Eluates from two  ChIPs were pooled and prepared as a single library using the standard Illumina ChIP-seq library preparation protocol.   Briefly, ~10 ng of input and ChIPed DNA were end-repaired followed by addition of “A” base to the 3’ end of the DNA fragments. The resulting modified DNA fragments were then ligated to the oligonucleotide adaptors and PCR amplified to construct the libraries. The libraries were size-selected in 200-300 bp range by agarose gel purification. Prior to sequencing, sample quality was assessed using Bioanalyzer  Hypersensitive DNA kit (Agilent). Library concentration was confirmed by qPCR. Samples were diluted to 10 nM and sent to the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley (http://qb3.berkeley.edu/gsl) for sequencing analysis on Illumina Hiseq2000 sequencer.

tag: chip antibody

value: none (input)


title: Ago1 ChIP-Seq

source_name: Ago1 IP

value: anti-Ago1; Wako (2A7)


title: Ago2 ChIP-Seq

source_name: Ago2 IP

value: anti-Ago2; Wako (4G8)


title: Input_DNA_H190

first: Martin

data_processing:
Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.8).
Fastq files were generated by CASAVA only considering high quality sequences (PF-cluster).
Overall sequnecing quality was checked with the FastQC script.
Reads were aligned to the genome (mm9 (NPC), hg19 (MDA-MD-231)) with BOWTIE v0.12.7.
Peak calling was performed with MACS v1.4.2 using default parameters but a p value of 1e-10 and input samples as control files.
Genome_build: MGSCv37
Supplementary_files_format_and_content: MACS14 output bed file (contains peak localisation).

source_name: neuronal progenitor cells, input

tag: age

value: neuronal progenitor cells


title: H3k4me3 ChIP-Seq

source_name: H3k4me3 IP

value: anti-H3k4me3; Millipore (#07-473)


title: Miz1_ChIPseq_H190

source_name: neuronal progenitor cells, H190 ChIP

value: H190 (Santa Cruz, sc764)


title: cell-9

status: Public on Sep 26 2013

city: Rehovot

first: Yaniv

last: Lubling

address: POB 26

country: Israel

institute: Weizmann Institute of Science

description: single-cell Hi-C sample

data_processing:
Paired-end reads of each multiplexed lane were paired-up and separated to single cell datasets based on the 3 bp unique identification tags prefixing each read. Read-pairs of each single cell were then processed independently. We mapped read ends separately to the Mus musculus genome (assembly mm9) using the Maq program with standard parameters and retained pairs of reads with unique hits of high quality (q ≥ 30) at both ends. The first RE1 (Bgl II or Dpn II) restriction site downstream of the read was identified and used as the fragment-end (fend) associated with the read. We retained read-pairs that reflect informative ligation events and with both ends mapped near the first RE2 (Alu I) site upstream of RE1 site. We discarded fend-pairs that were covered only once and used the list of unique fend-pairs, ignoring the coverage of each pair. Fend-pairs with problematic fragments (without a RE2 site or with a non-uniquely mapped start) were discarded. Samples that confidently originated from single cell, with substantial number of fend-pairs and with low noise levels were selected for the analysis.
Th1_bgl_pool.txt - Pool of 60 single-cell Hi-C samples
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include the list of unique fend-pairs of the sample (pair of genomic coordinates)

source_name: T-helper cells (Th1)

growth_protocol: CD4+ Th1 cells were prepared from spleens of male C57BL/6 mice by stimulating the single cell suspension from spleen with 1 µg/ml anti-CD3 (eBioscience) for 3 days in RPMI1640 medium with L-glutamine and 5% fetal calf serum, purified using magnetic beads coated with anti-CD4 (Miltenyi Biotec), and further expanded in the presence of 20 ng/ml IL-2 (Sigma).

extract_protocol:
Single cells treated according to the modified Hi-C protocol were isolated in PBS and incubated at 65 degrees C for overnight.
The biotin-labelled DNA from each cell was bound to Dynabeads M-280 streptavidin magnetic beads (Life Technologies), digested with Alu I (New England Biolabs), A-tailed with Klenow Fragment (3'->5' exo-) (New England Biolabs) and dATP, ligated with customised Illumina adapter with T4 DNA ligase (New England Biolabs), then the library was amplified by PCR with library amplification primers, and size-selected between 300 and 700 bp on an agarose gel.

value: Spleen

tag: restriction enzyme

value: Bgl II

value: T-helper cells (Th1)


title: cell-6

description: single-cell Hi-C sample


title: cell-10

description: single-cell Hi-C sample


title: cell-8

description: single-cell Hi-C sample

value: Dpn II


title: cell-7

description: single-cell Hi-C sample