title: mic_time0-2

description: INVIVO.xlsx


title: Sample 2 of control P180 endocrine pancreas

status: Public on Dec 03 2014

type: SRA

city: Houston

first: Ge

last: Li

state: TX

address: 1100 Bates St.

department: Pediatrics

country: USA

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Quality control was checked by FastQC (version 0.10.1).
Sequencing adptors and remaining MSA adaptors were trimmed by cutadapt program.
The trimmed reads were alignned to mouse genomes using bowtie aligner (version 0.12.9)
Sum of number of reads overlapping for each SmaI/XmaI interval wer counted.
The SmaI/XmaI intervals refer to genomic regions with SmaI/XmaI cut sites (cccggg) at both ends and within the distance of 60bp to 3kb, which are the regions that examined by MSA-seq.
Genome_build: NCBI37/mm9 mouse genome (Jul 2006 release)
Supplementary_files_format_and_content: The processed data are presented in .xlsx format, and present the read depth of each sample in each SmaI/XmaI interval.

molecule: genomic DNA

organism: Mus musculus

source_name: endocrine pancreas

growth_protocol: SL mice were reared as 4 pups per litter from P1 to P21, and C mice were reared as 9 pups per little from P1 to P21.

extract_protocol:
Genomic DNA was isolated with phenol/chloroform extraction followed by ethanol precipitation
Libraries were constructed by MSA-seq. As a brief description of the MSA: 500ng of genomic DNA was serially digested with SmaI and XmaI followed by an adaptor ligation and adaptor mediated PCR amplification (Waterland et al, 2010 Plos Genetics). MSA products were sheared to 200-500bp, ligated to sequencing adaptors for paired-end read, and submitted for sequencing by Illumina HiSeq.

tag: cell type

value: pancreatic islets

tag: strain

value: FVB

tag: litter size

tag: age


title: Sleckman-C5L-ZF-12-Ind5-ATCGAGCATCTCG_S8_L001_R2_001

city: St. Louis

first: Jacqueline

last: Payton

state: MO

address: 660 S. Euclid Ave

department: Pathology and Immunology

institute: Washington University School of Medicine

description: LigaseIV -/- 53BP1 -/- Line C ZF #12 PCR of Zinc Finger Nuclease induced Double Stranded DNA Break

data_processing:
Paired end reads from the MiSeq Desktop Sequencer were de-multiplexed by the sample indexes allowing for a maximum 1 base pair mismatch within the index.
For samples where the same Index was used, but different primer sequences were used, the appropiate sequences were first extracted by the appropaite primer sequence and then by the Index sequence.
Adaptor sequences were then clipped from reads 1 and 2 using FLEXBAR version 2.4 (parameters: -m 10 -u 5 -ae RIGHT -r -aa -at 0.5).  (Dodt, M., Roehr, J.T., Ahmed, R., and Dieterich, C. (2012). FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology (Basel) 1, 895-905.).
Paired reads were assembled using FLASH-1.2.7 software (parameters: -m 10 -M 100 -x 0.25). (Magoc, T., and Salzberg, S.L. (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963.).
The assembly parameters were adjusted based on the read length distribution of a particular sample. When a sample was dominated by short reads that resulted in 100% sequence overlap between read 1 and 2,  ~50 bases from the end of the reads was removed using PrinSeq in order to the prevent mis-assembly. Schmieder, R., and Edwards, R. (2011). Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864.
The trimmed reads were assembled again by FLASH.
Individual assembled reads (contigs) were then aligned pairwise to the reference sequence using the MUSCLE aligner as a scheduled batch job using The Genome Institute clusters (parameters: default, reference sequences: for Igkappa GenBank NG_005612.1, for TCRbeta AC117678.16, for recombination substrate refer to Bredemeyer, A.L., Sharma, G.G., Huang, C.Y., Helmink, B.A., Walker, L.M., Khor, K.C., Nuskey, B., Sullivan, K.E., Pandita, T.K., Bassing, C.H., and Sleckman, B.P. (2006) ATM stabilizes DNA double-strand-break complexes during V(D)J recombination. Nature 442, 466-470).
Using customized Perl scripts, alignments with >5bp deletions on either strand (mis-assembled sequences due to poor sequence quality) were removed.
Using customized Perl scripts, alignments without >10 bps of continuous reference sequence (primer dimers) were removed.
Using customized Perl scripts, alignments where assembled sequences appeared to be longer than the full length coding end (usually mis-assembled reads, small deletions near coding end or insertions) were removed.
Using customized perl scripts, DNA end structures were then calculated and the structures from triplicate PCR reactions were pooled together into a single file. As a convention for calculation of DNA end structure, nucleotides at the ligation junction that could be assigned to either the 5’ or 3’ end were assigned to the 5’ end except for the analysis of Cas9 and Eb:ZFN DNA ends where the nucleotides were assigned to generate blunt and 4 nucleotide 5’ overhangs, respectively, when possible.
Using R, products smaller than 50 base pairs and products with only single reads were removed from further analysis.
Graphs were generated using customized R scripts.
Genome_build: For Igkappa GenBank NG_005612.1, for TCRbeta AC117678.16, for recombination substrate refer to Bredemeyer et al. Nature 442, 466-470)
Supplementary_files_format_and_content: .txt files reporting: ced (The distance of a particular 5' end from the double stranded DNA break), overhang (The length of the overhang associated with that particular 5' end. A negative value means a 5' overhang and a positive value means a 3' overhang. A zero value means a blunt end.), and u2..3. (The number of sequencing reads that had that particular  DNA end structure (position of 5' end and overhang).

source_name: Abelson transformed pre-B cells

growth_protocol: Abelson transformed pre-B cells were grown as previously described in the following paper: Bredemeyer, A.L., Sharma, G.G., Huang, C.Y., Helmink, B.A., Walker, L.M., Khor,  K.C., Nuskey, B., Sullivan, K.E., Pandita, T.K., Bassing, C.H., and Sleckman, B.P.  (2006). ATM stabilizes DNA double-strand-break complexes during V(D)J  recombination. Nature 442, 466-470.

extract_protocol:
DNA extraction was done as described in the following paper. Blondal, T., Thorisdottir, A., Unnsteinsdottir, U., Hjorleifsdottir, S., Aevarsson, A.,  Ernstsson, S., Fridjonsson, O.H., Skirnisdottir, S., Wheat, J.O., Hermannsdottir,  A.G., et al. (2005). Isolation and characterization of a thermostable RNA ligase 1  from a Thermus scotoductus bacteriophage TS2126 with good single-stranded  DNA ligation properties. Nucleic Acids Res 33, 135-142.
Sequencing adaptors for Illumina MiSeq Sequencing was done by PCR as described for the HCoDES procedure in the reference above. Amplified PCR products were then pooled in apporxomately equimolar concentrations for Illumiina MiSeq using 40% Phi-X.

treatment_protocol: Genomic DNA was isolated from Abelson kinase transformed pre-B cells harboring single double stranded DNA breaks. The genomic DNA was treated with single stranded DNA ligase followed by sodium bisulphite treatment and PCR as described for HCoDES in the following paper: Yair Dorsett1, Yanjiao Zhou2,3, Anthony T. Tubbs1, Bo-Ruei Chen1,  Caitlin Purman1, Baeck-Seung Lee1, Rosmy George1, Andrea L. Bredemeyer1,  Jiang-yang Zhao1, Erica Sodergen3*, George M. Weinstock3*,  , Nathon, D, Han4, Alejandro Reyes1,4,+, Eugene M. Oltz1, Dale Dorsett5, Ziva Misulovin5,  Jacqueline E. Payton1 and Barry P. Sleckman1 (2014), Molec Cell In Press

tag: sequencing run

value: set 7

value: Abelson transformed pre-B cells

tag: genotype/variation

value: LigaseIV -/- 53BP1 -/- Line C ZF #12 PCR of Zinc Finger Nuclease-induced DSB


title: Sleckman-C5L-ZF-12-Ind6-TACTCTAATCTCG_S9_L001_R2_001


title: mic_time0-1

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description: INVIVO.xlsx

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
alignment: tophat with deafult parameters
Expression table done using ESAT http://garberlab.umassmed.edu/software/esat/
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: total RNA

source_name: Microglia sorted from spinal cord of injured mice

growth_protocol: In vivo-sorted cells

extract_protocol:
miRNeasy (Qiagen)
see Jaitin et. al., Science 2014

treatment_protocol: The spinal cords of deeply anesthetized mice were exposed by laminectomy at T12, and contusive (200 kdynes) centralized injury was  performed using the Infinite Horizon spinal cord impactor (Precision  Systems)

tag: organ

value: Spinal cord

tag: selection marker

value: Time following spinal cord injury

tag: treatment

value: spinal cord injury

tag: time

value: time 0


title: Sleckman-ALig4-Cas9-Eb9314-Ind12-TAACAAG_S3_L001_R1_001

description: LigaseIV -/- Line A CJ #1 PCR of Cas9 + Eb guide RNA induced break

value: set 8

value: LigaseIV -/- Line A CJ #1 PCR of Cas9 + Eb guide RNA-induced break


title: Sleckman-H2AX-LigaseIV-Line-5-312-Substrate-53BP1-LigaseIV-Line-C-shNT-Substrate-Ind-13-GAGGCGTATCTCG_S4_L001_R1_001

description: LigaseIV -/- 53BP1 -/- Line C PCR of RAG induced Double Stranded DNA Breaks at the Recombination Substrate . Sequences mixed with distal substrate PCR sequences. Pull out sequences of interest using primer specific primer sequence.

value: set 6

value: LigaseIV -/- 53BP1 -/- Line C PCR of RAG-induced DSBs at the Recombination Substrate. Sequences mixed with distal substrate PCR sequences. Pull out sequences of interest using primer specific primer sequence.


title: mic_day7-2

description: INVIVO.xlsx

value: 7 days


title: Sample 5 of small litter P21 endocrine pancreas


title: Sample 1 of control P180 endocrine pancreas


title: mic_day7-1

description: INVIVO.xlsx


title: Sleckman-H2AX-LigaseIV-Line-5-312-Substrate-53BP1-LigaseIV-Line-C-shNT-Substrate-Ind-13-GAGGCGTATCTCG_S4_L001_R2_001


title: Sleckman-53BP1-LigaseIV-Line-C-shNT-Substrate-Ind-11-CCATCATATCTCG_S13_L001_R1_001

description: LigaseIV -/- 53BP1 -/- Line C  PCR of RAG induced Double Stranded DNA Breaks at the Recombination Substrate

value: LigaseIV -/- 53BP1 -/- Line C  PCR of RAG-induced DSBs at the Recombination Substrate


title: Sleckman-BLig4-Cas9-Eb9314-Ind9-CCGATTA_S6_L001_R1_001

description: LigaseIV -/- Line B CJ #7 PCR of Cas9 + Eb guide RNA induced break

value: LigaseIV -/- Line B CJ #7 PCR of Cas9 + Eb guide RNA-induced break


title: Sleckman-53BP1-LigaseIV-Line-C-shNT-Substrate-Ind-11-CCATCATATCTCG_S13_L001_R2_001


title: Sleckman-53BP1-LigaseIV-Line-C-shNT-Substrate-Ind-12-TAACAAGATCTCG_S14_L001_R1_001


title: Sample 4 of small litter P21 endocrine pancreas


title: Sample 4 of control P180 endocrine pancreas


title: Sleckman-C5L-ZF-12-Ind4-CACCTCCATCTCG_S7_L001_R1_001


title: mic_day3-2

description: INVIVO.xlsx

value: 3 days


title: Sleckman-53BP1-LigaseIV-Line-C-shNT-Substrate-Ind-12-TAACAAGATCTCG_S14_L001_R2_001


title: B-Lig4-CJ-7-48hr-Kappa-shNT-Ind-43-TGTGCCA_S15_L001_R1_001

description: LigaseIV -/- Line B CJ #7 PCR of RAG induced Double Stranded DNA Breaks at Jk1 of IgKappa locus

value: set 4

value: LigaseIV -/- Line B CJ #7 PCR of RAG-induced DSBs at Jk1 of IgKappa locus


title: B-Lig4-CJ-7-48hr-Kappa-shNT-Ind-44-AACGGAG_S16_L001_R1_001


title: Sample 3 of small litter P21 endocrine pancreas

value: pancreatic islets

value: FVB


title: Sample 2 of small litter P21 endocrine pancreas


title: mic_day3-1

description: INVIVO.xlsx


title: B-Lig4-CJ-7-48hr-Kappa-shNT-Ind-45-GATAGTT_S17_L001_R1_001

value: Abelson transformed pre-B cells


title: B-Lig4-CJ-7-48hr-Subst-shNT-Ind-66-GACACAG_S20_L001_R1_001

description: LigaseIV -/- Line B CJ #7  PCR of RAG induced Double Stranded DNA Breaks at the Recombination Substrate

value: LigaseIV -/- Line B CJ #7  PCR of RAG-induced DSBs at the Recombination Substrate


title: Sample 1 of small litter P21 endocrine pancreas


title: B-Lig4-CJ-7-48hr-Subst-shNT-Ind-68-TTTTCGG_S22_L001_R1_001


title: Sleckman-LH8-110-inv-B5L-P548-K-Ind29-GTTCTCA_S22_L001_R1_001

description: Ligase IV -/- H2AX -/- Line #8 CJ #148 Substrate PCR for de novo DSBs. Sequences mixed with regular substrate PCR sequences. Pull out sequences of interest using primer specific primer sequence.

value: set 5


title: mic_day1-2

description: INVIVO.xlsx

value: Spinal cord

value: Time following spinal cord injury

value: spinal cord injury

value: 1 day


title: Sample 5 of control P21 endocrine pancreas


title: B-Lig4-CJ-7-48hr-Subst-shNT-Ind-67-AGGACCT_S21_L001_R1_001


title: Sleckman-LH8-110-inv-B5L-P548-K-Ind30-CTGGTGG_S23_L001_R1_001

value: Ligase IV -/- H2AX -/- Line #8 CJ #148 Substrate PCR for de novo DSBs. Sequences mixed with regular substrate PCR sequences. Pull out sequences of interest using primer specific primer sequence.


title: mic_1hr-2

description: INVIVO.xlsx

value: 2 hr


title: Sleckman-LH8-110-inv-B5L-P548-K-Ind31-TGCCCAT_S24_L001_R1_001


title: Sample 4 of control P21 endocrine pancreas


title: ALig4-48hr-Kappa-Ind1-TGAGGTT_S1_L001_R1_001

description: LigaseIV -/- Line A CJ #1 Kappa PCR of RAG induced Double Stranded DNA Breaks at Jk1 of IgKappa locus

value: LigaseIV -/- Line A CJ #1 Kappa PCR of RAG-induced DSBs at Jk1 of IgKappa locus


title: mic_1hr-1

description: INVIVO.xlsx

value: 1 hr


title: Sample 3 of control P21 endocrine pancreas


title: MboII-Ind-7-KpnI-Ind7-AGACTGA_S65_L001_R1_001

description: KpnI control sample. Sequences mixed with other recombination substrte sequences. Pull out KpnI sequences using specific primer sequence for KpnI control.

value: KpnI control sample. Sequences mixed with other recombination substrate sequences. Pull out KpnI sequences using specific primer sequence for KpnI control.


title: Sample 2 of control P21 endocrine pancreas


title: mic_16hr-1

description: INVIVO.xlsx

value: 16 hr


title: ALig4-48hr-Kappa-Ind2-GCTTAGA_S2_L001_R1_001

value: set 4


title: Sample 1 of control P21 endocrine pancreas


title: mic_16hr-2

description: INVIVO.xlsx


title: ALig4-48hr-Kappa-Ind1-TGAGGTT_S1_L001_R2_001


title: ALig4-48hr-Kappa-Ind2-GCTTAGA_S2_L001_R2_001


title: ALig4-48hr-Kappa-Ind3-ATGACAG_S3_L001_R2_001


title: ALig4-48hr-Subst-Ind-11-CCATCAT_S7_L001_R1_001

description: LigaseIV -/- Line A CJ #1  PCR of RAG induced Double Stranded DNA Breaks at the Recombination Substrate

value: LigaseIV -/- Line A CJ #1  PCR of RAG-induced DSBs at the Recombination Substrate


title: b03_WT_Irf7_t2

data_processing:
Basecalls performed using CASAVA version 1.4
alignment using bowtie 0.12 using default parameters
tdf command - igvtools count -w 5 -e 200
Genome_build: mm9
Supplementary_files_format_and_content: tdf files

source_name: GM-CSF treated myeloid cells

growth_protocol: GM-CSF supplemented culture

extract_protocol:
Cells were fixated, lyzed and nuclei were sonicated. Sonicated nuclei were mixed with protein G magnetic dynabeads coupled to target antibbody.
Libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

treatment_protocol: LPS treatment 2hr

value: Myeloid cells

tag: tissue

value: Bone marrow

tag: chip antibody


title: ALig4-48hr-Subst-Ind-12-TAACAAG_S8_L001_R1_001

value: Abelson transformed pre-B cells


title: b02_WT_Irf7_t1


title: ALig4-48hr-Subst-Ind-11-CCATCAT_S7_L001_R2_001


title: mic_day1-1

description: INVIVO.xlsx


title: ALig4-48hr-Subst-Ind-13-GAGGCGT_S9_L001_R1_001


title: B53BP1Lig4-48hr-Kappa-Ind4-CACCTCC_S4_L001_R2_001

description: Ligase IV -/- 53BP1 -/- Line B CJ #6 PCR of RAG induced Double Stranded DNA Breaks at Jk1 of IgKappa locus

value: Ligase IV -/- 53BP1 -/- Line B CJ #6 PCR of RAG-induced DSBs at Jk1 of IgKappa locus


title: ALig4-48hr-Subst-Ind-13-GAGGCGT_S9_L001_R2_001


title: B53BP1Lig4-48hr-Kappa-Ind4-CACCTCC_S4_L001_R1_001


title: ALig4-48hr-Kappa-Ind3-ATGACAG_S3_L001_R1_001


title: ALig4-48hr-Subst-Ind-12-TAACAAG_S8_L001_R2_001


title: B53BP1Lig4-48hr-Kappa-Ind5-ATCGAGC_S5_L001_R1_001


title: B53BP1Lig4-48hr-Kappa-Ind6-TACTCTA_S6_L001_R1_001


title: ChIP-seq gamma-H2A_Pfh1 depleted_2

city: Umeå

first: Nasim

last: Sabouri

address: Linnaeus väg

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Umeå University

description: Reads from replicate 1 and 2 were merged to one file when performing peak calling with MACS

data_processing:
Reads were analyzed using Galaxy platform
Both input and IP reads were mapped with Bowtie, permitting two mismatches in the seed length (seed length 28 bp)
Replicates were merged and peaks were called.
Peaks were identified using MACS 1.4 using settings: bandwith 300; p-value cutoff 10-5; tag size 101.
Genome_build: Pombase_09052011

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe SA60

growth_protocol: Cells were grown to a of concentration 8x106 cells per ml

extract_protocol:
Lysates were clarified by centrifugation and chromatin was sonicated with Covaris E210 and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit TruSeq DNA sample preparation kit v2 (Illumina Cat nr. FC-121-2001). Library fragments of ~650 bp (insert plus adaptor and PCR primer sequences) were isolated from an e-gel, which corresponded to ~400 bps on the bioanalyzer. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were crosslinked in 1% formaldehyde for 5 min at 25 degrees C.

tag: antibody

value: anti-gamma-H2A, source C.Redon

tag: media

value: EMMS with 10 ug/ml thiamine

tag: pfh1 status


title: B53BP1Lig4-48hr-Kappa-Ind5-ATCGAGC_S5_L001_R2_001


title: ChIP-seq gamma-H2A_Pfh1 depleted_1


title: b01_WT_Irf7_t0


title: B53BP1Lig4-48hr-Subst-Ind-15-GGTCCTC_S11_L001_R2_001

description: Ligase IV -/- 53BP1 -/- Line B CJ #6 PCR of RAG induced Double Stranded DNA Breaks at the Recombination Substrate

value: Ligase IV -/- 53BP1 -/- Line B CJ #6 PCR of RAG-induced DSBs at the Recombination Substrate


title: ChIP-seq gamma-H2A_1

value: EMMS


title: b04_WT_Irf7_t4


title: B53BP1Lig4-48hr-Subst-Ind-15-GGTCCTC_S11_L001_R1_001


title: Input_gamma-H2A_2


title: Input_gamma-H2A_1


title: ChIP-seq Cdc20-3HA_Pfh1 depleted_2

source_name: Schizosaccharomyces pombe NS119

value: anti-HA; Santa Cruz Cat nr. sc.7392x


title: B53BP1Lig4-48hr-Subst-Ind-16-CGGTGGC_S12_L001_R1_001


title: B53BP1Lig4-48hr-Subst-Ind-16-CGGTGGC_S12_L001_R2_001


title: ChIP-seq Cdc20-3HA_Pfh1 depleted_1


title: B53BP1Lig4-48hr-Subst-Ind-14-TTTAACT_S10_L001_R1_001


title: N.europaea + N.winogradskyi co-culture, rep. 3

city: Corvallis

first: Luis

last: Sayavedra-Soto

state: OR

address: Cordley Hall 2082

department: Botany and Plant Pathology

institute: Oregon State University

data_processing:
Aligned reads using Bowtie version 2.1.0 to a Bowtie index containing the genomes of both organisms, with options "--no-mixed --threads 8 --reorder --no-unal --all --trim5 6 --trim3 10 -1 $sample/mate_1.fastq -2 $sample/mate_2.fastq -S $sample/alignments.sam"
Custom Python script matched alignments to gene annotations. Gene expression counts were aggregated from reads aligning unambiguously to each gene. A small list of homologs was used to resolve reads aligning ambiguously between the homologous genes to a single gene count.
NBPSeq version 0.1.8 was used to calculate differential gene expression by pairwise comparison.
Genome_build: N.europaea: gi|30407130|emb|AL954747.1| Nitrosomonas europaea ATCC 19718, complete  genome
Genome_build: N.winogradskyi: NC_007406.1, Contig6  [organism=Nitrobacter winogradskyi] [strain=Nb-255]
Supplementary_files_format_and_content: differential gene expression is tab-separated text output from NBPSeq

organism:
Nitrobacter winogradskyi
Nitrosomonas europaea

source_name: cultures

growth_protocol: Chemostat cultures at D=0.008 h-1; N. europaea with 60 mM NH4+; N. winogradskyi with 60 mM NO2-; Co-culture with 60 mM NH4+;

extract_protocol:
Three biological replicates. Total RNA obtained using FastRNA kit (MP Biomedical). rRNA  removed with MICROBExpress (Ambion).
Standard illumina protocol; high-throughput; mRNASeq

treatment_protocol: Transcritome comparison of single cultures to co-culture

tag: phenotype

value: Ammonia oxidizer + Nitritre oxidizer co-culture

value: 60 mM NH4+


title: LH5-CJ48-Kappa-Ind-31-TGCCCAT_S25_L001_R2_001

description: Ligase IV -/- H2AX -/- Line #5 CJ #48 PCR of RAG induced Double Stranded DNA Breaks at Jk1 of IgKappa locus

value: Ligase IV -/- H2AX -/- Line #5 CJ #48 PCR of RAG-induced DSBs at Jk1 of IgKappa locus


title: B53BP1Lig4-48hr-Kappa-Ind6-TACTCTA_S6_L001_R2_001


title: ChIP-seq gamma-H2A_2


title: B53BP1Lig4-48hr-Subst-Ind-14-TTTAACT_S10_L001_R2_001


title: LH5-CJ48-Kappa-Ind-31-TGCCCAT_S25_L001_R1_001


title: N.europaea, single-culture, rep. 3

organism: Nitrosomonas europaea

tag: cell line

value: Ammonia oxidizer


title: ChIP-seq Cdc20-3HA_2


title: ChIP-seq Cdc20-3HA_1


title: Input_Cdc20-3HA_1

description: Replicate 1 and 2 were merged when performing peak calling with MACS


title: N.europaea, single-culture, rep. 1


title: LH5-CJ48-Kappa-Ind-33-ACCATAC_S27_L001_R2_001

tag: cell type


title: N.europaea, single-culture, rep. 2


title: ChIP-seq Pfh1-13Myc_2

source_name: Schizosaccharomyces pombe NS29

tag: strain

value: anti-Myc; Clontech Cat. nr 631206

value: YES


title: N.europaea + N.winogradskyi co-culture, rep. 2


title: ChIP-seq Pfh1-13Myc_1


title: N.europaea + N.winogradskyi co-culture, rep. 1


title: LH5-CJ48-Subst-Ind-48-GTAAAAA_S31_L001_R1_001

description: Ligase IV -/- H2AX -/- Line #5 CJ #48 PCR of RAG induced Double Stranded DNA Breaks at the Recombination Substrate

value: set 4

value: Ligase IV -/- H2AX -/- Line #5 CJ #48 PCR of RAG-induced DSBs at the Recombination Substrate


title: LH5-CJ48-Subst-Ind-48-GTAAAAA_S31_L001_R2_001


title: Input_Pfh1-13Myc_2


title: Input_Pfh1-13Myc_1


title: LH8-CJ-148-48hr-Kappa-Ind-25-CGTCGCT_S19_L001_R1_001

description: Ligase IV -/- H2AX -/- Line #8 CJ #148 PCR of RAG induced Double Stranded DNA Breaks at Jk1 of IgKappa locus

value: set 2

value: Ligase IV -/- H2AX -/- Line #8 CJ #148 PCR of RAG-induced DSBs at Jk1 of IgKappa locus


title: LH5-CJ48-Subst-Ind-49-GTCTGAT_S32_L001_R2_001

value: Abelson transformed pre-B cells


title: LH5-CJ48-Kappa-Ind-33-ACCATAC_S27_L001_R1_001


title: LH5-CJ48-Subst-Ind-49-GTCTGAT_S32_L001_R1_001


title: LH8-CJ-148-48hr-Kappa-Ind-25-CGTCGCT_S19_L001_R2_001


title: LH5-CJ48-Subst-Ind-50-CAATATC_S33_L001_R1_001


title: LH8-CJ-148-48hr-Kappa-Ind-26-TCAACTG_S20_L001_R2_001


title: LH8-CJ-148-48hr-Kappa-Ind-26-TCAACTG_S20_L001_R1_001


title: LH5-CJ48-Kappa-Ind-32-AAACCTT_S26_L001_R2_001


title: LH5-CJ48-Kappa-Ind-32-AAACCTT_S26_L001_R1_001


title: LH8-CJ-148-48hr-Subst-Ind-51-CTCCCGA_S34_L001_R1_001

description: Ligase IV -/- H2AX -/- Line #8 CJ #148 PCR of RAG induced Double Stranded DNA Breaks at the Recombination Substrate

value: Ligase IV -/- H2AX -/- Line #8 CJ #148 PCR of RAG-induced DSBs at the Recombination Substrate


title: LH8-CJ-148-48hr-Kappa-Ind-27-TGTTTGT_S21_L001_R2_001


title: LH8-CJ-148-48hr-Subst-Ind-52-GCCGTTT_S35_L001_R1_001


title: 1725-SB-6

city: Nashville

first: Daniel

last: LePage

state: TN

address: U7214 MRBIII 465 21st Ave S

institute: Vanderbilt University

description: CHG.analysis and CpG.analysis

data_processing:
Illumina 2000 100 bps Paired-end Whole-Genome Bisulfite Sequencing
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to dmel_r5 whole genome using bowtie v0.12.7 with -q --phred33-quals -n 1 -k 2 --best --chunkmbs 512
The number of reads containing converted cytosines and the number of reads containing unconverted cytosines at covered cytosines were counted based on Bismark's mapping results. Only sequences with greater than or equal to 10x coverage were analyzed.
SEQMONK used for visualization
Genome_build: dmel_r5.43_FB2012_01
Supplementary_files_format_and_content: .txt files (SeqMonk) for CpG, CHG analysis

organism: Drosophila melanogaster

source_name: adult testes

growth_protocol: Flies were reared on conrmeal-molasses media at 25 degrees C.

extract_protocol:
Genomic DNA was extracted with the PurGene Tissue Kit
Genomic DNA was fragmented by Covaris shearing and submitted to Vanderbilt Technologies for Advanced Genomics (VANTAGE). PE-75bp llibrary was prepared using the TruSeq kit with methylated adapters. DNA was then bisulfite treated, PCR amplified, and sequenced on an Illumina HiSeq 2000.

tag: wolbachia infection

value: infected

tag: strain of infection

value: wMel


title: LH8-CJ-148-48hr-Subst-Ind-53-TAGGTAA_S36_L001_R1_001

tag: sequencing run


title: 1725-SB-5

description: CHG.analysis and CpG.analysis

value: uninfected

value: Not applicable


title: LH5-CJ48-Subst-Ind-50-CAATATC_S33_L001_R2_001.

tag: genotype/variation


title: LH8-CJ-148-48hr-Subst-Ind-52-GCCGTTT_S35_L001_R2_001


title: LH8-CJ-148-48hr-Subst-Ind-53-TAGGTAA_S36_L001_R2_001


title: IFNAR1 KO DMSO: alpha19  (replicate 2)

city: New Haven

first: Christian

last: Harman

state: Connecticut

address: 300 Cedar Street, The Anlyan Center

department: Genetics/Immunobiology

institute: Yale University

description: cDNA from Poly(A) selected RNA from Interferon-alpha receptor 1 (IFNAR1) Knockout Mouse embryonic fibroblasts treated DMSO.

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Fragments were mapped to the mouse genome (mm9) with Tophat2 (Kim et al., 2013), using default parameters.
A reference transcriptome consisting of UCSC known genes (Hsu et al., 2006) was used for isoform-level quantification and differential analysis using Cuffdiff2 (Trapnell et al., 2013).
Quality control analysis and visualization were done using the CummeRbund package (Trapnell et al., 2012), which is part of the R/Bioconductor suite of utilities (Gentleman et al., 2004).
Differentially expressed genes between samples were selected with a Benjamini-Hochberg corrected q-value <0.05, deemed by the Cuffdiff2 program as significant, with the additional parameter of at least a 5-fold difference being used.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files including RPKM values for each sample.
Supplementary_files_format_and_content: gene_exp.diff: Gene differential FPKM. Tests differences in the summed FPKM of transcripts sharing each gene_id
Supplementary_files_format_and_content: genes.count_tracking: Gene counts. Tracks the summed counts of transcripts sharing each gene_id
Supplementary_files_format_and_content: genes.fpkm_tracking: Gene FPKMs. Tracks the summed FPKM of transcripts sharing each gene_id
Supplementary_files_format_and_content: genes.read_group_tracking: Gene read group tracking. Tracks the summed expression and counts of transcripts sharing each gene_id in each replicate
Supplementary_files_format_and_content: run.info: Tab delimited text file listing information about Cuffdiff run.
Supplementary_files_format_and_content: geneIDs_sig_5fold.txt: Processed list of significantly differentially expressed genes (Benjamini-Hochberg corrected q-value <0.05) with at least a 5-fold difference

molecule: polyA RNA

source_name: Mouse Embryonic Fibroblasts IFNAR1-KO

growth_protocol: Primary MEFs were generated from IFNAR1 KO mice and respective littermate control embryos (E16.5-18.5). All primary MEFs used for experiments were from passage 4 or less. Control immortalized MEFs were provided by Dr. C. Thompson (University of Pennsylvania) (Wei et al., 2001)

extract_protocol: RNA was extracted from duplicate samples and libraries generated for sequencing using the directional RNA-Seq library prep at the Yale Center for Genome Analysis.

treatment_protocol: Q-VD-OPH (MP Biomedicals) was used at 10 μg/ml.

value: Mouse Embryonic Fibroblasts

tag: genotype

value: DMSO


title: WT QVDOPH: alpha10  (replicate 2)

description: cDNA from Poly(A) selected RNA from wild-type Mouse embryonic fibroblasts treated with the broad spectrum caspase inhibitor Q-VD-OPh.

source_name: Mouse Embryonic Fibroblasts Wild Type

value: wild type

value: Q-VD-OPh


title: IFNAR1 KO QVDOPH: alpha22  (replicate 2)

description: cDNA from Poly(A) selected RNA from Interferon-alpha receptor 1 (IFNAR1) Knockout Mouse embryonic fibroblasts treated with the broad spectrum caspase inhibitor Q-VD-OPh.


title: WT DMSO: alpha7  (replicate 2)

description: cDNA from Poly(A) selected RNA from wild-type Mouse embryonic fibroblasts treated with DMSO.


title: IFNAR1 KO DMSO: alpha13 (replicate 1)


title: RNA_LTR (lane 6)

city: Novosibirsk

first: Evgeniy

last: Brenner

state: Russia

address: Lavrentiev av., 8

country: Russia

institute: ICBFM SB RAS

description: total RNA (rRNA depleted)

data_processing:
Mapping was performed by Bioscope v.1.3 software
Analysis of differential expression was performed by Cufflinks v.2.0.1 software
Genome_build: Mus musculus NCBI37/mm9
Supplementary_files_format_and_content: file «fpkm.txt» is a flat tab-delimited text file that includes gene name, locus and FPKM values for case and control libraries. File «gene_exp.diff» is standard Cufflinks output file that includes FPKM values and test statistics (p value, q_value, test statistics and significance flag) for each gene in studied genome.

source_name: Lewis lung carcinoma after RNase A treatment

extract_protocol:
total RNA was extracted from homogenized tumor pieces using Trizol Reagent and was subsequently rRNA depleted using RiboMinus™ Eukaryote System v2 (Invitrogen, cat.no. A15026).
Standard protocol for SOLiD™ Total RNA-Seq Kit (Invitrogen, cat.no. 4445374) was followed; Standard fragment library

tag: Sex

value: female

tag: age

value: 12 - 14 weeks

value: epithelial


title: IFNAR1 KO QVDOPH: alpha17  (replicate 1)

tag: treatment


title: RNA_LTC (lane 5)

description: total RNA (rRNA depleted)

source_name: Lewis lung carcinoma before RNase A treatment

tag: tissue


title: WT DMSO: alpha1 (replicate 1)


title: n2a-Dali-R3

city: Oxford

first: Vladislava

last: Chalei

address: Sherrington building, Parks road

department: MRC FUnctional Genomics Unit, Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

data_processing:
(1) alignment: 50bp, paired-end reads were mapped to the mouse genome (mm9) using bowtie with the options “-m1 –v2 –best –strata –a”
(2) peak-calling: Peak calls were made using the MACS2 algorithm (Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137) (https://github.com/taoliu/MACS/blob/master/README) with the options “--mfold 10 30 --gsize=2.39e9 --qvalue=0.01”. Peak calls were then filtered such that only peak calls with a -log10 qvalue > 5 were retained (FDR < 0.001%). Peaks were called for each combination of the three Dali CHART-seq pull-down cocktails and three control samples (two LacZ CHART-seq pull-downs and one input sample: GSM1269955, GSM1269956 & GSM1269959).
(3) construction of final peak set: The final peakset comprises of peaks common to all nine Dali vs LacZ/input control comparisons. Overlapping peaks were merged in this analysis.
Genome_build: mm9
Supplementary_files_format_and_content: A single bed file containing the final Dali peak set. The average MACS2 peak score is reported in the score column.

source_name: neuro 2A (N2A) neuroblastoma cell line

growth_protocol: N2A mouse neuroblastoma cells were grown in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
CHART Enrichment and RNase H Mapping experiments were performed as previously described (Simon, 2013, Capture hybridization analysis of RNA targets (CHART). Curr Protoc Mol Biol Chapter 21: Unit 21 25). CHART extract was prepared from approximately 3 × 10^8  N2A cells per pull down and hybridized with 810 pmol biotinylated oligonucleotide cocktail overnight with rotation at room temperature. Complexes were captured using 250ml MyOneC1 streptavidin beads (Invitrogen) overnight at room temperature with rotation. Bound material was extensively washed and eluted using RNase H (New England Biolabs) for 30 min at room temperature. Samples were treated with Proteinase K and cross-links were reversed. DNA was sheared to an average fragment size of 150-300 bp using a Bioruptor (Diagenode).
Fragmented DNA was end-repaired, A-tailed and adapter-ligated before size selection and amplification. The prepared libraries were QC’ed and multiplexed before paired end sequencing over one lane of a Illumina HiSeq flow cell. For more information contact the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics, Oxford.

treatment_protocol: None.

value: neuro 2A (N2A)

value: neuroblastoma cell line


title: WT QVDOPH: alpha4 (replicate 1)


title: Input_Cdc20-3HA_2

value: EMMS


title: n2a-Dali-R2


title: n2a-Dali-R1


title: LH8-CJ-148-48hr-Kappa-Ind-27-TGTTTGT_S21_L001_R1_001

value: set 2

value: Ligase IV -/- H2AX -/- Line #8 CJ #148 PCR of RAG-induced DSBs at Jk1 of IgKappa locus


title: LH8-CJ-148-48hr-Subst-Ind-51-CTCCCGA_S34_L001_R2_001

value: Abelson transformed pre-B cells

value: Ligase IV -/- H2AX -/- Line #8 CJ #148 PCR of RAG-induced DSBs at the Recombination Substrate


title: mRNA from HBx transgenic line

status: Public on Dec 02 2014

city: Taipei

first: Wangta

last: Liu

address: Academia Rd.

country: Taiwan

institute: Institute of Cellular and Organismic Biology,  Academia Sinica

description: HBx

data_processing:
HBx_count.txt; genome build: Zv9
Counts: Sequence reads were obtained and mapped to the zebrafish (Zv9) genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.

organism: Danio rerio

source_name: zebrafish liver

growth_protocol: Zebrafish were cultured and maintained with a controlled light cycle of 14 h light/10 h dark at 28 °C.

extract_protocol: The total RNA from liver tissue was extracted using a TRIzol Reagent kit (Invitrogen). For transcriptome sequencing, the poly(A) RNA from total RNA was isolated by using the Poly(A)PuristTM MAG Kit (Ambion). After construction of whole transcriptome library and template beads preparation, the sequencing run was performed by using SOLiD 3 System. Data analysis  was performed with SOLiD Analysis Tool Pipeline.

treatment_protocol: Transgenic zebrafish were generated by Tol2 transposon mediated transgenesis

value: HBx transgenic

value: liver


title: mRNA from AB strain

description: WT

data_processing:
WT_count.txt; genome build: Zv9
Counts: Sequence reads were obtained and mapped to the zebrafish (Zv9) genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.

value: AB


title: mRNA from HCP transgenic line

description: HCP

data_processing:
HCP_count.txt; genome build: Zv9
Counts: Sequence reads were obtained and mapped to the zebrafish (Zv9) genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.

value: HCP transgenic


title: Dorsal Peconic ChIP-exo (Drosophila embryos) Rep 2

city: Kansas City

first: Julia

last: Zeitlinger

institute: Stowers Institute for Medical Research

data_processing:
Peconic LLC performed data processing as described by Rhee and Pugh (Cell 2011)
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand
Genome_build: UCSC dm3

growth_protocol: D. melanogaster embryos were collected and aged on yeasted apple juice plates at 25C and 60 % humidity

extract_protocol:
embryos were cross-linked in 1.8% formaldehyde. Embryos were then dounced to break down cells and extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. 300 ul soluble chromatin from ~100 mg embryos was used
Peconic LLC performed library construction as described by Rhee and Pugh (Cell 2011)

treatment_protocol: no treatment, only fixation by formaldehyde

value: whole-embryo

tag: time point

value: 02 to 04 h AEL

tag: chip antibody

value: anti-Dorsal rabbit polyclonal, custom (GenScript)

value: Oregon-R


title: Dorsal Peconic ChIP-exo (Drosophila embryos) Rep 1


title: Twist Peconic ChIP-exo (Drosophila embryos) Rep 2

description:
dmel_embryo_twi_chipexo_02
Protocol: ChIP-exo

data_processing:
Peconic LLC performed data processing as described by Rhee and Pugh (Cell 2011)
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand

value: anti-Twist rabbit polyclonal, custom (Covance)


title: Doxy 50 #3_Pterygium

city: Logroño

first: Ignacio

middle: M

last: Larrayoz

state: Please Select

address: C\ Piqueras 98, Ed CIBIR

department: Oncology Area

country: Spain

institute: CIBIR

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to NCBI Build 37.2  genome sequence indexes  using tophat 2.0.10
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1 following the protocol from Trapnell et al.,Nature Protocols, 2012.
Library siggenes in R was applied to select the differentially expressed loci using the FDR-based SAM method.
Genome_build: Human NCBI genome build 37.2
Supplementary_files_format_and_content: FPKM.txt is an text  file containing the Fragments Per Kilobase of exon per Megabase of library size for each ensembl ID/gene

organism: Homo sapiens

source_name: Pterygium

growth_protocol: Cells were cultured in DMEM/F-12 medium supplemented with 10% fetal calf serum, 200 mM L-glutamine, 0.5 % DMSO, and 1% penicillin/streptomycin/amphotericin.

extract_protocol: Total RNA was isolated from pterygium cell cultures using TRIzol, purified using an RNeasy Mini kit  and treated with DNase I. Library preparation and ultrasequencing were performed following Illumina´s (San Diego, CA) protocols. First, the integrity and quality of total RNA were assessed with the Experion Automated Electrophoresis system. Then, mRNA was isolated from 5 g of total RNA using poly-T oligo-attached magnetic beads. And it was fragmented into pieces of approximately 200 bp using divalent cations under elevated temperature. The cleaved RNA fragments were reverse transcribed into first strand cDNA using reverse transcriptase and random primers. Next, the second strand was synthesized using DNA polymerase I and RNAse H. These double-stranded cDNA fragments were end-repaired by T4 DNA polymerase and Klenow DNA polymerase, and phosphorylated by T4 polynucleotide kinase. The cDNA products were incubated with Klenow DNA polymerase to generate 3’ Adenine overhangs, therefore allowing ligation to Illumina indexing adapters to the double stranded cDNA ends. The adapter-ligated products were purified with Ampure XP magnetic beads ( and libraries were amplified by 15 cycles of PCR with Phusion DNA polymerase. Pools of 6 indexed libraries were mixed (multiplexed) at equimolar ratios to yield a total oligonucleotide mix concentration of 10 nM. Finally the resulting libraries were sequenced on the Genome Analyzer IIx platform (Illumina) to generate 150 bp single reads. Six pooled indexed libraries were sequenced in each flow cell lane.

treatment_protocol: For each patient, cells were subjected to 4 treatments: 0 (control), 50, 200, and 500 microg/ml doxycycline for 24 h.

value: Pterygia

tag: race

value: Caucasian


title: Doxy 200 #2_Pterygium


title: Doxy 500  #3_Pterygium


title: Control #3_Pterygium


title: Doxy 200 #3_Pterygium


title: Doxy 500  #2_Pterygium


title: Doxy 50 #2_Pterygium


title: Doxy 50 #1_Pterygium


title: Doxy 500  #1_Pterygium


title: Doxy 200 #1_Pterygium


title: mRNA from HBx+HCP transgenic line

description: HBx+HCP

data_processing:
HBx+HCP_count.txt; genome build: Zv9
Counts: Sequence reads were obtained and mapped to the zebrafish (Zv9) genomes using the SOLiD Analysis Tool Pipeline. All reads mapping with fewer mismatches were retained.

value: intrahepatic cholangiocarcinoma

value: HBx+HCP transgenic


title: Doxy 500  #10

data_processing: Aggressive adapter removal, mRNA alignment to DNA performed by Tophat (an intron aware wrapper of Bowtie DNA aligner) and results were sorted and indexed using Samtools. Coverage vectors for each sample were extracted under R statistical environment using Rsamtools library. Human GTF annotation from Ensembl was applied as reference for the exon genomic ranges, parsed into R data structures. Exon expression was calculated as the median coverage for every exon genomic range as stated by annotation. Exon expression data from our 40 different samples were normalized by quantile normalization and locus expression was calculated by simple addition of all the expression hits from distinct exons annotated to a single locus. Library siggenes in R was applied to select the differentially expressed loci using the FDR-based SAM method. The reference genome version used was GRCh37, Ensembl version 63.

extract_protocol: Total RNA was isolated from pterygium cell cultures using TRIzol, purified using an RNeasy Mini kit  and treated with DNase I. Library preparation and ultrasequencing were performed following Illumina's (San Diego, CA) protocols. First, the integrity and quality of total RNA were assessed with the Experion Automated Electrophoresis system. Then, mRNA was isolated from 5 ug of total RNA using poly-T oligo-attached magnetic beads. And it was fragmented into pieces of approximately 200 bp using divalent cations under elevated temperature. The cleaved RNA fragments were reverse transcribed into first strand cDNA using reverse transcriptase and random primers. Next, the second strand was synthesized using DNA polymerase I and RNAse H. These double-stranded cDNA fragments were end-repaired by T4 DNA polymerase and Klenow DNA polymerase, and phosphorylated by T4 polynucleotide kinase. The cDNA products were incubated with Klenow DNA polymerase to generate 3’ Adenine overhangs, therefore allowing ligation to Illumina indexing adapters to the double stranded cDNA ends. The adapter-ligated products were purified with Ampure XP magnetic beads ( and libraries were amplified by 15 cycles of PCR with Phusion DNA polymerase. Pools of 6 indexed libraries were mixed (multiplexed) at equimolar ratios to yield a total oligonucleotide mix concentration of 10 nM. Finally the resulting libraries were sequenced on the Genome Analyzer IIx platform (Illumina) to generate 150 bp single reads. Six pooled indexed libraries were sequenced in each flow cell lane.

value: Pterygia cells

tag: passages

value: Doxy 500

tag: patient


title: Doxy 500  #9


title: Doxy 50 #10

value: Doxy 50


title: Control #10

value: Control


title: Doxy 200 #10

value: Doxy 200


title: Control #9


title: Doxy 50 #9


title: Doxy 200 #9


title: Twist Peconic ChIP-exo (Drosophila embryos) Rep 1

description:
dmel_embryo_twi_chipexo_01
Protocol: ChIP-exo


title: Doxy 200 #8


title: Doxy 500  #8


title: Control #8


title: Doxy 50 #8


title: Doxy 500  #7


title: Control #2_Pterygium


title: Doxy 200 #7


title: Control #7


title: Doxy 50 #7


title: Doxy 500  #6


title: Control #6


title: Doxy 200 #6


title: Control #5


title: Doxy 500  #4


title: Doxy 200 #5


title: Doxy 50 #5


title: Control #1_Pterygium


title: Doxy 200 #4


title: Doxy 500  #3


title: Control #4


title: Doxy 50 #4


title: Doxy 50 #3


title: Doxy 200 #3


title: Doxy 500  #2


title: Doxy 50 #2


title: Control #2


title: Doxy 500  #1


title: Doxy 200 #1


title: Doxy 50 #1


title: Control #1


title: GATA6_RNAseq_day6_rep2

city: Los Angeles

first: Minjie

last: Zhang

state: CA

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

data_processing:
Illumina Casava1.7 software was used for basecalling.
Low quality reads were filteref and adaptor sequence were trimmed using our in-house software.
ChIP-Seq: reads were  aligned to a reference sequence (GRCm38/mm10) with bowtie2 software.
ChIP-Seq: peaks were called using MACS software (version v1.4.2) with parameters -g mm --nomodel --shiftsize=150 -w -S 2
RNA-Seq: reads were aligned to a reference sequence (GRCm38/mm10) with Tophat alignment software tools (version v2.0.9).
RNA-Seq: the expression values of each gene were calculated with Cufflinks software (version v2.0.2) and normalized using FPKM.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: ChIP-Seq: wig files and BED files;   RNA-Seq: tab-delimited text files for each sample include FPKM values.

source_name: mouse embryonic fibroblasts

extract_protocol:
ChIP-Seq: After sonicating nuclei, histone-DNA complexes were isolated with antibody.
ChIP-Seq: Libraries were constructed according to Illumina's NEXTflexTM ChIP-Seq Kit (Catalog # 5143-02).
RNA-Seq: Total RNA was extracted from each cell line using TRIzol reagent.
RNA-Seq: 1 ug of total RNA was used to prepare libraries according to Illumina TruSeq RNA Sample Prep Kit (Part # 15027084).

tag: gata transcription factors in infectionfect

tag: days

value: post-induction at day6


title: GATA6_RNAseq_day6_rep1

tag: strain


title: Doxy 500  #5

tag: cell type


title: Doxy 50 #6


title: GATA6_RNAseq_day2_rep2

value: post-induction at day2


title: GATA6_RNAseq_day4_rep2

value: post-induction at day4


title: GATA6_RNAseq_day2_rep1


title: GATA6_RNAseq_day4_rep1


title: GATA6_RNAseq_day0_rep1

value: post-induction at day0


title: GATA4_RNAseq_day4_rep2


title: GATA4_RNAseq_day6_rep1


title: GATA4_RNAseq_day6_rep2


title: GATA6_RNAseq_day0_rep2


title: GATA4_RNAseq_day2_rep2


title: GATA4_RNAseq_day4_rep1


title: GATA4_RNAseq_day0_rep2


title: Control #3


title: GATA4_Input_DNA


title: GATA6_ChIPSeq_rep2

value: GATA6 (R&D system, AF1700, lot KWT0112101)


title: GATA6_Input_DNA


title: GATA4_RNAseq_day0_rep1


title: GATA4_ChIPSeq_rep1

value: GATA4 (R&D system, AF2606, lot VAZ0312091)


title: GATA6_ChIPSeq_rep1


title: GATA4_ChIPSeq_rep2


title: non-stable SCV (RNA)

city: Adelaide

first: Long

last: Bui

state: South Australia

address: North Terrace Campus

department: Microbiology

country: Australia

institute: University of Adelaide

data_processing:
Bowtie2 to align reads from samples
Samtools and Bedtools to generate a mapped read count for the reference genes
Differential expression analysis was performed using R program with DESeq
Genome_build: NC_007795
Supplementary_files_format_and_content: read counts for reference genes, DESeq output and excel worksheet file with analyzed data.

organism: Staphylococcus aureus

source_name: WCH

growth_protocol: Strain WCH-SK2 was cultured in batch culture condition and in a prologned continuous culture (chemostat) for 60 days

extract_protocol:
Total RNA was extracted using RNAeasy minikit, a volume of 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Ion Torrens protocols

treatment_protocol: Cells were harvested and treated with RNA protect (Qiagen)

tag: phenotype

value: MRSA

tag: medium

value: day 30 of continuous culture -CDM

tag: stress

value: low level of stress (0.0078%)


title: WT batch (RNA)

value: batch culture - TSB

value: no stress


title: stable SCV (RNA)

value: day 55 of continuous culture -CDM

value: high level of stress (0.03%)


title: control (Sample 1)

first: Areum

last: Han

address: 6577 MacDonald Research Lab. 675 Charles E. Young Dr. South

institute: UCLA

description: Sample 1

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome and transcriptome using tophat with parameters --coverage-search --microexon-search --library-type=fr-firststrand --min-isoform-fraction=0.
Gene expression values, FPKM, were calculated using a cufflinks program.
Exon inclusion ratios were calculated using a splicetrap program.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM
*genes.fpkm_tracking.txt: fpkm for gene,
*isoforms.fpkm_tracking.txt: fpkm for isoform,
*transcripts.gtf: gene description
and exon inclusion level values for each Sample (splicetrap*.txt)

growth_protocol: ouse neuroblastoma (N2A) cells were cultured in DMEM with 10% FBS and 2mM L-glutamine.

extract_protocol:
Total RNA was collected using Trizol (Invitrogen) according to the manufacturer's instructions. The RNA was further treated with DNase I to avoid DNA contamination.
RNA-seq libraries were constructed following standard protocols (Illumina TruSeq RNA Sample Prep Kit). To make strand-specific libraries, we added two extra steps to the protocol. After first strand cDNA synthesis, remaining dNTPs were removed by a size selection using beads (AMPure XP). Second-strand cDNA was synthesized with dNTP mix with dUTP instead of dTTP. After sequencing adaptors were ligated, USER (Uracil-Specific Excision Reagent enzyme;NEB) was added to reactions to degrade the second strand cDNA with uracil. The samples were incubated for 15min at 37°C and the reaction were inactivated at 94°C for 5min. The samples were put in ice and preceded to next PCR amplification step.
The libraries were subjected to 100bp paired-end sequencing (Illumina HiSeq2000 platform).

treatment_protocol: At 70 to 80% confluency, cells were trypsinized and suspended in the growth medium. DNAâLipofectamine 2k (Invitrogen) complexes were prepared and mixed with cells in a tube according to manufacturerâs instructions. Tubes were incubated for 5 h with mixing in every half hour. Then cells were centrifuged and cultured in plates for 3 d. Proteins and RNA was extracted from collected cells.

value: neuroblastoma cell (N2a)

tag: transfected with

value: shControl

tag: genotype/variation

value: shRNA transfection control


title: ptbp1kd (Sample 2)

description: Sample 2

value: single knock down of ptbp1


title: F1_B6xWSB tunicamycin replicate2

city: Ithaca

first: Clement

middle: Y

last: Chow

state: NY

address: 227 Biotech Bldg

institute: Cornell University

data_processing:
Image analysis and base calling were performed with the provided Illumina software.
Quality assessment of the Illumina RNA-seq reads was performed using FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for all samples
Positions with low Q-score at the end of the reads were trimmed by FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html).
Adapter sequences were trimmed by Trimmomatic software
RNA-seq reads were aligned to the strain-specific reference mouse genome assembly using TopHat v1.4.1  with three mismatches allowed.
Total expression level for each transcript, measured in FPKM (Fragments Per Kilobase-pair of exon Model), was calculated based on all mapped reads
Read counts were normalized across all samples using the default normalization method (TMM) in the edgeR package in R
For each strain and condition, principal components analysis was used to identify outlying samples. Within a strain, we required that control samples be clustered together and TM treated samples be clustered together. If a sample was not clustered with the appropriate condition, it was removed from analysis. After removal of outlying samples, there remained at least two replicates for each strain and condition combination.
Remaining samples were re-normalized.
TM-induced gene expression changes were assessed by comparing control vs TM treated samples using linear models with the edgeR package in R
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: .csv text files include FPKM values for each Sample

source_name: F1_B6xWSB tunicamycin replicate2

growth_protocol: All MEFs were thawed at passage three or four and cells were split 1:3 every 3 days (fewer than three passages) before treatment. MEFs were maintained in DMEM containing 4.5 g/L glucose (Invitrogen), 10% fetal bovine serum, L-glutamine, and pen/strep (Invitrogen).

extract_protocol:
At the end of the treatment, medium was aspirated out and Trizol (Invitrogen) was added for immediate isolation of total RNA by standard procedures.
Single-end 100 bp mRNA-seq libraries were made with 1.5 ug of total RNA using the Illumina TruSeq RNA Sample Preparation kit (Illumina Inc., CA), per manufacturer’s guidelines. The samples were multiplexed and sequenced on a total of eight lanes using the Illumina HiSeq 2500 instrument.

treatment_protocol: MEFs were plated at a concentration of 2 x 105 cells/well in six-well plates. Cells were plated at least 18 h before treatment. TM stocks were prepared at 2 mg/ml in DMSO. To induce ER stress, MEFs were treated with a final concentration of 2 ug/ml of TM. Control cells were treated with 0.1% DMSO. MEFs were treated for 4 h.

value: primary Mouse Embryonic Fibroblasts


title: F1_B6xWSB tunicamycin replicate1

source_name: F1_B6xWSB tunicamycin replicate1


title: F1_B6xWSB tunicamycin replicate3

source_name: F1_B6xWSB tunicamycin replicate3


title: F1_B6xWSB control replicate3

source_name: F1_B6xWSB control replicate3


title: ptbp2kd (Sample 3)

description: Sample 3

growth_protocol: Mouse neuroblastoma (N2A) cells were cultured in DMEM with 10% FBS and 2mM L-glutamine.

treatment_protocol: At 70 to 80% confluency, cells were trypsinized and suspended in the growth medium. DNA–Lipofectamine 2k (Invitrogen) complexes were prepared and mixed with cells in a tube according to manufacturer’s instructions. Tubes were incubated for 5 h with mixing in every half hour. Then cells were centrifuged and cultured in plates for 3 d. Proteins and RNA was extracted from collected cells.

value: single knock down of ptbp2


title: ptbp1ptbp2kd (Sample 4)

description: Sample 4

source_name: N2A_shptbp1 and shptbp2_RNA-seq

value: shptbp1 and shptbp2

value: double knock down of ptbp1 and ptbp2


title: F1_B6xWSB control replicate2

source_name: F1_B6xWSB control replicate2


title: F1_B6xWSB control replicate1

source_name: F1_B6xWSB control replicate1


title: F1_B6xNZO tunicamycin replicate1

source_name: F1_B6xNZO tunicamycin replicate1


title: GATA4_RNAseq_day2_rep1

value: post-induction at day2


title: F1_B6xNZO control replicate3

source_name: F1_B6xNZO control replicate3


title: F1_B6xNZO control replicate1

source_name: F1_B6xNZO control replicate1


title: F1_B6xNZO tunicamycin replicate3

source_name: F1_B6xNZO tunicamycin replicate3


title: F1_B6xNOD tunicamycin replicate1

description: F1_C57BL6JxNODShiLtJ_control_TM_FPKM.csv

source_name: F1_B6xNOD tunicamycin replicate1


title: F1_B6xCAST tunicamycin replicate3

source_name: F1_B6xCAST tunicamycin replicate3


title: F1_B6xNOD tunicamycin replicate2

source_name: F1_B6xNOD tunicamycin replicate2


title: F1_B6xNZO control replicate2

source_name: F1_B6xNZO control replicate2


title: F1_B6xNOD control replicate3

source_name: F1_B6xNOD control replicate3


title: F1_B6xNOD control replicate2

source_name: F1_B6xNOD control replicate2


title: F1_B6xCAST tunicamycin replicate2

source_name: F1_B6xCAST tunicamycin replicate2


title: F1_B6xCAST control replicate3

source_name: F1_B6xCAST control replicate3


title: F1_B6xCAST tunicamycin replicate1

source_name: F1_B6xCAST tunicamycin replicate1


title: F1_B6x129 control replicate3

description: F1_C57BL6Jx129S1SvImJ_control_TM_FPKM.csv

source_name: F1_B6x129 control replicate3


title: F1_B6x129 tunicamycin replicate2

source_name: F1_B6x129 tunicamycin replicate2


title: WSB Tunicamycin replicate2

source_name: WSB Tunicamycin replicate2

value: WSB/EiJ


title: F1_B6xNZO tunicamycin replicate2

source_name: F1_B6xNZO tunicamycin replicate2


title: F1_B6xNOD control replicate1

source_name: F1_B6xNOD control replicate1


title: F1_B6xCAST control replicate2

source_name: F1_B6xCAST control replicate2


title: F1_B6x129 tunicamycin replicate1

source_name: F1_B6x129 tunicamycin replicate1


title: PWK Tunicamycin replicate1

source_name: PWK Tunicamycin replicate1

value: PWK/PhJ


title: F1_B6x129 tunicamycin replicate3

source_name: F1_B6x129 tunicamycin replicate3


title: PWK control replicate3

source_name: PWK control replicate3


title: F1_B6x129 control replicate1

source_name: F1_B6x129 control replicate1


title: PWK control replicate2

source_name: PWK control replicate2


title: NZO Tunicamycin replicate3

source_name: NZO Tunicamycin replicate3


title: PWK control replicate1

source_name: PWK control replicate1


title: WSB Tunicamycin replicate3

source_name: WSB Tunicamycin replicate3


title: WSB Tunicamycin replicate1

source_name: WSB Tunicamycin replicate1


title: WSB control replicate3

source_name: WSB control replicate3


title: PWK Tunicamycin replicate3

source_name: PWK Tunicamycin replicate3


title: WSB control replicate2

source_name: WSB control replicate2


title: NZO Tunicamycin replicate2

source_name: NZO Tunicamycin replicate2


title: NZO control replicate3

source_name: NZO control replicate3


title: NZO control replicate2

source_name: NZO control replicate2


title: NOD Tunicamycin replicate3

source_name: NOD Tunicamycin replicate3

value: NOD/ShiLtJ


title: PWK Tunicamycin replicate2

source_name: PWK Tunicamycin replicate2


title: NOD Tunicamycin replicate2

source_name: NOD Tunicamycin replicate2


title: NOD Tunicamycin replicate1

source_name: NOD Tunicamycin replicate1


title: CAST Tunicamycin replicate3

source_name: CAST Tunicamycin replicate3

value: CAST/EiJ


title: CAST control replicate3

source_name: CAST control replicate3


title: NZO Tunicamycin replicate1

source_name: NZO Tunicamycin replicate1


title: CAST control replicate1

source_name: CAST control replicate1


title: B6 control replicate2

source_name: B6 control replicate2


title: AJ Tunicamycin replicate2

source_name: AJ Tunicamycin replicate2

value: A/J


title: F1_B6x129 control replicate2

source_name: F1_B6x129 control replicate2


title: AJ control replicate3

source_name: AJ control replicate3


title: AJ control replicate1

source_name: AJ control replicate1


title: AJ Tunicamycin replicate1

source_name: AJ Tunicamycin replicate1


title: 129 Tunicamycin replicate3

source_name: 129 Tunicamycin replicate3


title: 129 control replicate3

source_name: 129 control replicate3


title: 129 control replicate2

source_name: 129 control replicate2


title: Doxy 200 #2

source_name: Pterygium

value: Pterygia cells

value: Doxy 200


title: NOD control replicate1

source_name: NOD control replicate1


title: NOD control replicate3

source_name: NOD control replicate3


title: CAST Tunicamycin replicate2

source_name: CAST Tunicamycin replicate2


title: B6 Tunicamycin replicate1

source_name: B6 Tunicamycin replicate1


title: B6 Tunicamycin replicate3

source_name: B6 Tunicamycin replicate3


title: B6 control replicate3

source_name: B6 control replicate3


title: yw male, replicate 2

city: Detroit

first: Victoria

middle: H

last: Meller

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

description: smallRNA Seq

data_processing:
Ilumina Small RNA-Seq adapters were removed from the sequenced tags
Tags with an abundance count less than 5 were removed
Tags ending in a homopolymer run with at least 9 nucleotides were removed
Genome_build: UCSC dm3/BDGP R5
Supplementary_files_format_and_content: Tag count

source_name: third instar male larvae

growth_protocol: Groups of 50 third instar males of the appropriate genotypes were collected.

extract_protocol:
Total RNA was isolated by homogenization of 50 larvae in Qiazol reagent. Small  RNA was enriched using the miRNeasy kit (Qiagen).
Illumina SmallRNA TruSeq Kit 3

tag: genotype

value: laboratory reference strain

tag: development stage

value: third instar male larvae


title: 129 Tunicamycin replicate2

source_name: 129 Tunicamycin replicate2


title: AJ control replicate2

source_name: AJ control replicate2


title: 129 Tunicamycin replicate1

source_name: 129 Tunicamycin replicate1


title: anti-CMS_brep_1_trep_2

city: Heidelberg

first: Lukas

last: Chavez

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Sample 2

data_processing:
library strategy: CMS-seq
CMS-IP and CMS-Input sequencing data were mapped against a fully in-silico converted C. cinerea genome (C.cinerea_okayama7#130 including all supercontigs downloaded from the Broad institute (GCF_000182895.1)) using the Bismark software v0.6.4 (-q -n 2 --chunkmbs 1028 bowtie-0.12.7)
CpG coverage, saturation, and correlation have been calculated by the Bioconductor software package MEDIPS v1.10.0 (extend=250, uniq=T, window_size=100, pattern=”CG”, BSgenome=custom genome generated from C.cinerea_okayama7#130)
For the identification of 5hmC enriched regions (HERGs), we have first combined the mapping results of the technical replicates per biological replicate resulting in two independent CMS-IP and two independent CMS-Input samples. Subsequently, we calculated differential coverage between the group of CMS-IP and the group of CMS-Input samples using MEDIPS v1.10.0 (same parameters as above but window_size=300, and diff.method=edgeR, p.vale=1e-3)
In an alternative approach, we converted CMS-IP and CMS-Input sequencing data (custom scripts) and mapped against the in-silico converted C. cinerea genome using bowtie-0.12.7 allowing for up to 100 different mapping positions per read (-q -k 100 --best --chunkmbs 512). Subsequently, an alternative set of HERGs was calculated as described above (same parameter settings) but using the alternative multiple mapping results.
Genome_build: C.cinerea_okayama7#130 including all supercontigs downloaded from the Broad institute (GCF_000182895.1)
Supplementary_files_format_and_content: Result table contain the counts, rpkm, log2FC, and p-values at genome wide 300 bp windows as returned by the MEDIPS software for both approaches (considering reads that map to i) only one or ii) up to 100 different positions in the genome).

organism: Coprinopsis cinerea

extract_protocol:
DNeasy Plant Mini Kit (Qiagen)
Truseq DNA LT sample prep kit (Illumina)

tag: developmental stage

value: Oidia

tag: ip antibody

value: anti-CMS (non-commercial)

tag: ip antibody info


title: anti-CMS_brep_1_trep_3

description: Sample 3


title: male, 1.688x snapback, replicate 1

description: smallRNA Seq

value: ectopic expression of ds 1.688 RNA


title: Twist ChIP-seq (Drosophila embryos) Rep 1

description:
dmel_embryo_twi_chipseq_01
Illumina multiplex barcode: ACAGTG

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were trimmed to 50 bp and aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

extract_protocol:
embryos were cross-linked in 1.8% formaldehyde. Embryos were then dounced to break down cells and extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. 300 ul soluble chromatin from ~100 mg embryos was used
DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

tag: tissue

value: whole-embryo

tag: time point

value: 02 to 04 h AEL

tag: chip antibody

value: anti-Twist rabbit polyclonal, custom (Covance)

value: Oregon-R


title: anti-CMS_brep_2_input

description: Sample 7


title: anti-CMS_brep_2_trep_1

description: Sample 4


title: anti-CMS_brep_1_trep_1

description: Sample 1


title: anti-CMS_brep_1_input

description: Sample 6


title: male, 1.688x snapback, replicate 2

description: smallRNA Seq


title: AJ Tunicamycin replicate3

source_name: AJ Tunicamycin replicate3

value: primary Mouse Embryonic Fibroblasts


title: yw male, replicate 1

description: smallRNA Seq


title: Myc ChIP-nexus (Drosophila S2 cells) Rep 2

description:
dmel_s2_myc_chipnexus_02
Protocol: ChIP-nexus
Illumina multiplex barcode: GCCAAT

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and saved in BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand

source_name: Schneider 2

growth_protocol: grown at 25C in HyClone SFX-Insect Cell Culture Media with penicillin and streptomycin

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer to extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. 300 ul soluble chromatin from ~ 20 million cells was used
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

tag: cell line

value: Schneider 2 cells

value: anti-Myc rabbit polyclonal, Santa Cruz Technology, catalog # sc-28207, lot # D-2704


title: Twist ChIP-nexus (Drosophila embryos) Rep 2

description:
dmel_embryo_twi_chipnexus_02
Protocol: ChIP-nexus
Illumina multiplex barcode: CGATGT

source_name: Oregon-R

extract_protocol:
embryos were cross-linked in 1.8% formaldehyde. Embryos were then dounced to break down cells and extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. 300 ul soluble chromatin from ~100 mg embryos was used
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.


title: spoIIID- rep3 (S33)

city: Burlington

first: Julie

last: Dragon

state: VT

address: 95 Carrigan Dr

department: MMG

institute: UNIVERSITY OF VERMONT & ST AGRIC COLLEGE

data_processing:
Illumina CASAVA 1.8.2 for basecalling
Read pairs were aligned to the SN:AM180355.1_Clostridium_difficile630 LN:4290252 genome using BWA 0.6.1.
Read pairs were mapped to the modified gene annotation using the countOverlaps procedure of the R/Bioconductor I Ranges package.
Hypothesis testing was based on the R/Bioconductor package DESeq
Genome_build: NC_009089.1

organism: Clostridioides difficile 630

source_name: Cells grown on 70:30 sporulation plates

growth_protocol: Strains were transferred from BHIS agar plates onto 70:30 agar plates at time 0. The samples were grown under anaerobic conditions (85% N2, 5% CO2, 10% H2) at 37˚C for 18 hr after which the triplicate samples were harvested and processed as indicated.

extract_protocol:
Cell pellets were resuspended in RNA Pro solution and transferred to RNA Pro Blue tubes. The sample was homogenized using the FastPrep-24 automated homogenizer (MP Bio) for 30 s at setting 6.0 (homogenization was repeated a total of 3 times), and RNA was harvested according to the manufacturer's direction.
30 µg of total RNA was subjected to 2 rounds of DNase I treatment in solution, followed by one DNase I treatment using a Qiagen Rneasy kit. The samples were tested for genomic contamination using quantitative PCR for 16S rRNA and the sleC gene. 5 µg of the DNase-treated RNA was ribosomally depleted using a Ribo-Zero Gram-positive ribosomal RNA depletion kit (EpiCentre). The enriched RNA was analyzed using a Pico kit on a Bioanalyzer. 100 ng of the enriched RNA was used to carry out cDNA synthesis and library construction using the TruSeq stranded mRNA kit (without polyA selection) according to the manufacturer's instructions.

treatment_protocol: Cells were harvested from the plates and resuspended in PBS. The sample used to harvest RNA was removed from the cell suspension, pelleted and processed accordingly.

value: spoIIID- (targetron insertion in bp 546)

tag: timepoint

value: 18 hr

tag: growth condition

value: 70:30 agar plates


title: Myc ChIP-nexus (Drosophila S2 cells) Rep 1

description:
dmel_s2_myc_chipnexus_01
Illumina multiplex barcode: ACAGTG
ChIP-nexus

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and saved in BigWig format
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand
Genome Build:
dmel_s2_myc_chipnexus_01_positive.bw: UCSC dm3
dmel_s2_myc_chipnexus_01_negative.bw: UCSC dm3

source_name: Drosophila melanogaster_Schneider 2 cells


title: Dorsal ChIP-seq (Drosophila embryos) Rep 1

description: UCSC dm3

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Reads were trimmed to 50 bp and aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were extended to each library's estimated insert size
Genome-wide coverage counts were calculated and saved in BigWig format
Supplementary_files_format_and_content: BigWig files contain pileup counts for each base

value: anti-Dorsal rabbit polyclonal, custom (GenScript)

tag: strain

tag: multiplex barcode

value: ACAGTG


title: Max ChIP-seq (Drosophila S2 cells) Rep 1

description: UCSC dm3

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer to extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. 300 ul soluble chromatin from ~ 20 million cells was used
DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

value: anti-Max rabbit polyclonal, Santa Cruz Technology, catalog # sc-28209, lot # D-2504

value: TGACCA


title: Max ChIP-nexus (Drosophila S2 cells) Rep 2

description:
dmel_s2_max_chipnexus_02
Protocol: ChIP-nexus
Illumina multiplex barcode: ACAGTG


title: Dorsal ChIP-nexus (Drosophila embryos) Rep 1

description:
dmel_embryo_dl_chipnexus_01
Illumina multiplex barcode: TTAGGC
ChIP-nexus

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and saved in BigWig format
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand
Genome Build:
dmel_embryo_dl_chipnexus_01_positive.bw: UCSC dm3
dmel_embryo_dl_chipnexus_01_negative.bw: UCSC dm3

source_name: Drosophila melanogaster_whole-embryo


title: anti-CMS_brep_2_trep_2

description: Sample 5

value: Oidia


title: Dorsal ChIP-nexus (Drosophila embryos) Rep 2

description:
dmel_embryo_dl_chipnexus_02
Illumina multiplex barcode: TGACCA
ChIP-nexus

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and saved in BigWig format
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand
Genome Build:
dmel_embryo_dl_chipnexus_02_positive.bw: UCSC dm3
dmel_embryo_dl_chipnexus_02_negative.bw: UCSC dm3


title: sigE- rep1 (E1)

value: sigE- (targetron insertion in bp 119)


title: Max ChIP-nexus (Drosophila S2 cells) Rep 1

description:
dmel_s2_max_chipnexus_01
Illumina multiplex barcode: TTAGGC
ChIP-nexus

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and saved in BigWig format
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand
Genome Build:
dmel_s2_max_chipnexus_01_positive.bw: UCSC dm3
dmel_s2_max_chipnexus_01_negative.bw: UCSC dm3


title: WT rep 2 (R2)

value: wild type


title: spoIIID- rep1 (S31)


title: spoIIID- rep2 (S32)


title: sigE- rep2 (E2)


title: sigK- rep3 (K3)

value: sigK- (targetron insertion in bp 230)


title: sigK- rep2 (K2)


title: sigK- rep1 (K1)


title: WT rep 3 (R3)


title: WT rep1 (R1)


title: ZR751_PKC412_R2

city: Vienna

first: Sebastian

last: Nijman

address: Lazarettgasse 14

country: Austria

institute: Research Center for Molecular Medicine

data_processing:
Illumina Casava 1.82 software used for base calling
Elimination of low quality reads with Triagetools. Alignement with Tophat 2 with refSeq annotation.
Expression estimates by read counting on refSeq gene models
Genome_build: hg19
Supplementary_files_format_and_content: gene-level expression measured in FPKM

source_name: Breast cancer cell line (luminal)

growth_protocol: Cell lines were grown according to ATCC recommendations

extract_protocol:
Cells were put on ice, medium was aspirated, washed with ice-cold PBS 2x followed by Trizol RNA extraction.
Illumina Sequencing Protocol

treatment_protocol: Treatment with DMSO or PKC412 (1µM) was performed in 10 cm dishes. 6h treatment time before harvesting.

tag: subtype

value: luminal

tag: agent


title: Twist ChIP-nexus (Drosophila embryos) Rep 1

description:
dmel_embryo_twi_chipnexus_01
Protocol: ChIP-nexus
Illumina multiplex barcode: ATCACG

value: whole-embryo

value: 02 to 04 h AEL

value: anti-Twist rabbit polyclonal, custom (Covance)


title: ZR751_PKC412_R1


title: ZR751_PKC412_R3


title: MDAMB468_PKC412_R1

source_name: Breast cancer cell line (basal)

value: basal


title: ZR751_DMSO_R1

value: DMSO


title: MDAMB468_PKC412_R3


title: BF39

city: Madison

first: Reid

last: Alisch

state: WI

address: 6001 Research Park Blvd.

department: Department of Psychiatry

institute: University of Wisconsin School of Medicine

description: Sample 22

data_processing:
Bismark (version 0.11.1) was used to map the bisulfite treated reads to human genome
Only reads with a depth greater than 5 and less than 1000 were considered for further analysis
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated text file giving methylation at each CpG position

organism: Macaca mulatta

source_name: Central nucleus of the Amygdala

extract_protocol:
DNA and RNA extraction was performed using AllPrep DNA/RNA mini kit (Qiagen).
Genome-wide methylation data was generated for each monkey using reduced representation bisulfite sequencing (RRBS). Briefly, genomic DNA (1ug) was digested with MspI and the fragments were end-repaired and ligated to Illumina Truseq adapters (methylated) following the manufacturer’s protocol (Illumina). Adapter-ligated DNA fragments, ranging from 200 to 400 base pairs (bp), were purified by gel electrophoresis (2.5% NuSieve GEG agargose) and then treated with sodium bisulfite (ZymoResearch EZ DNA methylation gold kit), which converts unmethylated cytosines to uracil and leaves methylated cytosines unchanged. Converted libraries of DNA fragments were then amplified using TruSeq adapter primers (Illumina) and amplicons were purified (MiniElute PCR purification kit; Qiagen 28004) and sequenced on a Next-Generation sequencer (Illumina HiSeq2000).

tag: age (yrs)

tag: mean at score

tag: hemisphere

value: Right

value: Central nucleus of the Amygdala


title: sigE- rep3 (E3)

tag: genotype

value: 18 hr

value: 70:30 agar plates


title: LTMR cluster rep 3

first: Katrin

last: Schrenk-Siemens

address: Im Neuenheimer Feld 366

department: Institute of Pharmacology

institute: University Heidelberg

data_processing:
Raw reads were aligned using ELAND in the Illumina CASAVA pipeline
BAM files were processed using SAM tools (http://www.ncbi.nlm.nih.gov/pubmed/19505943)
Read counts were generated using HTSeq (http://biorxiv.org/content/early/2014/02/20/002824) and a UCSC Refseq HG19 gene model
For comparison of expression levels between different samples all read counts were normalized to the total number of reads assigned to the gene model for a given sample
Differential expression was analyzed using DeSeq (http://genomebiology.com/content/11/10/R106)
Genome_build: UCSC Refseq HG19
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each Sample

source_name: peripheral sensory neurons

growth_protocol: Neuroectodermal spheres were derived from hES cells and further differentiated into neural crest like cells. These neural crest like cells were then incubated in differentiation medium containing retinoic acid and various growth factors to induce sensory neuron differentiation.

extract_protocol:
RNA of human ESC-derived sensory neuron clusters (10-20 cells)  and neural crest like cells was isolated using PicoPure (Life Technologies) and amplified using the Ovation RNA Amplification System V2 (NuGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 23 DIV


title: MDAMB468_DMSO_R2


title: MDAMB468_PKC412_R2


title: r09076

description: Sample 23


title: MDAMB468_DMSO_R1


title: r09081

description: Sample 20

value: Left


title: BE99

description: Sample 21


title: LTMR cluster rep 1


title: r09069

description: Sample 17


title: NCCs rep 3

source_name: neural crest like cells

value: 0 DIV


title: BE85

description: Sample 19


title: r09060

description: Sample 18


title: BE75

description: Sample 16


title: r09078

description: Sample 14


title: NCCs rep 1


title: TBP ChIP-seq (Human K562 cells) Rep 1

description: UCSC hg19

source_name: TBP ChIP-seq (Human K562 cells) Rep 1

growth_protocol: grown at 37C, 5% CO2 w/ humidity in Iscove's DMEM media with 10% fetal bovine serum

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then dounced to bread down cells and extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp.  300 ul soluble chromatin from ~ 10 million cells was used
DNA-protein-complexes were isolated with specific antibodies. Sequencing libraries were prepared following Illumina's instructions: DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs were ligated to the adenylated fragments, and after a size-selection step using AmPure beads (200-250 bp) the adapter modified DNA was PCR-amplified. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

value: K562 cells

value: anti-TBP rabbit polyclonal, Santa Cruz Technology, catalog # sc-204X (ChIP-grade), lot # C-0513

value: GTGGCC


title: BF10

description: Sample 15


title: r09024

description: Sample 11


title: BE97

description: Sample 12


title: NCCs rep 2


title: ZR751_DMSO_R2


title: TBP ChIP-nexus (Human K562 cells) Rep 2

description:
hsap_k562_tbp_chipnexus_02
Illumina multiplex barcode: GCCAAT
ChIP-nexus

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and saved in BigWig format
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand
Genome Build:
hsap_k562_tbp_chipnexus_02_positive.bw: UCSC hg19
hsap_k562_tbp_chipnexus_02_negative.bw: UCSC hg19

source_name: Homo sapiens_K562 cells

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then dounced to bread down cells and extract nuclei. Chromatin was sonicated by bioruptor to an average size of 300~500 bp.  300 ul soluble chromatin from ~ 10 million cells was used
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment (Klenow polymerase) and T4 polynucleotide kinase. A single 3'-A overhang was added to the blunted ends using Klenow 3'-5' exo- polymerase. Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.


title: BE60

description: Sample 6


title: BE50

description: Sample 7


title: BD60

description: Sample 1


title: RNA-seq oidia, replicate 2

description: Coprinus cinereus

data_processing:
Paired-end RNA sequencing data were mapped against the C. cinerea genome using tophat (Trapnell et al., 2009) (-g 1 -r 115 --mate-std-dev=70 --no-coverage-search --library-type=fr-secondstrand) employing bowtie-0.12.7 (Langmead et al., 2009). Read counts per gene (and other annotations) have been calculated based on the mapping results using custom scripts.
Genome_build: C.cinerea_okayama7#130 including all supercontigs downloaded from the Broad institute (release date 6/9/2010).
Supplementary_files_format_and_content: DESeq result table.

source_name: Oidia

extract_protocol: C. cinerea oidia mRNA was isolated using the Qiagen RNeasy plant mini kit. 5 µg mRNA was used for 2 rounds of polyA selection following the manufacturer’s instructions (Life Technologies, Poly(A)PuristTM MAG kit). For oidia, RNA purified library preparation was done using SOLiDTM Total RNA-seq kit (Life Technologies). For hyphae, RNA library preparation was done after polyA selection using NEB NEBNext® Ultra™ RNA Library Prep Kit for Illumina® kit. Library quality was analyzed using Agilent 2100 Bioanalyzer platform.

tag: strain/background

tag: developmental stage

value: oidia


title: LTMR cluster rep 2


title: r09020

description: Sample 2

tag: tissue


title: r09019

description: Sample 8


title: BF36

description: Sample 9


title: r09051

description: Sample 10


title: r09012

description: Sample 3


title: RNA-seq hyphae, replicate 2

description: Coprinus cinereus

source_name: Hyphae

value: hyphae


title: BD94

description: Sample 4


title: RNA-seq hyphae, replicate 1

description: Coprinus cinereus


title: RNA-seq oidia, replicate 1

description: Coprinus cinereus


title: r09006

description: Sample 5


title: h_BrainF10_MBD_M

status: Public on Dec 01 2014

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

data_processing:
Library strategy: MBD-Seq
Library selection: MeCP2 protein methyl-CpG binding domain
Sequenced reads were mapped to hg18 genome using MAQ with parameters -n 2 -m 0.001 -e 70 -a 250
Reads with a poor mapping score were filtered out using bamtools with the paramater -mapQuality ">=20"
BAM files were converted into wig format using bedtools
Genome_build: hg18
Supplementary_files_format_and_content: Merged files containing the combined read data for all replicates for that sample. Columns represent: chromosome, start position, stop position & read_coverage. A single header row provides additional information for the browser.

source_name: Hippocampus

extract_protocol:
DNA was extracted and sheared to approximately 400 bp using sonication and then ligated to Illumina's adapters. Methylated DNA was purified by two step MBD Affinity Purification as described in Skene et al., 2010.
Libraries were prepared as follows using enzymes from New England Biolabs (NEB). End Repair was carried out by incubating fragmented DNA with T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase for 30 minutes at 20 C. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP for 30 minutes at 37 C to yield a protruding 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligated DNA was ethanol precipitated and then reconstituted in running buffer prior to MAP-purification. Purified DNA was PCR amplified with Illumina primers for 10-12 cycles. Library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were isolated by gel extraction. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a Genome Analyzer following the manufacturer's protocols. Sequencing was performed at the Wellcome Trust Sanger Institute; Hinxton, Cambridge, UK.

tag: individual

tag: gender

value: Male

tag: neuropathological status

value: Control

value: Hippocampus


title: h_BrainG1_MBD_F

value: Female


title: h_BrainF2_MBD_F


title: h_BrainF1_MBD_M


title: h_BrainF3_MBD_M


title: h_BrainF9_MBD_M


title: h_BrainF4_MBD_M


title: h_BrainE9_MBD_F


title: h_BrainE8_MBD_M


title: h_BrainF5_MBD_M


title: h_BrainE7_MBD_M


title: h_BrainE5_MBD_M


title: h_BrainF6_MBD_F


title: h_BrainE3_MBD_F


title: h_BrainE4_MBD_F


title: h_BrainE1_MBD_M

value: Schizophrenia


title: h_BrainE2_MBD_M


title: h_BrainG2_MBD_F


title: h_BrainD10_MBD_M


title: h_BrainD7_MBD_F

value: Depression


title: h_BrainD6_MBD_M


title: h_BrainF8_MBD_M


title: h_BrainF7_MBD_M


title: h_BrainD5_MBD_M


title: h_BrainD4_MBD_M


title: h_BrainD3_MBD_M


title: h_BrainD2_MBD_F


title: h_BrainD1_MBD_F


title: h_BrainC7_MBD_F

value: Bipolar


title: h_BrainE6_MBD_M


title: h_BrainC8_MBD_F


title: h_BrainC9_MBD_F


title: h_BrainC3_MBD_M

source_name: Parietal

value: C

value: Parietal


title: h_BrainC6_MBD_M


title: h_BrainC4_MBD_F


title: h_BrainC2_MBD_M

source_name: Cerebellum

value: Cerebellum


title: h_BrainB8_MBD_M

source_name: Occipital

value: Occipital


title: h_BrainD9_MBD_M


title: h_BrainB7_MBD_M

source_name: Frontal

value: Frontal


title: h_BrainB9_MBD_M

source_name: Thalamus

value: Thalamus


title: h_BrainB10_MBD_M

source_name: Temporal

value: Temporal


title: h_BrainB6_MBD_M

source_name: Pons

value: B

value: Pons


title: h_BrainB5_MBD_M


title: h_BrainB4_MBD_M


title: h_BrainB2_MBD_M


title: h_BrainA10_MBD_M


title: h_BrainB3_MBD_M


title: h_BrainA9_MBD_M


title: h_BrainB1_MBD_M


title: h_BrainA7_MBD_M

value: A


title: r09061

description: Sample 13

value: Left

value: Central nucleus of the Amygdala


title: h_BrainC10_MBD_F

value: Hippocampus


title: h_BrainA6_MBD_M

value: Male

value: Control


title: h_BrainA5_MBD_M


title: h_BrainC1_MBD_M


title: h_BrainA3_MBD_M


title: h_BrainA2_MBD_M


title: DamID_mel-28 Male

city: Bern

first: Peter

last: Meister

state: Schweiz

address: Baltzerstrasse 4

department: Institute of Cell Biology

country: Switzerland

institute: University of Bern

description:
C. elegans (+contaminating E.coli)
DamID reads

data_processing:
DamID adapter sequences were cut from raw reads using cutadapt with following parameters:  -g CGCGGCCGAG -e 0.15
Cut reads were mapped to ce10 C. elegans genome with bowtie, using -m 1 -- best parameters
sam file converted to bam using samtools before import into R
genomic intervals from bowtie were imported to R, intervals not starting with GATC were removed (plus strand) as well as intervals not ending with GATC (minus strand). Number of reads per 100 kb regions was then counted (file: GATC_read_counts_per_100kb_bin.tab)
GATC counts per 100 kb bin was normalized to the total number of GATC reads. For all intervals, the ratio between lmn-1/mel-28 and gfp frequency was calculated (file:Ratios_per_100kb_bin.tab)
Genome_build: ce10
Supplementary_files_format_and_content: GATC_read_counts_per_100kb_bin.tab DamID read counts per 100 kb bin for all strains (males and hermaphrodites, summed for repeats)
Supplementary_files_format_and_content: Ratios_per_100kb_bin.tab Ratio between localized dam (lmn-1/mel-28) and free dam (gfp) for males and hermaphrodites, per 100 kb bin

organism: Caenorhabditis elegans

source_name: Entire animals (20)

growth_protocol: Worm were grown at 25°C on a E. coli bacterial lawn

extract_protocol:
PCR product was purified on a Qiaquick column following the instructions of the manufacturer, except that an additional 35% guanidine hydrochloride was introduced before the PE washes
PCR fragments were end-repaired using End-It (Epicentre), A-tailed using Klenow fragment and ligated to Y-shaped library primers. Indexed primers were used to amplify (6 cycles) the library.

treatment_protocol: 10 worms were pooled together in a single PCR tube containing 1ul of lysis buffer (10 mM Tris-Ac, 10 mM MgAc, 50 mM KAc, 0.67% Tween20, 0.67% NP40), snap-frozen in liquid nitrogen. Frozen worms were thawed and 2 ul of lysis buffer with ProtK (final concentration in 3 ul 0.67 mg/ml) was added. Worms were then digested for 4 hours at 42°C, ProtK was inactivated at 80°C for 10'. Lysates were then digested with 0.1 ul DpnI restriction enzyme, together with 7 ul One-Phor-All buffer (10 mM TrisAc pH7.5, 50 mM KAc, 10 mM MgAc), 6 hours at 37°C. ds DamID adapters (0.2 ul 50 uM) were then ligated at 16°C overnight (hybridized 5’-CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA and 5’-TCCTCGGCCGCG) with 0.5 ul T4 ligase and 2 ul T4 ligase buffer in a total volume of 20 ul. Ligated fragments were then PCR amplified using 5’-NNNNGTGGTCGCGGCCGAGGATC.

value: Strain expressing a fusion between DNA adenine methyltransferase (dam) and mel-28, under transcriptional control of the uninduced hsp-16.41 promoter

value: L4 stage


title: DamID_mel-28 Hermaphrodite

value: Hermaphrodite