title: scc2-4_wce_1

city: Kansas City

first: Musinu

last: Zakari

state: Missouri

address: 1000E 50th Street

institute: Stowers Institute for Medical Research

data_processing:
CASAVA-1.8.2 used for base calling.
Reads were aligned UCSC sacCer3 using the bowtie aligner using the following parameters:  bowtie --best --strata -v 2 -m 1, reporting unique alignments with up to 2 mismatches
Unique alignments with the fewest mismatches were reported. Reads without unique alignments for a permissible number of mismatches were not reported
Genome_build: SacCer3
Supplementary_files_format_and_content: The bigWig files contain rpm normalized coverage for each sample calculated as follows: read mappings were extended in silico to 150 bases and coverage depth across the genome was assessed. Coverage at each base was then divided by the number of mapped reads and converted to reads per million

organism: Saccharomyces cerevisiae BY4741

growth_protocol: Cultures were innoculated from overnight cultures and grown till exponential phase (OD=0.8).

extract_protocol:
Chromatin was extracted from cells and histone-DNA complexes extracted with antibody
Libraries were constructed using 10ng each of sample using Illumina KAPA HTP sample preparation kit with instructions

value: scc2-4 mutant

tag: replicate


title: scc2-4_wce_2

status: Public on Jun 15 2015

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

tag: genotype


title: ES_Tsix-stop_serum Undiff

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

library_source: transcriptomic

data_processing:
Initial data processing and base calling was performed using the Illumina Analysis Pipeline. FASTQ files were mapped using GSNAP version 2011-03-10 (Wu et al., 2010). To avoid bias in the mapping of either the Cast- or the 129-derived reads, the alternative alleles of polymorphic sites between the 129- and Cast-genome (see above) are included in the reference during mapping (GSNAP SNP-tolerant mapping; flag –v). Only sequence tags aligning to a single position on the genome were considered for further analysis on the 32-42 bp aligned sequence reads. Further analysis was performed with the 32-42 bp aligned sequence.
The data was converted to Browser Extensible Data (BED) files for downstream analysis. To compensate for differences in sequencing depth and mapping efficiency among samples, the total number of unique reads of each sample was uniformly equalized relative to the sample with the lowest number of sequence reads, allowing quantitative comparisons. Wiggle (WIG) files for viewing the data in the UCSC Genome Browser were generated from the normalized files.
To obtain RNA-Seq gene expression values (RPKM), we used Genomatix (www.genomatix.de; ElDorado 12-2010) selecting RefSeq genes.
Known polymorphic sites between the mouse species 129 and Cast were collected using polymorphic sites determined by (i) the Sanger mouse sequencing project using the March 2011 release (Keane et al., 2011; Yalcin et al., 2011) (http://www.sanger.ac.uk/resources/mouse/genomes/; we used the ftp-mouse.sanger.ac.uk/REL-1003/20100301-high-confidence-snps.tab file for the species 129S1, C57BL and CAST) and (ii) the NIEHS/Perlegen mouse resequencing project (Frazer et al., 2007) (http://phenome.jax.org/db/q?rtn=projects/projdet&reqprojid=198; we used the b04_Chr*_genotype.dat files for the species 129S1/SvImJ, CAST/EiJ and the C57BL/6J reference genome of NCBI Build 36 (Waterston et al., 2002)). This resulted in a total of 20,785,351 polymorphic sites between the genomes of 129 and Cast.
Within the individual samples, we used the mapped tags to determine the sequence tag coverage per allele for each of the 20,785,351 polymorphic sites using GSNAP tally. A total of 7,854,031 polymorphic sites were covered at least once in any of the samples used for this study. Per single polymorphic nucleotide, the pile-ups were subsequently assigned to either the 129- or the Cast-allele using custom Perl-based scripts (see supplementary table Polymorphic_sites_of_Tsix_stop_with_counts.txt.gz). To avoid including counts from positions which were reported to be polymorphic in the Sanger sequencing project and/or the NIEHS/Perlegen resequencing projects, but which were not present in the genotypes used for the current study, we selected polymorphic sites that were covered at least twice from both the 129 and the Cast allele. This resulted in a total of 1,121,809 polymorphic sites used in further analysis. Counts over polymorphic sites within exons of individual RefSeq genes for either 129 or Cast were summed to obtain allele-specific gene expression counts for both species. The ratio between the 129 counts or the Cast counts versus the total counts (129 + Cast) represent the relative contribution of the 129 or Cast allele, respectively, to expression of a particular gene. To calculate allele specific expression values, we multiplied the relative contribution of either 129 or Cast with the total RPKM expression value of a gene. For the ESC differentiation timecourse, only genes that contained a count of >80 over the complete timecourse from both the 129 as well as from the Cast allele were included for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated according to general instructions and were used for analysis; Wig files can be directly uploaded to the UCSC genome browser. The domains within Domains.txt were determined using the HiC data

molecule: polyA RNA

organism: Mus musculus

source_name: Embryonic Stem Cells (ESCs)

growth_protocol: ESCs were cultured without feeders in the presence of leukemia inhibitory factor (LIF; 1000 U ml-1) either in Glasgow modification of Eagles medium (GMEM) containing 10% fetal calf serum (called “serum” medium), or in serum-free N2B27 supplemented with MEK inhibitor PD0325901 (1 μM), GSK3 inhibitor CH99021 (3 μM), penicillin (100 U ml-1), streptomycin (100 mg ml-1), glutamine (1 mM), non-essential amino acids (0.1 mM), β-mercaptoethanol (0.1 mM) (together called “2i” medium; Ying et al., 2008). For adaptation to 2i, serum ESCs were transferred to 2i medium and cultured for >12 days (>6 passages) in 2i medium. ESCs used in this study include the female lines ES_Tsix-stop (Luikenhuis et al., 2001), ES_Xist-del (a polymorphic 129:Cast female ESC line that show non-random XCI due to a deletion in the Xist gene on the 129 allele; Csankovszki et al. (1999)), TNGA (Chambers et al., 2007) and XT67E1 (a polymorphic 129:PGK female ESC line that show non-random XCI due to a deletion in the Xist gene on the 129 allele; Penny et al., 1996), and the male ESC lines E14Tg2a (E14) and Rex1GFPd2 lines (Wray et al., 2011; Marks et al., 2012). Derivation and culture of the EpiSCs was described previously (Maruotti et al. 2010; Veillard et al., 2014). Derivation of NPC lines, including culture conditions and further details, has been described in Splinter et al. (2011).

extract_protocol:
Total RNA was isolated with Trizol (Invitrogen) according to the manufacturer’s recommendations. 100 μg total RNA was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit; QIAGEN), followed by DNaseI treatment (QIAGEN). 100–200 ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 s and purified (RNAeasy Minelute Kit; QIAGEN). cDNA was synthesized using 5 μg random hexamers by Superscript III Reverse Transcriptase (Invitrogen). Ds cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer’s recommendations and purified (Minelute Reaction Cleanup Kit; QIAGEN). Strand-specific rRNA depleted ds cDNA profiling used for the NPC lines was performed with the ScriptSeq kit (cat. no. SS10924) from Illumina, according to the instructions of the manufacturer. rRNA depletion was performed with the Ribo-Zero rRNA Removal Kit using 5 μg of total RNA (Human/Mouse/Rat; cat. no. RZH110424). Collection of the cells for Hi-C and the HiC sample preparation procedure was performed as previously described (Lieberman-Aiden et al., 2009), with the slight modification that DpnII was used as restriction enzyme during initial digestion.
For the PolyA+ samples, cDNA was prepared for sequencing by end repair of 20 ng ds cDNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and 14 cycles of PCR amplification. Quality control of the adaptor-containing DNA libraries of both PolyA+ and ScriptSeq samples was performed by qPCR and by running the products on a Bioanalyzer (BioRad). Cluster generation and sequencing (32-42 bp) was performed with the Illumina Genome Analyzer IIx or Hi-Seq 2000 platforms according to standard Illumina protocols. For HiC, paired-end libraries were prepared according to Lieberman-Aiden et al. (2009) and sequenced on the NextSeq 500 platform using 2*75 bp sequencing.

treatment_protocol: Induction of ESC differentiation has been described by Barakat et al. (2011). In short, ESCs were split, and pre-plated on non-gelatinised cell culture dishes for 60 minutes. ESCs were then seeded in non-gelatinised bacterial culture dishes containing differentiation medium to induce embryoid body (EB) formation. EB-medium consisted of IMDM-glutamax, 15% foetal calf serum, 100 U ml-1 penicillin, 100 mg ml-1 streptomycin, non-essential amino acids, 37.8 μl l-1 monothioglycerol and 50 μg ml-1 ascorbic acid. EBs were plated on coverslips 1 day prior to harvesting, and allowed to grow out.

tag: cell type

value: ESCs

tag: strain background

value: 129/SV-Jae x Cast

tag: treatment

value: Undifferentiated in serum and LIF


title: ES_Xist-del replica

value: 129/SV-Jae x Cast/B6

value: Undifferentiated in Ndiff and 2i+LIF


title: ES_Xist-del_serum Undiff


title: total scnRNAs from PDD1 MAC&MIC-KO cells @3 hpm

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

data_processing:
Following removal of the adapter sequences from the sequence reads, the reads from rRNAs, tRNA, snRNAs, the mitochondrial genome, and mixed phiX174 phage DNA were removed.
Supplementary_files_format_and_content: Normalized numbers (RPKM) of sequenced 26-32-nt RNAs that map uniquely to the compiled 1462 MIC genome supercontigs (ordered by their lengths) are shown as histograms with 100-b bin. The 1,464 supercontigs (Tetrahymena Comparative Sequencing Project, Broad Institute of Harvard and MIT) were ordered by length, concatenated as 157.7 Mb of linear DNA, and used as the MIC genome for this study.

molecule: total RNA

organism: Tetrahymena thermophila

source_name: Conjugating cells at 3 hpm

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30 °C. For conjugation, growing cells (~5-7 x 105/ml) of two different mating types were washed, pre-starved (~12-24 hr) and mixed in 10 mM Tris (pH 7.5) at 30 °C.

extract_protocol: RNA libraries were prepared for sequencing according to Noto et al. (2014) Methods in Molecular Biology 1093,209-24

tag: genotype/variation


title: scnRNAs co-IPed with zygotically-expressed HA-Twi11p @10.5 hpm

source_name: Conjugating cells at 10.5 hpm

value: zygotically expressing HA-Twi1p


title: total scnRNAs from wild-type cells @12 hpm

source_name: Conjugating cells at 12 hpm

value: wild-type


title: total scnRNAs from wild-type cells @3 hpm


title: WK33-HA Bc 14h rep2

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Trimming and filtering of LinDA adapters and low quality sequences was performed using 1) cutadapt  v1.2.1 with options –e 0.2, -n 2 and –m 36 and 2) PRINSEQ lite v0.20.2 with options –trim_qual_right/left 20, trim_tail_right/left 3 –min_len 36, -min_qual_mean 25
Sequenced reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie v0.12.7 with options –best –m 1
Peak calling was performed for each replicate using the program QuEST v2.4 in transcription factor mode (option “2”) with permissive parameter settings (option “3”) and suppling the corresponding input or mock-treated sample as negative controls in peak calling
For samples where several negative controls were available, only peaks that were identified against all used negative controls (high confidence peaks) were retained for further analysis
Annotation of peak locations with respect to annotated gene features in TAIR10 was performed using the annotatePeaks.pl function from the Homer suite
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files with peak coordinates, enrichment scores, and annnotation information

organism: Arabidopsis thaliana

source_name: 4 week old mature leaves

growth_protocol: Arabidopsis Col-0 plants were grown for 4 weeks under short-day conditions in closed cabinets (Schneijder chambers: 16 h light/ 8 h dark cycle at 22-24°C, 60% relative humidity) on 42mm Jiffy-7 pots (Jiffy) to prevent contaminations from garden soil. Before sewing, the Jiffy pot peat pellets were re-hydrated in water containing 0.1% liquid fertilizer Wuxal (Manna). B. cinerea strain 2100 was cultivated on potato dextrose plates at 22°C for 10 days. Spores were collected, washed, and frozen at -80C in 0.8% NaCl at a concentration of 10 to the power of 7 spores mL-1.

extract_protocol:
Lysates were clarified from sonicated nuclei and WRKY33-DNA complexes were isolated with an HA antibody. ChIP DNA was purified using a QIA quick PCR Purification kit (Qiagen) and subjected to a linear DNA amplification (LinDA) protocol (Shankaranarayanan et al., 2011) which included two rounds of ‘in vitro transcription’ by T7 RNA polymerase.
The resulting LinDA DNA was used to generate sequencing libraries bearing barcodes using a NEBNext ChIP-Seq Library Pre Reagent Set for Illumina kit (New England Biolabs).

treatment_protocol: For inoculation of Arabidopsis plants the spores were diluted in Vogel buffer. 2.5x10 to the power of 5 spores mL-1 were used for spray inoculations of 4-week old intact plants. For mock treatment, Vogel buffer was used. Plants were kept prior to and during infection under sealed hoods at high humidity.

tag: tissue

value: leaves

tag: ecotype

tag: chip antibody

value: rabbit polyclonal antibodies to HA (Sigma)

value: 14 hour post inoculation with spores of Botrytis cinerea 2100


title: wt_ip_2

value: wildtype

tag: antibody

value: Myc-Tag (9B11)

tag: antibody manufacturer

value: Cell Signaling

tag: antibody catalog number

tag: antibody lot/batch number


title: ES_Tsix-stop replica


title: scc2-4_ip_1


title: WK33-HA mock 14h rep2

value: 14 hour mock treated


title: ES_Rex1GFPd2_2i Undiff

value: Undifferentiated in Ndiff and 2i


title: total scnRNAs from wild-type cells @10.5 hpm


title: ES_XT67E1_serum Undiff


title: Ago2_R792A_C793A

city: Nagoya

first: Hiroshi

middle: I.

last: Suzuki

address: 65 Tsurumai-cho, Showa-ku

department: DIvision of Molecular Oncology, Graduate School of Medicine

country: Japan

institute: Nagoya University

description: Ago2-bound RNA

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Paired-end reads were trimmed to remove adapter sequences, and reads larger than 15 bp were subjected to subsequent analysis using custom scripts.
The first read of the pair was used for expression analyses and mapped to mm9 assembly with the TopHat program (version 2.0.9.) (Trapnell et al., 2009) with parameter --b2-very-sensitive.
miRNA expression levels were computed as the number of reads that mapped to miRBase v18., allowing two mismatches per alignment region.
Genome_build: mm9
Supplementary_files_format_and_content: counts

source_name: mouse embryonic stem cells

growth_protocol: mESCs were grown on gelatinized tissue culture plates in Dulbecco’s Modified Essential Media supplemented with HEPES pH 7.0, 15% fetal bovine serum (Hyclone/Thermo Scientific), 1000U/mL leukemia inhibitory factor (Chemicon/Millipore), 0.1 mM nonessential amino acids, 0.1 mM L-glutamine, 0.1 mM Pen/Strep and 0.11 mM β- mercaptoethanol

extract_protocol:
Ago2-bound small RNAs were collected by immunoprecipitation of Flag-tagged Ago2 proteins.
Ago2-bound small RNAs were subjected to library preparation using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs)  and analyzed by Illumina HiSeq 2000.

value: embryonic stem cells

value: anti-Flag

value: Ago2 R792A C793A


title: scc2-4_ip_2

value: scc2-4 mutant


title: WT Bc 14h rep2

value: WT


title: wt_wce_1


title: Ago2_K566A

description: Ago2-bound RNA

value: Ago2 K566A


title: empty

description: Ago2-bound RNA

value: control


title: wt_ip_1


title: Ago2_PGKTP_AAAAA

description: Ago2-bound RNA

value: Ago2 PGKTP AAAAA


title: Ago2_GKT_GKGT

description: Ago2-bound RNA

value: Ago2 GKT GKGT


title: Ago2_Q548A

description: Ago2-bound RNA

value: Ago2 Q548A


title: Ago2_WT

description: Ago2-bound RNA

value: Ago2 WT


title: wt_wce_2


title: NPC_129-Xi_10p

source_name: Neural Progenitor Cells (NPCs)

value: NPCs

value: 129/SV-Jae x Cast

value: NPCs in N2B27 with FGF and EGF


title: EpiSC_female_NT

source_name: EpiStem Cells (EpiSC)

value: EpiSC

value: Undifferentiated EpiSCs


title: NPC_129-Xi


title: *NPC_129-Xi_10p


title: ES_Tsix-stop T=0d

value: ESCs

value: Undifferentiated in Ndiff and 2i+LIF


title: ES_Tsix-stop T=8d

value: 8 days released from Ndiff and 2i+LIF (EB formation)


title: *NPC_129-Xi


title: ES_Tsix-stop T=2d

value: 2 days released from Ndiff and 2i+LIF (EB formation)


title: NPC_Cast-Xi


title: ES_Tsix-stop T=3d

value: 3 days released from Ndiff and 2i+LIF (EB formation)


title: ES_Tsix-stop T=4d

value: 4 days released from Ndiff and 2i+LIF (EB formation)


title: Mex3-1 RNAi 1fd12

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

data_processing:
Base calls were made using the Illumina pipeline v. 1.6 for Illumina GAIIx and v. OLB 1.9 for HiSeq2000
Untrimmed reads were aligned to the transcritpome associated with BioProject 215411 using the program Bowtie2 version 2.2.4.  Raw counts were extracted from resulting SAM files and normalized to the number of mapped reads to calculate Counts Per Million reads (CPM).
Pseudocounts of 1 were added to all CPM values.
To determine differentially expressed transcripts in the X1 and X2 replicate experiments vs. irradiated controls, the program DeSeq was used and resulting false discovery rate probabilities are provided in the processed data file.
Genome_build: NCBI BioProject 215411, SmedASXL_transcripts_20130210.nt
Genome_build: SmedAsxl_v1.1
Supplementary_files_format_and_content: Excel tab delimited.  RPM values for each sample for each transcript are listed as well as baySeq p values.

organism: Schmidtea mediterranea

source_name: mex3-1(RNAi) animals at 1 feed day 12 post feed

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to RNAi feeding, fed 5x, then collected 12 days later (5fd12).

extract_protocol:
All 3 tissue samples were RNA extracted in Trizol reagent, and RNA quality was analyzed on a bioanalyzer.  RNA samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.
RNA-seq.  Illumina TruSeq library prep kit with v4 chemistry.

treatment_protocol: Only for purified X1 and X2 cells:  animals were dissociated and sorted on a Becton-Dickenson FACSaria and cell fractions collected and RNA subsequently purified as in Labbe, et al., 2012.

tag: strain

value: Asexual CIW4

value: whole animals

value: RNAi


title: Control RNAi 1fd12

source_name: unc22(RNAi) animals at 1 feed day 12 post feed


title: X2 sample

source_name: stem cell progeny FACS fraction

value: sorted cells

value: Hoechst stain and FACS


title: Population STARR-seq Input Plasmid Library

city: Durham

first: Christopher

last: Vockley

state: NC

address: 101 science drive rm 2193

institute: Duke University

data_processing:
library strategy: self-transcribing active regulatory region sequencing (STARR-seq)
Base-calling was performed on instrument using CASAVA software
bowtie2-build haplotype.fasta haplotypes
bowtie2 -N 0 --mp 100 --rdg 100,100 --rfg 100,100 -x haplotypes -1 Read1.fastq -2 Read2.fastq
filtering: discard any variant with read counts less than 1
significance evaluation: Fisher's Exact Test was applied to RNA vs. DNA read counts for reference vs. alternate alleles; P-values were adjusted via multiple hypothesis correction to control for False Discovery Rate (FDR) via procedure p.adjust() in R.
Genome_build: hg19
Supplementary_files_format_and_content: SNP-fdr.txt contains output of significance evaluation
Supplementary_files_format_and_content: haplotype.fasta.gz contains the reference used to generate alignment files

organism: Homo sapiens

source_name: Human gDNA cloned into STARR-seq backbone

growth_protocol: HepG2 cells were obtained through the Duke University Cell Culture Facilities and were maintained in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was purified via RNA midi prep (Qiagen) including DNAse I treatment steps.  70 ug of RNA total RNA was used as input for poly-a selection and ribosomal RNA depletion using the dynabead OligoDT mRNA purificatin kit (invitrogen). RNA was treated with turbo DNAse (invitrogen) then repurified using a a RNAeasy colum (Qiagen).
cDNA was generated using SuperScript III reverse transcriptase using a reporter gene specific primer that bound the transcript generated from the plamsid. Libraries were constructed in two rounds. cDNA generated from spliced mRNA was amplified using a splice specific PCR primer. Then sequencing libraries were amplified from the reporter cDNA as per methods section.

treatment_protocol: Cells were transfected with reporter vectors using Fugene HD (promega) at a 5:1 Fugene to DNA ratio

tag: molecule subtype

value: Population STARR-seq Input DNA


title: (-NO)1

city: Richardson

first: Stephen

last: Spiro

state: TX

address: 800 W Campbell Road

department: Biological Sciences

institute: University of Texas at Dallas

description:
Δhmp ΔnrfA ΔnorVW
rRNA depleted total RNA

data_processing:
RNA-seq reads were aligned to the CFT073 genome using bowtie (version 0.12.8)
TPM (transcripts per million) was calculated by RSEM(version 1.2.19)
Genome_build: CFT073(AE014075.1)
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; column1: transcript id; column2: TPM value

organism: Escherichia coli CFT073

source_name: uropathogenic Escherichia coli (UPEC) grown without nitrosative stress

growth_protocol: Samples were grown anaerobically in MOPS minimal media supplemented with casamino acids using glucose as the carbon source. 20mM nitrate was added to (+NO) cultures for inducing nitrosative stress.

extract_protocol:
Total Rna was extracted from cultures using Qiagen RNeasy Protect Bacteria Mini Kit. For rRNA depletion, samples were treated with the MICROBExpressTM Bacterial mRNA Enrichment Kit (Life Technologies) according to the manufacturer’s instructions.  Samples were cleaned with the Zymo RNA Clean and ConcentratorTM (Zymo Research) and then subjected to a second cycle of rRNA depletion.  RNA was recovered by ethanol precipitation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: deltahmp deltanrfA deltanorVW


title: (+NO)3

source_name: uropathogenic Escherichia coli (UPEC) grown with nitrosative stress


title: (+NO)2


title: ES_Xist-del T=0d

value: 129/SV-Jae x Cast/B6


title: (-NO)3


title: (+NO)1


title: (-NO)2


title: X1 sample

source_name: stem cell FACS fraction


title: Population STARR-seq Rep 7

source_name: RNA from plasmid transfected into HepG2 cells

tag: cell line

tag: transfected with

value: reporter vector

value: Population STARR-seq mRNA


title: Population STARR-seq Rep 6


title: Irrad sample

source_name: Irradiated whole animals 60 Gy. Day 7

value: 60 Gy. Gamma irradiation


title: Population STARR-seq Rep 5


title: scnRNAs co-IPed with ectopically-expressed Twi1p @10.5 hpm

value: FLAG-HA-TWI1 was expressed at 5 hpm


title: Population STARR-seq Rep 2


title: new MAC DNA from TWI1 MAC-KO cells @36 hpm

description: library strategy: DNA-seq

data_processing:
The first 36-nt sequences of the reads that map the micronuclear genome were used in downstream analyses
The number of normalized (RPKM) sequence reads from purified new MACs mapping to each IES was calculated and divided by the number of reads that map the flanking MAC-destined sequences of the IES.
For the flanking sequences, 1 kb sequences located 500 bp upstream and downstream from the IES were used.
Supplementary_files_format_and_content: Retention Index (RI) of individual IESs

source_name: Exconjugant cells @ 36 hpm

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% proteose peptone at 30 °C. For conjugation, growing cells (~5-7 x 105/ml) of two different mating types were washed, pre-starved (~12-24 hr) and mixed in 10 mM Tris (pH 7.5) at 30 °C

extract_protocol: Genomic DNA was extracted from the new MACs and fragmented into ~250 bp segments by sonication. Genomic DNA libraries were generated from 20 ng of the fragmented DNA using NEBNext DNA Library Prep Reagent Set for Illumina (NEB) and KAPA Real-Time Library Amplification Kit (KAPA Biosystems). The libraries were sequenced using a HiSeq2000 platform with 50-nt single reads.

treatment_protocol: Nuclei from exconjugants at 36 hpm were dissociated and stained with DAPI in TMSNP buffer (0.25 M sucrose, 10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 3 mM CaCl2, 0.016% NP-40, 1 mM PMSF, 1x complete proteinase inhibitor cocktail (Roche), 0.1 µg/mL DAPI) by a dounce homogenizer with 15 strokes. The nuclear fraction was collected by centrifugation at 4,500 g at 4°C for 5 min, washed with TMSN buffer (TMSNP buffer without PMSF) 3 times, and stored at -80˚C. The nuclear fraction was resuspended with TMSN buffer containing 2 mM EDTA and 0.016 or 0.1% NP-40, and the new MACs were collected by FACSAriaIII (BD biosciences) according to size and DAPI intensity. The purity of the new Mac was assessed by immunostaining using an anti-H3K4me3 antibody (Abcam) and DAPI staining, with H3K4me3-negative nuclei counted as MICs; H3K4me3-positive, DAPI-poor small nuclei counted as new MACs; and H3K4me3-positive, DAPI-rich large nuclei counted as parental (old) MACs. Contamination with the parental (old) MACs was rare (<1 %), and most of the contaminants in our new MAC preparations were MICs. Genomic DNA libraries were constructed only when the purity of the new MAC sample was above 90%.

value: TWI1 MAC-KO cells


title: new MAC DNA from TWI1 TWI11 double MIC-KO cells @36 hpm

description: library strategy: DNA-seq

value: TWI1 TWI11 double MIC-KO cells


title: Population STARR-seq Rep 4


title: total scnRNAs from EZL1 MAC-KO cells @10.5 hpm

value: EZL1 MAC-KO


title: total scnRNAs from PDD1 MAC&MIC-KO cells @10.5 hpm


title: Tat_RNA-Seq rep1

city: Dallas

first: Ivan

last: D'Orso

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

description: rRNA-minus total RNA

data_processing:
RNA-Seq reads were mapped and aligned to the reference genome hg19 with TopHat v2.0
Differential expression was detected using Cufflinks v1.3.0 with the default significance threshold (p-value < 0.05)
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: csv generated by Cufflinks

source_name: Jurkat T cells

growth_protocol: CD4+ Jurkat T cells (clone E6.1) were cultured in RPMI1640 (HyClone) with 10% fetal bovine serum, 100 U/mL penicillin and 100 mg/mL streptomycin (Invitrogen). Jurkat T-Rex cells were maintained in the same conditions but in the presence of 10 mg/ml Blasticidin as indicated by the manufacturer's instructions (Invitrogen).  The derived Jurkat T-Rex clones (GFP bearing the Strep/Flag (SF) epitope and Tat bearing the SF epitope) were selected with 300 mg/ml of zeocin for four weeks and later cultured with 10 mg/ml Blasticidin and 100 mg/ml zeocin (Invitrogen). To generate the stable GFP:SF and Tat:SF expressing cell lines, the parental Jurkat T-Rex was electroporated with 2 mg of Ssp1-linearized pcDNA4\TO vector (Invitrogen) bearing either insert using a nucleofector kit V and a Nucleofector II (Lonza).

extract_protocol:
For RNA-seq, total RNA samples were prepared from biological duplicate samples with TRIzol (Invitrogen).  rRNA-depleted total RNA was then prepared using the Ribominus isolation kit (Invitrogen) and used for library preparation using the SOLiD Total RNA-Seq kit (Applied Biosystems).
Briefly, 500 ng of rRNA-depleted RNA was fragmented and adapters ligated before cDNA synthesis.  The cDNA was then size selected, amplified, purified with AmpureXP beads (Beckton Coulter) and quality checked on a Bioanalyzer (Agilent).  Samples were quantified by qPCR using SOLiD adapter primers per the manufacturer's instructions (Applied Biosystems) and the EZ-Bead system was used to amplify the libraries onto the sequencing beads for high-throughput sequencing on a SOLiD 5500xl instrument (Applied Biosystems).

treatment_protocol: To induce expression of GFP:SF and Tat:SF for RNA-Seq and ChIP-Seq the stable cell lines were treated with 1 μg/ml doxycycline for 16 hrs.

value: T Cells

value: Jurkat

tag: transgene

value: Tat


title: Population STARR-seq Rep 3


title: GFP_RNA-Seq rep2

description: rRNA-minus total RNA

value: GFP


title: Tat_RNA-Seq rep2

description: rRNA-minus total RNA


title: GFP_RNA-Seq rep1

description: rRNA-minus total RNA


title: GFP_Input_DNA_ChIPSeq

data_processing:
ChIP-Seq reads were aligned to the reference genome hg19 using bowtie v1.1. The flag "-m 1" was used
Peaks were called using macs2 using the default fdr threshold of p-value < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-Seq: Tab-delimited peak files generated by macs2
Note: When converting SRA files to FASTQ files using fastq-dump (tested with sra toolkit v2.8.0), please refer to submitter recommendations in README file linked as supplementary file on GSE65687 record.

extract_protocol:
Chromatin was cross-linked with 1% formaldehyde for 10 min at room temperature in culture media, and the reaction was stopped by the addition of glycine (125 mM final).  Cells were washed twice with PBS and re-suspended in 1 ml of nuclei extraction buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, protease inhibitor (Roche)) at 2x107 cells/ml and incubated for 10 min at 4°C.  Cell nuclei were collected by centrifugation at 3000 rpm for 5 min at 4°C, and re-suspended in Szak's RIPA buffer (50 mM Tris-HCl pH 8.0, 1% NP-40, 150 mM NaCl, 0.5% deoxycholate, 0.1% SDS, 5 mM EDTA, 0.5 mM PMSF, protease inhibitor) at 5x107 nuclei/ml.  Nuclear pellets were sonicated using the Bioruptor water bath sonicator (Diagenode) using the high setting with 20 sec on 30 sec off for 45 min to generate 100-300 bp DNA fragments.  Chromatin DNA was quantified with NanoDrop 1000 (Agilent).  For the ChIP step, 1–3 mg of antibody was conjugated with 15 ml of protein G dynabeads (Invitrogen) and blocked with 0.16% bovine serum albumin for 16 hrs at 4°C.  Antibody-conjugated dynabeads were incubated with 30–50 μg of chromatin DNA for 2 hr at 4°C.  Then the beads were sequentially washed sequentially two times with the following buffers: low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton, 0.1% SDS, 2 mM EDTA), high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% Triton, 0.1% SDS, 2 mM EDTA), LiCl wash buffer (0.25M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 20 mM Tris, pH 8.0), and 1 mM Tris-EDTA pH 8.0.  Chromatin immunocomplexes were eluted by incubation for 10 min at 65°C with 1% SDS and 100 mM NaHCO3, and cross-linking was reversed by incubation in the solution adjusted to 200 mM NaCl and proteinase K (20 μg) for 1 hr at 65°C.
ChIP DNA was submitted to McDermott Center Sequencing Core at UT Southwestern Medical Center for library preparation and high-throughput sequencing.  ChIP DNA was quantified on a Qubit® 2.0 Fluorometer (Invitrogen) and libraries from ~10 ng ChIP DNA were prepared using the SOLiDTM ChIP-Seq Kit with modifications for the 5500xl instrument (Applied Biosystems). Samples were end repaired, 3’-end adenylated and barcoded with multiplex adapters (Applied Biosystems).  After purification with Ampure XP beads (Beckton Coulter), samples were PCR amplified (~14 cycles), size selected with Ampure XP beads, and quantified on the Agilent 2100 Bioanalyzer.  Emulsion PCR was then performed and beads enriched on the EZ-Bead system.


title: new MAC DNA from wild-type cells @36 hpm

description: library strategy: DNA-seq

value: wild-type


title: ES

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences Bldg

institute: Louisiana State University

data_processing:
Trimming raw sequence reads smaller than 40 bp long out of a fastq file with a custome-made Python script
Mapping raw sequence reads to a custom-made database containing bisulfite-converted IAP LTR sequences using Bowtie2
Grouping a number of sequences reads to each IAP LTR locus using a custome-made Perl script
Trimming out raw sequence reads for a given IAP LTR locus that do not have a sufficient sequence coverage for DNA methylation analyses
Running a batch analysis of BiQanalyzerHT for DNA methylation levels of IAP LTR with a custom-made Perl script
Genome_build: mm9
Supplementary_files_format_and_content: BiQAnalyzerHT output files showing total percent methylation, read-based standard deviation, methylation stats on a CpG site-specific basis and methylation heatmap

source_name: AB2.2 embryonic stem cells

extract_protocol:
Genomic DNA was isolation ES and Neuro2A cell stock using phenol-chloroform extraction protocol, precipitated using ethanol precipitation protocol and resuspended in 1X TE buffer.
In brief, genomic DNA isolated from ES and Neuro2A cells were fractionated by sonication, ligated to an adaptor and modified with bisulfite conversion protocol. It was then amplified with a PCR scheme designed to enrich IAP LTR-genomic regions, and finally size-fractionated with agarose gel electrophoresis. The prepared libraries were sequenced with a Next-Generation-Sequencing protocol. [For somatic cell protocol, see "protocol" field under SAMPLES.]

value: embryonic stem cells


title: Neuro2A

source_name: Brain neuroblastoma

value: A albino

value: brain neuroblastoma


title: NPC_Cast-Xi_10p

value: NPCs

value: 129/SV-Jae x Cast

value: NPCs in N2B27 with FGF and EGF


title: Tat_Input_DNA_ChIPSeq


title: total scnRNAs from TWI1 TWI11 double MIC-KO cells @12 hpm

source_name: Conjugating cells at 12 hpm

value: TWI1 TWI11 double MIC-KO


title: total scnRNAs from RDR1 MIC-KO cells @10.5 hpm

source_name: Conjugating cells at 10.5 hpm

value: RDR1 MIC-KO


title: total scnRNAs from TWI1 MAC-KO cells @10.5 hpm

value: TWI1 MAC-KO


title: total scnRNAs from EZL1 MAC-KO cells @3 hpm

source_name: Conjugating cells at 3 hpm


title: H3K4me1_Tat_ChIPSeq

value: H3K4me1 (Abcam; ab8895)


title: H3K9me3_Tat_ChIPSeq

value: H3K9me3 (Abcam; ab8898)


title: total scnRNAs from TWI1 TWI11 double MIC-KO cells @10.5 hpm


title: H3K4me1_GFP_ChIPSeq


title: S5P_GFP_ChIPSeq

value: Pol II S5P (Abcam; ab5131)


title: S2P_Tat_ChIPSeq

value: T Cells

value: Pol II S2P (Abcam; ab5095)


title: scnRNAs co-IPed with maternally-expressed FLAG-HA-Twi1p @10.5 hpm

value: maternally expressing FLAG-HA-Twi1p


title: total scnRNAs from wild-type cells @7 hpm

source_name: Conjugating cells at 7 hpm


title: HEK293T_Input

city: Bronx

first: Julie

last: Nadel

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
Fastq files were generated through the Illumina CASAVA pipeline (v1.8).  Sequencing reads were then run through the Wasp System (WASP v3.1.5 rev. 6632) hosted pipeline for primary data processing.
The reads were aligned to the hg19 reference genome using Bowtie (v0.12.7), using non-default parameters of --tryhard, -I 50 and -X 650.
Alignments were generated in SAM format, which were then transformed into BAM files using Samtools (version 0.1.8).  The aligned sequences in BAM format had PCR duplicates removed, and peaks were called based on input and IP files using MACS v1.4.2.
All peaks containing “N” nucleotides were discarded.
Due to using directional sequencing through the incorporation of dUTP, we were able to determine the RNA-derived sequence of the RNA:DNA hybrids.  To do this, we sorted sequencing reads by their bit flag and intersected the reads representing the RNA-derived sequences (which had bit flag 147 or 163) with our RDIP-seq peaks.  By assessing the number of RNA reads aligned to the positive or negative reference strand for each peak, we assigned each RDIP-seq peak a “strandedness” value, with +1 being all RNA-derived reads aligned to the positive strand and -1 to the negative strand.  Because there were some peaks that had intermediate values of strandedness, we wanted to be confident in assigning the strand to each peak, so we eliminated the middle 10% of strandedness values for peaks (and corresponding peaks) from our dataset.
Genome_build: hg19
Supplementary_files_format_and_content: bed - contains peak chr, start, stop, peak id, reads aligned to pos strand, reads aligned to minus strand, strandedness value, skewing value

source_name: HEK293T cells

growth_protocol: Both cell lines were grown in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum and 2mM Penicillin-Streptomycin (Invitrogen), at 37°C in 5% CO2.  The cells were allowed to reach 80-90% confluence before harvesting with trypsin-EDTA.

extract_protocol:
Whole cell nucleic acid was isolated through a modified salting out extraction protocol.  Nucleic acid was sonicated to an average size of 400-600 bp using the Covaris sonicator.  The fragmented nucleic acid was then treated with RNase I (Ambion AM2294) to remove any ssRNA from the sample, phenol/chloroform purified and re-suspended in EB buffer.
Libraries were prepared using elements of a directional RNA-seq protocol.  Starting the library preparation at the second strand synthesis step, the RNA of the RNA:DNA hybrid was nicked using RNase H treatment to serve as a primer for the DNA polymerase.  The second strand was formed while incorporating dUTP to allow for directional sequencing and the identification of the RNA strand of the RNA:DNA hybrid.  Next, the ends of fragments were repaired, adenosine tails added, and Illumina Tru-Seq strand-specific adaptors ligated.  UNG treatment was utilized to degrade the dUTP-containing RNA strand of the RNA:DNA hybrid, and barcoded PCR primers were used to amplify the library while maintaining directionality.  Libraries were multiplexed and combined for sequencing using Illumina HiSeq 2500 150 bp paired-end sequencing in our institutional Epigenomics Shared Facility.

treatment_protocol: Three micrograms of nucleic acid sample was then incubated overnight with the S9.6 antibody, following which the RNA:DNA hybrids were enriched by immunomagnetic precipitation using Dynabeads (M-280 Sheep anti-mouse IgG).  The sample was then extracted through phenol/chloroform purification, precipitated in the presence of glycogen and re-suspended in EB buffer.

value: Epithelial fetal human kidney cells

tag: cell modifications

value: Contains SV40 T-antigen

tag: ip antibody


title: total scnRNAs from wild-type cells @7.5 hpm

source_name: Conjugating cells at 7.5 hpm

value: wild-type


title: total scnRNAs from wild-type cells @8 hpm

source_name: Conjugating cells at 8 hpm


title: HEK293T_RDIP

tag: cell type

value: S9.6 (ATCC hybridoma - HB08730)


title: scc2-4 rep3 [ribo-depletion]

description: Ribo-zero depleted RNA

data_processing:
Reads were aligned UCSC sacCer3 using the bowtie aligner using the following parameters:  bowtie --best --strata -v 2 -m 1, reporting unique alignments with up to 2 mismatches
RPKM values were determined by counting reads on the intervals for each gene and dividing by the length in kb and total number of reads per sample in millions.
Genome_build: sacCer3

source_name: Yeast

growth_protocol: Yeast cells were cultured in YPD+CSM media to an exponential phase (O.D. of 0.7)

extract_protocol:
RNA was extracted using acidic phenol-chloroform. Total WT RNA was divided into 2 and processed into libraries either directly or following ribo-depletion.
RNA libraries were constructed using standard Illumina Truseq RNA library preparation kit

treatment_protocol: Cells growing in exponential phase in YPD+CSM were pelleted by centrifugation.

tag: replicate

tag: rna purification

value: ribo-depletion

tag: genotype

value: scc2-4 mutant


title: H3K9me3_GFP_ChIPSeq

value: Jurkat

value: GFP


title: Pol II_2_GFP_ChIPSeq

value: Pol II CTD 4F8(Active motif; 61081)


title: Pol_II_2_Tat_ChIPSeq

value: Tat

value: Pol II CTD 4F8 (Active motif; 61081)


title: Pol II_GFP_ChIPSeq

value: Pol II CTD 4H8 (Abcam; ab5408)


title: IMR90_Input

source_name: IMR-90 cells (ATCC CCL-186)

value: Female human lung fibroblasts


title: WT rep3 [total RNA]

description: Total RNA (no poly-A selection)

value: total RNA

value: WT


title: IMR90_RDIP


title: Pol II_Tat_ChIPSeq

value: T Cells


title: scc2-4 rep1 [ribo-depletion]

description: Ribo-zero depleted RNA


title: S5P_Tat_ChIPSeq

value: Pol II S5P (Abcam; ab5131)


title: H3K79me3_GFP_ChIPSeq

value: H3K79me3 (Abcam; ab2621)


title: WT rep3 [ribo-depletion]

description: Ribo-zero depleted RNA


title: H2C

description: DNase-treated, rRNA-depleted mRNA

data_processing:
After sequencing, fastq file generation was completed using the Illumina CASAVA pipeline (v1.8).
Post-sequencing analysis was performed using the WASP pipeline (v3.1.5 rev. 6632), involving read alignment using gsnap (2012-07-20), with htseq (v0.5.3p3) used to determine read quantitation.
Biological replicates were normalized using DESeq (Bioconductor) and RefSeq gene identifiers were assigned using biomaRt.
Only gene expression assigned a RefSeq identifier was used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed file - containing gene chr, start, stop, refseq id, ensemble id, expression, strand, and expression quartile

extract_protocol:
RNA was isolated from HEK 293T and IMR-90 cells using TRIzol extraction.  Four biological replicates from each cell line were DNase treated, and Ribo-Zero rRNA removal (Ribo-Zero, Epicentre) was utilized for three of the four RNA samples, leaving a non-Ribo-Zero depleted sample for rRNA expression analysis.
cDNA synthesis was performed by using oligo-dT as well as random hexamers. Actinomycin D was added to the reaction to prevent any possible amplification from contaminating genomic DNA. During second strand synthesis, a dU/VTP mix was used to create directional libraries. Before library preparation, cDNA samples were Covaris-fragmented to 300 bp fragments. The samples were then end-filled, 3’ terminal A-extended and ligated to pre-annealed TruSeq indexed Illumina adapters.  Uracil-DNA-glycosylase (UDG) treatment preceded the PCR reaction to cleave the uridine-containing strand and therefore identify the orientation of each transcript.  The samples were multiplexed and sequenced using 100 bp single-end read sequencing on the Illumina HiSeq 2500 in our institutional Epigenomics Shared Facility.

value: Epithelial fetal human kidney cells

value: Contains SV40 T-antigen


title: H2D

description: DNase-treated, rRNA-depleted mRNA


title: WT rep2 [ribo-depletion]

description: Ribo-zero depleted RNA


title: H2B

description: DNase-treated, rRNA-depleted mRNA


title: H3K79me3_Tat_ChIPSeq


title: WT rep2 [total RNA]

description: Total RNA (no poly-A selection)


title: NsrR_input

data_processing:
ChIP-seq reads were aligned to the CFT073 genome using bowtie (version 0.12.8)
peaks were called using MACS2 with default parameters
Genome_build: CFT073(AE014075.1)
Supplementary_files_format_and_content: bed format peak file generated from MACS2

source_name: uropathogenic Escherichia coli (UPEC)

growth_protocol: samples were grown aerobically in rich media

extract_protocol:
Cells were disrupted by sonication and NsrR bound DNA was isolated with anti-Flag antibody.
DNA fragments were treated with Epicentre End-It DNA End Repair Kit and 3’ A overhangs were added with DNA polymerase I (Klenow fragment).  Adapters from the IlluminaTruSeq DNA sample preparation kit were ligated using LigFast (Promega) and DNAs were amplified by PCR using primers provided in the IlluminaTruSeq DNA sample preparation kit and Phusion DNA polymerase (NEB).  Products of the ligation reaction and PCR amplification in the range 300-400 bp were purified by 2% agarose gel electrophoresis.  DNA concentrations were measured using Qubit™ dsDNA HS Assay Kits (Invitrogen).

value: CFT073 nsrR::3X-Flag tag


title: H3K27Ac_GFP_ChIPSeq

value: H3K27Ac (Abcam; ab4729)


title: H3K4me3_GFP_ChIPSeq

value: H3K4me3 (Abcam; ab8580)


title: WT rep1 [ribo-depletion]

description: Ribo-zero depleted RNA

value: ribo-depletion


title: scc2-4 rep2 [ribo-depletion]

description: Ribo-zero depleted RNA

value: scc2-4 mutant


title: WT rep1 [total RNA]

description: Total RNA (no poly-A selection)


title: I3A-R

description: Dnase-treated mRNA


title: NsrR_ChIPSeq_rep3

value: Monoclonal ANTI-FLAG  M5(Sigma-Aldrich, catalog number:F4042 )


title: I2A

description: DNase-treated, rRNA-depleted mRNA


title: H3K4me3_Tat_ChIPSeq

value: Jurkat

value: Tat


title: H3K36me3_Tat_ChIPSeq

value: H3K36me3 (Abcam; ab9050)


title: H3K27Ac_Tat_ChIPSeq


title: H2B-R

description: Dnase-treated mRNA


title: I3A

description: DNase-treated, rRNA-depleted mRNA

value: Female human lung fibroblasts


title: H3K36me3_GFP_ChIPSeq

value: GFP


title: Flag_Tat_ChIPSeq

value: Flag (Sigma; F3165)


title: NsrR_ChIPSeq_rep1


title: NsrR_ChIPSeq_rep2


title: Flag_GFP_ChIPSeq

value: T Cells


title: Library 2 RNA bound (Gag 1:10 RNA)

status: Public on Jun 13 2015

city: Strasbourg

first: Redmond

middle: P

last: Smyth

state: Alsace

address: 15 rue Rene Descartes

department: Architecture et Réactivité de L'ARN

institute: IBMC CNRS

description: In vitro transcribed RNA

data_processing:
Demultiplex reads using novobarcode (Novocraft) using parameters -F ILMFQ -l 6
Trim reads using trim galore! (Babraham Bioinformatics) with the parameters -q 30 --phred64 --paired
Trimmed reads we aligned to the HIV-1 genome using novoalign (Novocraft) with the parameters -F STDFQ -o SAM -o SoftClip -r None
Data processing was performed using a Python script using the Numpy, Pysam and Numba (Continuum Analytics) modules. Briefly, this script parses SAM files containing reads aligned to the reference sequence. It fetches alignment matches by decoding the CIGAR and reads are translated into sequence matches or mismatches in comparison to the reference sequence. It then merges match patterns derived from aligned paired-end reads removing redundancy and sequencing errors where overlapping paired reads disagree. Absolute nucleotide occurrences are counted using one of the three modes: The ‘1d’ mode counts the number of A, C, G, U at each position, the ‘2d’ mode is used for inferring the effect of single mutations on protein binding. It counts all non-redundant combinations of two positions (i,j); i ∈I,j ∈J;I={1…532}; J=I \j; and fills an array containing the number of dinucleotide occurrences for each pair of positions [number of AA,AC,…TG,TT]. The ‘3d’ mode is used for inferring epistatic effects and structural elements. It is similar to the ‘2d’ mode except that it counts all non-redundant combinations of three positions. Results are serialized to a binary .npy file. A separate script converts these numpy arrays into text files compatible with statistical tools written in MATLAB (MathWorks).
Genome_build: ViralProj15476, HIV-1 NL4-3 nucleotides 1-532 of RNA genome
Supplementary_files_format_and_content: 1D processed text file list genome position and the number of A, T, C, and G nucleotide found at that position. 2D and 3D files are similar, but list non redundant pairs or triplets of genome positions and the number of dinucleotides (AA, AT, AC…) or trinucleotides (AAA, AAT, AAC...) found at these postions

organism: Human immunodeficiency virus 1

source_name: In vitro transcribed HIV RNA

extract_protocol:
RNA was bound to protein and bound RNA was separated from unbound RNA using magnetic beads. RNA was proteinase K digested, phenol/chloroform extracted and EtOH precipitated
RNA was reverse transcribed into cDNA and a specific region of the RNA was PCRed into dsDNA. This dsDNA was then randomly fragmented before library construction for sequencing on the Illumina HiSeq2000 in 100 paired end read mode. Libraries were prepared by ligating preanneled Illumina multiplex adaptors P-GATCGGAAGAGCACACGTCT and ACACTCTTTCCCTACACGACGCTCTTCCGATCT  to the blunted and A-tailed dsDNA. This was then amplified using primer PCR1.0 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT and an index containing primer CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT where NNNNNN is replaced with one of the Illumina TruSeq indexes

tag: library

tag: bound

value: Yes


title: Library 2 RNA bound (Gag 1:1 RNA)

description: In vitro transcribed RNA


title: Library 2 RNA bound (Gag 10:1 RNA)

description: In vitro transcribed RNA


title: Library 1 RNA bound (Gag 10:1 RNA)

description: In vitro transcribed RNA


title: Library 1 RNA bound (Gag 1:1 RNA)

description: In vitro transcribed RNA


title: Library 1 RNA bound (Gag 1:10 RNA)

description: In vitro transcribed RNA


title: WT RNA bound (Gag 1:1 RNA)

description: In vitro transcribed RNA

value: Wild-Type


title: WT RNA bound (Gag 10:1 RNA)

description: In vitro transcribed RNA


title: CD4_H3K4me3_JMJD3-KO_Rep2_GA2537

city: Cincinnati

first: Iouri

last: Chepelev

state: OH

address: 3200 Vine St

institute: US Department of Veterans Affairs Medical Center

description: Biological replicate 2

data_processing:
Sequencing reads were mapped to mm8 genome using ELAND software. The uniquely aligned reads were then subjected to redundancy filtering by retaining only one aligned read per genomic position per strand. The positions of the resulting reads were then shifted by 75bp (half of nucleosomal DNA length) and counted in 200bp consecutive windows in the genome. The counts were normalized to the library size of 10 million uniquely aligned non-redundant reads in order to facilitate comparison across samples. The resulting normalized counts are reported in bedGraph files.
Genome_build: mm8
Supplementary_files_format_and_content: bedGraph

source_name: JMJD3-KO Naïve CD4+ T cells

growth_protocol: Jmjd3 flox/flox (Jmjd3f/f) mice were generated by targeting exons 15-21 (encoding the JmjCcatalytic domain) using a Cre-LoxP system. Jmjd3f/f mice were then crossed with CD4-Cre mice (Taconic) to generate Jmjd3 cKO (conditional knockout) mice. C57BL/6 mice were obtained from the Jackson Laboratory.

extract_protocol:
Mouse thymocytes were isolated using a negative selection kit (StemCell) and stained for CD4, CD25, CD44, and CD62L. Naïve CD4+ (CD4+ CD25- CD44low CD62L+) cells were sorted by BD FACSAria II to >95% purity.
Library construction was as described in Barski et al. Cell 129(4): 823-837 (2007).

tag: phenotype

value: JMJD3 cKO

value: CD4+ T cells


title: Library 2 RNA Unbound (Gag 1:10 RNA)

description: In vitro transcribed RNA

value: No


title: Library 2 RNA Unbound (Gag 1:1 RNA)

description: In vitro transcribed RNA


title: Library 2 RNA Unbound (Gag 10:1 RNA)

description: In vitro transcribed RNA


title: WT RNA bound (Gag 1:10 RNA)

description: In vitro transcribed RNA


title: CD4_H3K4me3_WT_Rep2_GA2536

description: Biological replicate 2

source_name: WT Naïve CD4+ T cells

value: Wild Type


title: CD4_H3K27me3_WT_Rep2_GA2538

description: Biological replicate 2


title: I2B

description: DNase-treated, rRNA-depleted mRNA


title: Library 1 RNA Unbound (Gag 1:1 RNA)

description: In vitro transcribed RNA


title: CD4_H3K27me3_JMJD3-KO_Rep1_GA1977

description: Biological replicate 1


title: CD4_H3K27me3_WT_Rep1_GA1976

description: Biological replicate 1


title: Library 1 RNA Unbound (Gag 1:10 RNA)

description: In vitro transcribed RNA


title: S2P_GFP_ChIPSeq

tag: chip antibody

value: Pol II S2P (Abcam; ab5095)


title: Library 1 RNA Unbound (Gag 10:1 RNA)

description: In vitro transcribed RNA


title: WT RNA Unbound (Gag 1:10 RNA)

description: In vitro transcribed RNA


title: WT RNA Unbound (Gag 1:1 RNA)

description: In vitro transcribed RNA


title: Population STARR-seq Rep 1

source_name: RNA from plasmid transfected into HepG2 cells

value: reporter vector

value: Population STARR-seq mRNA


title: WT RNA Unbound (Gag 10:1 RNA)

description: In vitro transcribed RNA


title: Soy + E2 replicate 2

city: Little Rock

first: Horacio

last: Gomez-Acevedo

state: Arkansas

address: 4301 W. Markham St

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

data_processing:
Illumina Casava v 1.7 software used for basecalling with sequence length of 36 and Illumina encoding 1.5.
Reads were filtered with FASTX toolkit v 0.0.13.2 with parameter values p=0.95 and q=25
Alignment was carried out with TopHat v. 2.0.9 and Bowtie2 v 2.1.0
Assembling the expressed genes and transcripts was conducted with Cufflinks v. 2.1.1
Genome_build: rn4

organism: Rattus norvegicus

source_name: Uterus

extract_protocol:
Total RNA was isolated from rat uterus (N= 6 per group) using a combination of TRI reagent and RNeasy-mini columns (Qiagen), including on-column DNAse digestion. Three biologically separate pools containing equal amounts of RNA from two individual uterus were utilized for each diet.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

tag: tissue

value: Uterus

tag: age

value: Post natal day 65

tag: diet

value: Soy + E2


title: Soy replicate 2

tag: strain

value: Soy


title: CD4_H3K4me3_WT_Rep1_GA1974

description: Biological replicate 1


title: Soy replicate 3


title: Soy + E2 replicate 1


title: Caseine replicate 1

value: Caseine


title: Caseine + E2 replicate 3

value: Caseine + E2


title: Caseine + E2 replicate 2


title: mms21RINGD rep2

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Ribo-zero depleted RNA

data_processing:
Base calls were performed using CASAVA-1.8.2
Reads were aligned to UCSC sacCer3 using tophat version 2.0.8 with default parameters.
Uniquely mapping reads were quantified on genes using the countOverlap function in the Bioconductor package GenomicFeatures.
RPKM values were determined using Bioconductor package edgeR version 3.8.6 using the count of uniquely mapped reads on the intervals for each gene.
Genome_build: sacCer3

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were cultured in YPD+CSM media to an exponential phase (O.D. of 0.6)

extract_protocol:
RNA was extracted using acidic phenol-chloroform. Total RNA was processed into libraries following ribo-depletion.
RNA libraries were constructed using standard Illumina Truseq RNA library preparation kit

treatment_protocol: Cells grown in exponential phase in YPD+CSM were pelleted by centrifugation.

value: ribo-depletion

value: mms21RINGD mutant


title: Caseine replicate 3


title: Caseine replicate 2


title: mms21RINGD rep3

description: Ribo-zero depleted RNA


title: CD4_H3K4me3_JMJD3-KO_Rep1_GA1975

description: Biological replicate 1


title: Caseine + E2 replicate 1


title: WT rep3

description: Ribo-zero depleted RNA

value: WT


title: KO1

status: Public on Jun 12 2015

city: Chapel Hill

first: Joshua

last: Starmer

state: NORTH CAROLINA

address: 120 Mason Farm Road

institute: University of North Carolina at Chapel Hill

data_processing:
Initial processing and basecalling was done using the Illumina Pipeline (v.1.8.2)
Low quality reads were filtered using trimmomatic
Alignment to the mm9 genome was performed using Tophat2 and Bowtie2
Reads counts per gene and repetitive elements (RepeatMasker) were generated using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited text files contain read counts per feature

source_name: E10.5 embryo

extract_protocol:
Total RNA was extracted from embryos with Trizol, DNase I-digested and cleaned up with RNeasy columns (Qiagen) and polyA RNA was extracted with KAPA kit.
RNA-seq library was prepared with KAPA Stranded mRNA-Seq Kit (Kapabiosystems, cat. KK8420) following the manufacturer's instructions, with 85C for 6 minutes at the RNA fragmentation step.

value: whole embryo

value: mixed C57BL/6 CD1 129

value: H3f3afl/-; H3f3bfl/-; Sox2-CreTg/0; Trp53-/-

tag: developmental stage

value: E10.5 embryo


title: WT rep2

description: Ribo-zero depleted RNA


title: WT rep1

description: Ribo-zero depleted RNA


title: KO3


title: KO2


title: Soy + E2 replicate 3


title: CD4_H3K27me3_JMJD3-KO_Rep2_GA2539

description: Biological replicate 2

value: JMJD3 cKO

value: CD4+ T cells


title: Dm_Rpb3_X_ChIP_(20140917_3)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Total RNA Polymerase II chromatin immunoprecipitations was performed in Drosophila S2 cells using an antibody against Rpb3.
library strategy: Modified ChIP-seq (see PMID 22025700)

data_processing: 1. We used Novoalign (v2.08.03) with options "-F STDFQ -a -r Random" to map paired-end 25bp reads to release 5.51 of the D.melanogaster genomic sequence obtained from FlyBase. 2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig)

organism: Drosophila melanogaster

source_name: Crosslinked MNase digested chromatin

extract_protocol: Drosophila S2 cells were crosslinked using formaldehyde for 10 minutes at room temperature. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. Chromatin was immunoprecipitated using an antibody against Rpb3. DNA was extracted from the immunoprecipitated chromatin and subjected to Illumina (Solexa) sequencing.

tag: cell line

value: Drosophila S2 cells

tag: antibody


title: Control 1

value: H3f3afl/+; H3f3bfl/+; Sox2-CreTg/0; Trp53-/-


title: Soy replicate 1

value: Sprague Dawley

value: Uterus


title: Control 3


title: Control 2


title: JB8 H3K4me1_ChIPSeq

city: Houston

first: Lisha

last: Zhu

address: 7000 fannin st

institute: UT Health Science Center at Houston

data_processing:
Basecalling : illumina RTA 1.18.64.  FASTQ Generation : Casava 1.8.2
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Alignment ( BWA) with default parameters in bwa aln and bwa samse
peaks were called using MACS version 2 with the following settings:-B --broad --nomodel --extsize 150 -q 0.01 --broad-cutoff 0.1
MACS2 bdgcmp was used to generate fold-enrichment and logLR track with parameters -m FE and -m logLR -p 0.00001
Genome_build: hg19
Supplementary_files_format_and_content: BROADPEAK file reports peaks with FDR q <0.1

source_name: Neutrophil, Chromatin IP against  H3K4me1

extract_protocol: Chromatin was fixed in 1% formaldehyde, sheared to 100-900bp using Micrococcal nucleasean (Cell Signalling Technologies Inc.) and ultrasonic sonicator (FB-705, Fisher Scientific), immunoprecipitated using the indicated antibodies, purified and sequenced using Illumina HiSeq 2500 as recommended by the manufacturer.

treatment_protocol: Whole blood was drawn into 10 mL citrated Cell Preparation Tubes (Becton Dickinson, Franklin Lakes, NJ, USA). Cell separation procedures were started within one hour from the time the specimens were drawn. Peripheral blood mononuclear cells were separated from neutrophils and red blood cells by subjecting the CPT tubes directly to density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis.

value: Neutrophil

tag: condition

value: healthy

value: Rabbit polyclonal to Histone H3 (mono methyl K4) - ChIP Grade (ab8825)


title: JB7 input DNA

source_name: Neutrophil


title: mms21RINGD rep1

city: Kansas City

description: Ribo-zero depleted RNA


title: JB8 input DNA


title: JB6 input DNA


title: JB8 H3K27ac_ChIPSeq

source_name: Neutrophil, Chromatin IP against  H3K27ac

value: Rabbit polyclonal to Histone H3 (acetyl K27) - ChIP Grade (ab4729)


title: JB6 H3K4me1_ChIPSeq


title: JB7 H3K27ac_ChIPSeq


title: JB7

data_processing:
Basecalling : illumina RTA 1.18.64.  FASTQ Generation : Casava 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome using tophat v2.0.10 default parameters
Fragments Per Kilobase of exon per million fragments mapped (FPKM) were calculated using cuffnorm v2.2.1 with default paramters
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Neutrophil RNA from an adult

extract_protocol:
Total RNA was extracted using TRIzol™ reagent according to the manufacturer's directions. RNA was further purified using a RNeasy MiniElute cleanup kit including a DNase digest according to the manufacturer's instructions (Qiagen, Valencia, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Whole blood was drawn into 10 mL citrated Cell Preparation Tubes (Becton Dickinson, Franklin Lakes, NJ, USA). Cell separation procedures were started within one hour from the time the specimens were drawn. Peripheral blood mononuclear cells were separated from neutrophils and red blood cells by subjecting the CPT tubes directly to density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis, and neutrophils were then immediately placed in TRIzol™ reagent (Invitrogen, Carlsbad, CA, USA) and stored at -80°C.

value: adult

tag: gender

value: male


title: Mm_GFP_IN_(20140617_13)

description: MNase-seq, no size selection. Mouse embryonic fibroblasts were crosslinked and the chromatin digested with micrococcal nuclease, followed by sequencing of the extracted DNA.

data_processing: 1. We used Bowtie2 (v2.2.4) with options "--no-unal --local --very-sensitive-local --no-discordant --no-mixed --contain --overlap --dovetail --phred33 -I 10 -X 700" to map paired-end 25bp reads to release mm9 of the M.musculus genomic sequence obtained from UCSC. 2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig)

extract_protocol: Mouse embryonic fibroblasts (MEFs) were crosslinked using formaldehyde. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. DNA was extracted from the solubilized chromatin and subjected to Solexa sequencing.

tag: cell type

value: Mouse embryonic fibroblasts (MEFs)

tag: transgene

value: GFP (negative control)

tag: selection

value: size non-selected


title: JB6 H3K27ac_ChIPSeq


title: JB8


title: Mm_GFP_1.1x_IP_(20150213_13)

description: MNase-seq size selected (1.1 vol Ampure). Mouse embryonic fibroblasts were crosslinked and the chromatin digested with micrococcal nuclease, followed by sequencing of the extracted DNA with an Ampure bead size selection.

data_processing: 1. We used Bowtie2 (v2.2.1) with options "--no-unal --local --very-sensitive-local --no-discordant --no-mixed --contain --overlap --dovetail --phred33 -I 10 -X 700" to map paired-end 25bp reads to release mm9 of the M.musculus genomic sequence obtained from UCSC. 2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig)

extract_protocol: Mouse embryonic fibroblasts (MEFs) were crosslinked using formaldehyde. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. DNA was extracted from the solubilized chromatin and subjected to Solexa sequencing. After linker ligation, short insert lengths were enriched by recovering the unbound fraction from an Ampure bead selection using a volumetric ratio of DNA:beads of 1.1x.

value: size selected Ampure 1.1 vol


title: p2Cell_67

status: Public on Jun 11 2015

first: Yan

last: Xu

state: Ohio

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cicinnati children's Hospital Medical Center

data_processing:
CASAVA 1.8.2 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
adapter sequences were removed using cutadapt-1.2.1
trimming by base quality was performed and low complexity reads were removed using prinseq-lite-0.20.3
paired reads were aligned against mm9 using bowtie2-2.1.0 and tophat-2.0.8
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for 148 cells

source_name: whole e16.5 developing mouse lung, sacculation stage

growth_protocol: Mice were housed in filtered cages and all experiments were performed in accordance with approved IACUC protocols.

extract_protocol:
Microdissected mouse e16.5 lung buds were finely minced and triturated using a glass capillary pipette in protease serum free media, and suspended in approximately 100 uL of PBS and loaded into the Fluidigm C1 lab chip according to manufacturer protocol v1.x.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: e16.5 pc pregnant females were euthanized via C02 and embryos were isolated and microdissected for developing lung buds; approximately 12 lung buds were combined to make a cell suspension to load into the Fluidigm C1

value: lung

value: e16.5 fetal mouse

tag: genotype

value: wt


title: p2Cell_70


title: p2Cell_69


title: JB6


title: p2Cell_65


title: p2Cell_53_61


title: p2Cell_68


title: p2Cell_56_64


title: JB7 H3K4me1_ChIPSeq


title: p2Cell_46


title: p2Cell_42


title: p2Cell_43


title: p2Cell_66


title: p2Cell_41


title: p2Cell_48


title: p2Cell_47


title: Mm_GFP_1.2x_IP_(20150213_13_2)

description: MNase-seq size selected (1.2 vol Ampure). Mouse embryonic fibroblasts were crosslinked and the chromatin digested with micrococcal nuclease, followed by sequencing of the extracted DNA with an Ampure bead size selection.

extract_protocol: Mouse embryonic fibroblasts (MEFs) were crosslinked using formaldehyde. Chromatin was fragmented using MNase and then sonicated to ensure complete extraction of chromatin and associated proteins. DNA was extracted from the solubilized chromatin and subjected to Solexa sequencing. After linker ligation, short insert lengths were enriched by recovering the unbound fraction from an Ampure bead selection using a volumetric ratio of DNA:beads of 1.2x.

value: size selected Ampure 1.2 vol


title: p2Cell_44


title: p2Cell_45


title: p2Cell_51_59


title: p2Cell_38


title: p2Cell_55_63


title: p2Cell_50_58


title: p2Cell_36


title: p2Cell_34


title: p2Cell_35


title: p2Cell_29


title: p2Cell_33


title: p2Cell_40


title: p2Cell_37


title: p2Cell_32


title: p2Cell_27


title: p2Cell_39


title: p2Cell_49_57


title: p2Cell_24


title: p2Cell_31


title: p2Cell_28


title: p2Cell_30


title: p2Cell_21


title: p2Cell_25


title: p2Cell_23


title: p2Cell_19


title: p2Cell_18


title: p2Cell_20


title: p2Cell_22


title: p2Cell_17


title: p2Cell_16


title: p2Cell_15


title: p2Cell_14


title: p2Cell_9


title: p2Cell_26


title: p2Cell_5


title: p2Cell_8


title: p2Cell_4


title: p2Cell_12


title: p2Cell_13


title: Cell_94


title: p2Cell_3


title: p2Cell_10


title: p2Cell_1


title: p2Cell_11


title: Cell_91


title: p2Cell_7


title: p2Cell_2


title: Cell_95


title: p2Cell_52_60


title: p2Cell_54_62


title: Cell_90


title: p2Cell_6


title: Cell_9


title: Cell_93


title: Cell_92


title: Cell_87


title: Cell_89


title: Cell_85


title: Cell_88


title: Cell_83


title: Cell_86


title: Cell_82


title: Cell_84


title: Cell_96


title: Cell_81


title: Cell_8


title: Cell_74


title: Cell_75


title: Cell_73


title: Cell_79


title: Cell_77


title: Cell_76


title: Cell_72


title: Cell_70


title: Cell_80


title: Cell_65


title: Cell_61


title: Cell_69


title: Cell_63


title: Cell_64


title: Cell_66


title: Cell_68


title: Cell_67


title: Cell_62


title: Cell_60


title: Cell_56


title: Cell_59


title: Cell_54


title: Cell_58


title: Cell_52


title: Cell_57


title: Cell_50


title: Cell_71


title: Cell_44


title: Cell_49


title: Cell_45


title: Cell_47


title: Cell_48


title: Cell_43


title: Cell_41


title: Cell_42


title: Cell_40


title: Cell_37


title: Cell_55


title: Cell_53


title: Cell_51


title: Cell_39


title: Cell_35


title: Cell_34


title: Cell_36


title: Cell_32


title: Cell_33


title: Cell_31


title: Cell_29


title: Cell_3


title: Cell_27


title: Cell_26


title: Cell_30


title: Cell_25


title: Cell_23


title: Cell_20


title: Cell_2


title: Cell_15


title: Cell_24


title: Cell_22


title: Cell_19


title: Cell_4


title: Cell_11


title: Cell_38


title: Cell_16


title: BXD60

city: Berkeley

first: Takeshi

last: Morita

state: CA

address: 355 LSA

department: Molecular and Cell Biology

institute: University of California - Berkeley

data_processing:
Base calling with CASAVA v1.8.0
Sequenced reads were mapped to C57BL/6J genome (NCBIM37) and DBA/2J genome (modified NCBIM37 genome using Sanger SNP database from 'REL-1211-SNPs_Indels'), using Tophat v2.0.9 with parameters: -N 0 --max-insertion-length 0 --max-deletion-length 0 --no-novel-juncs --no-novel-indels
Gene level counts were measured using htseq-counts with parameters -m intersection-strict
Gene level counts were normalized across samples using EDASeq package for R, using upper quartile normalization
Genome_build: NCBIM37 (mm9)
Supplementary_files_format_and_content: normalized read counts

source_name: Dorsal root ganglia

extract_protocol:
Dorsal root ganglion RNA was extracted using Trizol reagent
Libraries were prepared using Illumina TruSeq RNA Sample Prep kit v2

tag: strain background

value: BXD

tag: strain info.

value: C57BL6/J x DBA2/J F2 recombinant inbred strain

value: 8 weeks

value: Dorsal root ganglia


title: BXD55


title: BXD48


title: Cell_10


title: BXD42


title: Cell_21


title: BXD44


title: Cell_1


title: BXD40


title: BXD89


title: BXD15


title: BXD77


title: BXD73


title: BXD36


title: BXD14


title: Cell_17


title: BXD34


title: BXD87


title: BXD28


title: BXD5


title: BXD13


title: BXD16


title: Whole cell extract of Smchd1 null NSCs

city: Roseworthy

first: Ruijie

last: Liu

state: South Australia

address: Mudla Wirra Rd

country: Australia

institute: the university of Adelaide

description:
Sample name: ChIP_11_D1_WCE
N/A, control data for ChIP_14&18_D1H3K4me3, ChIP_16&20_D1H3K27me3, MBD_seq_NPC1&2&3

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq or MBD-seq reads were aligned to the mm10 genome assembly using Rsubread
Data were filtered using the following specifications
Smchd1 peaks were called using MACS version 2 with the following setting: callpeak (call peaks from alignment), pvalue(0.0005 and 0.005) using the wild type data as input and Smchd1 null data as control
H3K4me3 enriched regions and MBD binding sites (DNA methylation enriched regions) were called using MACS2 version 2 with the following setting: callpeak (call peaks from alignment), pvalue(0.0005) using the ChIP-seq or MBD-seq data as input and whole cell extracts as control. H3K27me3 enriched regions were identified using the same method, except peak calling with MACS2 verson 2 was performed with following setting: callpeak (call peaks from alignment), pvalue(0.0005), broad-cutoff(broad region calling is on).
Genome_build: mm10
Supplementary_files_format_and_content: bdg files were generated using macs2, bed files were generated using macs2, contains all peaks from macs2 peak calling under the specified p-value settings.For ctcf chips, it contains macs2 output for D1 vs Chip67,Wtnons vs Chip67 and Wtun vs Chip 67.

source_name: Neural stem cells

growth_protocol: NSCs were derived as described (Wang et al. 2012) from E14.5 mouse brains. NSCs were cultured in NeuroCult NSC Basal Medium (Mouse) (StemCell Technologies) containing NeuroCult Proliferation Supplement (Mouse) (StemCell Technologies), 0.2% Heparin Solution (StemCell Technologies), recombinant human epidermal growth factor (EGF, 20 ng/ml; StemCell Technologies) and recombinant human basic fibroblast growth factor (bFGF, 20 ng/ml; StemCell Technologies). Cells were plated onto polyornithine (15 ng/ml; Sigma) and laminin (10 ng/ml; Sigma) coated plates at a density of 200,000 cells/cm2. Cells were grown in 37°C, 5% CO2 incubator and passaged every two days using Accutase (Sigma-Aldrich) to detach the cells from the plates.

extract_protocol:
For ChIP-seq, nuclei were isolated from formaldehyde crosslinked NSCs and chromatin was fragmented by sonication. Chromatin immunoprecipitation was performed with corresponding antibodies for Smchd1, H3K4me3 and H3K27me3. DNA was extracted from the immunoprecipitated fraction following reverse-crosslinking. For MBD-seq, genomic DNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen) and methylated DNA was isolated via binding to the methyl-CpG binding domain of human MBD2 protein coupled beads using the MethylMiner methylated DNA enrichment kit (Life Technologies) according to the manufacturer’s instructions.
Sequencing libraries was generated with Illumina's TruSeq DNA Sample Preparation Kit or Ovation Ultralow system (NuGen) according to manufacturer's instruction.

value: C57BL/6 x FVB/N

value: E14.5 mouse brain derived neural stem cells

tag: genotype/variation

value: Smchd1MommeD1/MommeD1 (Smchd1 null)

value: none (Whole cell extract)


title: BXD11


title: BXD2


title: BXD9


title: BXD1


title: MBD-seq in Smchd1 null NSCs replicate 3

description:
Sample name: MBD_seq_NPC3
Affinity-purified DNA
macs2WTMBD_5e-4_summits.bed, macs2WTMBD_5e-4_treat_pileup.bedgraph

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq or MBD-seq reads were aligned to the mm10 genome assembly using Rsubread
Data were filtered using the following specifications
Smchd1 peaks were called using MACS version 2 with the following setting: callpeak (call peaks from alignment), pvalue(0.0005 and 0.005) using the wild type data as input and Smchd1 null data as control. H3K27me3 enriched regions were identified using the same method, except peak calling with MACS2 verson 2 was performed with following setting: callpeak (call peaks from alignment), pvalue(0.0005), broad-cutoff(broad region calling is on).
H3K4me3 enriched regions and MBD binding sites (DNA methylation enriched regions) were called using MACS2 version 2 with the following setting: callpeak (call peaks from alignment), pvalue(0.0005) using the ChIP-seq or MBD-seq data as input and whole cell extracts as control. H3K27me3 enriched regions were identified using the same method, except peak calling with MACS2 verson 2 was performed with following setting: callpeak (call peaks from alignment), pvalue(0.0005), broad-cutoff(broad region calling is on).
Genome_build: mm10
Supplementary_files_format_and_content: bdg files were generated using macs2, bed files were generated using macs2, contains all peaks from macs2 peak calling under the specified p-value settings.For ctcf chips, it contains macs2 output for D1 vs Chip67,Wtnons vs Chip67 and Wtun vs Chip 67.

extract_protocol:
For ChIP-seq, nuclei were isolated from formaldehyde crosslinked NSCs and chromatin was fragmented by sonication. Chromatin immunoprecipitation was performed with corresponding antibodies for Ctcf, Smchd1, H3K4me3 and H3K27me3. DNA was extracted from the immunoprecipitated fraction following reverse-crosslinking. For MBD-seq, genomic DNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen) and methylated DNA was isolated via binding to the methyl-CpG binding domain of human MBD2 protein coupled beads using the MethylMiner methylated DNA enrichment kit (Life Technologies) according to the manufacturer’s instructions.
Sequencing libraries was generated with Illumina's TruSeq DNA Sample Preparation Kit or Ovation Ultralow system (NuGen) according to manufacturer's instruction.

value: male

tag: affinity purification method


title: MBD-seq in wild type NSCs replicate 1

description:
Sample name: MBD_seq_NPC4
Affinity-purified DNA
macs2D1MBD_5e-4_summits.bed, macs2D1MBD_5e-4_treat_pileup.bedgraph

value: Smchd1 wild-type

value: MethylMiner methylated DNA enrichment kit (Life Technologies)


title: Whole cell extract of wild type NSCs

description:
Sample name: ChIP_1_WT_WCE
N/A, control data for ChIP_4&8_WTH3K4me3, ChIP_6&10_H3K27me3, MBD_seq_NPC4&5&6

tag: chip antibody


title: MBD-seq in wild type NSCs replicate 3

description:
Sample name: MBD_seq_NPC6
Affinity-purified DNA
macs2D1MBD_5e-4_summits.bed, macs2D1MBD_5e-4_treat_pileup.bedgraph


title: Ctcf ChIP in Smchd1 null NSCs  replicate 2

description:
Sample name: Ctcf_ChIP_10_D1_Un_b
Immunoprecipitated DNA
macs2ctcfD1UnVS67_5e-4_summits.bed, macs2ctcfD1UnVS67_5e-4_treat_pileup.bedgraph


title: Ctcf ChIP in Smchd1 null NSCs  replicate 1

description:
Sample name: Ctcf_ChIP_9_D1_Un_a
Immunoprecipitated DNA
macs2ctcfD1UnVS67_5e-4_summits.bed, macs2ctcfD1UnVS67_5e-4_treat_pileup.bedgraph


title: MBD-seq in wild type NSCs replicate 2

description:
Sample name: MBD_seq_NPC5
Affinity-purified DNA
macs2D1MBD_5e-4_summits.bed, macs2D1MBD_5e-4_treat_pileup.bedgraph


title: Ctcf ChIP in wild type untransduced NSCs  replicate 2

description:
Sample name: Ctcf_ChIP_8_WT_Un_b
Immunoprecipitated DNA
macs2ctcfWTUnVS67_5e-4_summits.bed, macs2ctcfD1UnVS67_5e-4_treat_pileup.bedgraph


title: H3K27me3 ChIP in Smchd1 null NSCs replicate 2

description:
Sample name: ChIP_20_D1_17 H3K27me3
Immunoprecipitated DNA
macs2D1H3K27me3_5e-4_summits.bed, macs2D1H3K27me3_5e-4_treat_pileup.bedgraph


title: BXD68

tag: age

tag: tissue


title: BXD21

tag: strain


title: MBD-seq in Smchd1 null NSCs replicate 2

description:
Sample name: MBD_seq_NPC2
Affinity-purified DNA
macs2WTMBD_5e-4_summits.bed, macs2WTMBD_5e-4_treat_pileup.bedgraph


title: MBD-seq in Smchd1 null NSCs replicate 1

description:
Sample name: MBD_seq_NPC1
Affinity-purified DNA
macs2WTMBD_5e-4_summits.bed, macs2WTMBD_5e-4_treat_pileup.bedgraph


title: BXD6


title: Ctcf ChIP in wild type NSCs transduced with Ctcf.7 shRNA

description:
Sample name: Ctcf_ChIP_12_WT_Ctcf7
Immunoprecipitated DNA
Control data for Ctcf_ChIP_5_WT_Nons_a, Ctcf_ChIP_6_WT_Nons_b, Ctcf_ChIP_7_WT_Un_a, Ctcf_ChIP_8_WT_Un_b, Ctcf_ChIP_9_D1_Un_a and Ctcf_ChIP_10_D1_Un_b

value: Smchd1 wild-type, Ctcf null


title: H3K27me3 ChIP in Smchd1 null NSCs replicate 1

description:
Sample name: ChIP_16_D1_01 H3K27me3
Immunoprecipitated DNA
macs2D1H3K27me3_5e-4_summits.bed, macs2D1H3K27me3_5e-4_treat_pileup.bedgraph


title: Ctcf ChIP in wild type NSCs transduced with Non-silencing shRNA replicate 2

description:
Sample name: Ctcf_ChIP_6_WT_Nons_b
Immunoprecipitated DNA
macs2ctcfWTNonsVS67_5e-4_summits.bed, macs2ctcfWTNonsVS67_5e-4_treat_pileup.bedgraph


title: Ctcf ChIP in wild type untransduced NSCs  replicate 1

description:
Sample name: Ctcf_ChIP_7_WT_Un_a
Immunoprecipitated DNA
macs2ctcfWTUnVS67_5e-4_summits.bed, macs2ctcfD1UnVS67_5e-4_treat_pileup.bedgraph


title: H3K4me3 ChIP in Smchd1 null NSCs replicate 2

description:
Sample name: ChIP_18_D1_17 H3K4me3
Immunoprecipitated DNA
macs2D1H3K4me3_5e-4_summits.bed, macs2D1H3K4me3_5e-4_treat_pileup.bedgraph


title: H3K27me3 ChIP in wild type NSCs replicate 2

description:
Sample name: ChIP_10_WT_04 H3K27me3
Immunoprecipitated DNA
macs2WTH3K27me3_5e-4_summits.bed, macs2WTH3K27me3_5e-4_treat_pileup.bedgraph


title: Ctcf ChIP in wild type NSCs transduced with Non-silencing shRNA replicate 1

description:
Sample name: Ctcf_ChIP_5_WT_Nons_a
Immunoprecipitated DNA
macs2ctcfWTNonsVS67_5e-4_summits.bed, macs2ctcfWTNonsVS67_5e-4_treat_pileup.bedgraph


title: Smchd1 ChIP in Smchd1 null NSCs replicate 2

description:
Sample name: ChIP_17_D1_17 Smchd1
Immunoprecipitated DNA
N/A, control data for ChIP_3_WT_13 Smchd1, ChIP_7_WT_04 Smchd1

value: Smchd1 (Abcam, ab31865, lot GR52946-1)


title: H3K27me3 ChIP in wild type NSCs replicate 1

description:
Sample name: ChIP_6_WT_13 H3K27me3
Immunoprecipitated DNA
macs2WTH3K27me3_5e-4_summits.bed, macs2WTH3K27me3_5e-4_treat_pileup.bedgraph


title: H3K4me3 ChIP in Smchd1 null NSCs replicate 1

description:
Sample name: ChIP_14_D1_01 H3K4me3
Immunoprecipitated DNA
macs2D1H3K4me3_5e-4_summits.bed, macs2D1H3K4me3_5e-4_treat_pileup.bedgraph


title: Ctcf ChIP in wild type NSCs transduced with Ctcf.6 shRNA

description:
Sample name: Ctcf_ChIP_11_WT_Ctcf6
Immunoprecipitated DNA
Control data for Ctcf_ChIP_5_WT_Nons_a, Ctcf_ChIP_6_WT_Nons_b, Ctcf_ChIP_7_WT_Un_a, Ctcf_ChIP_8_WT_Un_b, Ctcf_ChIP_9_D1_Un_a and Ctcf_ChIP_10_D1_Un_b


title: Smchd1 ChIP in wild type NSCs replicate 1

description:
Sample name: ChIP_3_WT_13 Smchd1
Immunoprecipitated DNA
macs2WTsmchd1_5e-4_summits.bed, macs2WTsmchd1_5e-4_treat_pileup.bedgraph, macs2WTsmchd1_5e-3_summits.bed, macs2WTsmchd1_5e-3_treat_pileup.bedgraph


title: Smchd1 ChIP in wild type NSCs replicate 2

description:
Sample name: ChIP_7_WT_04 Smchd1
Immunoprecipitated DNA
macs2WTsmchd1_5e-4_summits.bed, macs2WTsmchd1_5e-4_treat_pileup.bedgraph, macs2WTsmchd1_5e-3_summits.bed, macs2WTsmchd1_5e-3_treat_pileup.bedgraph


title: Smchd1 null replicate 3

description: Sample name: NPC_RNA_13

data_processing:
Instrument control: HiSeq control software v2.0.12.0
Base calling and quality scoring: Real-Time Analysis v1.17.21.3
FASTQ file generation and de-multiplexing: CASAVA pipeline version 1.8.2
Sequenced reads were mapped using the align function in the Rsubread package (version 1.10.5, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.10.5) using the in-built mm10 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise linear models (Smyth, SAGMB 2004) with observational level weights (Law et al. Genome Biology 2014) were fitted to summarize the values from replicates samples using functionality from the limma package (version 3.22.0, Smyth, 2005).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

extract_protocol:
Cells were harvested, washed in 1X PBS and total RNA was isolated using the AllPrep DNA/RNA Mini Kit (Qiagen) as per manufacturer's instructions.
RNA libraries were prepared for sequencing from 1 µg total RNA using standard Illumina protocols (TruSeq RNA Sample Preparation Kit v2, and TruSeq SR Cluster Kit v3-cBot-HS and TruSeq SBS Kit v3-HS chemistry for all samples).


title: H3K4me3 ChIP in wild type NSCs replicate 1

description:
Sample name: ChIP_4_WT_13 H3K4me3
Immunoprecipitated DNA
macs2WTH3K4me3_5e-4_summits.bed, macs2WTH3K4me3_5e-4_treat_pileup.bedgraph


title: Smchd1 null replicate 2

description: Sample name: NPC_RNA_12


title: Wild type replicate 3

description: Sample name: NPC_RNA_14


title: Smchd1 null replicate 1

description: Sample name: NPC_RNA_11


title: shSamd14-infected rep3

city: Madison

first: Kyle

last: Hewitt

state: Wisconsin

address: 1111 Highland Ave.

institute: University of Wisconsin

data_processing:
Illumina Casava-1.8.2 base calling
RSEM reference preparation: RSEM v1.2.15 with Bowtie v1.0.1, rsem-prepare-reference run with options "--bowtie --gtf" Gene annotation: Ensembl v75 filtered for genes of type "protein_coding" or "lincRNA" on standard chromosomes
RSEM abundance estimation: RSEM v1.2.15 with Bowtie v1.0.1, rsem-calculate-expression run with options "--no-bam-output --time -p 10"
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values and counts for each Sample

source_name: E14.5 fetal liver

growth_protocol: Blood progenitors were isolate from E14.5 fetal liver using EasySep Hematopoietic Progenitor Isolation (STEMCELL technologies cat#19856) and grown ex vivo for 3 days in StemPro-34 medium (Life Technologies cat# 10639).

extract_protocol:
2x10^5 Ter119 and CD71 negative cells were isolated at day 3 and lysed in Trizol prior to RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Retroviral infections of control- or shSamd14 shRNAs were performed immediately following isolation.

tag: developmental stage

value: liver

tag: cell markers


title: shSamd14-infected rep1


title: shSamd14-infected rep2


title: Wild type replicate 2

description: Sample name: NPC_RNA_114


title: Smchd1 ChIP in Smchd1 null NSCs replicate 1

description:
Sample name: ChIP_13_D1_01 Smchd1
Immunoprecipitated DNA
N/A, control data for ChIP_3_WT_13 Smchd1, ChIP_7_WT_04 Smchd1


title: P17 33C

city: Cambridge

first: Katrin

middle: Alice

last: Mooslehner

state: Cambridgeshire

address: Hills Road

department: Paediatrics

country: United Kingdom

institute: Addenbrookes Hospital

data_processing:
Basecalls performed using CASAVA version 1.8 Sequencing Analysis Software
Sequence reads were aligned to the latest version of the C57/BL6 mus musculus reference genome (NCBI37/mm9) using Real Time Analysis (RTA) 1.10, CASAVA 1.8 Sequencing analysis software. For P17 37°C 85269237 reads out of 92901239 raw reads were mapped, for P17 33°C 51480433 reads out of 64560744 raw reads were mapped and for PC1 control 46952666 reads out of 56095836 raw reads were mapped. Genomic regions and peaks were determined using MACS peak finder (Zhang et al., 2008). Data tables showing the peak analysis results listed as chromosome number, peak region start and end position on target (bp), length of the peak region (bp), the position of the peak maximum relative to the start position (summit) [bp], the peak intensity value representing the number of reads per peak region (tags) and the statistical significance of the peak, i.e. how likely calls MACS the peak as true signal by accident (=pValue). The length of the peak regions does not match the length of the isolated gel fraction in the agarose gel. Average Peak region length for PC1 33C is 773bps, for P17 33C: 795bps and P17 37C: 2.8kb.
Genome_build: mm9
Supplementary_files_format_and_content: Data tables showing the peak analysis results listed as chromosome number, peak region start and end position on target (bp), length of the peak region (bp), the position of the peak maximum relative to the start position (summit) [bp], the peak intensity value representing the number of reads per peak region (tags) and the statistical significance of the peak, i.e. how likely calls MACS the peak as true signal by accident (=pValue).

source_name: proliferating, tagged WT AR

extract_protocol: P17 cells were derived from the mouse epididymal cell line PC1 by genetic modification to express a tagged wild type mouse AR cDNA (N-TAP-mAR). N-TAP-mAR allows purification of multi-protein complexes and their genomic targets with FLAG antibody coupled magnetic beads under native conditions. 200 to 300bp DNA fraction purified from an agarose gel was submitted to Source BioScience for library preparation. Nano drop measurements were: PC1 33C: 2.7 ng/ul in 25ul and PC17 33C: 7.7 ng/ul in 30ul and PC17 37C: 6.3 ng/ul in 30ul. Linkers used for library preparation are unknown. For library validation Source Bioscience checks routinely fragment size, yield and concentration with Agilent Bioanalyzer. Technical Specifications point out that for cluster generation, the library hybridized to the flow cell and series of bridge amplification occurred resulting in the generation of approximately 1000 copies for each template. They expected to see up to 25 million high quality clusters formed on each lane of the flow cell. Sequencing was done by synthesis with nucleotides designed to have reversible termination property, which allows each cycle of the sequencing reaction to occur simultaneously for all 4 nucleotides.

value: proximal caput epididymus

tag: passages

value: passage 20-25

value: FLAG


title: P17 37C

source_name: non-proliferating, tagged WT-AR


title: control-infected rep3


title: control-infected rep2


title: control-infected rep1


title: WT rep 2

city: New York

first: Juan

middle: R

last: Cubillos-Ruiz

department: Medicine

institute: Weill Cornell Medicine

data_processing:
Align to contamination (mm9 related) (chrM and Ribosomal RNA) and get rid of chrM and ribo mapped reads
None aligned reads from step 2 are the possible reads coming from mRNAs. Use these reads to estimate isoform/gene level raw read counts using RSEM package (1).
Normalize read raw counts from rsem using edgeR bioconductor R package (2).Filter low count genes from complete data set.Normalize using Upper quartile normalization
Use edgeR to find differentially expressed genes.
Result will be sorted based on adjusted p-value and genes has small adjusted p-value are considered as differentially expressed based on comparison.
Genome_build: MM9
Supplementary_files_format_and_content: text, csv -  Estimated counts, Normalized estimated counts

source_name: ovarian cancer ascites_WT

growth_protocol: in vivo tumor and ascites

extract_protocol:
Total RNA from sorted tumor-associated DCs (N=3/genotype) was independently isolated using the miRVANA kit Life Technologies and further purified and concentrated using minElute columns (Qiagen). RNA integrity was confirmed using an Agilent Bioanalyzer 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

value: ID8-based tumors (day 23)

value: sorted tumor-associated DCs


title: XBP1-KO rep1

source_name: ovarian cancer ascites_XBP1-KO

value: conditional knockout selectively deleting XBP1 in CD11c positive cells


title: PC1 33C

source_name: proliferating, non-tagged WT AR


title: H3K4me3 ChIP in wild type NSCs replicate 2

description:
Sample name: ChIP_8_WT_04 H3K4me3
Immunoprecipitated DNA
macs2WTH3K4me3_5e-4_summits.bed, macs2WTH3K4me3_5e-4_treat_pileup.bedgraph

value: C57BL/6 x FVB/N


title: XBP1-KO rep3


title: WT rep 3


title: XBP1-KO rep2


title: Sf_M_24

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

description: Small RNA

data_processing:
CLC Genomic Workbench (version 7.0.4) was used to remove adapter sequences and reads with low quality score from datasets. To avoid any impurity in sequences we also discarded the reads without 3’ adapters and less than 16 nt in length after trimming.
FASTQ/A Collapser of FASTX-toolkit was used to produce copy number based sequence lists. The tab separated files with the read sequences and their counts were used as input file for further analysis.
miRanalyzer, a powerful web-based server for next generation sequencing analysis of miRNAs was used
Genome_build: Silkworm (Bombyx mori P50T 2.0)
Supplementary_files_format_and_content: .txt files are final reports

organism: Spodoptera frugiperda

source_name: SF9 Cells

growth_protocol: The S. frugiperda cell line (Sf9) was  maintained in SF900-II serum-free medium (Invitrogen) as a  monolayer in a cell culture flask at 27 uC.

extract_protocol:
Total RNA was extracted from cells using Tri-reagent  according to the manufacturer’s instructions (Molecular Research  Center). RNA concentrations were measured using a spectrophotometer,  and integrity was ensured through analysis of RNA on a 1%  (w/v) agarose gel and bioanalyser.
Small RNA libraries were generated from both samples by using the Illumina Truseq Small RNA Preparation kit at LC Sciences. The purified cDNA libraries were sequenced on Illumina GAIIx, and raw sequence reads (36 nt) were obtained by using Illumina’s Sequencing Control Studio software version 2.8 followed by real-time sequencing image analysis and base-calling by Illumina’s Real-Time Analysis version 1.8.70 (LC Sciences).

treatment_protocol: For AcMNPV infection,  26106 cells were infected at an m.o.i. of 5 as described by King &  Possee (1992).

value: ovarian tissue

tag: infection status

value: Mock

tag: Stage

value: Control


title: Sf_BV_72

description: Small RNA

value: Infected with baculovirus AcMNPV

value: cells collected 72  hours post infection


title: ds080_293T_GFP_PD_WT_GFP_FOXM1_RA

first: Giovanni

last: Marsico

address: Robinson Way

institute: CRUK Cambridge Institute

description: experiment 3

data_processing:
fastq files were aligned to the reference genome using bowtie2
bam files from the alignment were cleaned (q > 10, no Encode balcklist) using samtools
peaks were called on the cleaned bam files using macs2 with the inputs from each respective experiment (see samples description) and defualt parameters
Genome_build: hg19
Supplementary_files_format_and_content: bed format; content is peaks called by macs

source_name: HEK293 Flp-In cells

growth_protocol: HEK293 Flp-In cells were obtained from Invitrogen (Life Technologies Ltd) and grown in Eagle's Minimum Essential Media (Invitrogen) supplemented with 10% tetracycline free fetal bovine serum (Clontech) and 100 μg/ml Zeocin (Invitrogen). The Flp-In cell line was first transfected with pcDNA6/TR (Invitrogen) and selected with 5 μg/ml Blasticidine (Sigma) to generate HEK293 TetR Flp-In cells. To generate the GFP-FOXM1 stable cells lines the TetR Flp-In cells were transfected with pcDNA5FRT containing an insert coding for either WT or DNA binding domain mutated (H287A or R286A) full length FOXM1B with an N-terminal EGFP tag and a control cell line expressing only EGFP was also generated. Insertion of the FOXM1 sequence occured following co-transfection of the pOG44 recombinase plasmid (Invitrogen) and positive cells were selected with 100 μg/ml hygromycin (Invitrogen) to generate GFP-FOXM1 HEK293TetR cells.

extract_protocol:
IP was carried out as described in Schmidt et al. (2009) (PMID 19275939). In brief, cells were cross-linked using 1% formaldehyde for 10 min at RT, reaction was quenched with 1/20th volume 2.5M Glycine and cell pellets were collected after scraping plates. Nuclear lysates were prepared by lysing with LB1 (50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton-X plus PI) 10 min at 4°C and LB2 (10mM Tris-HCl, pH8.0, 200mM NaCl, 1mM EDTA, 0.5M EGTA plus PI) 5 min at 4°C, followed by sonication in LB3 (10mM Tris-HCl, pH8.0, 100mM NaCl, 1mM EDTA, 0.5M EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine plus PI) using a diagnode sonicator to give a fragment size of ~200-300bp. Sonicated lysate was combined with 100ul protein-A magnetic beads preloaded with either 10 ug anti-FOXM1 antibody (GeneTex (USA); cat no. GTX-1000276 and GTX102170) or 10 μl anti-GFP antibody (Abcam, Cambridge, UK; ab290) O/N at 4°C. Beads were washed X6 in RIPA buffer (50mM HEPES pH7.6, 1mM EDTA, 0.7% Na deoxycholate, 1% NP-40, 0.5M LiCl) and DNA was eluted for 16 hr at 65°C in elution buffer (50mM Tris-HCl, pH8.0, 10mM EDTA, 1% SDS). Extracted DNA was treated with RNase A for 30 min at 37°C, followed by Proteinase K for 1 hr at 55°C, and DNA was purified by phenol-chloroform extraction and quntified by bioanalyzer and quibit.
Illumina ChIP-seq kit sample prep kit was used to prepare duplicate/triplicate samples

treatment_protocol: Cells were plated in 4 x 150 cm2 dishes (1 x 10E7 per dish), cultured overnight, and treated with doxycycline (1 μg/ml) for 24 h prior to extraction .

tag: cell type

value: 293 GFP-foxm1 R/A

tag: antibody

value: anti-GFP (ab290)


title: ds079_293T_GFP_PD_WT_GFP_FOXM1_HA

description: experiment 3

value: 293 GFP-foxm1 H/A


title: ds081_293T_GFP_PD_WT_GFP_FOXM1_RA

description: experiment 3


title: ds078_293T_GFP_PD_WT_GFP_FOXM1_HA

description: experiment 3


title: Sf_BV_24

description: Small RNA

value: cells collected 24 hours post infection


title: Wild type replicate 1

description: Sample name: NPC_RNA_113

value: E14.5 mouse brain derived neural stem cells

value: Smchd1 wild-type

tag: gender

value: male


title: WT rep 1

value: wild type


title: ds076_293T_GFP_PD_WT_GFP_FOXM1

description: experiment 3

value: 293 GFP-foxm1 WT


title: ds070_293T_input

description: experiment 2


title: ds075_293T_input

description: experiment 3


title: ds072_293T_GFP_PD_WT_GFP_FOXM1_HA_mut_set1

description: experiment 2

value: 293 GFP-foxm1 H/A mut


title: ds077_293T_GFP_PD_WT_GFP_FOXM1

description: experiment 3


title: ds071_293T_GFP_PD_WT_GFP_FOXM1_set1

description: experiment 2


title: ds069_293T_GFP_2

description: experiment 1


title: ds068_293T_GFP_1

description: experiment 1


title: ds067_293T_FOXM1_GTX_2

description: experiment 1

value: 293 Flp


title: ds065_293T_Input

description: experiment 1