title: Lib152

value: pMY56 (control)

value: vector control


title: ΔpinT infection 8 h replicate 1

status: Public on Dec 11 2015

type: SRA

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:08_h:R1

library_source: transcriptomic

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20 (version 0.0.13)
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 20 nt (via READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (via READemption version 0.3.5)
Counting of reads per gene (READemption version 0.3.5)
Genome_build: Human: hg19/GRCh37; Salmonella enterica Typhimurium SL1344: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: CSV (tab separated), Number of reads per gene and condition

molecule: total RNA

organism:
Homo sapiens
Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: cell culture infection model

growth_protocol: HeLa-S3 cells were cultured according the guidelines provided by the ENCODE consortium (http://genome.ucsc.edu/encode/protocols/cell/human/Stam_15_protocols.pdf). Cells were grown in DMEM (Gibco) supplemented with 10% fetal calf serum (FCS; Biochrom), 2 mM L-glutamine (Gibco) and 1 mM sodium pyruvate (Gibco) in T-75 flasks (Corning) in a 5% CO2, humidified atmosphere at 37°C.  All further cell lines used in this study (THP-1, CaCo-2, AGS, HEK, MEF and RAW264.7) were cultured in RPMI (Gibco) supplemented with 10% FCS, 2 mM L-glutamine, 1 mM sodium pyruvate in a 5% CO2, humidified atmosphere at 37°C.For the differentiation of bone marrow derived macrophages the marrow of femur and tibia was isolated from 8-12 week old female C57BL/6 wild-type mice and stored in RPMI supplemented with 10% FCS. The cell suspension was centrifuged for 5 min at 250 g and the leukocyte pellet was resuspended in differentiation medium consisting of X-vivo-15 medium (Lonza) supplemented with 10% FCS and 10% L929 conditioned DMEM medium (same composition as above). Cells were cultured for 3 days at 3*106 cells per 10 mL in a T-75 flask. At day 3 another 3 mL of differentiation medium were added and cells were further cultured until day 5. Successful macrophage differentiation was validated by microscopy on day 5 upon which the cells were disattached using a rubber scraper (Sarstedt) and seeded into 6-well plates at 105 cells per well in fresh differentiation medium. Infection was carried out on day 7 as described below.

extract_protocol:
miRvana kit for total RNA (Ambion) or TRIzol (Invitrogen) as indicated
The total RNA samples were first fragmented using ultrasound (4 pulses of 30 s each). Then, RNAs <20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics). This was followed by a dephosphorylation with Antarctic Phosphatase (AP, NEB) and re-phosphorylation with T4 Polynucleotide Kinase (PNK, NEB). Oligonucleotide adapters were ligated to the 5' and 3' ends of the RNA samples. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The resulting cDNAs were amplified with PCR using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. An aliquot of the size fractionated pool was analyzed by capillary electrophoresis.

treatment_protocol: Infection samples: In vitro infection was carried out following the protocol of (Schulte et al., 2011) with the indicated Salmonella Typhimurium (SL1344) strain in 6-well format. At the indicated time point post-infection, cells were fixed with RNAlater (Qiagen) and sorted for invaded (GFP+) and non-infected (GFP-) host cells using a FACSAria III device (BD). Total RNA from the sorted cells was extracted following the miRvana protocol (Ambion). "0 h" refers to RNA extracted from mixed lysates of extracellular Salmonella and host cells.

tag: human cell line

value: HeLa-S3 (ATCC CCL-2.2)

tag: infection agent

value: Salmonella Typhimurium SL1344 delta-pinT

tag: organism

value: mixed sample (human cell line HeLa-S3 + Salmonella typhimurium SL1344)


title: 4 h WT GFP- replicate 3

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX (version 0.0.13)
Size filtering: discarding reads shorter than 20 nt (via READemption version 0.3.5)
Read mapping using segemehl version 0.2.0  (via READemption version 0.3.5)
Counting of reads per gene (READemption version 0.3.5)
Genome_build: Human: hg19/GRCh37; Salmonella enterica Typhimurium SL1344: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: CSV (tab separated), Number of reads per gene and condition

extract_protocol:
miRvana for total RNA (Ambion)
miRvana kit for total RNA (Ambion) or TRIzol (Invitrogen) as indicated
cDNA libraries for Illumina sequencing were generated by Vertis Biotechnology AG, Freising-Weihenstephan, Germany (http://www.vertisbiotech.com/). A minimal amount of ~100 ng of total RNA was required for cDNA library preparation. DNase I-treated total RNA samples were first sheared via ultra-sound sonication (4 pulses of 30 s at 4°C each) to generate on average ~200-400 bp fragmentation products. Then, fragments <20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics). As an internal quality control for this pilot experiment, spike-in RNA (sequence of spike: 5’-AAAUCCGUUCGUACGGGCCC-3’; was 5’-monophosphorylated and gel-purified) was added to a final concentration of 0.5%. The samples were then poly(A)-tailed using poly(A) polymerase and the 5’triphosphate (and eukaryotic cap) structures were removed using tobacco acid pyrophosphatase (TAP). Afterwards, an RNA adapter was ligated to the 5’monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase (NEB). The resulting cDNA was PCR-amplified to about 20-30 ng/µL using a high fidelity DNA polymerase (barcode sequences for multiplexing were part of the 3’primers). The cDNA library was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis (Agilent Technologies).

value: Salmonella typhimurium SL1344


title: 4 h WT GFP+ replicate 3


title: Lib175

city: New York

first: Robert

last: Roeder

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequenced reads were mapped to reference genome hg19 using BWA with default settings through GALAXY.
ChIPseq peaks were called by SICER software with parameter settings as W=200,G=400, and FDR=0.001
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using rpkmforgenes.py developed by Sandberg.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each RNA-seq Sample; bedGraph files were generated for each ChIP-Seq sample.

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The human AML cell line THP1 and the human ALL cell line CCRF-CEM were grown in RPMI-160 medium supplemented with 10% FBS and 2% Penicillin/Streptomycin.

extract_protocol:
For ChIP assays, normally, cells were fixed with 0.4% (v/v) formaldehyde at room temperature for 10 min. For improving the ChIP efficiency of non-DNA binding factors, double fixation was used. For double fixation with EGS (Pierce, Cat. no. 21565) and formaldehyde, cells were fixed initially with 1.5 mM EGS at room temperature for 30 min, and subsequently with 0.4% formaldehyde at room temperature for 10 min. For double fixation with DMA (Pierce, Cat. no. 20660) and formaldehyde, cells were fixed initially with 25 mM DMA at room temperature for 1 hour, and subsequently with 0.4% formaldehyde at room temperature for 10 min. After two washes with PBS, fixed cells were resuspended in ice-cold RIPA-0.3 buffer (10 mM Tris-HCl, 1mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% NaDOC, and 0.3 M NaCl, pH7.4) at the concentration of 40 million/ml, and chromatin was disrupted by sonication to the size range of 100 to 500 bp. Antibodies were diluted in RIPA-0.3, and bound to Dynabeads protein A (Life Technologies, cat. no. 10002D) by incubating at 4 °C for 3 hours. The bead-antibody complexes were washed with RIPA-0.3 twice, and then incubated with sonicated chromatin at 4 °C overnight. The second day, after 2 washes with RIPA-0.5, 1 wash with RIPA-0.3, 1 wash with RIPA-0, 2 washes with LiCl buffer (10 mM Tris-HCl, 0.25 M LiCl, 0.25% NP-40, and 0,25% NaDOC, pH7.4), and 2 washes with TE buffer, bound protein-DNA complexes were resuspended in elution buffer (10 mM Tris-HCl, 1mM EDTA, and 1% SDS, pH7.4) supplemented with 10 µg/ml RNase A for elution and RNA digestion, and incubated at 55 °C for 1 hour. Afterwards, proteinase K was added to the final concentration of 100 µg/ml, and 30 min later, the temperature of incubation was increased to 65 °C for decrosslinking.  After decrosslinking for 4–6 hours, DNA was purified by ChIP DNA Clean & Concentrator (Zymo Research, cat. no. D5205). RNA was extracted from cells using RNeasy Plus Mini Kit (Qiagen, cat. no. 74134) or Quick-RNA MiniPrep Kit (Zymo, R1054) by following the manufacturer’s protocol (Qiagen, cat. no. 74134).
ChIP-seq libraries were constructed with 5 to 10 ng immunoprecipitated DNA. RNA-seq libraries were prepared by following a previously published strand-specific protocol. Samples were sequenced on HiSeq 2000 or 2500 by following the manufacturer's protocols.

treatment_protocol: For knockdown experiments with lentiviral shRNAs, TRC control or gene-specific shRNA was transduced into cells by spin infection. Around 15 hours after transduction, cells were washed with PBS twice, and re-suspended in fresh medium. Puromycin (2 μg/ml, final conc.) was added to the culture medium 24 hours later. Cells were harvested for ChIP or RNA extraction 3 days after puromycin selection. For flavopiridol (Sigma, cat. no. F3055) treatment of THP1 cells, flavopiridol was solubilized in DMSO and added to culture medium at 1 μM (final conc.). Meanwhile, an equal volume of DMSO was added to control cells. After 1 more hour in culture, cells were fixed for ChIP.

tag: cell line

value: CCRF-CEM

tag: cell type

value: human acute lymphocytic leukemia (ALL) cell line

tag: treatment

value: pMY137 (PAF1 shRNA #2)

tag: genotype/variation

value: PAF1 knockdown

tag: chip antibody

tag: chip antibody vendor

value: Bethyl

tag: chip antibody cat. #

tag: fixation

value: EGS+ FA


title: ΔpinT infection 8 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:08_h:R2


title: ΔpinT infection 4 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:04_h:R3


title: Wild-type infection 16 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:WT:16_h:R1

value: Salmonella Typhimurium SL1344


title: Lib135

value: human acute monocytic leukemia (AML) cell line

value: pMY136 (PAF1 shRNA #1)

value: Santa Cruz

value: DMA + FA


title: Lib140

source_name: THP1 ChIP-seq

value: Pol II

value: Millipore


title: 21yo Hippocampus astro

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

data_processing:
The FASTQ files were first groomed using the FASTQ groomer and then mapped using TopHat2, which invokes Bowtie as an internal read mapper (Trapnell et al., 2009). The paired end option was selected and human genome version 19 (hg19) was used as the reference genome. We then ran Cufflinks to assemble transcripts and estimate expression level as fragments per kilobase of transcript sequence per million mapped fragments (FPKM) (Trapnell et al., 2010).
Genome_build: Hg19 or mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Hippocampus

extract_protocol:
Tissue was dissociated in papain (30units / ml) for 1.5 hours before trituration. Cells were immunopanned on a sequence of plates in the following order: CD45 --> GalC --> GalC --> Thy1 --> HepaCAM. Cells bound to HepaCAM plate were then scraped in Qiazol to harvest RNA
Nugen Ovation V2 kit (7102-32), followed by sonication in the Covaris machine, followed by indexing with NEB Next Ultra kit (E7530L)

tag: age

value: 21 years old

tag: cell subtype

value: HepaCAM positive cells

value: Astrocyte


title: ΔpinT infection 4 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:04_h:R2

value: HeLa-S3 (ATCC CCL-2.2)

value: Salmonella Typhimurium SL1344 delta-pinT

value: mixed sample (human cell line HeLa-S3 + Salmonella typhimurium SL1344)


title: Lib134

value: pMY56 (control)

value: vector control


title: 4 h mock GFP- replicate 3

value: Salmonella typhimurium SL1344


title: 0 h WT input replicate 3


title: 65yo tumor core astro

source_name: Adult tumor core

value: 65 years old


title: ΔpinT infection 4 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:04_h:R1


title: ΔpinT infection 2 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:02_h:R3


title: 64yo tumor core astro

value: 64 years old


title: 59yo tumor core astro

value: 59 years old


title: PolII_S5P-ChIP

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
Alignment: Sequence reads were obtained using the Illumina CASAVA v1.8.2. Reads were aligned against the human hg18 reference genome (NCBI Build 36.1) using the Bowtie aligner. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Peaks: Peak detection and Superenhancer identification were performed with the HOMER software suite (http://biowhat.ucsd.edu/homer/).
Genome_build: hg18
Supplementary_files_format_and_content: bowtie files are alignments made from fastq files with the Bowtie aligner; bedGraph files were generated on Homer and can be visualized on the UCSC genome browser; peak and superenhancer files were generated using Homer.

source_name: human LX2 cells

growth_protocol: LX-2 cells were cultured as described by Xu, L., Hui, A.Y., Albanis, E., Arthur, M.J., O'Byrne, S.M., Blaner, W.S., Mukherjee, P., Friedman, S.L., and Eng, F.J. (2005). Human hepatic stellate cell lines, LX-1 and LX-2: new tools for analysis of hepatic fibrosis. Gut 54, 142-151.

extract_protocol: Standard Illumina DNA library construction

treatment_protocol: LX-2 cells were treated with DMSO (0.1%) or JQ1(500nM) for 16 hrs.

value: human hepatic stellate cells


title: 24 h WT GFP- replicate 2


title: 0 h WT LB replicate 3


title: 24 h mock GFP- replicate 2


title: ΔpinT infection 0 h replicate 3

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:00_h:R3


title: 24 h WT GFP+ replicate 2


title: PolII_S5P-ChIP + JQ1


title: PolII_S2P-ChIP + JQ1


title: 22yo Hippocampus astro

value: 22 years old


title: PolII_S2P-ChIP


title: ΔpinT infection 2 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:02_h:R1


title: 63yo ctx 1 astro

source_name: Adult temporal lobe

value: 63 years old


title: 63yo ctx 2 astro


title: 4 h WT GFP- replicate 2


title: 59yo tumor periphery astro

source_name: Adult tumor periphery


title: ΔpinT infection 0 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:00_h:R2


title: 60yo ctx astro

value: 60 years old


title: ΔpinT infection 0 h replicate 1

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:00_h:R1


title: PolII-ChIP

value: PolII


title: PolII-ChIP + JQ1


title: 53yo ctx astro

value: 53 years old


title: 16h_WT+_RiboZero

extract_protocol:
miRvana for total RNA (Ambion)
miRvana kit for total RNA (Ambion) or TRIzol (Invitrogen) as indicated
cDNA libraries for Illumina sequencing were generated by Vertis Biotechnology AG, Freising-Weihenstephan, Germany (http://www.vertisbiotech.com/). For the total RNA sample ~500 ng were used for cDNA library preparation. DNase I-treated total RNA samples were first sheared via ultra-sound sonication (4 pulses of 30 s at 4°C each) to generate on average ~200-400 bp fragmentation products. Then, fragments <20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics). The samples were then poly(A)-tailed using poly(A) polymerase and the 5’triphosphate (and eukaryotic cap) structures were removed using tobacco acid pyrophosphatase (TAP). Afterwards, an RNA adapter was ligated to the 5’monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase (NEB). The cDNA library for the rRNA-depleted sample was constructed similarly, except for the following modifications in the protocol: Upon the fragmentation of the RNA, a dephosphorylation step with Antarctic Phosphatase (AP, NEB) and a re-phosphorylation with T4 Polynucleotide Kinase (PNK, NEB) were performed. Oligonucleotide adapters were ligated to both the 5' and 3' end of the RNA samples. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. In any case, the resulting cDNA was PCR-amplified to about 20-30 ng/µL using a high fidelity DNA polymerase (barcode sequences for multiplexing were part of the 3’primers). The cDNA library was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis (Agilent Technologies).


title: BRD4-ChIP


title: ΔpinT infection 2 h replicate 2

description:
total RNA after RNA depletion
HeLa-S3:DeltapinT:02_h:R2


title: 51yo ctx astro

value: 51 years old

value: HepaCAM positive cells


title: 16h_WT+_total

value: HeLa-S3 (ATCC CCL-2.2)


title: 0 h WT input replicate 2


title: 47yo ctx astro

value: 47 years old

value: Astrocyte


title: BRD3-ChIP + JQ1


title: BRD3-ChIP


title: 0 h WT LB replicate 2

value: mixed sample (human cell line HeLa-S3 + Salmonella typhimurium SL1344)


title: BRD2-ChIP + JQ1


title: 22yo ctx astro


title: Elp3cKO_mRNA_rep2

city: Münster

first: Danny

middle: D.

last: Nedialkova

address: Von-Esmarch-Str. 54

department: Max Planck Research Group for RNA Biology

institute: Max Planck Institute for Molecular Biomedicine

data_processing:
Basecalls were performed with Illumina Casava 1.8.
The FastX-toolkit was used to remove 3' adapter sequences.
Reads were aligned to rRNA genes with Bowtie 1.0.0. Non-rRNA reads were mapped with Bowtie to reference sets consisting of UCSC canonical genes containing 18 nt of genomic flanking regions. Only reads with unique matches to the sense strand and a maximum of one mismatch in the seed sequence were retained for further analysis.
Raw read counts were determined using custom scripts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing gene annotations and raw read count data.

organism: Mus musculus

source_name: Forebrains

extract_protocol:
Frozen tissues were homogenized in 20 mM Tris (pH=7.5), 100 mM NaCl, 10 mM MgCl2, 1% Triton X100, 0.25% sodium deoxycholate. Total RNA was isolated from Proteinase K-treated extracts using acid phenol. Following treatment with DNase I, libraries from polyA-selected RNA were generated using the TruSeq RNA Sample Preparation Kit v2 (Illumina).
Total RNA was isolated from Proteinase K-treated extracts using acid phenol. Following treatment with DNase I, libraries from polyA-selected RNA were generated using the TruSeq RNA Sample Preparation Kit v2 (Illumina).

tag: developmental stage

value: E14.5 mouse embryos

tag: replicate


title: 4 h WT GFP+ replicate 2

value: Salmonella typhimurium SL1344


title: BRD2-ChIP


title: 24 h mock GFP- replicate 1


title: 24 h WT GFP- replicate 1


title: 4 h WT GFP- replicate 1


title: BRD4-ChIP + JQ1


title: 4 h WT GFP+ replicate 1


title: 16yo ctx astro

value: 16 years old


title: 24 h WT GFP+ replicate 1


title: 21yo ctx astro

value: 21 years old


title: 4 h mock GFP- replicate 2


title: 13yo ctx astro

value: 13 years old


title: 4 h mock GFP- replicate 1


title: WT_mRNA_rep2

value: wild type


title: 8yo ctx astro

value: 8 years old


title: WT_mRNA_rep1


title: 0 h WT input replicate 1


title: Fetal ctx 6 astro

source_name: Fetal cortex

value: 18.5 gestational weeks


title: Elp3cKO_ribo_rep2

extract_protocol:
Frozen tissues were homogenized in20 mM Tris (pH=7.5), 150 mM NaCl, 5 mM MgCl2, 1% Triton X100, 1 mM DTT, 100 µg/mL cycloheximide, 25 U/mL Turbo DNase (Ambion). RNase-treated extracts were resolved on sucrose gradients, and RNA from monosome fractions was extracted by hot phenol.  Ribosome footprints of 28-32 nt were purified by size selection and gel extraction.
Footprints were dephosphorylated and ligated to a preadenylated 3' linker. Following reverse transcription, cDNA was circularized and amplified by PCR.


title: 35yo ctx astro

value: 35 years old


title: Fetal ctx 5 astro


title: 0 h WT LB replicate 1


title: Elp3cKO_mRNA_rep1


title: WT_ribo_rep2


title: Fetal ctx 3 astro


title: cec-4_2

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
The RNA-seq data were mapped to the c.elegans genome (ce6) with the R package QuasR (www.bioconductor.org/packages/3.1/bioc/html/QuasR.html) using the included spliced alignment algorithm SpliceMap. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce6",splicedAlignment=TRUE)". Gene expression was quantified by counting the number of reads that started within any of the exons beloning to a particular gene (WormBase, WS190). The command used to create the count table was qCount(proj,exons,orientation="same") which counts the reads on the same strand as the gene. To compensate for differences in the read depths of the various libraries, we divided each sample by the total number of reads and multiplied by the average library size. Log2 expression levels were calculated after adding a pseudocount of 8 (y=log2(x+8). This was done to minimize the large differences in expression that would otherwise be caused by genes with small number of counts. As an alternative to gene-centric expression profiling we also quantified RNA expression in windows tiled along the genome. For that we partitioned the genome into non-overlapping windows of 500bp and counted all the reads starting within each window (without considering strand information). Normalization was performed the same way as for the gene expression table described above.
Genome_build: ce6

organism: Caenorhabditis elegans

source_name: Early embryo extracts

growth_protocol: Wild-type, met-2 set-25, cec-4 mutant strains were grown in two independent biological replicas. For each strain, 100,000 - 200,000 L1 worms were grown synchronously in 250 ml S-medium containing HB101 E. coli strain under continuous agitation (180 rpm) at 20ºC until gravid adults with early embryos were observed (between 60-65 hours depending on strain). Embryonic progeny was harvested using hypochlorite treatment, re-suspended in 500ul Trizol® and snap-freeze in liquid nitrogen.

extract_protocol:
Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). Total RNA was purified using RNeasy kit (QIAGEN 74104) including DNase treatment. Depletion of ribosomal RNA was done for 5 µg of total RNA with Ribo-Zero™ Margnetic Gold Kit (Epicentre MRGZG12324) and further concentrated with RNA Clean & Concentrator™ kit (Zymo Research R1015) according to corresponding manufacturer’s instructions.
From the depleted RNA 50ng were used for library preparation with the ScriptSeq v2 RNA-seq Library preparation kit (Epicentre). Equimolar pools of 3 samples were created and loaded on an Illumina HiSeq v3 flowcell using a cBot. Sequencing was performed on a HiSeq 2500 sequencer for 51 cycles running RTA 1.17.21.3. Samples were demultiplexed and FastQ files were generated using blc2fastq-1.8.4.

value: early embryo

tag: strain


title: met-2 set-25_2

value: met-2 set-25_delta_delta


title: wild-type_2

value: wild-type


title: Fetal ctx 2 astro

value: 18 gestational weeks

value: HepaCAM positive cells


title: Cry11Aa LC50 9Hr replicate 1

city: Gainesville

first: Pablo

middle: Emiliano

last: Canton

state: Florida

address: Natural Area Dr.

department: Entomology and Nematology

institute: University of Florida

data_processing:
Reads were checked for quality with FastQC utility and trimmed to 72 bp if necessary to remove adapter and low quality ends using Fastx trimmer
Reads were aligned to Aedes aegypti transcripts v 3.2 with TopHat2  v2.0.12 in Transcriptome mode with the following parameters: -N 2 -r 150 --mate-std-dev 50
Reads counts were summarized using HTSeq-Count v0.5.4p5 with the following parameters: -m intersection-nonempty -s no -t gene -i gene_id using Aaegl3.2 basefeatures.gtf
A count table for all samples was derived from HTSeq-Count outputs
Differential expression predictions were determined with EdgeR  v3.6.8 and DESeq2 v1.4.5, both in GLM mode using treatment tim and biological replicate in model design.
Genome_build: AaegL3.2
Supplementary_files_format_and_content: For each sample, data files contain tab separated gene ID, as identified in Vectorbase Database, counts summarized by HTSeq-Count, and normalized abundance from DEseq2 and EdgeR.

molecule: polyA RNA

organism: Aedes aegypti

source_name: intestine

growth_protocol: Mosquito larvae were reared in controlled temperature and humidity, fed with yeast diet, until 4th instar

extract_protocol:
Total RNA was isolated by TRIzol reagent, treated with DNAseI, and purified by RNeasy columns
PolyA RNA cDNA library was prepared with Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: Larvae were fed with a LC50 of purified Cry11Aa toxin crystals starting at same hour for each replicate. At 0,3,6,9 or 12 hours, dead and dying larvae were discarded and all others dissected to extract intestinal tissue

value: 4th instar

tag: breed

value: IBT-UNAM

tag: tissue

value: intestine

tag: timepoint

value: 9 hr


title: Cry11Aa LC50 12Hr replicate 1

value: 12 hr


title: Cry11Aa LC50 3Hr replicate 2

value: 3 hr


title: WT_ribo_rep1

extract_protocol:
Frozen tissues were homogenized in20 mM Tris (pH=7.5), 150 mM NaCl, 5 mM MgCl2, 1% Triton X100, 1 mM DTT, 100 µg/mL cycloheximide, 25 U/mL Turbo DNase (Ambion). RNase-treated extracts were resolved on sucrose gradients, and RNA from monosome fractions was extracted by hot phenol.  Ribosome footprints of 28-32 nt were purified by size selection and gel extraction.
Footprints were dephosphorylated and ligated to a preadenylated 3' linker ((5' rAppNNNNCTGTAGGCACCATCAAT/3ddC/ 3'). Following reverse transcription, cDNA was circularized and amplified by PCR.

value: E14.5 mouse embryos


title: cec-4_1


title: Cry11Aa LC50 0Hr replicate 2

value: 0 hr


title: Fetal ctx 1 astro

value: Astrocyte


title: met-2 set-25_1


title: Cry11Aa LC50 6Hr replicate 2

value: 6 hr


title: GM12878_SMC3_nexus

city: Farmington

first: Oscar

middle: J.

last: Luo

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

description: ChIP-nexus

data_processing:
Data processing of ChIA-PET reads was performed as previously described in Li et al., 2012 with slight modifications.
Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing.  After trimming the linkers, the sequences flanking the linker were mapped to the human reference genome (hg19) using bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained.  PCR duplicates were removed using the MarkDuplicates tool of the Picard Tools library (http://broadinstitute.github.io/picard/).  Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
PETs with a genomic span less than 8 kb are classified as self-ligation PETs and are used as a proxy for ChIP fragments since they are derived in a manner analogous to ChIP-Seq mapping for protein binding sites. PETs with a genomic span greater than 8 kb are classified as inter-ligation PETs and represent the long-range interactions of interest. To accurately represent the frequency of interaction between two loci and to define the interacting regions, both ends of inter-ligation PETs were extended by 500 bp along the reference genome, and PETs overlapping at both ends (with extension) were clustered together as one PET cluster.
ChIP-nexus sequencing raw reads (including the fixed and random barcodes) were first reduced for PCR redundancy, and then the fixed and random barcodes (read positions 1-9) were trimmed. The remaining sequences were aligned to human genome assembly hg19 by bwa-mem (Li and Durbin, 2010) and only uniquely aligned (MAPQ ≥ 30) PETs were retained.
The sequence alignment results were used as input to MACE (v1.2) (Wang et al., 2014) to identify RAD21 and SMC3 occupancy borders (footprints).
genome build: hg19
processed data files format and content: Tab-delimited file documenting the genomic coodinates and frequency of each interaction PET cluster. For ChIP-nexus, the processed data is the MACE processed genome coverage profile in bigwig format.

growth_protocol: GM12878 and HeLa cells (ATCC®) were cultured following manufacture’s instruction.

extract_protocol:
Chromatin was obtained and subjected to fragmentation with an average length of 300 bp by sonication. The anti-PolII monoclonal antibody 8WG16 (Covance, MMS-126R) and anti-CTCF antibody (Abcam, ab70303) were used to enrich PolII and CTCF-bound chromatin fragments, respectively.
ChIP DNA on beads was used for ChIA-PET library preparation. After performing the end-repair and A-tailing using T4 DNA polymerase (NEB) and Klenow enzyme, the ChIP DNA ends were proximity-ligated by the single biotinylated bridge-linker with the 3' nucleotide T over-hanging on both strands. Proximity ligation DNA was reverse cross-linked and fragmented and added sequencing adaptors simultaneously by using Tn5 transposase (Nextera kit, Illumina). DNA fragments contained the bridge-linker at ligation junctions were captured by Streptividin beads, and used as templates for PCR amplification. These DNA products were then subjected to size-selection and paired-end sequencing (2×150 bp) using Illumina Hi-Seq 2500.

treatment_protocol: Approximately 100-200 million cells were harvested and fixed by 30 ml of 1.5 mM EGS (ethylene glycol bis[succinimidylsuccinate]) in PBS buffer for 45 minutes at room temperature. Next, formaldehyde was added to final concentration of 1% to cross-link the cells for another 20 minutes at room temperature and then neutralized by using glycine. The cross-linked cells were lysed by cell lysis buffer and nuclear lysis buffer.

tag: factor


title: Cry11Aa LC50 6Hr replicate 1


title: GM12878_RAD21_nexus

description: ChIP-nexus

tag: cell line


title: wild-type_1


title: HeLa_RNAPII

description:
Combined
ChIA-PET

value: RNAPII

tag: antibody

value: anti-PolII monoclonal antibody 8WG16 (Covance, MMS-126R)


title: Cry11Aa LC50 3Hr replicate 1


title: Cry11Aa LC50 0Hr replicate 1


title: Elp3cKO_ribo_rep1


title: INPUT

city: Austin

middle: M

last: Phelps

state: TX - Texas

address: 34 Patterson Labs, 2401 Speedway

department: Integrative biology

institute: University of Texas at Austin

data_processing:
Reads from 8 individuals were combined
ChIP and INPUT reads were aligned to the vole genome (MicOch1.0) using bwa 0.7.12
Bwa alignments were improved usng STAMPY v1.0.21
Non-unique and low quality alignments (Phred =<20) were removed using samtools 0.1.19
We used Model-based Analysis of ChIP-Seq (MACS2 2.0.10) to find peaks with significant enrichment compared to the INPUT control (q value cutoff = 0.05).
Genome_build: MicOch1.0
Supplementary_files_format_and_content: Significant peak regions (q value < 0.05) reported by MACS2 are tabulated in .xls format

organism: Microtus ochrogaster

source_name: Retrosplenial cortex (RSC)

extract_protocol:
The retrosplenial cortex was dissected from freshly harvested brains and immediately fixed. Cells and nuclei were lysed on ice. Chromatin was extracted and sheared. Antibody against H3K4me1 was used to isolate putative enhancer DNA.
Libraries were prepared for Illumina sequencing using KAPA Library Preparation Kit (cat# KK8230) according to manufacturer's protocol.

tag: Sex

value: Male

value: Brain/RSC


title: H3K4me1-ChIP-seq


title: Fetal ctx 4 astro

value: 18.1 gestational weeks

tag: cell type


title: S2

status: Public on Dec 10 2015

city: qinhuangdao

first: xiaoyan

last: zhang

address: kangle road

country: China

institute: Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences

data_processing:
The cDNA libraries  for pair-end sequencing were constructed for each pooled RNA sample using the TruSeqTM RNA Sample Preparation Kit (Illumina, Inc.) according to the manufacturer’s instructions. The tagged cDNA libraries were pooled in equal ratio and used for 125 bp paired-end sequencing in a single lane of the Illumina HiSeqTM 2500 with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.
The clean reads were then aligned to Macrobrachium nipponense genome (RNA denovo) using the bwa_mem (Version: 0.7.8-r455). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 15 --ins 6 --del 6 --non-canonical) to provide the largest information on the AS events.
We applied HTseq to calculate the mRNA counts based on the mapping result
Genome_build: de novo assembly. FASTA file is available on the series record.
Supplementary_files_format_and_content: text file with count data

organism: Paralichthys olivaceus

extract_protocol:
Gonads were removed, flash frozen in liquid nitrogen, and RNA was harvested using RNeasy Mini Kit.The cDNA libraries were constructed for each pooled RNA sample using the TruSeqTM RNA sample preparation kit (Illumina, Inc.) according to the manufacturer’s instructions. The tagged cDNA libraries were pooled in equal ratio and used for 101 bp paired-ends sequencing with an Illumina HiSeqTM 2000
RNA libraries were prepared for sequencing using standard Illumina protocols

value: five years old

value: gonad

tag: Stage

value: stage Ⅲ


title: F3

value: stage Ⅴ


title: S3


title: S1


title: F2


title: F1


title: shSREBP1 (2)

city: Los Angeles

last: Bensinger

address: 615 Charles E Young Dr

department: MIMG

institute: UCLA

data_processing:
The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in paired-end mode. We followed a 2-pass alignment strategy: in the first round, reads were aligned to a genome index that included both the genome sequence (GRCh37 primary assembly) and the exon/intron structure of known gene models (Ensembl GRCh37.71). Novel splice junctions were then included in the junction database to generate a new genome index for re-alignment. Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%, minimum intron length=21, minimum alignment overhang for novel junctions=10, infinite penalty for non-canonical splice sites
Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-nonemtpy” mode for version v0.6.1p2).
Expression estimates in units of FPKMs (fragments per kilobase of mappable gene length and million reads) were obtained after normalizing the counts matrix with sequencing depth and gene effective length. These expression levels, which are expected to correlate with mRNA relative abundance within each sample (within-sample normalization), were used for rank-order classifier in comparative analyses for individual samples. Differential expression or global clustering across samples was  carried out after inter-sample normalization.
Genome_build: GRCh37
Supplementary_files_format_and_content: Expression estimates in units of FPKMs. Format: Ensembl Gene id / Gene symbol / RefSeq id / Description / locus / biotype / Average expression estimates for each sample

source_name: THP1 cell line

growth_protocol: Modified THP1 cells were passaged in RPMI media with 10% FBS +  puromyocin.

extract_protocol:
Cells were lysed into Trizol and RNA was purified using a Trizol/Qiagen RNEasy Kit combined protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 72 hr prior to RNA extraction, cells were plated at 1.2e6 cells/well in 6 well dishes in the presence of 80nM PMA in RMPI + 10% FBS.

value: THP1 monocytic cells

tag: lentivirus-introduced modification

value: Stably transduced with  shRNA to SREBF1

tag: cell culture condition

value: 80nM PMA for 72h


title: shSREBP2 (1)

value: Stably transduced with  shRNA to SREBF2


title: shControl (2)

value: Stably transduced with Non-targeting shRNA


title: shControl (1)


title: ADARB1.Short.02

first: Jinkai

last: Wang

address: 650 Charles E. Young Drive South, CHS 33-228

institute: University of California, Los Angeles

data_processing:
Paired-end RNA-Seq reads were first mapped to Ensembl transcripts and the unmapped were then mapped to human genome (hg19) using tophat (version 1.4.1).
FPKMs were calculated using Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: Supplemental excel file includes the FPKM values of all samples.

growth_protocol: HEK293 cell line was grown in DMEM with 10% FBS.

extract_protocol:
48 hours after transfection, cells were collected for RNA extraction using TRIzol reagent (Life technologies) and protein lysates with RIPA buffer. Total RNA samples were treated with DNaseI (Fermentas) and reverse transcribed using the High-Capacity cDNA RT kit (Applied Biosystem).
RNA-Seq libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Cells were transiently transfected with Lipofectamine 2000 reagent according to the manufacturer’s protocol.

tag: transfection

value: ADARB1 short isoform


title: ADARB1.Long.02

value: ADARB1 long isoform


title: ADARB1.Long.03


title: hRRP6 (EXOSC10)_iCLIP_biological replicate1

city: Copenhagen

first: Mireya

last: Plass

address: Robert-Rössle Str. 10

institute: MDC-Berlin

description:
reads.plus.bedGraph
reads.min.bedGraph

data_processing:
Reads were demultiplexed using their fixed barcodes
Reads were trimmed at the 3'end to remove adapter sequences and low-quality sequences using custom python scripts. Reads shorter than 25 nt were discarded.
Duplicated reads were collapsed using random barcodes (first 5 nucleotides) to discriminate between identical sequences.
Reads were mapped to the Human genome (hg19) + exon junction index +exome (ensembl70) using BWA-PSSM with parameters -n 0.04 -l 1024-m 400 -P 0.99.
Confidently mapped reads with a posterior probability > 0.99 were kepts for further analyses.
Reads from the two replicates were merged and significant clusters were identified using Pyicos (Althammer et al 2011).
Only clusters with a false discovery rate (FDR) < 0.01 were further used
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files containing the significant clusters identified in the plus and the minus strands using the merged datasets.

growth_protocol: HEK293T transiently transfected with FLAG-hRRP6 (wild type) were expanded in 15 cm plates to 95% confluency

extract_protocol:
HEK293T were irradiated, lysed and epitope-tagged proteins were purified following protocol from Konig et al. 2011
iCLIP libraries were constructed FLAG-hRRP6 immunoprecipitates following the protocol from Konig et al. 2011
iCLIP library strategy can be found in Konig et al. 2011

tag: protocol

value: anti-FLAG M2 magnetic beads (Sigma Aldrich, catalog# M8823)

tag: adaptor

tag: random barcode

value: NNNCCGGNN


title: ADARB1.Long.01


title: hRRP6 (EXOSC10)_iCLIP_biological replicate2

description:
reads.plus.bedGraph
reads.min.bedGraph

value: transiently transfected with FLAG-hRRP6 (wild type)


title: New MAC DNA from exconjugants @ 36 hpm from PDD1 KO cells rescued with PDD1-MIM22 mutant

city: Montpellier

first: Kazufumi

last: Mochizuki

address: 141 rue de la Cardonille

country: France

institute: Institute of Human Genetics, CNRS

description:
Sample 8
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.

data_processing:
Library strategy: DNA-Seq
The first 36-nt sequences of the reads that map to the micronuclear genome were used in downstream analyses.
The numbers of normalized sequence reads (RPMs) from the purified new MACs that mapped to each IES were calculated and divided by the average numbers of reads from the purified, wild-type-derived MICs (from B2086 and CU428) that mapped to the corresponding IES to give the Retention Indexes (RIs) of the IESs.
Genome_build: Draft MIC genome sequence (version 2, supercontigs) obtained from the Tetrahymena Comparative Sequencing Project (Broad Institute of Harvard and MIT) (http://www.broadinstitute.org/annotation/genome/Tetrahymena/MultiHome.html).
Supplementary_files_format_and_content: IES_Position_for_DNA_elimination_assay.txt: Explains positions of predicted Internal Eliminated Sequences (IESs) in the MIC supercontigs used in this study.
Supplementary_files_format_and_content: *_IES_HitRPM.txt: Number of sequence reads mapping each IES (RPM and RPKM). 'length' in the files does not indicate actual length of IES but sum of the length of unique sequences within each IES.

organism: Tetrahymena thermophila

source_name: Exconjugant cells @ 36 hpm, PDD1 KO rescued with PDD1-MIM22 mutant, new MACs

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% protease peptone at 30⁰C overnight. To induce conjugation, exponentially growing cells (~3-5x 10^5/ml) of two different mating types were starved in 10 mM Tris-HCl (pH 7.5) at 30°C for 8-14 h and mixed for conjugation (7x 10^5/ml) 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 HiSeq 2000 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%.

tag: genotype/variation

value: PDD1 KO rescued with PDD1-MIM22 mutant


title: ADARB1.Short.01


title: shSREBP2 (2)


title: New MAC DNA from exconjugants @ 36 hpm from PDD1 KO cells rescued with wild-type PDD1

description:
Sample 7
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.

source_name: Exconjugant cells @ 36 hpm, PDD1 KO rescued with wild-type PDD1, new MACs

value: PDD1 KO rescued with wild-type PDD1


title: EV.02

value: Control (empty vector)


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

description:
Sample 3
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.

source_name: Exconjugant cells @ 36 hpm, wild-type, new MACs

value: wild-type


title: New MAC DNA from exconjugants @ 36 hpm from PDD1 KO cells

description:
Sample 6
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.

source_name: Exconjugant cells @ 36 hpm, PDD1 KO, new MACs

value: PDD1 KO


title: New MAC DNA from exconjugants @ 36 hpm from TWI1 KO cells

description:
Sample 5
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.

source_name: Exconjugant cells @ 36 hpm, TWI1 KO, new MACs

value: TWI1 KO


title: MIC DNA from vegetative wild-type CU428 cells

description: Sample 2

source_name: Exconjugant cells @ 36 hpm, wild-type, MIC DNA

tag: strain/background


title: ADARB1.Short.03


title: New MAC DNA from exconjugants @ 36 hpm from JUB1 KO cells

description:
Sample 4
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.

source_name: Exconjugant cells @ 36 hpm, JUB1 KO, new MACs

value: JUB1 KO


title: MIC DNA from vegetative wild-type B2086 cells

description: Sample 1


title: shSREBP1 (1)

value: THP1 monocytic cells


title: ChIP_seq_Chaf1a.2122_Sox2_input_day3

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

description:
Chaf1a.2122 knockdown
Processed data file: WTC.binding.positions.evalue.Day3_Chaf1a.2122_Sox2.input.Day3_Chaf1a.2122_WCE.txt

data_processing:
For ATAC-seq data, The reads were aligned to the mouse genome mm9 using BWA version 0.7.8 with -q 5 -l 32 -k 2 and paired option. Non-primary mapping, failed QC, duplicates and non-paired reads were filtered. Reads from different chromosomes and chrM were also filtered. Only uniquely mapped reads were used for the analysis. The read density profiles were generated using 150 bp window with a 20 bp step and were normalized by the library size.
For Sono-seq and Sox2 ChIP-seq data, the reads were aligned to mm9 using Bowtie with a unique mapping option. The smoothed tag density profiles were generated using get.smoothed.tag.density function of the SPP R package with a 100-bp window, 50-bp step and library size normalization. The positions of promoters and enhancers in mESC and MEF were obtained from publicly available data set (Shen et al Nature 2012). For the peak comparison in Sox2 between CAF-1 KD and Renilla KD, first the reads were subsampled to make the sequencing depth the same from each condition as the number of peaks called tends to increase as sequencing depth is deeper. The significantly enriched peaks compared inputs were detected using SPP find.binding.positions function with e-value = 10.
Genome_build: mm9
Supplementary_files_format_and_content: wig and tag density profiles; txt and peak calling results; csv and tag density values at given coordinates

source_name: OKSM reprogramming intermediates   from Mouse Embryonic Fibroblasts

growth_protocol: Reprogramming of fibrobasts was performed in standard serum/LIF ESC media supplemented with Doxycycline and Ascorbate

extract_protocol:
To generate ATAC-seq libraries, total of 50000 cells were used and libraries were constructed as previously described46. Briefly, cells were washed in PBS twice, counted and nuclei were isolated from 100000 cells using 100ul hypotonic buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) to generated two independent transposition reactions. Nuclei were split in half and treated with 2.5 μL Tn5 Transposase (Illumina) for 30min at 37°C. DNA from transposed nuclei was then isolated and PCR amplified using barcoded Nextera primers (illumina). For all ChIP experiments 10e7 reprogramming intermediates were collected per library. Chromatin precipitation assays were performed as previously described69 using goat polyclonal Anti-Sox2 (AF2018, R&D). Briefly, cells were cross-linked on plate in 1% methanol free formaldehyde and snap frozen in liquid nitrogen until processed. Nuclei were isolated using 1ml of Cell lysis buffer (20mM Tris pH8, 85mM KCL, 0.5% NP40 and 1X HALT protease inhibitor cocktail) and resuspended in nuclear lysis buffer (10mM Tris-HCL pH7.5, 1% NP40, 0.5% Na deoxycholate, 0.1% SDS, 1X HALT protease inhibitor cocktail) and sonicated using optimized pulses of branson sonifier (1min ON/OFF pulses for 5 cycles) for ChIP-seq libraries and S220 Covaris sonicator (Settings: duty cycle 5%, intensity 6, cycles/burst 200, pulse length 60s, 20 cycles, 8°C) for sono-seq input preparations. Sonications were verified for both methods using the 2100 Bioanalyzer. Immunoprecipitations were carried out by first adjusting salt concentration in sheared chromatin to 167mM NaCL and adding antibodies (6ug of Sox2 antibody) and incubated for 3-4 hrs at 4C. 50μl Protein G Dynabeads (Invitrogen) were prepared for each IP reaction by washing 2-3 times in chip dilution buffer (16.7mM Tris-HCl pH 8.1, 167mM NaCl, 0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA) and added for an additional hour to pull down bound chromatin. Beads complexes were then washed 6 times in RIPA buffer (20mM Tris-HCL pH8.1, 1mM EDTA, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% Na deoxyhcholate), then two times with RIPA with high salt concentration (500mM), then 2 washes in LiCL buffer (10mM tris-HCL pH8.1, 1mM EDTA, 1% DOC, 1% NP40, 250mM LiCL) and two final washes in TE. Complexes were then eluted and reverse cross-linked in 50ul ChIP elution buffer (10mM Tris-HCL pH8, 5mM EDTA, 300mM NaCl, 01% SDS) and 8ul of reverse crosslinking buffer (250mM Tris-HCl pH 6.5, 1.25M NaCl, 62.5mM EDTA, 5mg/mL Proteinase K, 62.5ug/mL RNAse A by incubation at 65°C for 6h. DNA was isolated using Ampure SPRI beads and yield quantified using Qubit fluorometer.
Libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: MEFs were treated with Doxycycline (2ug/ml) to induce reprogramming. iPSCs were established upon Dox withdrawal for 4 days followed by 5 passages in serum/LIF.

tag: strain

value: Mouse Embryonic Fibroblasts

tag: age

value: E13.5 embryos

tag: genotype

value: Col1a1::tetOP-OKSM ; R26-M2rtTA


title: ChIP_seq_Chaf1a.2122_Sox2_IP_day3

tag: tissue

value: goat polyclonal Anti-Sox2 (AF2018, R&D); lot#:KOY0213101


title: Jub1p ChIP from new MACs of PDD1 KO rescued with PDD1-MIM22 mutant

description:
Sample 14
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
The anti-Jub1p antibody was produced by ourselves. Rabbits were immunized with a peptide (CRSFDKQAQGKKNSS) corresponding to amino acids 838-851 (underlined) of Jub1p (DDBJ/EMBL/GenBank EAS04546.2).
Reads mapped to LMR locus: 13538_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 13538Red_IES_flank_hit_UL.txt

data_processing:
The first 36-nt sequences of the reads that map to the micronuclear genome were used in downstream analyses.
The numbers of normalized sequence reads (RPMs) from the ChIP sample that mapped to each 100-bp bin were divided by the numbers of reads from the Input sample, and these normalized scores were mapped to a representative 100-kb MIC locus, the LMR, as previously described (Schoeberl et al. (2012) Genes Dev 26, 1729-42) and to a modeled IES consisting of the 5,606 predicted IESs that range from 1-5 kb in length along with their flanking sequences.
Genome_build: LMR locus: Described in Schoeberl et al. (2012) Genes Dev 26, 1729-42.
Genome_build: IESs: Listed in Schoeberl et al. (2012) Genes Dev 26, 1729-42.
Supplementary_files_format_and_content: Histograms of mapped normalized sequence read numbers.

source_name: New MACs @ 12 hpm, PDD1 KO rescued with PDD1-MIM22 mutant, Jub1p ChIP

growth_protocol: Cells were grown in SPP medium (Gorovsky et al., 1975) containing 2% protease peptone at 30⁰C overnight. To induce conjugation, exponentially growing cells (~3-5x 10^5/ml) of two different mating types were starved in 10 mM Tris-HCl (pH 7.5) at 30°C for 8-14 h and mixed for conjugation (7x 105/ml) at 30°C.

extract_protocol: Chromatin immunoprecipitation was performed with the new MACs only when their purity was above 80%. Chromatin from the new MACs was sheared into 150-500 bp fragments (peak ~300 bp) in Sonication buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 0.1% SDS, 1x complete protease inhibitor cocktail, 1 mM PMSF) using a probe sonicator. For ChIP, 20 mg of Protein A Sepharose CL-4B beads (GE Healthcare) was washed with TE twice and with ChIP buffer (25 mM Tris-HCl pH 8.0, 167 mM NaCl, 5 mM EDTA, 0.05% SDS, 1% Triton X-100, 1x complete protease inhibitor cocktail, 1 mM PMSF) 3 times and was then pre-incubated with 90 µl of ChIP buffer containing 10 µl of 10 mg/ml BSA (NEB) (total ~200 µl suspension) at 4°C for 1 h. The fragmented chromatin from 2 million new MACs in Sonication buffer was diluted with an equal volume of 2x ChIP dilution buffer (334 mM NaCl, 2% Triton X-100, 1x complete protease inhibitor cocktail), adjusted to 1 ml with ChIP buffer and incubated with a 25 µl suspension of the beads at 4°C for 2 h for the pre-absorption. To couple an antibody to the beads, the 10 µl suspension of the beads pre-incubated with BSA was incubated with an antibody (50 µl anti-Jub1p [in-house] or 5 µg anti-Pdd1p [Abcam ab5338]) in 0.5 ml of ChIP buffer at 4°C for 2 h and was then washed with ChIP buffer 3 times. The pre-absorbed chromatin was incubated with the antibody-coupled beads at 4°C overnight. The beads were washed once with Low-salt wash buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) and twice each with High-salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), LiCl wash buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1 mM EDTA, 1% sodium deoxycholate, 1% NP-40) and TE. The immunoprecipitated chromatin was eluted with Elution buffer (0.1 M NaHCO3, 1% SDS). For cross-linking reversal, the NaCl concentration of the sample was adjusted to 200 mM, and the sample was incubated at 65°C for ~12 h. The DNA was extracted, and DNA libraries were generated from the immunoprecipitated DNA and 20 ng of the fragmented chromatin DNA without immunoprecipitation (Input) using the NEBNext DNA Library Prep Reagent Set for Illumina (NEB) and the KAPA Real-Time Library Amplification Kit (KAPA Biosystems). The libraries were sequenced using the HiSeq 2000 platform (Illumina) with 50-nt single-end reads.

treatment_protocol: Nuclei from cells at 12 hpm were dissociated and stained with DAPI in TMSN 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) using a dounce homogenizer with 15 strokes. The nuclear fraction was collected by centrifugation at 4,500 g at 4°C for 5 min and then washed with TMSN buffer once and with TMSN(-) buffer (TMSN buffer without complete proteinase inhibitor cocktail) twice. The nuclei were fixed with 1.25 mg/ml Di(N-succinimidyl) glutarate (Sigma) in PBSN buffer (PBS with 0.016% NP-40) at room temperature for 30 min, collected by centrifugation at 9,000 g at 4°C for 5 min, and washed with PBSN buffer twice. The DSG-fixed nuclei were re-fixed with 1% paraformaldehyde (Sigma) in PBSN buffer at room temperature for 10 min. The paraformaldehyde was quenched with 0.25 M glycine at room temperature for 5 min. The nuclei were washed with PBSN buffer containing 0.1 µg/ml DAPI twice and then with PBSN(+) buffer (PBSN with 1x complete proteinase inhibitor cocktail and 0.1 µg/ml DAPI) once, and the nuclear pellet was stored at -80°C. The nuclei were resuspended in PBSN(+), and the new MACs were collected according to their size and DAPI intensity using a FACSAria III (BD Biosciences). The purity of the collected new MACs was assessed by immuno-DNA-FISH using a Cy3-labeled probe against Tlr1 and an anti-Pdd1p antibody (Abcam) for wild-type, JUB1 KO, WT-rescue and MIM22 cells or an anti-H3K4me3 (Abcam) antibody for PDD1 KO cells: Tlr1-negative nuclei were counted as parental (old) MACs; Tlr1-positive, and Pdd1p- or H3K4me3-positive nuclei were counted as new MACs; Tlr1-positive but Pdd1p- or H3K4me3-negative nuclei were counted as MICs. Contamination of the parental MACs was rare (<2%), and most of the contaminants in our new MAC preparations were MICs.

tag: chip antibody


title: ATAC_seq_Renilla_rep2_day0

description:
Renilla control knockdown
Processed data file: renilla_merged_t0.uniq.norm.tagdensity.bigwig

data_processing:
Library strategy: ATAC-seq
For ATAC-seq data, The reads were aligned to the mouse genome mm9 using BWA version 0.7.8 with -q 5 -l 32 -k 2 and paired option. Non-primary mapping, failed QC, duplicates and non-paired reads were filtered. Reads from different chromosomes and chrM were also filtered. Only uniquely mapped reads were used for the analysis. The read density profiles were generated using 150 bp window with a 20 bp step and were normalized by the library size.
For Sono-seq and Sox2 ChIP-seq data, the reads were aligned to mm9 using Bowtie with a unique mapping option. The smoothed tag density profiles were generated using get.smoothed.tag.density function of the SPP R package with a 100-bp window, 50-bp step and library size normalization. The positions of promoters and enhancers in mESC and MEF were obtained from publicly available data set (Shen et al Nature 2012). For the peak comparison in Sox2 between CAF-1 KD and Renilla KD, first the reads were subsampled to make the sequencing depth the same from each condition as the number of peaks called tends to increase as sequencing depth is deeper. The significantly enriched peaks compared inputs were detected using SPP find.binding.positions function with e-value = 10.
Genome_build: mm9
Supplementary_files_format_and_content: wig and tag density profiles; txt and peak calling results; csv and tag density values at given coordinates

tag: antibody


title: ATAC_seq_Renilla_rep1_day0


title: ATAC_seq_Chaf1a.2122_rep2_day0

description:
Chaf1a.2122 knockdown
Processed data file: Chaf1a.2122_merged_t0.uniq.norm.tagdensity.bigwig


title: EV.03

tag: cell line


title: EV.01


title: Pdd1p ChIP from new MACs of PDD1 KO rescued with PDD1-MIM22 mutant

description:
Sample 13
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
Reads mapped to LMR locus: 13261_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 13261Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, PDD1 KO rescued with PDD1-MIM22 mutant, Pdd1p ChIP


title: ATAC_seq_Chaf1a.166_rep2_day0

description:
Chaf1a.164 knockdown
Processed data file: Chaf1a.166_merged_t0.uniq.norm.tagdensity.bigwig


title: ATAC_seq_Chaf1a.2122_rep1_day0


title: Input for ChIP (Sample 13 & 14) from new MACs of PDD1 KO rescued with PDD1-MIM22 mutant

description:
Sample 12
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
Reads mapped to LMR locus: 13260_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 13260Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, PDD1 KO rescued with PDD1-MIM22 mutant, input


title: ATAC_seq_Chaf1a.2122_rep2_day6

description:
Chaf1a.2122 knockdown
Processed data file: Chaf1a.2122_merged_day6.uniq.norm.tagdensity.bigwig


title: ATAC_seq_Chaf1a.166_rep1_day0


title: ATAC_seq_Chaf1a.2122_rep2_day3

description:
Chaf1a.2122 knockdown
Processed data file: Chaf1a.2122_merged_day3.uniq.norm.tagdensity.bigwig


title: Jub1p ChIP from new MACs of PDD1 KO rescued with wild-type PDD1

description:
Sample 11
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
The anti-Jub1p antibody was produced by ourselves. Rabbits were immunized with a peptide (CRSFDKQAQGKKNSS) corresponding to amino acids 838-851 (underlined) of Jub1p (DDBJ/EMBL/GenBank EAS04546.2).
Reads mapped to LMR locus: 13544_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 13544Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, PDD1 KO rescued with wild-type PDD1, Jub1p ChIP


title: ATAC_seq_Chaf1a.2122_rep1_day3


title: ATAC_seq_Chaf1a.2122_rep1_day6


title: ChIP_seq_ChaF1a_166_day3_H3K9me3_IP

description: Chaf1a.164 knockdown

data_processing:
For H3K9me3 ChIP-seq data, the reads were aligned to mm10 using Bowtie with a unique mapping option and allowing up to 3 mismatches.
For RNA-Seq data, adaptor sequences were trimmed using Reaper and reads shorter than 15 nucleotides, and low complexity reads were removed. Reads mapping to rRNA sequences were filtered out using Bowtie. The remaining reads were aligned to the mm10 genome using Bowtie with a unique mapping option and allowing up to 3 mismatches.
Genome_build: mm10 for H3K9me3 ChIP-seq and RNA-seq
Supplementary_files_format_and_content: wig density profiles in bigWig format

source_name: OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts

extract_protocol:
see methods section in main text
Libraries for sequencing were prepared using standard Illumina protocols.


title: Pdd1p ChIP from new MACs of PDD1 KO rescued with wild-type PDD1

description:
Sample 10
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
Reads mapped to LMR locus: 13267_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 13267Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, PDD1 KO rescued with wild-type PDD1, Pdd1p ChIP


title: Input for ChIP (Sample 10 & 11) from new MACs of PDD1 KO rescued with wild-type PDD1

description:
Sample 9
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
Reads mapped to LMR locus: 13266_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 13266Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, PDD1 KO rescued with wild-type PDD1, input


title: ChIP_seq_ChaF1a_166_day0_H3K9me3_IP

description: Chaf1a.164 knockdown


title: ChIP_seq_ChaF1a_2122_day0_H3K9me3_IP

description: Chaf1a.2122 knockdown


title: ChIP_seq_Renilla_day3_H3K9me3_IP

description: Renilla control knockdown


title: Input for ChIP (Sample 8) from PDD1 KO new MACs

description:
Sample 7
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
Reads mapped to LMR locus: 13291_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 13291Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, PDD1 KO, input


title: ChIP_seq_Renilla_day0_H3K9me3_IP

description: Renilla control knockdown


title: ChIP_seq_ChaF1a_166_day3_H3K9me3_input

description: Chaf1a.164 knockdown


title: Jub1p ChIP from wild-type new MACs

description:
Sample 6
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
The anti-Jub1p antibody was produced by ourselves. Rabbits were immunized with a peptide (CRSFDKQAQGKKNSS) corresponding to amino acids 838-851 (underlined) of Jub1p (DDBJ/EMBL/GenBank EAS04546.2).
Reads mapped to LMR locus: 12995_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 12995Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, wild-type, Jub1p ChIP


title: ChIP_seq_ChaF1a_2122_day0_H3K9me3_input

description: Chaf1a.2122 knockdown


title: ChIP_seq_Renilla_day3_H3K9me3_input

description: Renilla control knockdown


title: ChIP_seq_ChaF1a_166_day0_H3K9me3_input

description: Chaf1a.164 knockdown


title: ChIP_seq_ChaF1a_2122_day3_H3K9me3_input

description: Chaf1a.2122 knockdown


title: Input for ChIP (Sample 6) from wild-type new MACs

description:
Sample 5
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
Reads mapped to LMR locus: 12992_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 12992Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, wild-type, input


title: ChIP_seq_Renilla_day0_H3K9me3_input

description: Renilla control knockdown


title: Pdd1p ChIP from JUB1KO new MACs

description:
Sample 4
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
Reads mapped to LMR locus: 12649_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 12649Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, JUB1 KO, Pdd1p ChIP


title: RNA_seq_CAF1_day6-rep3

description: CAF-1 knockdown (shRNA pool)


title: Input for ChIP (Sample 4) from JUB1 KO new MACs

description:
Sample 3
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
Reads mapped to LMR locus: 12648_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 12648Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, JUB1 KO, input


title: ChIP_seq_ChaF1a_2122_day3_H3K9me3_IP

description: Chaf1a.2122 knockdown


title: RNA_seq_CAF1_day6-rep2

description: CAF-1 knockdown (shRNA pool)


title: Pdd1p ChIP from wild-type new MACs

description:
Sample 2
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
Reads mapped to LMR locus: 12639_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 12639Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, wild-type, Pdd1p ChIP


title: RNA_seq_Renilla_day6-rep3

description: CAF-1 knockdown (shRNA pool)


title: Jub1p ChIP from PDD1 KO new MACs

description:
Sample 8
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
The anti-Jub1p antibody was produced by ourselves. Rabbits were immunized with a peptide (CRSFDKQAQGKKNSS) corresponding to amino acids 838-851 (underlined) of Jub1p (DDBJ/EMBL/GenBank EAS04546.2).
Reads mapped to LMR locus: 13293_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 13293Red_IES_flank_hit_UL.txt

source_name: New MACs @ 12 hpm, PDD1 KO, Jub1p ChIP


title: RNA_seq_Renilla_day6-rep2

description: CAF-1 knockdown (shRNA pool)


title: RNA_seq_Renilla_day6-rep1

description: CAF-1 knockdown (shRNA pool)


title: Input for ChIP (Sample 2) from wild-type new MACs

description:
Sample 1
All experiments were done with cells in or after sexual reproduction, in which two different strains (derived from B2086 and CU428) were mixed.
Reads mapped to LMR locus: 12638_plus_ChIP36ntRedMicH_LMRL36hit_OriHist.txt
Reads mapped to the modeled IES: 12638Red_plus_IES_flank_hit_UL.txt


title: RNA_seq_CAF1_day3-rep2

description: CAF-1 knockdown (shRNA pool)


title: RNA_seq_CAF1_day3-rep1

description: CAF-1 knockdown (shRNA pool)


title: RNA_seq_Renilla_day3-rep3

description: CAF-1 knockdown (shRNA pool)


title: RNA_seq_Renilla_day3-rep2

description: CAF-1 knockdown (shRNA pool)


title: Mouse hindlimb muscle-P14 replicate 2

city: Columbus

first: Jinmo

last: Gu

state: OH

address: 460 W 12th Ave

department: CCC

institute: The Ohio State University

data_processing:
Casava 1.2-14 for demultiplexing and basecalling
Data filtering on raw reads: Remove reads with adaptors; Remove reads with unknown bases more than 5%; Remove low quality reads (which are defined as reads having more than 50% bases with quality value ≤ 10).
Quality Check : FastQC (version 0.10.1) tool is used to evaluate the list of paired end raw read files
Mapping: Tophat version 2.0.8 is used to map clean reads to mouse reference genome build GRCm38 with parameters  --library-type fr-firststrand  -p 8 -g 1 .
Quantification: Cufflinks software  version 2.2.1 from the tuxedo suite (http://cufflinks.cbcb.umd.edu/) is utilized to quantify the normalized counts for gene expression . Ensembl is used for gene annotation
Differential gene expression:  Cuffdiff software version 2.2.1 from the tuxedo suite is used to perform differential expression analysis then the log2 fold change values reported are transformed into regular fold change.
Genome_build: GRCm38
Supplementary_files_format_and_content: genes_fpkmonly_for_all_samples.xlsx: abundance measurements for each sample; DifferentialExpression_withingroup.xlsx: differential expression between the biological replicates within each group; DifferentialExpression_groupwise_comparison.xlsx: differential expression analysis between the groups using the two biological replicates within each group:

source_name: Mouse hindlimb muscle-P14

extract_protocol:
RNA were extracted from P2, P7, and P14 mouse hindlimb muscles with Trizol accrording to manufacturere's protocol. TruSeq stranded total RNA sample prep (ribosomal depletion) kit was used with 200ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: mixed

value: wild type

tag: developmental stage

value: postnatal day 14

value: skeletal muscle


title: Mouse hindlimb muscle-P14 replicate 1


title: Cflo.d1.brain.major.b4.mRNA

city: Philadelphia

first: Daniel

middle: Francis

last: Simola

state: PA

address: 1041 BRB II/III

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
DNA fragments sequenced following RNA isolation, polyA+ purification
Cflor.d1.major.minor.brain.rnaseq.normalized.txt

data_processing:
Base calling was performed using Bcl2FastQ 2.0
All sequenced reads were aligned to the custom diploid C. floridanus reference genome; The diploid reference was first split into two pseudo-haplotypes by randomly partitioning the two alleles at each single nucleotide polymorphism into two haploid genome sequences. Mapping was performed against each refernece haplotype using an updated version of Glimmr with calls to Bowtie2 with options (--end-to-end --very-sensitive) and allowing each read to display valid alignment for up to 10 distinct genomic locations (-k 10). Successfully mapped reads were then merged into a single alignment file by retaining the alignments for a given read that contain fewer mismatches to the particular reference haplotype. For RNA-seq data, remaining unmapped reads were also aligned to a reference transcriptome containing full-length transcripts for annotated genes. Remaining unmapped reads were then trimmed in an iterative manner from full-length 75nt reads, to 55nt reads, to 35nt reads, where the 10 outer bases on either end of the read were removed at each step.
RNA-seq: Relative mRNA transcript abundance Yij for gene i in sample j was estimated as fragments per kilobase per million reads (FPKM) using Cufflinks v2.2.1; with the following flags for strand specificity and multi-read correction (--library-type fr-firststand -u). Expression levels were estimated from FPKM data by log transformation as follows: log2(Yij + 1), where the +1 addend provides a variance stabilizing function for weakly expressed transcripts. Expression levels were then normalized in three steps as follows: (1) quantile normalization; (2) scaling by genes with invariant expression across samples; (3) for scout brain samples only, quantile normalized and corrected data were further scaled by the mean expression of ERCC spike-in oligos. Invariant genes in step (2) were identified as those genes that have non-zero expression in all samples and a standard error of expression among samples was in the bottom 25th percentile (SE < 0.388) of all genes in consideration; in this way a total of 1305 invariant genes v were identified. Actin (Cflo_10344) and GAPDH (Cflo_07234) were always included as known reference genes. Corrected quantile normalized expression levels Q*ij in a given sample j were obtained by subtracting the average expression of invariant genes in sample j relative to their global average expression over all samples; Finally, these corrected values were scaled conservatively using the ERCC spike-in controls, where Eij = log2(Zij + 1) was used for ERCC expression Zij for oligo i in sample j, as this transformation yielded the highest average pairwise Pearson correlation between all 21 samples (0.92). Here, a correction factor was estimated as the relative shift in median expression of sample data Q*ij compared to median expression of corresponding ERCC data; RNA-seq data from one day-old minor and major brains was normalized as above, but without ERCC normalization (step 3); that is, final expression estimates were determined by Q*ij.
ChIP-seq: ChIP-seq alignment maps were quantitated using Glimmr; and normalized using custom software. The posterior probability of binding was computed for every nucleotide in the genome for H3K9ac and H3K27ac by normalizing to input samples, setting the prior probability of binding equal to 0.4 for H3K9ac and H3K27ac samples and 0.5 for input samples and default parameters otherwise. Resulting probability scores Pij for locus i in sample j were converted to a Phred-like enrichment score Eij = -10log10(1 – Pij); and then log transformed and normalized to the 75th percentile of per-nucldeotide enrichment scores genome-wide, Pj(75): Zij = log2(Eij / Pj(75)). H. saltator chromatin spike-in data were analyzed in the same manner, except only full-length reads were mapped to the H. saltator reference genome to maximize specificity. These data were used to identify the normalization method that would minimize the per nucleotide standard error among samples. To this end, upper-quartile normalization was chosen (average technical replicate error = 0.11), and empolyed to normalize C. floridanus data as well.
Genome_build: Custom fork of C. floridanus assembly v3.0 (Bonasio et al, Science 329, 2010), yielding a diploid reference genome
Supplementary_files_format_and_content: ChIP-seq data files are provided in wiggle format at 25bp resolution; RNA-seq data files are provided as normalized FPKM matrices.
Genome_build: cflo.v3.3 http://hymenopteragenome.org/drupal/sites/hymenopteragenome.org.camponotus/files/data/Cflo_3.3_scaffolds.fa.gz, http://hymenopteragenome.org/camponotus/?q=genome_consortium_datasets

organism: Camponotus floridanus

source_name: Central brain from one day-old major

growth_protocol: Ant colonies have been maintained in a sealed environmental growth chamber kept at a constant temperature of 25°C with constant humidity of 50% and a 12:12 light:dark cycle. Ants are fed twice a week with an ample supply of water, 20% sugar water (sucrose cane sugar), and Bhatkar–Whitcomb diet

extract_protocol:
RNA extract protocol: A 15µL aliquot representing 15% of cells in a single brain was prepared after light sonication; Total RNA was purified by phenol:chloroform extraction and purification using RNAse-free Agencourt AMPure XP beads (Beckman Coulter, Inc.). 1µL of ERCC RNA Spike-In Mix (Ambion) was added to each 15µL aliquot to total RNA to facilitate transcript-level normalization relative to cell number and to control for technical variation during library preparation. The mRNA fraction of RNA was purified by selection for poly adenylated transcripts using oligo(dT)25 Dynabeads (Invitrogen); cDNA was produced from total RNA using SuperScript III Reverse Transcriptase (Invitrogen), and second strand synthesis was performed using dUTP to preserve strand specificity; Strand-specific RNA-seq libraries were subsequently produced for these dUTP incorporated dsDNA libraries after one round of linear amplification (LinDA)
ChIP extract protocol: Chromatin immunoprecipitation (ChIP) was performed on individual scout brains using 45µL of remaining cell material (60e3–75e3 cells) for a subset of the same brains used for RNA-seq according to Simola and Ye, et al, Genome Res 23, 2013; brain tissue was crosslinked with formaldeyde for 5 min.; After mixing C. floridanus (75µg/IP) and H. saltator (1.88µg/IP) chromatin, IPs were performed using 1µg antibody
NEB Next Ultra, NEB Multiplex Barcode Oligos

treatment_protocol: 15 25–30 day-old minors were isolated from the designated colony, placed into a 195c nest box, and provided with 0.5% DMSO, 50µM TSA or 50µM TSA in combination with 50µM or 100µM C646 dissolved in 0.5% DMSO in 20% sugar water; scouts were frozen on dry ice after 45 days of treatment

tag: colony

tag: dev. stage

value: Adult (post-eclosion)

tag: morphology

value: Major worker

tag: behavioral caste

value: Callow

tag: treatment

tag: treatment duration

tag: foundress origin

value: Florida Keys, FL, USA

tag: modification

value: dUTP-stranded RNA (polyA+)

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: Cflo.d1.brain.major.b3.mRNA

tag: age


title: RNA_seq_Renilla_day3-rep1

description: CAF-1 knockdown (shRNA pool)

tag: strain

tag: tissue

tag: genotype


title: RNA_seq_CAF1_day0-rep3

description: CAF-1 knockdown (shRNA pool)

tag: antibody


title: RNA_seq_CAF1_day0-rep1

description: CAF-1 knockdown (shRNA pool)


title: Mouse hindlimb muscle-P7 replicate 2

source_name: Mouse hindlimb muscle-P7

tag: strain background

tag: genotype/variation

tag: developmental stage

value: postnatal day 7


title: RNA_seq_CAF1_day0-rep2

description: CAF-1 knockdown (shRNA pool)


title: Cflo.d1.brain.major.b2.mRNA

tag: colony

tag: dev. stage

tag: morphology


title: RNA_seq_CAF1_day6-rep1

description: CAF-1 knockdown (shRNA pool)


title: Cflo.d1.brain.major.b1.mRNA

tag: behavioral caste

tag: treatment

tag: treatment duration


title: Mouse hindlimb muscle-P7 replicate 1


title: RNA_seq_Renilla_day0-rep3

description: CAF-1 knockdown (shRNA pool)


title: RNA_seq_Renilla_day0-rep1

description: CAF-1 knockdown (shRNA pool)


title: Cflo.d1.brain.minor.b5.mRNA

source_name: Central brain from one day-old minor

value: Minor worker

tag: foundress origin

tag: modification

tag: antibody vendor


title: Cflo.d1.brain.major.b5.mRNA

tag: age

tag: antibody catalog #

tag: antibody lot #


title: Mouse hindlimb muscle-P2 replicate 1

source_name: Mouse hindlimb muscle-P2

value: postnatal day 2

tag: tissue


title: Sono_seq_Renilla_rep3_day3

description:
Processed data file: coordinate.sonoseq.value.total.mESC.csv
library strategy: Sono-Seq

data_processing:
For ATAC-seq data, The reads were aligned to the mouse genome mm9 using BWA version 0.7.8 with -q 5 -l 32 -k 2 and paired option. Non-primary mapping, failed QC, duplicates and non-paired reads were filtered. Reads from different chromosomes and chrM were also filtered. Only uniquely mapped reads were used for the analysis. The read density profiles were generated using 150 bp window with a 20 bp step and were normalized by the library size.
For Sono-seq and ChIP-seq data, the reads were aligned to mm9 using Bowtie with a unique mapping option. The smoothed tag density profiles were generated using get.smoothed.tag.density function of the SPP R package with a 100-bp window, 50-bp step and library size normalization. The significantly enriched peaks compared to inputs were detected using SPP find.binding.positions function with e-value = 10.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig and tag density profiles; txt and peak calling results; .csv sono-seq results

tag: strain

tag: cell type

value: OKSM reprogramming intermediates from MEFs

tag: time

value: day 3

tag: antibody

tag: protocol

value: Renilla control knockdown


title: RNA_seq_Renilla_day0-rep2

description: CAF-1 knockdown (shRNA pool)

value: Mouse Embryonic Fibroblasts

value: E13.5 embryos

tag: genotype

value: Col1a1::tetOP-OKSM ; R26-M2rtTA


title: Sono_seq_Renilla_rep2_day3

tag: genotype/variation


title: Sono_seq_Renilla_rep1_day3


title: siRbfox1&3_Flag-Rbfox1_N_Rep2

city: LOS ANGELES

first: Chia-ho

last: Lin

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

description:
processed data files:
Expression_Cufflinks_siRbfox1&3+Flag-Rbfox1_N_compared_to_siRbfox1&3+EGFP.txt

data_processing:
illumina Casava software used for basecalling
Gene expression values, FPKM were calculated using a cufflinks program
Exon inclusion ratios were calculated using a splicetrap program
Genome_build: mm9
Supplementary_files_format_and_content: Text files include gene expression values and exon inclusion level values for each sample.
Supplementary_files_format_and_content: Expression_Cufflinks_*: pair comparison of gene expression data; Splicing_SpliceTrap*: pair comparison of splicing data

source_name: Hippocampal culture_Rbfox1 and Rbfox3 siRNAs_Flag_Rbfox1_N

growth_protocol: The mouse neurons were cultured as decribed by Ho et al. (PMID: 24784359).

extract_protocol:
Total RNA was extracted by RNeasy Mini kit (Qiagen) according to manufacturer's instruction.
Ribosomal RNA was removed using Ribo-Zero™ rRNA Removal Kits (Epicentre), and the cDNA libraries were prepared using TruSeq RNA Sample Preparation Kit (Illumina).
RNA-Seq HiSeq2000 (Illumina) paired-end 50 nt, non-strand specific.

treatment_protocol: Cultured hippocampal neurons (9 DIV) were transduced with AAV2/9 vectors at a concentration of 1500 genomic copies/cell for 12 hours and then removed. The neurons (10 DIV) were then incubated with Accell siRNA for 4 days at concentration of 1.2 mM (Dharmacon, Inc.) before RNA purification.

value: hippocampal neurons

value: 14 DIV

tag: sirna

value: Rbfox1 and Rbfox3

tag: treated with

value: AAV2/9-SynI-Flag-Rbfox1_N_siMt and Rbfox1 and Rbfox3 siRNAs


title: Sono_seq_CAF-1_rep3_day3

value: CAF-1 knockdown


title: siRbfox1&3_Flag-Rbfox1_N_Rep1


title: Cflo.d1.brain.minor.b3.mRNA

tag: colony

tag: dev. stage

value: Adult (post-eclosion)

tag: morphology

tag: behavioral caste

value: Callow

tag: treatment

tag: treatment duration


title: Sono_seq_CAF-1_rep2_day3

tag: age


title: Cflo.d1.brain.minor.b2.mRNA

tag: foundress origin

value: Florida Keys, FL, USA

tag: modification

value: dUTP-stranded RNA (polyA+)

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: Sono_seq_CAF-1_rep1_day3

tag: strain

tag: cell type

tag: time

tag: antibody

tag: protocol


title: ChIP_seq_Renilla_Sox2_input_day3

description: Processed data file: WTC.binding.positions.evalue.Day3_Renilla_Sox2.input.Day3_Renilla_WCE.txt

value: none (input)

tag: genotype/variation


title: siRbfox1&3_Flag-Rbfox1_C_Rep2

description:
processed data files:
Expression_Cufflinks_siRbfox1&3+Flag-Rbfox1_C_compared_to_siRbfox1&3+EGFP.txt

source_name: Hippocampal culture_Rbfox1 and Rbfox3 siRNAs_Flag_Rbfox1_C

tag: sirna

tag: treated with

value: AAV2/9-SynI-Flag-Rbfox1_C_siMt and Rbfox1 and Rbfox3 siRNAs


title: ChIP_seq_Renilla_Sox2_IP_day3

source_name: OKSM reprogramming intermediates from Mouse Embryonic Fibroblasts

value: OKSM reprogramming intermediates from MEFs

value: goat polyclonal Anti-Sox2 (R&D, catalog# AF2018, lot# KOY0213101)


title: Cflo.d1.brain.minor.b1.mRNA

tag: colony

tag: dev. stage

tag: morphology

value: Minor worker

tag: behavioral caste


title: ChIP_seq_Chaf1a.166_Sox2_IP_day3

description: Processed data file: WTC.binding.positions.evalue.Day3_Chaf1a.166_Sox2.input.Day3_Chaf1a.166_WCE.txt

tag: age

value: day 3

value: Chaf1a knockdown


title: ChIP_seq_Chaf1a.166_Sox2_input_day3

value: E13.5 embryos

value: Col1a1::tetOP-OKSM ; R26-M2rtTA


title: Cflo.larva.C646.Input

description:
Input DNA for ChIP
none

source_name: Whole larvae, pooled

value: Larva

tag: treatment

tag: treatment duration

value: 72h starve, then treated and frozen after 24h

tag: foundress origin

tag: modification

value: Input


title: siRbfox1&3_EGFP_Rep2

description:
processed data files:
Expression_Cufflinks_siRbfox1&3+EGFP_compared_to_siNT+EGFP.txt,
Expression_Cufflinks_siRbfox1&3+Flag-Rbfox1_C_compared_to_siRbfox1&3+EGFP.txt,
Expression_Cufflinks_siRbfox1&3+Flag-Rbfox1_N_compared_to_siRbfox1&3+EGFP.txt,
Splicing_SpliceTrap_CassetteExon_siRbfox1&3+EGFP_compared_to_siNT+EGFP.txt

source_name: Hippocampal culture_Rbfox1 and Rbfox3 siRNAs_EGFP

value: hippocampal neurons

value: 14 DIV

value: Rbfox1 and Rbfox3

value: AAV2/9-SynI-EGFP and Rbfox1 and Rbfox3 siRNAs


title: ATAC_seq_iPSC

description:
Processed data file: iPSC_MEFs_rep1.uniq.norm.tagdensity.bigwig
library strategy: ATAC-Seq

source_name: iPSCs derived from Mouse Embryonic Fibroblasts

tag: strain

value: induced Pluripotent Cells derived from MEFs

value: wild type uninfected


title: Cflo.larva.C646.H3

description:
DNA fragments sequenced following chromatin immunoprecipitation
D260_larva.C64625_H3.wig.txt

value: Florida Keys, FL, USA

tag: antibody vendor

value: Abcam

tag: antibody catalog #

tag: antibody lot #


title: Mouse hindlimb muscle-P2 replicate 2

tag: strain background

value: mixed

value: wild type

tag: developmental stage

value: postnatal day 2

tag: tissue

value: skeletal muscle


title: siRbfox1&3_EGFP_Rep1

tag: sirna

tag: treated with


title: ATAC_seq_Renilla_rep2_day6

description:
Processed data file: renilla_merged_day6.uniq.norm.tagdensity.bigwig
library strategy: ATAC-Seq

tag: cell type

value: OKSM reprogramming intermediates from MEFs

value: E13.5 embryos

tag: time

value: day 6

tag: antibody

tag: genotype/variation

tag: protocol

value: Renilla control knockdown


title: ATAC_seq_Renilla_rep1_day6

tag: age

value: Col1a1::tetOP-OKSM ; R26-M2rtTA


title: ATAC_seq_Renilla_rep1_day3

description:
Processed data file: renilla_merged_day3.uniq.norm.tagdensity.bigwig
library strategy: ATAC-Seq

value: day 3


title: Cflo.larva.C646.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
D260_larva.C64625_H3K27ac.wig.txt

tag: colony

tag: dev. stage

value: Larva

tag: morphology

tag: behavioral caste

tag: treatment

tag: treatment duration

value: 72h starve, then treated and frozen after 24h

tag: foundress origin


title: Cflo.larva.H2O.Input

description:
Input DNA for ChIP
none

tag: modification

value: Input

tag: antibody vendor

tag: antibody catalog #

tag: antibody lot #


title: ATAC_seq_Chaf1a.166_rep1_day6

description:
Processed data file: Chaf1a.166_merged_day6.uniq.norm.tagdensity.bigwig
library strategy: ATAC-Seq

tag: strain

tag: cell type

value: Chaf1a knockdown


title: siNT_EGFP_Rep1

description:
processed data files:
Expression_Cufflinks_siRbfox1&3+EGFP_compared_to_siNT+EGFP.txt,
Splicing_SpliceTrap_CassetteExon_siRbfox1&3+EGFP_compared_to_siNT+EGFP.txt

source_name: Hippocampal culture_Control siRNAs_EGFP

value: hippocampal neurons

value: 14 DIV

tag: sirna

value: Non-targeting

tag: treated with

value: AAV2/9-SynI-EGFP and Non-targeting siRNAs


title: ATAC_seq_Chaf1a.166_rep2_day6

tag: time

tag: antibody

tag: genotype/variation

tag: protocol


title: Cflo.larva.H2O.H3

description:
DNA fragments sequenced following chromatin immunoprecipitation
D260_larva.H2O_H3.wig.txt

tag: colony

tag: dev. stage

tag: age

tag: morphology

value: Florida Keys, FL, USA

value: Abcam


title: ATAC_seq_Chaf1a.166_rep1_day3

description:
Processed data file: Chaf1a.166_merged_day3.uniq.norm.tagdensity.bigwig
library strategy: ATAC-Seq


title: L8

city: Shanghai

first: Xu

last: Zhang

address: 320 Yue Yang Road

department: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

institute: Institute of neuroscience

data_processing:
Basecalls performed using CASAVA version 1.8.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the mm10 genome assembly using Tophat version 2.0.9 with parameters: -r 100 -I 50000  --max-segment-intron 50000 -a 10 -m 0 -g 2  --read-realign-edit-dist 1
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed using Fisher-test function package in R program version 2.10.0
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: lumbar DRG

growth_protocol: GFP-labled APL cells were expanded in vivo via transplantation into syngeneic mice.

extract_protocol:
Total RNA was extracted with AMBION AM1560 kit.
Following "TruSeq RNA Sample Preparation Guide".

tag: tissue

value: dorsal root ganglion (DRG)


title: siRbfox1&3_Flag-Rbfox1_C_Rep1

value: Rbfox1 and Rbfox3

value: AAV2/9-SynI-Flag-Rbfox1_C_siMt and Rbfox1 and Rbfox3 siRNAs


title: ATAC_seq_Chaf1a.166_rep2_day3

value: OKSM reprogramming intermediates from MEFs

value: E13.5 embryos


title: Flag_cytoplasm_forebrain

description: iCLIP with anti-Flag antibodies on a cytoplasmic fraction purified from cultured mouse forebrain neurons.

data_processing:
library strategy: iCLIP-seq
PCR duplicates were removed by comparing random portions of the sequenced barcodes. Unique reads were mapped to the mouse genome (mm9/NCBI37) using Bowtie, allowing up to two nucleotide mismatches. Mapped reads were further mapped to the Known Gene table .
iClip data analyses were performed following the published paper (Konig J*, Zarnack K*, Curk T, Gregor R, Kayikci M, Zupan,B, Luscombe NM, Ule J (2010))
Genome_build: mm9
Supplementary_files_format_and_content: The significant crosslinksites were selected based on the FDR <=0.01.Sites located within 20nt of one another were then clustered. Clusters with 1nt width were removed from the downstrean analyese,

source_name: Flag,cytoplasm,forebrain

growth_protocol: The mouse neurons were cultured as described by Ho et al. (PMID: 24784359).

extract_protocol:
The crosslinked RNA was extracted by immunoprecipitation with anti-Rbfox1 antibodies or anti-Flag antibodies as control.
The libraries were constructed following the protocols described by König et al. (PMID: 20601959) with few modifications described by Lee et al. (Lee et al., 2015, submitted).

treatment_protocol: Cultured forebrain neurons (14 DIV) were irradiated with UV (254 nm) at 500 mJ/cm2 on ice and then partially lysed in lysis buffer (20 mM HEPES [pH 7.0], 150 mM NaCl, and 0.1% Triton X-100) for 1 minute on ice. The eluate was collected for downstream immunoprecipitation and RNA sequencing.

value: Forebrain culture

tag: fraction

value: anti-Flag antibodies


title: L7


title: Rbfox1_cytoplasm_forebrain

description: iCLIP with anti-Rbfox1 antibodies on a cytoplasmic fraction purified from cultured mouse forebrain neurons.

value: anti-Rbfox1 antibodies


title: 418

source_name: lumbar DRG neuron


title: L4


title: L5


title: L3


title: 416

value: dorsal root ganglion (DRG) neurons


title: DRG Contralateral

city: San Francisco

first: Zhonghui

last: Guan

department: Anesthesia

institute: UCSF

description: DRG Con vs Ips mrna_gene_exp.diff.xls

data_processing:
Fastq sequencing data was aligned to mm9 using Tophat 1.4.0 with default parameters
Differential expression testing was performed using Cuffdiff 1.3.0 using default parameters. Resulting significant (FDR<0.05) gene lists were filtered for genes with an absolute fold change greater than 2
Genome_build: mm9
Supplementary_files_format_and_content: normalized counts

source_name: contrlateral DRG

extract_protocol:
QIAGEN RNeasy Mini Kit
Epicentre ScriptSeq mRNA-Seq Library Preparation Kit

treatment_protocol: Left side sciatic and femoral nerve transection, and RNA samples were purified 7 days later

tag: development

value: young adult

value: L4-6 DRG


title: Dorsal Cord Ipilateral

description: Dorsal Cord Ipsi vs Con mrna_gene_exp.diff.xls

source_name: ipsilateral dorsal cord

value: lumbar dorsal spinal cord


title: DRG Ipsilateral

description: DRG Con vs Ips mrna_gene_exp.diff.xls

source_name: ipsilateral DRG


title: Cflo.d1.brain.minor.b4.mRNA

description:
DNA fragments sequenced following RNA isolation, polyA+ purification
Cflor.d1.major.minor.brain.rnaseq.normalized.txt

value: Adult (post-eclosion)

value: Minor worker

tag: behavioral caste

value: Callow

tag: treatment

tag: treatment duration

tag: foundress origin

tag: modification

value: dUTP-stranded RNA (polyA+)

tag: antibody vendor

tag: antibody catalog #


title: 414

tag: strain


title: ATAC_seq_Renilla_rep2_day3

tag: cell type

tag: time

value: day 3

tag: antibody

tag: genotype/variation

value: Col1a1::tetOP-OKSM ; R26-M2rtTA

value: Renilla control knockdown


title: Dorsal Cord Contralateral

source_name: contralateral dorsal cord


title: siNT_EGFP_Rep2

value: hippocampal neurons

tag: age

value: 14 DIV

tag: sirna

value: Non-targeting

tag: treated with

value: AAV2/9-SynI-EGFP and Non-targeting siRNAs


title: 398

tag: tissue


title: RNA_seq_CAF1_day3-rep3

description: CAF-1 knockdown (shRNA pool)

value: Mouse Embryonic Fibroblasts

value: E13.5 embryos

tag: genotype


title: Small RNAs in WT C. elegans under alg-1 RNAi

city: Baltimore

first: Mallory

middle: Ann

last: Freeberg

state: MD

address: 3400 N Charles St

department: Department of Biology

institute: Johns Hopkins University

description:
small RNA
VK4

data_processing:
Reads were processed to remove low quality reads and trim artificial adapter sequences following BGI protocols. Briefly, reads were marked and removed for low quality if they had [either more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score was lower than 13]. 3’ adapter sequences were then trimmed from the remaining high-quality reads. Finally, reads were removed if they: (1) lacked a 3’ adapter sequence, (2) were 5’-3’ adapter ligation products, (3) were 5’-5’ adapter ligation products, (4) were shorter than 18 nt, or (5) contained only As (homopolymers).
High-quality reads were aligned to the reference C. elegans genome version WS220 using Bowtie2 with the following parameters: -f -N 0 -M 10.
Reads that aligned with zero mismatches to one genomic locus were annotated to mature miRNA coordinates from miRBase v19.
Mature miRNA read counts in each library were normalized to the number of total mapped reads in that library; mature miRNA abundance is reported as reads per million mapped reads (RPM).
Genome_build: WS220 (ce10)
Supplementary_files_format_and_content: Tab-delimited file containing matrix of mature miRNAs and their normalized read counts in each library.

source_name: Whole animal

growth_protocol: Wild-type worms were grown and maintained at 20°C. To synchronize worms, embryos isolated by standard alkaline/hypochlorite treatment were hatched overnight to obtain arrested L1 larvae.

extract_protocol:
Total RNA isolation was carried out using TriReagent (Ambion) following the vendor’s protocol with the following modifications: Samples in TriReagent were subjected to three rounds of freeze-thaw-vortex cycles to improve RNA extraction efficiency. RNAs were precipitated in isopropanol for 1 h at -80°C followed by three washes with 70% ethanol.
Total RNA was submitted to BGI for small RNA-seq library construction and deep sequencing.

treatment_protocol: RNAi was performed at 20°C starting from synchronized L1 larvae according to the standard feeding RNAi protocol. Since some genes are essential for viability, we optimized the duration (1 or 2 generations) and strength (by dilution of the bacterial RNAi clones with bacteria harboring the empty vector L4440) of RNAi to achieve efficient knockdown in viable animals: kin-3 RNAi (1 generation; undiluted), kin-10 RNAi (2 generations; 1/2 strength by diluting with vector culture).

tag: Stage

tag: RNAi treatment


title: Cflo.larva.H2O.H3K27ac

description:
DNA fragments sequenced following chromatin immunoprecipitation
D260_larva.H2O_H3K27ac.wig.txt

tag: colony

tag: dev. stage

value: Larva

tag: morphology

tag: behavioral caste

tag: treatment

tag: treatment duration

value: 72h starve, then treated and frozen after 24h

value: Florida Keys, FL, USA

value: Abcam

tag: antibody lot #


title: 396

tag: strain

value: dorsal root ganglion (DRG) neurons


title: Small RNAs in WT C. elegans under kin-10 RNAi

description:
small RNA
VK3


title: Small RNAs in WT C. elegans under kin-3 RNAi

description:
small RNA
VK2


title: 394


title: 393


title: 392


title: 395


title: 389


title: 387


title: 383


title: 388


title: 415


title: 386


title: 382


title: 381


title: 380


title: 379


title: 376


title: 375


title: 378


title: 369


title: 367


title: 410


title: 366


title: 365


title: 364


title: Small RNAs in WT C. elegans under L4440 RNAi

description:
small RNA
VK1

value: L4440 (vector)


title: 397


title: 363


title: 361


title: 356


title: 359


title: 352


title: 391


title: 351


title: 354


title: 350


title: 346


title: 344


title: 349


title: 342


title: 343


title: 357


title: 335


title: 333


title: 334


title: 332


title: 338


title: 340


title: 330


title: 341


title: 326


title: 327


title: 325


title: 323


title: 362


title: 322


title: 331


title: 321


title: 319


title: 318


title: 316


title: 317


title: 315


title: 345


title: 314