title: Dme_wts_cic_wingdisc_ChIP-nexus 2

description:
Sheared genomic DNA
Custom-made polyclonal rabbit anti-Cic (described in associated paper) and anti-Sd (described in Ikmi et al., 2014, Mol.Biol.Evol.) antibodies were generated and affinity purified by GenScript.

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

extract_protocol:
Third instar larvae were dissected in cold PBS and imaginal disc complexes (anterior one third of the larvae after removing the fat body and salivary glands) were fixed in 1 ml fixation buffer (50 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid [HEPES], pH 7.5; 1 mM ethylenediaminetetraacetic acid [EDTA]; 0.5 mM ethylene glycol tetraacetic acid [EGTA]; 100 mM NaCl; 2% formaldehyde) for 30 min at room temperature. Fixed disc complexes were washed 3x fast and 2x 20 minutes with PBST (PBS, pH 7.4; 0.1% Triton X-100; 0.1% Tween-20), and were stored at 4 C until enough discs were obtained. 100-500 wing discs were dissected away from the cuticle and resuspended in buffer A2 (15 mM HEPES, pH 7.5; 140 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 1% Triton X-100; 0.1% sodium deoxycholate; 0.1 % sodium dodecyl sulfate [SDS]; 0.5 % N-lauroylsarcosine; 1 Roche complete protease inhibitor cocktail, cat. no. 5056489001). Tubes were flash frozen in liquid nitrogen and stored at -80 C. Imaginal discs were pooled to reach 500 wt discs (or 100 mutant), and sonication was performed in a Bioruptor sonicator for 5 min (30 s on/off cycle at the high setting) in buffer A2. Following centrifugation (16,000 g; 10 min at 4 C), the supernatant containing soluble chromatin was transferred to fresh tubes, and used for ChIP-nexus.
Library preparation was done as described in He, Johnston and Zeitlinger, 2015 Nature Biotechnology.

value: hand dissections

value: wing discs

tag: genotype/variation

value: y w ubxflp/ y w; FRT82B M(3) ubiGFP/ FRT82B wts149

value: 3rd instar-day9

value: anti-Cic


title: C3CBFACXX.2.48hr_05_Left_K27ac

status: Public on Sep 26 2017

type: SRA

city: Lexington

first: Darrell

middle: Orlyn

last: Ricke

state: MA

address: 244 Wood Street

department: Group 48 Bioengineering Systems & Technology

country: USA

institute: MIT Lincoln Laboratory

description: 48 hours injured

library_source: genomic

data_processing:
Filter low read samples with custom getReadCounts.sh script
Call peaks with MACS2
Genome_build: mouse mm9
Supplementary_files_format_and_content: bed & gappedPeak

molecule: genomic DNA

organism: Mus musculus

source_name: tibialis anterior muscle

extract_protocol:
Frozen tissue thawed, homogenized, cells lysed
Chromatin sheared and incubated overnight at 4C with antibodies using constant agitation; co-immunoprecipitated

treatment_protocol: Freeze injury was induced by applying a 6 mm diameter steel probe (cooled to the temperature of dry ice, −70C) to the belly of the TA muscle (directly below incision site) for 10 seconds

tag: tissue

value: tibialis anterior muscle

tag: timepoint

value: 48 hours

tag: chip antibody

value: H3 K27ac (Active Motif 39133)

tag: treatment

value: freeze injury


title: Dme_wts_cic_wingdisc_ChIP-nexus 1

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

organism: Drosophila melanogaster

source_name: wing discs

growth_protocol: Normal fly food, 25 degrees.

tag: age


title: C36UVACXX.8.48hr_04_Right_K4me3

description: 48 hours control

value: control


title: Dme_wts_SD_wingdisc_ChIP-nexus 1

value: anti-Sd


title: Dme_wts_SD_wingdisc_ChIP-nexus 2


title: C3CBFACXX.2.48hr_05_Left_K4me1

description: 48 hours injured


title: C36UVACXX.8.48hr_04_Right_WCE

description: 48 hours control

value: WCE - whole cell extract


title: Dme_wtscic_SD_wingdisc_ChIP-nexus 3

value: y w ubxflp/ y w; FRT82B M(3) ubiGFP/ FRT82B cicQ474X wts149


title: C36UVACXX.8.48hr_04_Right_K4me1

description: 48 hours control


title: Dme_wtscic_cic_wingdisc_ChIP-nexus 2

description:
Sheared genomic DNA
ChIP against Cic in Cic mutant (input).
Custom-made polyclonal rabbit anti-Cic (described in associated paper) and anti-Sd (described in Ikmi et al., 2014, Mol.Biol.Evol.) antibodies were generated and affinity purified by GenScript.


title: Dme_wtscic_SD_wingdisc_ChIP-nexus 2


title: C3CBFACXX.1.48hr_04_Right_WCE

description: 48 hours control


title: C3CBFACXX.1.48hr_04_Right_K4me3

description: 48 hours control


title: C3CBFACXX.3.48hr_05_Left_K27ac

description: 48 hours injured


title: C36UVACXX.8.48hr_04_Right_K27ac

description: 48 hours control


title: C3CBFACXX.1.48hr_04_Right_K4me1

description: 48 hours control


title: Dme_wtscic_cic_wingdisc_ChIP-nexus 1


title: C3CBFACXX.1.48hr_04_Right_K27ac

description: 48 hours control


title: C3CBFACXX.2.48hr_05_Left_WCE

description: 48 hours injured


title: Dme_FRT82B_SD_wingdisc_ChIP-nexus 2

value: y w ubxflp/ y w; FRT82B M(3) ubiGFP/ FRT82B

value: 3rd instar-day5


title: C36UVACXX.8.48hr_02_Left_WCE

description: 48 hours injured


title: Dme_FRT82B_cic_wingdisc_ChIP-nexus 2


title: C36UVACXX.8.48hr_02_Left_K4me1

description: 48 hours injured


title: Dme_FRT82B_SD_wingdisc_ChIP-nexus 1


title: C3CBFACXX.2.48hr_05_Left_K4me3

description: 48 hours injured


title: C36UVACXX.8.48hr_02_Left_K27ac

description: 48 hours injured


title: C3CBFACXX.1.48hr_02_Left_WCE

description: 48 hours injured


title: Dme_wtscic_SD_wingdisc_ChIP-nexus 1


title: S. carpocapsae L1 rep 2

city: Minneapolis

first: Marissa

last: Macchietto

address: 117 Pleasant Street SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota, Minneapolis

description:
unstranded, paired-end, read_length= 43 bp
C322_L12

library_source: transcriptomic

data_processing:
Gene expression analyses. Unstranded, paired-end RNA-seq reads for all species were trimmed to 40 bp from their 3’ ends to remove low quality nucleotide sequences. Transcriptome indexes were prepared for S. carpocapsae (PRJNA202318 downloaded from WormBase ParaSite version WS254), S. feltiae (PRJNA204661 downloaded from WormBase ParaSite version WS254), C. elegans (WS220), and C. angaria (PRJNA51225 downloaded from Wormbase Parasite W254) using the RSEM command (version 1.2.12) rsem-prepare-reference (Li et al. 2011). Reads were mapped to each respective species’ annotations using bowtie 0.12.8 with the following options: -S, --offrate 1, -v 1, -k 10, --best, --strata, -m 10 (Langmead et al. 2009). Gene expression was quantified using the RSEM command, rsem-calculate-expression, with the following options: --bam, --fragment-length-mean (Li et al. 2011). For all analyses, gene expression was reported in Transcripts Per Million (TPM).
Genome_build: S. carpocapsae (PRJNA202318 downloaded from WormBase ParaSite version WS254), S. feltiae (PRJNA204661 downloaded from WormBase ParaSite version WS254), C. elegans (WS220), and C. angaria (PRJNA51225 downloaded from Wormbase Parasite W254)
Supplementary_files_format_and_content: [.results] report gene-level and isoform-level TPMs and FPKMs

molecule: polyA RNA

organism: Steinernema carpocapsae

source_name: S. carpocapsae L1

extract_protocol:
Pellets of embryos were resuspended in 2 mL of Ringer’s solution (made with DEPC water) + 0.01% tween 20. DEPC was used in the Ringer’s solution to limit RNase contamination, and tween 20 was used to prevent embryos from sticking to any surfaces. Resuspended embryos were passed through at 40 μm mesh filter into a 60mm x 15mm petri dish to remove debris. Enough Ringer’s solution + 0.01% tween 20 was added to coat the bottom of the petri dish and reduce the density of the embryos so that they could easily be collected. Embryos were visualized in the dish using an EVOS inverted microscope, and single embryos were imaged and collected in 1.5 μL using a micropipette. If more than one embryo was collected, embryos were diluted further by pipetting them into 20 μL Ringer’s solution + 0.01% tween 20 on a clean slide that was pretreated with RNase ZAP or 70% ethanol. Single embryos were collected in 1.5 μL into PCR tube strip, and 2 μL of lysis buffer (18 μL 0.3% Triton-X 100 + 2 μL RNase inhibitor SIGMA), 1 μL of oligo-dT primer, and 1 μL of dNTP mix were added to each embryo. Embryos were heated to reverse secondary structure of RNA, reverse transcribed and PCR amplified according to the Smart-seq2 protocol by Picelli (Picelli et al. 2014) (Supp. Figure 1). All embryos, regardless of embryonic stage, were amplified for 18 cycles through PCR. PCR primers were cleaned up from the embryo samples by adding a 1:1 ratio of Ampure XP beads to sample, which were both equilibrated to room temperature, incubated for 8 min, placed on a magnet, and washed with 200 μL of 80% ethanol 3 times. Beads were dried at room temperature for approximately 5 min (until the beads cracked), after which, 17.5 μL of EB was added and incubated off the magnet for 3 min. Samples were placed back on the magnet, and 15 μL of cDNA was collected for each sample. Sample cDNA concentration was quantified using the Qubit fluorometer and bioanalyzed using the Agilent 2100 Bioanalyzer to check the cDNA quality.
For library preparation, 20 ng of cDNA from each sample was prepared using the regular Nextera tagmentation protocol (Gertz et al. 2012). The protocol reagents were scaled down, so that 2 μL of transposase, 10 μL of buffer, and 8 μL of cDNA (20 ng total) were used yielding a total volume of 20 μL. Transposase was cleaned up from the tagmented DNA using the QIAGEN columns as follows. Three volumes of buffer PM was added to each sample, placed into a QIAGEN spin column and spun at 13,000 RPM for 1 min. Flow-through was removed, 750 μL of buffer PE (prepared with ethanol) was added, and samples were spun at 13,000 RPM for 1 min. Flow-through was removed, and samples were spun again at the previous settings to dry the columns. Columns were placed into new clean collection tubes, and 30 μL of EB prewarmed to 55oC was added to the center of each column and incubated for 1 min before spinning down at the same settings.
In a PCR tube, 30 μL of sample, 35 μL of Phusion high fidelity master mix, 2.5 μL 25 μM Nextera adapter ID, and 2.5 μL 25 μM Nextera adapter Ad_noMX were combined and mixed well with a pipette. Samples were spun down quickly, and amplified for 6 cycles using the PCR program with the following settings: 72 °C for 5 min, 98 °C for 30 s, [98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min] for 6 cycles, 72 °C for 5 min, and hold at 4 °C.
PCR amplified libraries were cleaned up using a 1:1 ratio of Ampure XP beads to sample, and prepared in the same way as the bead cleanup above, except that 30 μL of EB was added to the beads to resuspend the library sample, which was then collected in 27.5 μL after 2 min.
Sample library fragments were between 200-600 bps with an average size of 360 bps after the Nextera tagmentation protocol. Samples were sequenced as paired-end 43 bp on the Illumina NextSeq 500 to an average depth of ~10 million reads.

tag: strain

value: ALL

tag: developmental stage

value: whole organism


title: C36UVACXX.8.48hr_02_Left_K4me3

description: 48 hours injured


title: S. carpocapsae L1 rep 4

description:
unstranded, paired-end, read_length= 43 bp
C482_L15


title: S. carpocapsae L1 rep 1

description:
unstranded, paired-end, read_length= 43 bp
C320_L11


title: C. elegans L1 rep 4

description:
unstranded, paired-end, read_length= 43 bp
E618_EL12

organism: Caenorhabditis elegans

source_name: C. elegans L1


title: C. elegans moving rep 4

description:
unstranded, paired-end, read_length= 43 bp
E301_EMOV5

source_name: C. elegans moving

value: moving


title: C. elegans L1 rep 3

description:
unstranded, paired-end, read_length= 43 bp
E685_EL13


title: C. elegans L1 rep 1

description:
unstranded, paired-end, read_length= 43 bp
E702_EL15


title: C3CBFACXX.1.48hr_02_Left_K4me3

description: 48 hours injured


title: C. elegans L1 rep 2

description:
unstranded, paired-end, read_length= 43 bp
E700_EL14


title: C3CBFACXX.1.48hr_02_Left_K4me1

description: 48 hours injured


title: C4KDJACXX.8.48h_02_Left_K4me1

description: 48 hours injured


title: C. elegans moving rep 3

description:
unstranded, paired-end, read_length= 43 bp
E299_EMOV3


title: G418_10 3 Run 3

city: Saint Louis

first: Ezekiel

last: Maier

state: MO

address: 4515 McKinley Ave

department: Computer Science

institute: Washington University in Saint Louis

description: Grown in 37Â°C + 5% CO2 + high glucose DMEM for 90 min

data_processing:
Sequenced reads were aligned to the C. neoformans H99 reference sequence (v3) using TopHat version 2.0.14 and Bowtie version 0.12.9
Reads that aligned uniquely to the reference sequence were considered for gene expression quantification with HTSeq version 0.6.1. Gene boundaries were defined using the current C. neoformans genome annotation provided by the Broad institute.
Differential expression analysis comparing matched mutant and wild type expression profile replicate sets was performed with DESeq version 1.24.0 built under R 3.3.0 using an adjusted p-value threshold of 0.01. Expression was normalized using the DESeq standard estimateSizeFactors procedure.
Genome_build: C. neoformans H99 reference sequence 3.0 (Cryptococcus neoformans var. grubii H99 Sequencing Project)
Supplementary_files_format_and_content: Gene expression was quantified processing Tophat produced bam alignments with HTSeq 0.6.1 with the current H99 annotation (v3) provided by the Broad institute's Fungal Genome initiative. Expression was normalized with DESeq version 1.24.0 built under R 3.3.0 using the estimateSizeFactors procedure.

organism: Cryptococcus neoformans

source_name: cultured cells

growth_protocol: All strains were constructed in the C. neoformans KN99Î± background. Cells were cultured overnight in YPD to a density of 1-2 OD600.

extract_protocol:
RNA is isolated from liquid culture following the protocol for TRIzol RNA Isolation Reagent (Life Technologies 15596026). Poly-A RNA is separated using an mRNA Catcher Plus Plate (Invitrogen  K1570-02).  Once the library is made it is sequenced on a HiSeq 2500 by Illumina.
The libraries are made by chemically shattering the RNA in TURBO DNase I (Invitrogen NC9075048) buffer at 75 degrees for 10 min. To make first-strand cDNA, shattered genomic DNA is incubating with Random Primers (Invitrogen 48190-011) and dNTP mix (NEB N0447S) at 65 degrees for 5 min. The first strand is then synthesized by using SSIII kit (Invitrogen 18080-44) 5X First Strand Buffer, DTT, and SSIII enzyme; and adding RNase OUT (Invitrogen 10777-019). It is incubated as follows: 25 degrees for 5 min, 50 degrees for 50 min, 70 degrees for 15 min, and holding at 4 degrees.The second strand is made by adding 5X SS buffer (Invitrogen 10812-014), dNTP mix (NEB N0447S), E. coli DNA ligase (NEB M02056), DNA Polymerase I (Invitrogen 18010-025), RNase H (Invitrogen 18021-014) and incubating at 16 degrees for 2 hours. Then end repair is carried out using the NEB Quick Blunting Kit (E1201S), adding an A base using Klenow Fragment (3â€™ to 5â€™ exo, NEB M0212S) and 1mM dATP (Invitrogen 18252-015), and finally adding the Illumina adapters and indices.

treatment_protocol: Cells were transfered to grow for 90 minutes in either capsule-inducing (DMEM, 37 Â°C, 5% CO2) conditions prior to isolation of polyA RNA.

tag: genotype

value: insertion of kanMX at chr11:287563

tag: condition description

value: Capsule-inducing

tag: condition

tag: replicate

tag: induction date

tag: library date

tag: sample id


title: S. carpocapsae moving rep 3

description:
unstranded, paired-end, read_length= 43 bp
C387_MOV4

source_name: S. carpocapsae moving


title: C3CBFACXX.1.48hr_02_Left_K27ac

description: 48 hours injured


title: G418_10 2 Run 3


title: S. carpocapsae moving rep 2

description:
unstranded, paired-end, read_length= 43 bp
C354_MOV3


title: C36UVACXX.1.48hr_01_Left_K4me3

description: 48 hours injured


title: G418_10 1 Run 3


title: S. carpocapsae moving rep 1

description:
unstranded, paired-end, read_length= 43 bp
C150_MOV1


title: Dme_FRT82B_cic_wingdisc_ChIP-nexus 1

value: hand dissections

value: wing discs


title: C. elegans 2-fold rep 4

description:
unstranded, paired-end, read_length= 43 bp
E297_E2X4

source_name: C. elegans 2-fold


title: C. elegans moving rep 1

description:
unstranded, paired-end, read_length= 43 bp
E242_EMOV1


title: G418_7 3 Run 3


title: S. carpocapsae L1 rep 3

description:
unstranded, paired-end, read_length= 43 bp
C388_L14


title: S. carpocapsae moving rep 4

description:
unstranded, paired-end, read_length= 43 bp
C391_MOV5


title: S. carpocapsae 2-fold rep 4

description:
unstranded, paired-end, read_length= 43 bp
C179_2X8

source_name: S. carpocapsae 2-fold


title: C4KDJACXX.8.48h_01_Left_K4me1

description: 48 hours injured

value: tibialis anterior muscle


title: C. elegans 2-fold rep 3

description:
unstranded, paired-end, read_length= 43 bp
E293_E2X3


title: C36UVACXX.1.48hr_01_Left_K4me1

description: 48 hours injured

value: 48 hours


title: S. carpocapsae 2-fold rep 3

description:
unstranded, paired-end, read_length= 43 bp
C178_2X7


title: C. elegans moving rep 2

description:
unstranded, paired-end, read_length= 43 bp
E298_EMOV2


title: C4KDJACXX.8.48h_01_Left_K27ac

description: 48 hours injured

value: H3 K27ac (Active Motif 39133)


title: C. elegans 2-fold rep 1

description:
unstranded, paired-end, read_length= 43 bp
E247_E2X1


title: G418_7 1 Run 3


title: G418_6 3 Run 3


title: S. carpocapsae 2-fold rep 2

description:
unstranded, paired-end, read_length= 43 bp
C35_2X6


title: C. elegans 2-fold rep 2

description:
unstranded, paired-end, read_length= 43 bp
E284_E2X2


title: C. elegans 1.5-fold rep 3

description:
unstranded, paired-end, read_length= 43 bp
E312_E1.5X5

source_name: C. elegans 1.5-fold


title: S. carpocapsae 2-fold rep 1

description:
unstranded, paired-end, read_length= 43 bp
C165_2X1


title: C. elegans 1.5-fold rep 4

description:
unstranded, paired-end, read_length= 43 bp
E318_E1.5X6


title: G418_6 2 Run 3

description: Grown in 37Â°C + 5% CO2 + high glucose DMEM for 90 min


title: C36UVACXX.1.48hr_01_Right_WCE

description: 48 hours control


title: S. carpocapsae 1.5-fold rep 4

description:
unstranded, paired-end, read_length= 43 bp
C181_1.5X3

source_name: S. carpocapsae 1.5-fold


title: C36UVACXX.1.48hr_01_Right_K4me3

description: 48 hours control


title: S. carpocapsae 1.5-fold rep 3

description:
unstranded, paired-end, read_length= 43 bp
C161_1.5X4


title: C. elegans 1.5-fold rep 2

description:
unstranded, paired-end, read_length= 43 bp
E294_E1.5X3


title: C36UVACXX.1.48hr_01_Right_K4me1

description: 48 hours control


title: WT3 Run 3

value: wildtype


title: S. carpocapsae 1.5-fold rep 2

description:
unstranded, paired-end, read_length= 43 bp
C180_1.5X2


title: WT2 Run 3


title: G418_7 2 Run 3


title: C. elegans 1.5-fold rep 1

description:
unstranded, paired-end, read_length= 43 bp
E309_E1.5X4


title: C36UVACXX.1.48hr_01_Right_K27ac

description: 48 hours control

value: control


title: C. elegans comma rep 4

description:
unstranded, paired-end, read_length= 43 bp
E279_ECOM3

source_name: C. elegans comma

value: comma


title: S. carpocapsae 1.5-fold rep 1

description:
unstranded, paired-end, read_length= 43 bp
C253_1.5X1


title: WT1 Run 3


title: C36UVACXX.7.24hr_05_Left_K4me3

description: 24 hours injured

value: 24 hours

value: freeze injury


title: G418_6 1 Run 3


title: S. carpocapsae comma rep 4

description:
unstranded, paired-end, read_length= 43 bp
C169_COM5

source_name: S. carpocapsae comma


title: S. carpocapsae comma rep 3

description:
unstranded, paired-end, read_length= 43 bp
C171_COM8


title: C36UVACXX.7.24hr_05_Left_K27ac

description: 24 hours injured


title: C. elegans comma rep 2

description:
unstranded, paired-end, read_length= 43 bp
E280_ECOM4


title: C. elegans comma rep 3

description:
unstranded, paired-end, read_length= 43 bp
E600_ECOM5


title: G418_6 2 Run 2


title: G418_6 3 Run 2


title: C36UVACXX.7.24hr_05_Left_K4me1

description: 24 hours injured


title: G418_6 1 Run 2


title: C36UVACXX.6.24hr_05_Left_K4me3

description: 24 hours injured


title: C36UVACXX.6.24hr_05_Left_K27ac

description: 24 hours injured


title: C. elegans 64-78-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
E572_E64C4

source_name: C. elegans 64-78-cell


title: S. carpocapsae 64-78-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
C455_64C4

source_name: S. carpocapsae 64-78-cell


title: C36UVACXX.1.48hr_01_Left_K27ac_1

description: 48 hours injured


title: S. carpocapsae comma rep 1

description:
unstranded, paired-end, read_length= 43 bp
C159_COM3


title: WT1 Run 2


title: C36UVACXX.6.24hr_05_Left_K4me1

description: 24 hours injured


title: WT2 Run 2


title: C. elegans comma rep 1

description:
unstranded, paired-end, read_length= 43 bp
E276_ECOM2


title: C. elegans 64-78-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
E581_E64C8


title: WT3 Run 2

description: Grown in 37Â°C + 5% CO2 + high glucose DMEM for 90 min


title: S. carpocapsae comma rep 2

description:
unstranded, paired-end, read_length= 43 bp
C155_COM2


title: S. carpocapsae 64-78-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
C453_64C2


title: C36UVACXX.5.24hr_04_Left_WCE

description: 24 hours injured

value: WCE - whole cell extract


title: C. elegans 64-78-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
E576_E64C6


title: C. elegans 24-44-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
E558_E32C3

source_name: C. elegans 24-44-cell


title: G418_10 2 Run 1


title: C36UVACXX.5.24hr_04_Left_K4me1

description: 24 hours injured


title: C. elegans 64-78-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
E340_E64C1


title: C36UVACXX.5.24hr_04_Left_K4me3

description: 24 hours injured


title: S. carpocapsae 24-44-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
C382_32C3

source_name: S. carpocapsae 24-44-cell


title: G418_10 1 Run 1


title: C36UVACXX.5.24hr_04_Left_K27ac

description: 24 hours injured

source_name: tibialis anterior muscle


title: S. carpocapsae 64-78-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
C438_64C5


title: G418_10 3 Run 1


title: C. elegans 24-44-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
E570_E32C4


title: G418_7 3 Run 1


title: S. carpocapsae 24-44-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
C379_32C5


title: C. elegans 24-44-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
E332_E32C1


title: C36UVACXX.4.24hr_04_Left_WCE

description: 24 hours injured


title: S. carpocapsae 24-44-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
C383_32C4


title: C. elegans 24-44-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
E334_E32C2


title: C36UVACXX.4.24hr_04_Left_K4me3

description: 24 hours injured


title: S. carpocapsae 64-78-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
C454_64C3


title: C. elegans 8-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
E604_E8C4

source_name: C. elegans 8-cell


title: G418_7 1 Run 1


title: G418_7 2 Run 1


title: G418_6 3 Run 1


title: S. carpocapsae 24-44-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
C380_32C2


title: C. elegans 8-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
E603_E8C3


title: C36UVACXX.4.24hr_04_Left_K4me1

description: 24 hours injured


title: C36UVACXX.4.24hr_04_Left_K27ac

description: 24 hours injured


title: S. carpocapsae 8-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
C30_8C7

source_name: S. carpocapsae 8-cell


title: S. carpocapsae 8-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
C121_8C1


title: G418_6 2 Run 1

description: Grown in 37Â°C + 5% CO2 + high glucose DMEM for 90 min


title: C. elegans 8-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
E546_E8C1


title: C36UVACXX.2.24hr_04_Right_WCE

description: 24 hours control


title: S. carpocapsae 8-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
C137_8C3


title: NAT_7 3 Run 1

value: insertion of natMX6 at chr11:287563A


title: G418_6 1 Run 1


title: S. carpocapsae 8-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
C366_8C9

value: ALL


title: NAT_7 2 Run 1


title: C. elegans 8-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
E556_E8C2

value: whole organism


title: C. elegans 4-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
E539_E4C2

source_name: C. elegans 4-cell


title: C36UVACXX.2.24hr_04_Right_K4me1

description: 24 hours control


title: S. carpocapsae 4-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
C136_4C6

source_name: S. carpocapsae 4-cell


title: C. elegans 4-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
E557_E4C5


title: C36UVACXX.2.24hr_04_Right_K27ac

description: 24 hours control


title: S. carpocapsae 4-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
C128_4C4


title: C36UVACXX.5.24hr_03_Left_WCE

description: 24 hours injured


title: C. elegans 4-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
E554_E4C4


title: NAT_7 1 Run 1

source_name: cultured cells


title: S. carpocapsae 4-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
C134_4C5


title: NAT_6 3 Run 1


title: C. elegans 4-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
E542_E4C3


title: C. elegans 2-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
E571_E2C5

source_name: C. elegans 2-cell


title: S. carpocapsae 4-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
C122_4C3


title: NAT_6 2 Run 1


title: NAT_6 1 Run 1


title: C36UVACXX.5.24hr_03_Left_K4me3

description: 24 hours injured


title: C36UVACXX.5.24hr_03_Left_K27ac

description: 24 hours injured


title: C36UVACXX.5.24hr_03_Left_K4me1

description: 24 hours injured


title: C. elegans 2-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
E569_E2C4


title: C36UVACXX.2.24hr_04_Right_K4me3

description: 24 hours control


title: NAT_1 3 Run 1


title: C36UVACXX.4.24hr_03_Left_K4me3

description: 24 hours injured


title: NAT_1 2 Run 1


title: C36UVACXX.4.24hr_03_Left_WCE

description: 24 hours injured


title: S. carpocapsae 2-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
C25_2C7

source_name: S. carpocapsae 2-cell


title: NAT_1 1 Run 1


title: C. elegans 2-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
E541_E2C1


title: C. elegans zygote rep 4

description:
unstranded, paired-end, read_length= 43 bp
E749_EZY4

source_name: C. elegans zygote

value: zygote


title: C36UVACXX.4.24hr_03_Left_K4me1

description: 24 hours injured


title: WT3 Run 1

description: Grown in 37Â°C + 5% CO2 + high glucose DMEM for 90 min


title: S. carpocapsae 2-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
C139_2C3


title: S. carpocapsae zygote rep 4

description:
unstranded, paired-end, read_length= 43 bp
C362_ZY5

source_name: S. carpocapsae zygote


title: C. elegans zygote rep 3

description:
unstranded, paired-end, read_length= 43 bp
E748_EZY3


title: WT2 Run 1


title: C36UVACXX.4.24hr_03_Left_K27ac

description: 24 hours injured


title: C. elegans zygote rep 2

description:
unstranded, paired-end, read_length= 43 bp
E747_EZY2


title: S. carpocapsae 2-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
C151_2C5


title: C36UVACXX.2.24hr_03_Right_WCE

description: 24 hours control


title: S. carpocapsae zygote rep 2

description:
unstranded, paired-end, read_length= 43 bp
C363_ZY6


title: WT1 Run 1


title: C. elegans zygote rep 1

description:
unstranded, paired-end, read_length= 43 bp
E586_EZY1


title: C36UVACXX.2.24hr_03_Right_K4me3

description: 24 hours control


title: S. carpocapsae zygote rep 1

description:
unstranded, paired-end, read_length= 43 bp
C350_ZY2


title: S. carpocapsae 2-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
C24_2C6


title: C36UVACXX.2.24hr_03_Right_K4me1

description: 24 hours control


title: Long-read sequencing for plasmid library

city: Cambridge

first: Xinchen

last: Wang

address: 32 Vassar St, D514

institute: MIT

description:
1_*.1.[1/2].fastq.gz files have 250nt reads with sequence. Barcode files have information on random 4nt barcode (ATNNNNAT) corresponding to each fragment.
processed data file:
MiSeq_Counts_per_SNP_group_by_90percent_overlap.txt
MiSeq_Fragment_to_SNP_group_by_90percent_overlap.txt

data_processing:
Reads were split by sample barcode and aligned to hg19 using bowtie2 (v2.2.9) with flags -p 6, -q and --phred33.
Alignments were filtered using grep to remove unaligned fragments, and remove mitochondrial reads
We filtered reads mapping to multiple genomic locations in samtools v1.3.1 (-q 30 flag) and removed reads mapping to ENCODE blacklist regions (bedtools v2.26.0)
Finally, only fragments with size between 100-600nt were kept for further analysis
illumina MiSeq reads were first processed with cutadapt as read length was longer than minimum fragment size
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files for signal tracks were generated using genomeCoverageBed (bedtools), unionBedGraphs (bedtools), and bedGraphToBigWig (UCSC utilities). Matrix of count information for all samples and text file listing assignment of fragments to SNPs for illumina MiSeq_Fragment_to_SNP_group_by_90percent_overlap was generated using custom shell and perl scripts. Please see first lines of text files for more detailed description of processed files.

organism: Homo sapiens

source_name: GM12878_plasmid library

growth_protocol: Cells were grown in suspension in RPMI 1640 Medium with GlutaMAX Supplement with 15% fetal bovine serum and 1% pen/strep added in. Cells were split every 2-3 days to maintain a density between 2x10^5 and 1x10^6 cells/mL.

extract_protocol:
Plasmid DNA was extracted from MegaX DH10B electrocompetent bacteria transformed with cloned library using Qiagen's Plasmid Plus MegaPrep Kit following manufacturer's instructions
We used a custom library construction protocol, see Methods section in paper for detailed protocol. Briefly, for RNA, following PolyA+ selection we performed reverse transcription using a sgGFP reporter gene-specific primer and performed PCR to add barcoded Illumina sequencing adapters. For plasmid reporter library, we directly performed PCR to add sequencing adapters off of the plasmid.

tag: cell line

tag: cell type

value: lymphoblastoid cell line

tag: molecule subtype

value: Plasmid Reporter Library


title: S. feltiae L1 rep 4

description:
unstranded, paired-end, read_length= 43 bp
F436_FL14

organism: Steinernema feltiae

source_name: S. feltiae L1

value: SN

tag: tissue


title: h2az_ctlsh_2 [JLSL051]

city: Davis

first: Simon

middle: Jesse

last: Lopez

state: CA

address: One Shields Ave

department: MMI

institute: UC Davis

description:
control knockdown sample2
JLSL051
processed data file:
CTLSH_H2AZ_peaks.bed
chr15M_H2AZ_diff_peaks.bed
chr15M-minus_H2AZ_diff_peaks.bed
KDSH_H2AZ_diff_peaks.bed

data_processing:
WGBS: BS-Seeker2, DSS, bsseq, DMRfinder
RNA-seq: TopHat2, edgeR
ChIP-seq: bowtie2, MACS2
Genome_build: hg38
Supplementary_files_format_and_content: DMR_chr15M_hg19.bed: list of DMRs between samples JLSL012A-C vs JLSL050A-C
Supplementary_files_format_and_content: DMR_chr15M-minus_hg19.bed: list of DMRs between samples JLSL011A-C vs JLSL050A-C
Supplementary_files_format_and_content: DMR_KDSH_hg19.bed: list of DMRs between samples JLKD109-110B vs JLSL050A-C
Supplementary_files_format_and_content: DMR_KD15M_hg19.bed: list of DMRs between samples JLSL011A-C vs JLSL012A-C
Supplementary_files_format_and_content: *counts.txt: transcript counts for all genes
Supplementary_files_format_and_content: CTL15M_K4me3_peaks.bed: list of ChIP peaks for samples JLSL027 and JLSL029 vs JLSL025
Supplementary_files_format_and_content: CTL15M_H2AZ_peaks.bed: list of ChIP peaks for samples JLSL044 and JLSL045 vs JLSL043
Supplementary_files_format_and_content: CTLSH_K4me3_peaks.bed: list of ChIP peaks for samples JLSL037 and JLSL039 vs JLSL035
Supplementary_files_format_and_content: CTLSH_H2AZ_peaks.bed: list of ChIP peaks for samples JLSL049 and JLSL050 vs JLSL051
Supplementary_files_format_and_content: KD15M_K4me3_peaks.bed: list of ChIP peaks for samples JLSL022 and JLSL024 vs JLSL020
Supplementary_files_format_and_content: KD15M_H2AZ_peaks.bed: list of ChIP peaks for samples JLSL041 and JLSL042 vs JLSL040
Supplementary_files_format_and_content: KDSH_K4me3_peaks.bed: list of ChIP peaks for samples JLSL032 and JLSL034 vs JLSL030
Supplementary_files_format_and_content: KDSH_H2AZ_peaks.bed: list of ChIP peaks for samples JLSL047 and JLSL048 vs JLSL046
Supplementary_files_format_and_content: chr15M_H2AZ_diff_peaks.bed: differential peaks from MACS bdgdiff for samples JLSL044 and JLSL045 vs JLSL049 and JLSL050
Supplementary_files_format_and_content: chr15M_K4me3_diff_peaks.bed: differential peaks from MACS bdgdiff for samples JLSL027 and JLSL029 vs JLSL037 and JLSL039
Supplementary_files_format_and_content: chr15M-minus_H2AZ_diff_peaks.bed: differential peaks from MACS bdgdiff for samples JLSL041 and JLSL042 vs JLSL049 and JLSL050
Supplementary_files_format_and_content: chr15M-minus_K4me3_diff_peaks.bed: differential peaks from MACS bdgdiff for samples JLSL022 and JLSL024 vs JLSL037 and JLSL039
Supplementary_files_format_and_content: KDSH_H2AZ_diff_peaks.bed: differential peaks from MACS bdgdiff for samples JLSL047 and JLSL048 vs JLSL049 and JLSL050
Supplementary_files_format_and_content: KDSH_K4me3_diff_peaks.bed: differential peaks from MACS bdgdiff for samples JLSL032 and JLSL034 vs JLSL037 and JLSL039
Supplementary_files_format_and_content: KD15M_H2AZ_diff_peaks.bed: differential peaks from MACS bdgdiff for samples JLSL041 and JLSL042 vs JLSL044 and JLSL045
Supplementary_files_format_and_content: KD15M_K4me3_diff_peaks.bed: differential peaks from MACS bdgdiff for samples JLSL022 and JLSL024 vs JLSL027 and JLSL029

extract_protocol:
WGBS: Illumina TruSeq DNA Methylation Kit (Illumina EGMK81312)
RNA-seq: NEB NEBNext rRNA Depletion Kit (NEB E6310L) and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB E7420S)
ChIP-seq: KAPA Hyper Prep Kit (Kapa KK8504)

value: neuronal cell line

tag: sirna

value: siCTL

tag: genotype/variation

value: control knockdown

value: H2A.Z (Active Motif 39113, LOT#GR279096-1)


title: input_ctlsh_2 [JLSL049]

description:
input control knockdown
JLSL049
processed data file:
CTLSH_H2AZ_peaks.bed

tag: chip antibody

value: input


title: S. feltiae L1 rep 2

description:
unstranded, paired-end, read_length= 43 bp
F406_FL11


title: S. feltiae L1 rep 3

description:
unstranded, paired-end, read_length= 43 bp
F434_FL13


title: S. carpocapsae zygote rep 3

description:
unstranded, paired-end, read_length= 43 bp
C260_ZY4


title: msn2Δmsn4Δ-RNA-t10

city: Pittsburgh

first: Zheng

last: Kuang

state: PA

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

description: Additionally time points representing the relative time of WT samples in the RC phase

data_processing:
Sequence reads were mapped to the Saccharomyces.cerevisiae (sacCer2) using TopHat (--bowtie1 -i 40 --genome-read-mismatches 4 --no-coverage-search -G genes.gtf). FPKM counts were calculated by Cuffidff.
Supplementary_files_format_and_content: FPKM file contains FPKM values for each gene in 7 WT and 11 mutant cells.
Genome_build: sacCer2

organism: Saccharomyces cerevisiae

source_name: yeast cells in metabolic cycles

extract_protocol:
2 OD cycling cells were collected and flash frozen. RNA was extracted with the Qiagen RNeasy Mini kit (QIAGEN, 74104, Valencia, CA).
RNA-seq libraries were prepared using Illumina Trueseq RNAseq v2 library kit (Illumina, San Diego, CA). PolyA beads were used for mRNA selection. 500 ng of RNA per sample was used as input and 12 cycles of PCR were run for amplification.

value: ZKY763:CEN.PK MATa msn2<delta>::hygMX msn4<delta>::KanMX6

tag: time


title: C36UVACXX.3.24hr_02_Left_K4me1

description: 24 hours injured

value: tibialis anterior muscle

tag: timepoint

tag: treatment


title: h2az_kdsh_2 [JLSL048]

description:
UBE3A knockdown sample2
JLSL048
processed data file:
KDSH_H2AZ_peaks.bed
KDSH_H2AZ_diff_peaks.bed

value: UBE3A knockdown


title: msn2Δmsn4Δ-RNA-t9

tag: strain


title: S. feltiae L1 rep 1

description:
unstranded, paired-end, read_length= 43 bp
F428_FL15

tag: developmental stage


title: msn2Δmsn4Δ-RNA-t8


title: C36UVACXX.3.24hr_02_Left_K27ac

description: 24 hours injured

value: 24 hours

value: H3 K27ac (Active Motif 39133)

value: freeze injury


title: input_kdsh_2 [JLSL046]

description:
input UBE3A knockdown
JLSL046
processed data file:
KDSH_H2AZ_peaks.bed


title: msn2Δmsn4Δ-RNA-t7

description: Same time points as WT RNAseq


title: S. feltiae moving rep 4

description:
unstranded, paired-end, read_length= 43 bp
F404_FMOV3

source_name: S. feltiae moving

value: moving


title: C36UVACXX.3.24hr_01_Left_WCE

description: 24 hours injured

value: WCE - whole cell extract


title: S. feltiae moving rep 3

description:
unstranded, paired-end, read_length= 43 bp
F410_FMOV6

value: whole organism


title: C36UVACXX.3.24hr_01_Left_K4me3

description: 24 hours injured


title: S. feltiae moving rep 2

description:
unstranded, paired-end, read_length= 43 bp
F407_FMOV4


title: h2az_ctlsh_1 [JLSL050]

description:
control knockdown sample1
JLSL050
processed data file:
CTLSH_H2AZ_peaks.bed
chr15M_H2AZ_diff_peaks.bed
chr15M-minus_H2AZ_diff_peaks.bed
KDSH_H2AZ_diff_peaks.bed


title: C36UVACXX.3.24hr_01_Left_K4me1

description: 24 hours injured


title: h2az_ctl15m_1 [JLSL044]

description:
control knockdown sample1
JLSL044
processed data file:
CTL15M_H2AZ_peaks.bed
chr15M_H2AZ_diff_peaks.bed
KD15M_H2AZ_diff_peaks.bed

value: chromosome duplication model of Dup15q syndrome


title: C36UVACXX.3.24hr_02_Left_WCE

description: 24 hours injured


title: msn2Δmsn4Δ-RNA-t11


title: h2az_ctl15m_2 [JLSL045]

description:
control knockdown sample2
JLSL045
processed data file:
CTL15M_H2AZ_peaks.bed
chr15M_H2AZ_diff_peaks.bed
KD15M_H2AZ_diff_peaks.bed


title: C36UVACXX.3.24hr_02_Left_K4me3

description: 24 hours injured


title: msn2Δmsn4Δ-RNA-t4

description: Same time points as WT RNAseq


title: C36UVACXX.3.24hr_01_Left_K27ac

description: 24 hours injured


title: msn2Δmsn4Δ-RNA-t3

description: Same time points as WT RNAseq


title: S. feltiae 2-fold rep 4

description:
unstranded, paired-end, read_length= 43 bp
F23_F2X4

source_name: S. feltiae 2-fold


title: C4KGFACXX.4.10hr_07_Left_K4me3

description: 10 hours injured

value: 10 hours


title: C. elegans 2-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
E552_E2C2


title: msn2Δmsn4Δ-RNA-t2

description: Same time points as WT RNAseq


title: h2az_kd15m_2 [JLSL042]

description:
UBE3A knockdown sample2
JLSL042
processed data file:
KD15M_H2AZ_peaks.bed
chr15M-minus_H2AZ_diff_peaks.bed
KD15M_H2AZ_diff_peaks.bed


title: C4KGFACXX.4.10hr_07_Left_K4me1

description: 10 hours injured


title: h2az_kdsh_1 [JLSL047]

description:
UBE3A knockdown sample1
JLSL047
processed data file:
KDSH_H2AZ_peaks.bed
KDSH_H2AZ_diff_peaks.bed


title: S. feltiae 2-fold rep 2

description:
unstranded, paired-end, read_length= 43 bp
F21_F2X2

value: SN


title: msn2Δmsn4Δ-RNA-t5

description: Same time points as WT RNAseq


title: input_kd15m_2 [JLSL040]

description:
input UBE3A knockdown
JLSL040
processed data file:
KD15M_H2AZ_peaks.bed


title: S. feltiae moving rep 1

description:
unstranded, paired-end, read_length= 43 bp
F409_FMOV5


title: k4me3_ctlsh_2 [JLSL039]

description:
control knockdown sample2
JLSL039
processed data file:
CTLSH_K4me3_peaks.bed
chr15M_K4me3_diff_peaks.bed
chr15M-minus_K4me3_diff_peaks.bed
KDSH_K4me3_diff_peaks.bed

value: neuronal cell line

value: H3K4me3 (Active Motif 39159, LOT#GR288375-1)


title: C4KGFACXX.4.10hr_07_Right_K4me3

description: 10 hours control

value: control


title: S. feltiae 2-fold rep 1

description:
unstranded, paired-end, read_length= 43 bp
F109_F2X5


title: S. feltiae 1.5-fold rep 4

description:
unstranded, paired-end, read_length= 43 bp
F203_F1.5X5

source_name: S. feltiae 1.5-fold


title: k4me3_ctlsh_1 [JLSL037]

description:
control knockdown sample1
JLSL037
processed data file:
CTLSH_K4me3_peaks.bed
chr15M_K4me3_diff_peaks.bed
chr15M-minus_K4me3_diff_peaks.bed
KDSH_K4me3_diff_peaks.bed

value: siCTL

value: control knockdown


title: WT-RNA-t6

description: Same time points as msn2Δmsn4Δ RNAseq

value: BY5764:CEN.PK MATa


title: C4KGFACXX.4.10hr_07_Right_K4me1

description: 10 hours control

value: tibialis anterior muscle


title: input_ctl15m_2 [JLSL043]

description:
input control knockdown
JLSL043
processed data file:
CTL15M_H2AZ_peaks.bed

value: input


title: input_ctlsh [JLSL035]

description:
input control knockdown
JLSL035
processed data file:
CTLSH_K4me3_peaks.bed


title: h2az_kd15m_1 [JLSL041]

description:
UBE3A knockdown sample1
JLSL041
processed data file:
KD15M_H2AZ_peaks.bed
chr15M-minus_H2AZ_diff_peaks.bed
KD15M_H2AZ_diff_peaks.bed

value: UBE3A knockdown

value: H2A.Z (Active Motif 39113, LOT#GR279096-1)


title: S. feltiae 2-fold rep 3

description:
unstranded, paired-end, read_length= 43 bp
F20_F2X1


title: C4KGFACXX.4.10hr_07_Right_K27ac

description: 10 hours control

value: H3 K27ac (Active Motif 39133)


title: S. feltiae 1.5-fold rep 2

description:
unstranded, paired-end, read_length= 43 bp
F186_F1.5X3


title: k4me3_kdsh_2 [JLSL034]

description:
UBE3A knockdown sample2
JLSL034
processed data file:
KDSH_K4me3_peaks.bed
KDSH_K4me3_diff_peaks.bed


title: C4KDJACXX.2.10hr_06_Left_K4me3

description: 10 hours injured

value: freeze injury


title: k4me3_kdsh_1 [JLSL032]

description:
UBE3A knockdown sample1
JLSL032
processed data file:
KDSH_K4me3_peaks.bed
KDSH_K4me3_diff_peaks.bed


title: WT-RNA-t3

description: Same time points as msn2Δmsn4Δ RNAseq


title: C4KGFACXX.1.10hr_07_Left_K27ac

description: 10 hours injured


title: S. feltiae 1.5-fold rep 1

description:
unstranded, paired-end, read_length= 43 bp
F185_F1.5X2


title: WT-RNA-t2

description: Same time points as msn2Δmsn4Δ RNAseq


title: S. feltiae comma rep 4

description:
unstranded, paired-end, read_length= 43 bp
F197_FCOM7

source_name: S. feltiae comma

value: comma


title: input_kdsh [JLSL030]

description:
input UBE3A knockdown
JLSL030
processed data file:
KDSH_K4me3_peaks.bed


title: WT-RNA-t7

description: Same time points as msn2Δmsn4Δ RNAseq


title: C4KDJACXX.2.10hr_06_Left_K27ac

description: 10 hours injured

source_name: tibialis anterior muscle


title: k4me3_ctl15m_2 [JLSL029]

description:
control knockdown sample2
JLSL029
processed data file:
CTL15M_K4me3_peaks.bed
chr15M_K4me3_diff_peaks.bed
KD15M_K4me3_diff_peaks.bed


title: WT-RNA-t1

description: Same time points as msn2Δmsn4Δ RNAseq


title: C4KGFACXX.1.10hr_06_Right_K4me3

description: 10 hours control


title: S. feltiae 1.5-fold rep 3

description:
unstranded, paired-end, read_length= 43 bp
F187_F1.5X4

value: whole organism


title: k4me3_ctl15m_1 [JLSL027]

description:
control knockdown sample1
JLSL027
processed data file:
CTL15M_K4me3_peaks.bed
chr15M_K4me3_diff_peaks.bed
KD15M_K4me3_diff_peaks.bed

value: chromosome duplication model of Dup15q syndrome


title: S. feltiae comma rep 2

description:
unstranded, paired-end, read_length= 43 bp
F19_FCOM6


title: Msn4-ChIP-t6

description: Same time points as Msn2 ChIP

data_processing:
Raw reads were mapped to the reference genome (sacCer2) by bowtie and peaks were visualized by the CisGenome Browser
Supplementary_files_format_and_content: .txt files show the sequencing read intensity across the sacCer2 genome in CisGenome browser. The first column in the txt file is the name of the chromosome. The second column is the start position of each of the continuous 100 bp windows in the chromosome. The third column is the intensity of reads in this window.
Genome_build: sacCer2

extract_protocol:
~50 OD WT cycling cells per time point were collected for ChIP of Msn2 and Msn4. Antibodies are as following: Msn2 (y-300, sc-33631), Msn4 (yE-19, sc-15550). Validation is provided on the manufacturer’s website. 2.5 µg primary antibody was used per ChIP experiment. Briefly, cells were first fixed in 1% formaldehyde at 25℃ for 15 min and quenched in 125mM glycine at 25℃ for 10 min. Cells were pelleted and washed twice with TBS buffer before freezing. The frozen pellet was resuspended in 0.5 ml ChIP lysis buffer (50 mM HEPES•KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate (DOC), 0.1% SDS, 1 mM PMSF, 5 µM pepstatin A, Roche protease inhibitor cocktail) and split into two tubes and lysed by bead beating. Lysate were combined and expanded into 1 ml and sonicated for 16 cycles (30 sec on, 1 min off, high output) using a Bioruptor (Diagenode, Denville, NJ). The supernatant of the sonicated lysate was pre-cleared and incubated with 2.5 µg primary antibodies. After incubation overnight, 50 µl protein G magnetic beads (Invitrogen, Grand Island, NY, 10003D) were added and incubated for 1.5 h at 4 ℃. Beads were washed twice with ChIP lysis buffer, twice with DOC buffer (10 mM Tris•Cl pH 8.0, 0.25 M LiCl, 0.5% deoxycholate, 0.5% NP-40, 1 mM EDTA) and twice with TE. 100 µl of TES buffer (TE pH8.0 with 1% SDS, 150 mM NaCl, and 5 mM dithiothreitol) was added to resuspend the beads at 65°C for 20 min. Reverse crosslinking was performed by incubation for 6 h at 65°C. An equal volume of TE containing 1.25 mg/ml proteinase K and 0.4 mg/ml glycogen was added to the samples after reverse crosslinking and samples were incubated for 3 h at 37°C. DNA samples were purified using ChIP DNA Clean & Concentrator (ZYMO RESEARCH, D5205, Irvine, CA).
Library construction and sequencing were performed using KAPA Hyper Prep Kit (KAPABIOSYSTEMS, KK8502, Wilmington, MA). Briefly, DNA was end repaired and A-tailed. Barcoded adaptors were ligated and DNA was purified with Agencourt AMPure XP beads (Beckman Coulter, A63880, Indianapolis, IN) and amplified by 12-16 cycles. PCR products were gel-extracted and quantified on an Agilent Bioanalyzer.

value: Msn4(yE-19) [Santa Cruz, sc-15550]


title: msn2Δmsn4Δ-RNA-t1

description: Same time points as WT RNAseq

value: ZKY763:CEN.PK MATa msn2<delta>::hygMX msn4<delta>::KanMX6


title: S. feltiae comma rep 1

description:
unstranded, paired-end, read_length= 43 bp
F45_FCOM5

value: SN


title: C4KGFACXX.1.10hr_06_Right_K4me1

description: 10 hours control

value: 10 hours


title: input_ctl15m [JLSL025]

description:
input control knockdown
JLSL025
processed data file:
CTL15M_K4me3_peaks.bed


title: WT-RNA-t4

description: Same time points as msn2Δmsn4Δ RNAseq


title: C4KGFACXX.1.10hr_06_Right_K27ac

description: 10 hours control

value: control


title: Msn4-ChIP-t5

description: Same time points as Msn2 ChIP


title: S. feltiae 64-78-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
F432_F64C5

source_name: S. feltiae 64-78-cell


title: C4KDJACXX.2.10hr_06_Left_K4me1

description: 10 hours injured


title: Msn4-ChIP-t4

description: Same time points as Msn2 ChIP


title: S. feltiae comma rep 3

description:
unstranded, paired-end, read_length= 43 bp
F44_FCOM8


title: S. feltiae 64-78-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
F425_F64C3


title: k4me3_kd15m_1 [JLSL022]

description:
UBE3A knockdown sample1
JLSL022
processed data file:
KD15M_K4me3_peaks.bed
chr15M-minus_K4me3_diff_peaks.bed
KD15M_K4me3_diff_peaks.bed

value: H3K4me3 (Active Motif 39159, LOT#GR288375-1)


title: C36UVACXX.7.10hr_03_Left_WCE

description: 10 hours injured

value: WCE - whole cell extract


title: Msn4-ChIP-t3

description: Same time points as Msn2 ChIP

value: BY5764:CEN.PK MATa


title: WT-RNA-t5

description: Same time points as msn2Δmsn4Δ RNAseq


title: S. feltiae 64-78-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
F431_F64C4


title: input_kd15m [JLSL020]

description:
input UBE3A knockdown
JLSL020
processed data file:
KD15M_K4me3_peaks.bed


title: C36UVACXX.7.10hr_03_Left_K4me1

description: 10 hours injured

value: tibialis anterior muscle


title: S. feltiae 64-78-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
F193_F64C2


title: rna_kd15m_3 [JLSL041F]

description:
UBE3A knockdown sample3
JLSL041F

molecule: total RNA


title: k4me3_kd15m_2 [JLSL024]

description:
UBE3A knockdown sample2
JLSL024
processed data file:
KD15M_K4me3_peaks.bed
chr15M-minus_K4me3_diff_peaks.bed
KD15M_K4me3_diff_peaks.bed


title: Msn4-ChIP-t1

description: Same time points as Msn2 ChIP


title: C36UVACXX.6.10hr_03_Left_K27ac

description: 10 hours injured


title: S. feltiae 24-44-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
F218_F32C2

source_name: S. feltiae 24-44-cell


title: Msn2-ChIP-t6

description: Same time points as Msn4 ChIP


title: C36UVACXX.6.10hr_03_Left_WCE

description: 10 hours injured


title: rna_kd15m_1 [JLSL041D]

description:
UBE3A knockdown sample1
JLSL041D


title: msn2Δmsn4Δ-RNA-t6

description: Same time points as WT RNAseq


title: C36UVACXX.7.10hr_03_Left_K4me3

description: 10 hours injured


title: Msn2-ChIP-t5

description: Same time points as Msn4 ChIP


title: S. feltiae 24-44-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
F18_F32C3


title: Msn4-ChIP-t2

description: Same time points as Msn2 ChIP


title: C36UVACXX.6.10hr_03_Left_K4me1

description: 10 hours injured


title: rna_ctl15m_3 [JLSL041C]

description:
control knockdown sample3
JLSL041C

value: siCTL

value: control knockdown


title: C36UVACXX.6.10hr_03_Left_K4me3

description: 10 hours injured


title: rna_ctl15m_2 [JLSL041B]

description:
control knockdown sample2
JLSL041B


title: C36UVACXX.7.10hr_03_Left_K27ac

description: 10 hours injured


title: S. feltiae 8-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
F62_F8C8

source_name: S. feltiae 8-cell


title: C4KDJACXX.2.3hr_016_Left_K4me3

description: 3 hours injured

value: 3 hours


title: rna_ctl15m_1 [JLSL041A]

description:
control knockdown sample1
JLSL041A


title: rna_kdsh_3 [JLSL040F]

description:
UBE3A knockdown sample3
JLSL040F

value: neuronal cell line

value: UBE3A knockdown


title: Msn2-ChIP-t1

description: Same time points as Msn4 ChIP


title: S. feltiae 8-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
F110_F8C9


title: C4KDJACXX.2.3hr_016_Left_K27ac

description: 3 hours injured

value: H3 K27ac (Active Motif 39133)

value: freeze injury


title: rna_kdsh_2 [JLSL040E]

description:
UBE3A knockdown sample2
JLSL040E


title: S. feltiae 24-44-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
F216_F32C1

value: whole organism


title: S. feltiae 8-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
F10_F8C2


title: rna_kdsh_1 [JLSL040D]

description:
UBE3A knockdown sample1
JLSL040D


title: 2605745_TimePoint3_Whole Blood

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

institute: Emory University

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v2.7.7) with default parameters. Illumina bcl2fastq v2.17.1.14 was used for demultiplexing. FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
Reads were mapped to a composite reference assembly consisting of host, parasite, and ERCC control references with STAR (v2.5.2b) with default alignment parameters. Note all values for ERCC abundances will be zero as no spike ins were included in sequenced samples. See readme for details.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: RNA-Seq reads were mapped to both a host and parasite genome.  Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues.  The MacaM assembly has been deposited in GenBank under BioProject accession  PRJNA214746. Parasite: Plasmodium cynomolgi B strain genome assembly was used. The assembly has been deposited in GenBank under the BioProject accession PRJNA187987.
Supplementary_files_format_and_content: Excel files contain raw counts at the gene level, for each individual. Raw counts are further classified by experimental Time Point (1-3), and Specimen Type (Whole Blood).
Supplementary_files_format_and_content: Host and Parasite Raw Read Counts Column headers are defined as follows:    'Gene ID':  Identifiers of all Genes in the annotation.     'Gene Symbol': Symbols of all Genes in the annotation.    'Raw File List / Sample Identifier / Abundances': Samples were sequenced across multiple lanes, some samples were sequenced at extra depth, all fastq files are listed for each sample. Raw read counts of all genes, from the raw files listed in the column header. The raw file names and sample identifer both contain information regarding Specimen Type, NHP ID, and Time Point.      Notes:  There are 15 columns representing 5 animals for Time Points T01, T01B, and T03.    There is an read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0."

organism:
Macaca mulatta
Plasmodium cynomolgi strain B

source_name: Whole Blood

growth_protocol: Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.

extract_protocol:
Whole blood (3 ml) was collected in Tempus tubes (Applied Biosystems) that also preserve mRNA; these samples include erythrocytes, platelets and granulocytes in addition to mononuclear lymphocytes.  RNA was extracted using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 92 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate multiplexed sequencing on an Illumina HiSeq3000 at the Yerkes Genomics Core, aiming for 50 million paired-end 100 base pair (bp) reads per library.

treatment_protocol: The experiment included, 1 pre-inoculation day, 35 experiment days, and 10 post-experiment days.  Pre- and post-experiment days were used to prepare subjects and administer post-experiment curative treatments respectively.  The anti-malarial drugs primaquine and chloroquine were administered to all subjects at the end of the study for curative treatment of the liver and blood-stage infections, respectively.

tag: time point

tag: gender

value: Male

tag: non human primate individual id

tag: infected with

value: Plasmodium cynomolgi strain B


title: rna_kd15m_2 [JLSL041E]

description:
UBE3A knockdown sample2
JLSL041E

value: chromosome duplication model of Dup15q syndrome


title: C4KGFACXX.2.3hr_016_Right_K4me3

description: 3 hours control


title: S. feltiae 4-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
F102_F4C4

source_name: S. feltiae 4-cell

value: SN


title: S. feltiae 24-44-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
F47_F32C4


title: C4KGFACXX.2.3hr_016_Right_K4me1

description: 3 hours control

value: control


title: S. feltiae 4-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
F7_F4C2


title: rna_ctlsh_2 [JLSL040B]

description:
control knockdown sample2
JLSL040B


title: 2605707_TimePoint3_Whole Blood


title: Msn2-ChIP-t4

description: Same time points as Msn4 ChIP


title: S. feltiae 4-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
F6_F4C1


title: 2605726_TimePoint3_Whole Blood


title: Msn2-ChIP-t3

description: Same time points as Msn4 ChIP


title: S. feltiae 8-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
F426_F8C9


title: 2605688_TimePoint3_Whole Blood


title: S. feltiae 4-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
F48_F4C7


title: C4KDJACXX.2.3hr_016_Left_K4me1

description: 3 hours injured


title: 2603366_TimePoint1B_Whole Blood


title: wgbs_kdsh_3 [JLKD111B]

description:
UBE3A knockdown sample3
JLKD111B
processed data file:
DMR_KDSH_hg19.bed


title: C4KDJACXX.1.3hr_015_Left_K4me3

description: 3 hours injured


title: S. feltiae 2-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
F4_F2C4

source_name: S. feltiae 2-cell


title: C4KDJACXX.1.3hr_015_Left_K4me1

description: 3 hours injured


title: rna_ctlsh_3 [JLSL040C]

description:
control knockdown sample3
JLSL040C


title: 2605764_TimePoint3_Whole Blood


title: C4KDJACXX.1.3hr_015_Left_K27ac

description: 3 hours injured


title: Msn2-ChIP-t2

description: Same time points as Msn4 ChIP


title: C4KGFACXX.2.3hr_015_Right_K4me3

description: 3 hours control


title: 2603328_TimePoint1B_Whole Blood


title: 2603347_TimePoint1B_Whole Blood


title: S. feltiae 2-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
F5_F2C5


title: wgbs_kdsh_1 [JLKD109B]

description:
UBE3A knockdown sample1
JLKD109B
processed data file:
DMR_KDSH_hg19.bed


title: C4KGFACXX.2.3hr_016_Right_K27ac

description: 3 hours control


title: S. feltiae 2-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
F105_F2C7


title: rna_ctlsh_1 [JLSL040A]

description:
control knockdown sample1
JLSL040A


title: wgbs_kdsh_2 [JLKD110B]

description:
UBE3A knockdown sample2
JLKD110B
processed data file:
DMR_KDSH_hg19.bed


title: C4KGFACXX.2.3hr_015_Right_K4me1

description: 3 hours control


title: 2600654_TimePoint1B_Whole Blood


title: S. feltiae 2-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
F100_F2C6


title: wgbs_ctlsh_2 [JLSL050B]

description:
control knockdown sample2
JLSL050B
processed data file:
DMR_chr15M_hg19.bed
DMR_chr15M-minus_hg19.bed
DMR_KDSH_hg19.bed


title: 2602509_TimePoint1B_Whole Blood


title: wgbs_ctlsh_3 [JLSL050C]

description:
control knockdown sample3
JLSL050C
processed data file:
DMR_chr15M_hg19.bed
DMR_chr15M-minus_hg19.bed
DMR_KDSH_hg19.bed


title: S. feltiae zygote rep 4

description:
unstranded, paired-end, read_length= 43 bp
F213_FZY3

source_name: S. feltiae zygote

value: zygote


title: wgbs_ctlsh_1 [JLSL050A]

description:
control knockdown sample1
JLSL050A
processed data file:
DMR_chr15M_hg19.bed
DMR_chr15M-minus_hg19.bed
DMR_KDSH_hg19.bed


title: S. feltiae zygote rep 3

description:
unstranded, paired-end, read_length= 43 bp
F403_FZY6


title: 3h_12_Left_K4me3_C36PAACXX.7

description: 3 hours injured


title: wgbs_kd15m_3 [JLSL011C]

description:
UBE3A knockdown sample3
JLSL011C
processed data file:
DMR_chr15M-minus_hg19.bed
DMR_KD15M_hg19.bed


title: 3h_12_Left_K4me1_C36PAACXX.7

description: 3 hours injured


title: S. feltiae zygote rep 2

description:
unstranded, paired-end, read_length= 43 bp
F211_FZY2


title: 2589093_TimePoint1_Whole Blood


title: wgbs_kd15m_2 [JLSL011B]

description:
UBE3A knockdown sample2
JLSL011B
processed data file:
DMR_chr15M-minus_hg19.bed
DMR_KD15M_hg19.bed


title: 3h_12_Left_K27ac_C36PAACXX.7

description: 3 hours injured


title: wgbs_kd15m_1 [JLSL011A]

description:
UBE3A knockdown sample1
JLSL011A
processed data file:
DMR_chr15M-minus_hg19.bed
DMR_KD15M_hg19.bed


title: S. feltiae zygote rep 1

description:
unstranded, paired-end, read_length= 43 bp
F210_FZY1


title: 2589074_TimePoint1_Whole Blood


title: 2589055_TimePoint1_Whole Blood


title: wgbs_ctl15m_3 [JLSL012C]

description:
control knockdown sample3
JLSL012C
processed data file:
DMR_chr15M_hg19.bed
DMR_KD15M_hg19.bed


title: wgbs_ctl15m_2 [JLSL012B]

description:
control knockdown sample2
JLSL012B
processed data file:
DMR_chr15M_hg19.bed
DMR_KD15M_hg19.bed


title: 3h_12_Right_K27ac_C36PAACXX.7

description: 3 hours control


title: 3h_12_Right_K4me3_C36PAACXX.7

description: 3 hours control


title: 2589036_TimePoint1_Whole Blood


title: 3h_11_Left_K4me3_C36PAACXX.8

description: 3 hours injured


title: wgbs_ctl15m_1 [JLSL012A]

description:
control knockdown sample1
JLSL012A
processed data file:
DMR_chr15M_hg19.bed
DMR_KD15M_hg19.bed


title: C4KGFACXX.2.3hr_015_Right_K27ac

description: 3 hours control


title: 2589112_TimePoint1_Whole Blood


title: Sample84H_3M

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

country: China

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Aspergillus glaucus CCHA genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count( v0.5.4p2).
The normalized expression values for each gene were calculated by the number of uniquely mapped reads per kilobase of exon region per million mapped reads (RPKM)
Aspergillus glaucus CCHA
Genome_build: tab-delimited text files including RPKM values for each sample.

organism: Aspergillus glaucus

source_name: Aspergillus glaucus CCHA

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CCHA

value: cell

value: 3M NaCl for 84 h


title: 3h_11_Left_K27ac_C36PAACXX.8

description: 3 hours injured

value: tibialis anterior muscle


title: Sample84H_4M

value: 4M NaCl for 84 h


title: 3h_11_Left_K4me1_C36PAACXX.8

description: 3 hours injured

value: 3 hours


title: 3h_11_Right_WCE_C36PAACXX.8

description: 3 hours control

value: WCE - whole cell extract


title: Sample84H_0M

value: 0M NaCl for 84 h


title: Sample84H_1M

value: 1M NaCl for 84 h


title: Sample36H_3M

value: 3M NaCl for 36 h


title: 3h_11_Right_K4me3_C36PAACXX.8

description: 3 hours control


title: 3h_11_Right_K4me1_C36PAACXX.8

description: 3 hours control


title: C. angaria L1 rep 4

description:
unstranded, paired-end, read_length= 43 bp
A730_AL14

organism: Caenorhabditis angaria

source_name: C. angaria L1

value: whole organism


title: C. angaria L1 rep 3

description:
unstranded, paired-end, read_length= 43 bp
A729_AL13


title: Sample36H_1M

value: 1M NaCl for 36 h


title: C. angaria L1 rep 2

description:
unstranded, paired-end, read_length= 43 bp
A726_AL11


title: 3h_11_Right_K27ac_C36PAACXX.8

description: 3 hours control

value: H3 K27ac (Active Motif 39133)


title: C. angaria L1 rep 1

description:
unstranded, paired-end, read_length= 43 bp
A727_AL12


title: 3h_10_Left_K4me3_C36PAACXX.7

description: 3 hours injured

value: freeze injury


title: 3h_12_Right_K4me1_C36PAACXX.7

description: 3 hours control


title: C. angaria moving rep 4

description:
unstranded, paired-end, read_length= 43 bp
A650_AMOV5

source_name: C. angaria moving

value: moving


title: 3h_10_Left_WCE_C36PAACXX.7

description: 3 hours injured


title: C. angaria moving rep 3

description:
unstranded, paired-end, read_length= 43 bp
A647_AMOV4


title: 3h_10_Left_K27ac_C36PAACXX.7

description: 3 hours injured


title: 3h_10_Right_B_K4me1_C36PAACXX.8

description: 3 hours control

value: control


title: 3h_10_Left_K4me1_C36PAACXX.7

description: 3 hours injured


title: 3h_10_Right_B_K27ac_C36PAACXX.8

description: 3 hours control


title: C. angaria moving rep 2

description:
unstranded, paired-end, read_length= 43 bp
A646_AMOV3


title: C. angaria 2-fold rep 3

description:
unstranded, paired-end, read_length= 43 bp
A652_A2X3

source_name: C. angaria 2-fold


title: C. angaria 2-fold rep 4

description:
unstranded, paired-end, read_length= 43 bp
A658_A2X5


title: 3h_10_Right_A_K4me3_C36PAACXX.8

description: 3 hours control


title: C. angaria 2-fold rep 2

description:
unstranded, paired-end, read_length= 43 bp
A526_A2X2


title: C. angaria 2-fold rep 1

description:
unstranded, paired-end, read_length= 43 bp
A514_A2X1


title: C. angaria 1.5-fold rep 4

description:
unstranded, paired-end, read_length= 43 bp
A535_A1.5X4

source_name: C. angaria 1.5-fold


title: 3h_03_Left_K4me1_C36PAACXX.7

description: 3 hours injured


title: C. angaria 1.5-fold rep 3

description:
unstranded, paired-end, read_length= 43 bp
A530_A1.5X3


title: 3h_03_Right_B_K4me1_C36PAACXX.8

description: 3 hours control


title: 3h_03_Right_A_K4me3_C36PAACXX.8

description: 3 hours control


title: C. angaria 1.5-fold rep 2

description:
unstranded, paired-end, read_length= 43 bp
A517_A1.5X2


title: C. angaria comma rep 4

description:
unstranded, paired-end, read_length= 43 bp
A442_ACOM1

source_name: C. angaria comma

value: comma


title: KO_ZT20

description:
C57BL/6 Nfiil3 ΔIEC
Processed data file: genes.fpkm_tracking

data_processing:
Reads were mapped against mm10 using tophat with default parameters and FPKMs were calculated using cuffdiff with default parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: genes.fpkm_tracking: Comma-delimited text file with FPKM for each sample.

source_name: Ileum epithelial cells, Nfiil3 ΔIEC, chow diet, ZT20

extract_protocol:
RNA was extracted from intestinal epithelial cells isolated by laser capture microdissection. Extracted RNA was purified using PicoPure RNA Isolation Kit (Life Technology 12204-01).
Sequencing libraries were prepared using TruSeq RNA sample preparation kit v2 (Illumina).

treatment_protocol: Light box.

tag: strain/background

value: Nfiil3 <delta>IEC

value: Ileum epithelial cells

tag: diet

value: Chow

tag: circadian time


title: C. angaria comma rep 3

description:
unstranded, paired-end, read_length= 43 bp
A449_ACOM3


title: KO_ZT12

source_name: Ileum epithelial cells, Nfiil3 ΔIEC, chow diet, ZT12

tag: cell type


title: C. angaria comma rep 1

description:
unstranded, paired-end, read_length= 43 bp
A450_ACOM4

tag: tissue


title: C. angaria moving rep 1

description:
unstranded, paired-end, read_length= 43 bp
A531_AMOV2


title: C. angaria comma rep 2

description:
unstranded, paired-end, read_length= 43 bp
A446_ACOM2


title: C. angaria 64-78-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
A649_A64C3

source_name: C. angaria 64-78-cell


title: KO_ZT8

source_name: Ileum epithelial cells, Nfiil3 ΔIEC, chow diet, ZT8


title: KO_ZT4

source_name: Ileum epithelial cells, Nfiil3 ΔIEC, chow diet, ZT4


title: 3h_03_Left_K27ac_C36PAACXX.7

description: 3 hours injured

source_name: tibialis anterior muscle

value: tibialis anterior muscle


title: KO_ZT0

source_name: Ileum epithelial cells, Nfiil3 ΔIEC, chow diet, ZT0


title: Flox_ZT20

description:
C57BL/6 Nfiil3 fl/fl
Processed data file: genes.fpkm_tracking

source_name: Ileum epithelial cells, Nfiil3 fl/fl, chow diet, ZT20

value: Nfiil3 fl/fl


title: C. angaria 24-44-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
A657_A32C2

source_name: C. angaria 24-44-cell


title: C. angaria 64-78-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
A648_A64C2


title: 3h_03_Left_K4me3_C36PAACXX.7

description: 3 hours injured

value: 3 hours


title: Flox_ZT16

source_name: Ileum epithelial cells, Nfiil3 fl/fl, chow diet, ZT16


title: Flox_ZT12

source_name: Ileum epithelial cells, Nfiil3 fl/fl, chow diet, ZT12


title: C. angaria 24-44-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
A521_A32C1


title: C. angaria 24-44-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
A698_A32C4


title: C. angaria 1.5-fold rep 1

description:
unstranded, paired-end, read_length= 43 bp
A516_A1.5X1


title: 3h_03_Right_B_K27ac_C36PAACXX.8

description: 3 hours control


title: Flox_ZT8

source_name: Ileum epithelial cells, Nfiil3 fl/fl, chow diet, ZT8


title: Flox_ZT4

source_name: Ileum epithelial cells, Nfiil3 fl/fl, chow diet, ZT4


title: C. angaria 8-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
A534_A8C6

source_name: C. angaria 8-cell


title: KO_ZT16

source_name: Ileum epithelial cells, Nfiil3 ΔIEC, chow diet, ZT16


title: Flox_ZT0

source_name: Ileum epithelial cells, Nfiil3 fl/fl, chow diet, ZT0


title: C. angaria 24-44-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
A691_A32C3


title: 18S Zhao 0.5% DMS B

city: West Haven

first: Matthew

middle: D

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

description: 18S rRNA Targeted Structure Seq Analysis

data_processing:
Library strategy: Targeted Structure Seq
For both treated and untreated samples, FASTQ files resulting from sequencing were trimmed with Cutadapt to remove Illumina adaptor sequences and aligned to either mouse Xist or mouse 18S rRNA with Bowtie2 set to local alignment.
Paired-end reads were combined, where disagreements between paired reads were each resolved using the base call with the higher quality score. Multiple consecutive mismatches or deletions were treated as a single event on the 5’-most nucleotide of the cDNA. The 5’-most position of each combined read (start of reverse transcription) on the target sequence was matched with the expected starting position of the selected primers, with a 5-nt tolerance window. Reads without primer allocations were treated as misprimed off-target reads and discarded. Base-calls beyond 800 nt from the primer start position were discarded. Events for nucleotides in the primer sites were not counted to avoid analysis of the annealing site.
To calculate the probabilities of these events, the number of read-throughs was counted for each nucleotide as the number of times a nucleotide was included in the combined reads, including the gap between paired-ends. Depth was calculated as the number of times a nucleotide was included in the combined reads, excluding the gap between paired-ends. The probability of a stop event for a given nucleotide was then measured in sequencing data on the nucleotide immediately 3’ of the aligned section segment of the cDNA, where a modification would have been present and prompted a release of substrate by RT, as the number of stops divided by the number of read-through events plus the number of stops. The probability of mutation was calculated as the number of mismatches divided by the number of observations for a given nucleotide (depth). Nucleotides were subsequently filtered for total read-through above 100.
Genome_build: Alignment to RNA sequences Mus musculus 18S rRNA (NR_003278.3) or Mus musculus Xist (NR_001463).
Supplementary_files_format_and_content: csv file. Using data from samples treated with DMS, the probability of DMS-induced stop or mutation is indicated for each base in either 18S rRNA or Xist. Also present is the nucleotide number, the base identity (column "ref"), the number of readthroughs (column "RT"), the depth, and the number of deletions. The control values are preceded with a "c," the normalized treated values are preceded with an "n," and the original values are "Pmut" and "Pstop." Statistics based on a Wald test are preceded by "p."

source_name: Female MEF cells

growth_protocol: MEFs were cultured in DMEM + 10% FBS (Gibco) with penicillin and streptomycin to 90% confluency in duplicate 15 cm plates.

extract_protocol:
DMS-treated and untreated cells were collected in PBS by centrifugation (3 min, 1000 g, 4ᵒC). Then cells were lysed with a dounce homogenizer 15 times in 15 mM Tris pH 7.4, 60 mM KCl, 2 mM EDTA. The cells were collected by centrifugation (3 min, 1000 g), and the supernatant was discarded. The remaining pellet was resuspended in TRIzol LS (Life Technologies) and RNA was extracted according to the manufacturer’s instructions. Extracted RNA was treated with RQ1 DNase (Promega) for 1 hr at 37ᵒC, extracted with phenol/chloroform, and precipitated with ethanol.
For duplicate treated and untreated samples, RNA (1 μg) was brought to 12 μl with 10 pmol total of primers (primer sets were identical to those in Fang et al. 2015) The primer/RNA mix was brought to 70ᵒC for 5 min, then 4ᵒC for 2 min to anneal primers. Then 3 μl 5x reverse transcription buffer was added and mixed before incubating samples at 55ᵒC for 10 min. Then 5 μl RT mix was added  and reactions were incubated for 45 min at 55ᵒC for SSIII, 42ᵒC for AMV, or 60ᵒC for TGIRT-II. After reverse transcription, reactions were treated with 1 μl RNase A and 0.5 μl RNase H for 1 hr at 37ᵒC. Reverse transcription reaction cDNA products were purified with AMPure XP beads by adding 1 volume beads solution (at room temperature), 3 volumes PEG solution (2.5 M NaCl, 20% PEG 8000), and 1 volume iPrOH, mixed and allowed to sit at room temperature for 15 min. Beads were immobilized for 10 min on a magnetic rack, then washed twice with fresh 80% EtOH, allowed to dry for 10 minutes, then eluted in 16 μl dH2O. Ligation of 3’ adaptor was performed, and two subsequent rounds of PCR amplification, with Illumina indexes added in the second round.

treatment_protocol: Treated cells were washed with PBS and then incubated with 0.5% DMS in PBS (5 min, rt) before removing DMS solution and quenching with three washes of wash buffer (50 mM Tris pH 7.5, 100 mM NaCl, 3 mM MgCl2, 40 mM β-mercaptoethanol).

value: MEF

value: female

value: F1:129S1/CastEiJ x 129S1

tag: rt-primer set

value: 18S RT primers

tag: dms treatment

value: 0.5% DMS, 5 min


title: C. angaria 8-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
A533_A8C5

value: whole organism


title: 18S Zhao untreated A

value: Untreated


title: C. angaria 64-78-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
A654_A64C4


title: 18S Zhao untreated B


title: C. angaria 4-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
A524_A4C4

source_name: C. angaria 4-cell


title: 18S Zhao 0.5% DMS A


title: 18S TGIRT-II 0.5% DMS A


title: C. angaria 8-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
A519_A8C1


title: 18S TGIRT-II 0.5% DMS B


title: C. angaria 2-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
A523_A2C3

source_name: C. angaria 2-cell


title: C. angaria 4-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
A511_A4C1


title: C. angaria 2-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
A513_A2C2


title: C. angaria 4-cell rep 3

description:
unstranded, paired-end, read_length= 43 bp
A532_A4C5


title: 18S TGIRT-II untreated B


title: 18S TGIRT-II untreated A


title: 18S AMV 0.5% DMS A


title: 18S AMV 0.5% DMS B


title: C. angaria 2-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
A510_A2C1


title: C. angaria 2-cell rep 1

description:
unstranded, paired-end, read_length= 43 bp
A642_A2C4


title: C. angaria zygote rep 4

description:
unstranded, paired-end, read_length= 43 bp
A760_AZY3

source_name: C. angaria zygote

value: zygote


title: 18S AMV untreated A


title: C. angaria zygote rep 3

description:
unstranded, paired-end, read_length= 43 bp
A728_AZY2


title: C. angaria 8-cell rep 2

description:
unstranded, paired-end, read_length= 43 bp
A522_A8C3


title: 18S SSIII 0.5% DMS B


title: 18S AMV untreated B


title: C. angaria zygote rep 2

description:
unstranded, paired-end, read_length= 43 bp
A761_AZY4


title: C. angaria 4-cell rep 4

description:
unstranded, paired-end, read_length= 43 bp
A518_A4C3


title: C. angaria zygote rep 1

description:
unstranded, paired-end, read_length= 43 bp
A689_AZY1


title: 18S SSIII untreated B

description: 18S rRNA Targeted Structure Seq Analysis


title: 18S SSIII 0.5% DMS A


title: 18S SSIII untreated A


title: 18S SSIII 0.5% DMS


title: 18S SSIII untreated + Mn2+


title: 18S SSIII 0.5% DMS + Mn2+


title: 18S SSIII untreated


title: KP rep2

city: London

first: Gavin

last: Kelly

state: London

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick institute

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped and quantified to mm10 whole genome and refseq transcript RSEM v 1.2.11 (including bowtie v2.1.0) with parameters --bowtie2-sensitivity-level very_sensitive --estimate-rspd
Genome_build: mm10
Supplementary_files_format_and_content: Quantified reads were normalised by DESeq2 v1.10.1 in R v3.2, and saved in R-readable rds format.

source_name: lung adenocarcinoma cells

growth_protocol: Primary murine lung adenocarcinoma cells were obtained from p53 fl/fl; LSL-Kras-G12D (KP) or KP; cJun fl/fl (JKP) mice. Briefly, lung tumors were isolated macroscopically from mice 12 weeks post infection with AdV-CMV-Cre, subjected to collagen digest and then cultured on standard tissue culture plates in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with Pen/Strep and 10% fetal calf serum.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions
mRNA-seq libraries were prepared using TruSeq RNA Library Preparation Kit v2 (Illumina) according to the manufacturer’s instructions.

tag: mouse genotype

value: LSL-KrasG12D; p53 fl/fl

tag: replicate


title: KP rep1


title: KP rep3


title: JKP rep3

value: c-Jun fl/fl; LSL-KrasG12D; p53 fl/fl


title: JKP rep2


title: JKP rep1


title: Knock-out Mouse 3 Oocyte 8

status: Public on Sep 25 2017

city: La Jolla

first: Heidi

last: Cook-Andersen

state: California

address: 2880 Torrey Pines Scenic Drive, Rm 4811

department: Department of Reproductive Medicine

institute: University of California, San Diego

description: processed data header: K03

data_processing:
RNA-seq reads were mapped with the STAR pipeline against mm10 transcriptome hosted at TSCC.
The python script rpkmforgenes.py was used to quantify counts for each gene and scde was used to calculate differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes raw reads and RPKM values for each Sample.

source_name: mouse oocyte

growth_protocol: Five week-old F/F- and cKO-Zfp36l2 female mice were stimulated with 10 IU of PMSG by intraperitoneal injection. The mice were sacrificed 46 hrs after PMSG injection, ovaries were harvested and GV oocytes were collected following ovarian puncture in M2 media (Sigma) containing 5 μM Milrinone. Only oocytes completely enclosed in cumulus cells were collected and granulosa cells were mechanically removed using pipets of decreasing diameter. The zona pellucida was removed with a brief incubation in Acid Tyrode’s solution (Sigma) and the oocytes were immediately washed in PBS with 0.1% BSA.

extract_protocol:
RNA was isolated with Trizol and total RNA quality was assessed using an Agilent Bioanalyzer.
The RNA isolation and cDNA synthesis was carried out using the SMARTer® Ultra® Low Input RNA Kit for Sequencing - v3 (Clontech, Cat.no. 634851).

treatment_protocol: No treatment. Either F/F- or cKO-Zfp36l2 oocytes were isolated.

tag: genotype/variation

value: cKO-Zfp36l2 oocyte


title: Knock-out Mouse 4 Oocyte 2

description: processed data file header: KO4_2


title: Knock-out Mouse 4 Oocyte 3

description: processed data file header: KO4_3


title: Knock-out Mouse 4 Oocyte 6

description: processed data file header: KO4_6


title: Knock-out Mouse 4 Oocyte 7

description: processed data file header: KO4_7


title: Knock-out Mouse 4 Oocyte 5

description: processed data file header: KO4_5


title: Knock-out Mouse 3 Oocyte 7

description: processed data file header: KO3_7


title: Knock-out Mouse 4 Oocyte 8

description: processed data header: K04


title: Knock-out Mouse 4 Oocyte 4

description: processed data file header: KO4_4


title: Knock-out Mouse 4 Oocyte 1

description: processed data file header: KO4_1


title: Knock-out Mouse 3 Oocyte 6

description: processed data file header: KO3_6


title: Knock-out Mouse 2 Oocyte 8

description: processed data header: K02


title: Knock-out Mouse 3 Oocyte 1

description: processed data file header: KO3_1


title: Knock-out Mouse 3 Oocyte 3

description: processed data file header: KO3_3


title: Knock-out Mouse 3 Oocyte 2

description: processed data file header: KO3_2


title: Knock-out Mouse 2 Oocyte 6

description: processed data file header: KO2_6


title: Knock-out Mouse 2 Oocyte 5

description: processed data file header: KO2_5


title: Knock-out Mouse 2 Oocyte 4

description: processed data file header: KO2_4


title: Knock-out Mouse 3 Oocyte 4

description: processed data file header: KO3_4


title: Knock-out Mouse 2 Oocyte 3

description: processed data file header: KO2_3


title: Knock-out Mouse 2 Oocyte 2

description: processed data file header: KO2_2


title: Knock-out Mouse 1 Oocyte 5

description: processed data file header: KO1_5


title: Floxed Mouse 4 Oocyte 6

description: processed data file header: FF4_6

value: Floxed oocyte


title: Floxed Mouse 4 Oocyte 4

description: processed data file header: FF4_4


title: Floxed Mouse 4 Oocyte 7

description: processed data file header: FF4_7


title: Floxed Mouse 4 Oocyte 3

description: processed data file header: FF4_3


title: Knock-out Mouse 3 Oocyte 5

description: processed data file header: KO3_5


title: Floxed Mouse 4 Oocyte 1

description: processed data file header: FF4_1


title: Floxed Mouse 3 Oocyte 4

description: processed data file header: FF3_4


title: Floxed Mouse 3 Oocyte 7

description: processed data file header: FF3_7


title: Floxed Mouse 3 Oocyte 6

description: processed data file header: FF3_6


title: Floxed Mouse 3 Oocyte 5

description: processed data file header: FF3_5


title: Floxed Mouse 2 Oocyte 7

description: processed data file header: FF2_7


title: Floxed Mouse 3 Oocyte 3

description: processed data file header: FF3_3


title: Floxed Mouse 3 Oocyte 2

description: processed data file header: FF3_2


title: Knock-out Mouse 2 Oocyte 7

description: processed data file header: KO2_7


title: Floxed Mouse 2 Oocyte 4

description: processed data file header: FF2_4


title: Floxed Mouse 3 Oocyte 1

description: processed data file header: FF3_1


title: Floxed Mouse 2 Oocyte 2

description: processed data file header: FF2_2


title: Floxed Mouse 2 Oocyte 1

description: processed data file header: FF2_1


title: Floxed Mouse 2 Oocyte 3

description: processed data file header: FF2_3


title: Floxed Mouse 2 Oocyte 5

description: processed data file header: FF2_5


title: Floxed Mouse 1 Oocyte 8

description: processed data file header: FF1_8


title: Floxed Mouse 1 Oocyte 6

description: processed data file header: FF1_6


title: Floxed Mouse 1 Oocyte 5

description: processed data file header: FF1_5


title: Floxed Mouse 1 Oocyte 7

description: processed data file header: FF1_7


title: Krit1fl/fl rep3

first: Miguel

middle: Alejandro

last: Lopez-Ramirez

state: California/San Diego

address: 9500 Gilman Drive

department: School of Medicine

description: Krit1fl/fl rep3

data_processing:
Fastq files from RNA-seq experiments were mapped to individual genome for the mouse strain of origin using STAR with default parameters (mm10 for C57BL/6J) (Dobin, A. et al 2013, Bioinformatics).
Reproducibility between samples was analyzed using Irreproducibility discovery rate tool (IDR) (Li, Q.H. 2011, Ann Appl Stat). Homer (Heinz, S. 2010, Molecular Cell) was used for further analysis.
To measure gene expression, analyze repeats with the option RNA and condense Genes along with the default parameters was used. Subset-specific expression was defined with a 4-fold difference in expression between two experiments.
Genes with less than 16 tag counts were defined as not expressed. To map subset-specific peaks to gene expression, only expressed genes were considered.
Genome_build: mm10
Supplementary_files_format_and_content: Fastq files

source_name: BMEC

extract_protocol:
Primary BMEC total RNA were isolated using Trizol reagent, according to the manufacturer’s protocol (ThermoFisher).
RNA libraries were generated using Illumina’s TruSeq Stranded mRNA Sample Prep Kit using 400 ng of RNA. RNA libraries were multiplexed and sequenced with 100 basepair (bp) paired single end reads (SR100) to a depth of approximately 30 million reads per sample on an Illumina HiSeq2500.

value: Brain

tag: age

value: 2 months old


title: Krit1fl/fl rep2

description: Krit1fl/fl rep2

tag: strain


title: Floxed Mouse 4 Oocyte 5

description: processed data file header: FF4_5


title: Krit1ECKO rep3

description: Krit1ECKO rep3


title: Krit1ECKO rep1

description: Krit1ECKO rep1


title: Floxed Mouse 4 Oocyte 2

description: processed data file header: FF4_2


title: Krit1fl/fl rep1

description: Krit1fl/fl rep1


title: Krit1ECKO rep2

description: Krit1ECKO rep2


title: Floxed Mouse 2 Oocyte 6

description: processed data file header: FF2_6


title: Floxed Mouse 1 Oocyte 9

description: processed data file header: FF1_9


title: 17_Neonates_micro

city: La Jolla,

first: Inge

last: Holtman

department: CMM

institute: UCSD

data_processing:
Star Aligner 2.3.11 allowing for 2 mismatches to map reads to genome
SAM tools 0.1.19 to sort aligned reads
HT-seq 0.5.4 for quantification, mode=union, stranded=no, Ensembl version 71
EdgeR 3.12.0 for data exploration and differential expression
WGCNA 1.49 for co-expression network analysis and detection of modules
Genome_build: GRCm38
Supplementary_files_format_and_content: HT-seq count .txt files

source_name: Pure microglia

extract_protocol:
Ex vivo microglia isolation using CD11C and CD11B and CD45
Illumina TruSeq RNA-preparation kit standard protocol

tag: strain background

tag: microglia population

value: Neonatal mouse CD11C negative


title: 15_Neonates_CD11c_microglia

value: Neonatal mouse CD11C positive


title: 5_EAE_micro

value: EAE mouse CD11C negative


title: 23_unmanip_total_micro

value: Control mouse CD11C negative


title: 22_unmanip_total_micro


title: 4_EAE_micro


title: 3_EAE_CD11c_microglia

value: EAE mouse CD11C positive


title: 2_EAE_CD11c_microglia


title: 20_Neonates_micro


title: 19_Neonates_micro


title: 14_Neonates_CD11c_microglia


title: 6_EAE_micro


title: 21_unmanip_total_micro


title: 13_Neonates_CD11c_microglia


title: VA-ES-BJ_BAF47_HI-C_B

city: Boston

first: Cigall

last: Kadoch

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: VA-ES-BJ BAF47 Hi-C B

data_processing:
Sequencing      data      were       obtained   from   an Illumina HiSeq 2000 machine. The paired-end tags (PETs) from Hi-C libraries were mapped to the human reference genome (hg18) using bowtie240.  Only one uniquely mapped PET were considered at each genome coordinate.
The interaction matrices were binned using a binsize=50 kb, binstep=5kb, binmode=mean. First, we generated the matrices from the Hi-C interaction data using binstep of 5kb.
Each chromosome was separated into 50kb bins and interaction matrix of each chromosome was generated for Hi-C data. The interaction matrix was normalized by KR normalization. The normalized interaction matrix was used as input for identifying TAD by Armatus.
Genome_build: hg18

source_name: VA-ES-BJ (EpS)

growth_protocol: Cell lines were cultured either in DMEM/F12, RPMI1640, or DMEM medium (Gibco, Grand Island, NY, USA), supplemented with 10% fetal bovine serum, 1% Glutamax (Gibco) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10min at room temperature. The Hi-C assay was performed as previously described (Rao et. al, 2014) with the following modifications. Following cross-linking, the cells were lysed and digested with CviQ I + CviA II + Bfa I for 30min. Enzymes digested DNA ends were repaired and labeled with biotin-14-dATP with Klenow enzyme (large fragment). The proximity-based ligation of chromatin ends was performed using T4 DNA Ligase for overnight at 16°C. DNA was reverse cross-linked at 65°C for 6 hours and purified by phenol-chloroform extraction, which was followed by treatment with T4 DNA polymerase to remove biotin from unligated DNA-ends. DNA was sheared to 300-500bps by sonication. Biotinylated DNA was enriched using streptavidin beads and sequencing libraries were generated as described previously.
All library prep and sequencing were paired end on Illumina HiSeq 2000

treatment_protocol: Lentiviral particles were prepared in 293T packaging cells via polyethylenimine-mediated transfection as previously described (Bell et al 2012). The cells were harvested following 48-hour exposure to the lenti-virus and 5-day selection with 10 μg/ml of Blasticidin.

tag: cell line

value: VA-ES-BJ

value: epithelioid sarcoma


title: VA-ES-BJ_empty_Hi-C_B

description: VA-ES-BJ empty Hi-C B


title: VA-ES-BJ_empty_Hi-C_A

description: VA-ES-BJ empty Hi-C A


title: MEF+Ascl1_RNA_7d_B1

city: Singapore

first: Qian Yi

last: Lee

address: Biopolis Drive

department: R&D

country: Singapore

institute: Nuevocor

description: merged.genes.fpkm.txt

data_processing:
Raw sequences from previously published RNA-seq data for rtTA only and Ascl1 48 hrs (GSE43916: GSM1074345-8), as well as current MEF+Ascl1 7d samples are first trimmed with prinseq-lite-0.20.4 (-min_len 30 -trim_qual_right 25 -trim_left 15 -lc_method entropy -lc_threshold 65).
Trimmed sequences were mapped with tophat2 to mm9, then FPKM values were calculated with cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with FPKM output from cufflinks for each Sample

growth_protocol: Homozygous TauEGFP knock-in mice (Tucker et al., 2001) were bred with C57B/6 mice (Taconic) to generate heterozygous embryos. MEFs were isolated from E13.5 embryos and cultured in MEF media (5% cosmic calf serum + sodium pyruvate + pen/strep + MEM NEAA + 0.8% 2-Mercaptoethanol in DMEM).

extract_protocol:
Cells were trypsinzed and sorted for TauEGFP+ cells at 7 days post dox induction. Cells were sorted directly into TRIzol LS reagent and RNA was extracted according to manufacturer's protocol.
Stranded polyA-mRNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: MEFs were infected with Ascl1+rtTA. Doxycycline (dox) was added one day post infection. MEF media was replaced neuronal media (DMEM-F12 + N2 supplement + B27 supplement + insulin + dox) after 48hrs, and media was refreshed every 2-3 days.

tag: genotype

value: E13.5 fibroblast

tag: time post dox

value: 7 days


title: cTEC WT 3

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads were aligned to the mouse genome with Rsubread 1.26.1
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in RefSeq annotation.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: columns represent Entrez Gene ID, total gene length (total base count of all exons), and the number of reads mapping to that gene.

source_name: Thymic epithelium

extract_protocol:
Cell pellets were snap frozen on dry ice and and stored at -80°C, then RNA was isolated with miRNeasy Micro Kit (Qiagen)
First strand cDNA synthesis and cDNA amplification was performed using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories) according to manufacturer’s instructions. Complementary DNA libraries were prepared and indexed separately using the Nextera® XT DNA Library Preparation Kit (Illumina) following manufacturer’s instructions. Each indexed sample library was quantified using the Agilent Tapestation and the Qubit™ DNA BR assay kit for Qubit 3.0® Fluorometer (Life technologies). The indexed sample libraries were pooled and diluted to 1.5pM for 75 base paired-end sequencing on a a NextSeq 500 instrument using the v2 150 cycle High Output kit (illumina) as per manufacturer’s instructions.

value: Wild-type

tag: cell population

value: cortical thymic epithelial cells


title: cTEC WT 4


title: cTEC WT 2


title: mTEC KO

value: Mcl1 knock-out

value: medullary thymic epithelial cells


title: cTEC KO


title: 18_Neonates_micro


title: cTEC WT 1


title: 16_Neonates_CD11c_microglia


title: mTEC WT 2


title: 1_EAE_CD11c_microglia


title: mTEC WT 1


title: VA-ES-BJ_BAF47_HI-C_A

description: VA-ES-BJ BAF47 Hi-C A


title: TET2rescue-Mut-2i-1

middle: R

last: Branco

address: 4 Newark Street

institute: Blizard Institute

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! v0.3.3 with default parameters.
Trimmed reads were mapped to mm9 using tophat v2.0.9 with -g 1.
Raw read counts for each gene or repeat (from RepeatMasker annotation) were generated in Seqmonk with the RNA-seq quantitation pipeline. Reads from repeats belonging to the same class were pooled. Normalised gene and repeat expression values were calculated with the variance stabilizing transformation in DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files containing normalised gene expression values (log2) for each sample.

source_name: embryonic stem cells

growth_protocol: ESCs were cultured on gelatin-coated plates without feeders, in either: 1) serum media (DMEM supplemented with 15% fetal bovine serum and 1,000 U/ml LIF), or 2) 2i media (DMEM F-12 and neurobasal media supplemented with N2, B27, LIF, PD0325901 and CHIR99021).

extract_protocol:
RNA was extracted using either the AllPrep DNA/RNA mini kit (QIAGEN) and DNAse treated with the TURBO DNA-free kit (Ambion).
Non-directional mRNA-Seq libraries were generated using the Dynabeads mRNA purification kit (Life Technologies) and the NEBnext Ultra RNA library prep kit (NEB).

treatment_protocol: Lentiviral particles containing pLKO.1 shRNA vectors were produced by standard methods in 293T cells. Transduced ES cells were selected with 1 µg/ml puromycin 48 hours post-infection and collected after 3 days of selection.

value: Tet2 KO

tag: medium

tag: shRNA

tag: rescue

value: TET2 Mut


title: TET2rescue-WT-2i-2

value: TET2 WT


title: TET2rescue-Mut-serum-1

value: serum


title: TET2rescue-Mut-serum-3


title: TET2rescue-Mut-2i-2


title: TET2rescue-Mut-serum-2


title: TET2rescue-WT-2i-1


title: TET2rescue-Mut-2i-3


title: TET2rescue-WT-serum-3


title: MEF+Ascl1_5d_negative_B3_rep1

description: merged_macspeaks_all_wo.new.rtta_RPKM.quantile.filtered.stepminer.annotated.txt

data_processing:
Trimmed adaptors
Mapped with bowtie to mm9
Removed mitochondria reads and duplicate fragments
Called peaks with MACS2 (-q 0.01 --nomodel  --shift 0) based on reads aggregated from all replicates for that time point.
Merged peaks for relevant timepoints and compute RPKM of paired end read endpoints that fell within the region for all the biological replicates
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample at all peaks present at 1) early timepoints (12-48 hours) and 2) all samples

source_name: MEF+Ascl1 5d, Tau::EGFP-

growth_protocol: Homozygous TauEGFP knock-in mice (Tucker et al., 2001) were bred with C57B/6 mice (Taconic) to generate heterozygous embryos. MEFs were isolated from E13.5 embryos and cultured in MEF media (5% cosmic calf serum + sodium pyruvate + pen/strep + MEM NEAA + 0.8% 2-Mercaptoethanol in DMEM). Cortical neurons were isolated by dissecting cortical tissue from E15.5 embryos and sorting for TauEGFP+ cells.

extract_protocol: Cells were trypsinzed in 0.05% trypsin and processed at different time points post-dox. From day 5, cells were FAC sorted by TauEGFP. ATAC-seq protocol outlined by Buenrostro, et al (Nat. Methods, 2013)

treatment_protocol: MEFs were infected with rtTA alone or with Ascl1+rtTA. Doxycycline (dox) was added one day post infection. For cells harvested after 48 hours, MEF media was replaced neuronal media (DMEM-F12 + N2 supplement + B27 supplement + insulin + dox), and media was refreshed every 2-3 days.

tag: cell type

value: 5 days


title: MEF+Ascl1_5d_negative_B3_rep2


title: MEF+Ascl1_5d_negative_B2_rep2


title: MEF+Ascl1_RNA_7d_B2

description: merged.genes.fpkm.txt


title: TET2rescue-WT-serum-1


title: TET2rescue-WT-serum-2