title: DRSC_plate2_day2_G6_DRSC37529_FBgn0267821_da

description: 2day RNAi incubation

value: da


title: Sample 6_LUCH_lil-2_r2 MethylC-seq

status: Public on Apr 26 2017

type: SRA

city: La Jolla

first: Julie

middle: Ann

last: Law

state: CA

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

country: USA

institute: The Salk Institute for Biological Studies

library_source: genomic

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering and Mapping: Illumina sequence reads were filtered to remove duplicate reads either with prinseq [71], using the remove exact duplicates option (-derep 1), or the BSseeker2[72] filterReads.py script, using default conditions.  The reads were then mapped to the YJ or LUCH transgene sequences (LUC_transgene6.fa or LUC_transgene7.fa) using bsmap-2.74 [73] with the default parameters, allowing 2 mismatches (-v 2) and allowing uniquely mapping reads and multi-mapping reads with the maximum number of equal best hits set to 2 (-w 2). In addition, the reads were also mapped to the tair10 genome using the BSseeker2 bs_seeker2-align.py script, using the bowtie1 aligner (version bowtie-1.0.0)[74] and allowing for 2 mismatches (-m 2).
Methylation levels: The percent methylation level at each cytosine was calculated using the BSseeker2 bs_seeker2-call_methylation.py script requiring a minimum coverage of 4 reads (-r 4) for mapping to the Tair10 genome or the bsmap methratio.py script, reporting loci with zero methylation ratios (-z) for the YJ and LUCH transgenes. In house scripts were used to convert the resulting .CGmap or .txt files, respectively, into wiggle files containing the percent methylation levels of cytosines covered by at least 4 reads in the CG, CHG, and CHH contexts individually.
DMR calling: DMRs were identified using parameters outlined in Stroud et al. [54] using in house scripts. Briefly, the genome was split into 100bp, non-overlapping bins and the methylation level across each bin in the CG, CHG, or CHH context was calculated independently using the percent methylation values in the wiggle files. The methylation values in each bin were then compared between two samples to call DMRs with the following requirements: (1) To account for 100bp regions of the genome with low numbers of cytosines and for regions that display lower than average coverage, only bins with at least 4 cytosines in the given context that are covered by at least 4 reads in both samples being compared were included in the DMR analysis.  (2) Only bins with an absolute change in methylation of 0.4, 0.2, and 0.1 for the CG, CHG, and CHH contexts, respectively, and with an adjusted p-value of ≤0.01 were identified as DMRs.
Genome_build: TAIR10; LUC_Transgene6.fa; LUC_Transgene7.fa
Supplementary_files_format_and_content: wiggle (.wig) file, header with Chromosome, and two columns: position, % methylation
Supplementary_files_format_and_content: bed file, which has 3 columns:Chr#, start position, end position

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: LUCH_lil-2_r2 MethylC-seq

growth_protocol: Arabidopsis seeds were surface-sterilized and then planted on either half-strength Murashige and Skoog (MS) media supplemented with 8% agar and 1% sucrose or Linsmaier and Skoog (LS) media (Caissen, LSP03) supplemented with 8% agar. Seed were then stratified at 4°C for three days. Plants were grown in a growth incubator at 23°C under either continuous light or short day conditions (8 hrs light, 16 hrs dark). 10-day-old seedlings were used for all of the experiments.

extract_protocol:
For the MethylC-seq libraries corresponding to the “_r2, _r5, and_B” series (Table S4), genomic DNA was extracted using the DNeasy Plant Mini  Kit (Qiagen, Cat# 69104). One microgram of genomic DNA was sonicated into  fragments 150 to 300 bp in length using a Diagenode Bioruptor, followed by purification with the PureLink PCR Purification Kit (Invitrogen, Cat#  K3100-01). For all the remaining MethylC-seq libraries (Table S4), genomic  DNA was extracted from 10-day-old seedlings using the DNeasy Plant Mini Kit  (Qiagen, Cat# 69104). 2 ug of genomic DNA was sonicated into 200 bp fragments using a Covaris S2 Sonicator, followed by purification with Sera-Mag Magnetic SpeedBeads (ThermoScientific, Cat# 65152105050250)."
For the MethylC-seq libraries corresponding to the '_r2, _r5, and_B' series  (Table S4), the sonicated and purified genomic DNA fragments were repaired using the End-It DNA End-Repair Kit (Epicentre, Cat# ER0720), and the DNA fragments were purified using the Agencourt AMPure XP-PCR Purification system (Beckman Coulter, Cat# A63880). The purified DNAs were adenylated at the 3? end using the polymerase activity of Klenow Fragment (3?"5? exo-) (New England Biolabs, Cat# M0212), followed by purification using the Agencourt AMPure XP-PCR Purification system. The methylated adapters in the TruSeq DNA Sample Preparation Kit (Illumina, Cat# FC-121-2001) were ligated to the DNA fragments using T4 DNA Ligase (New England Biolabs, Cat# M0202). After purification using AMPure XP beads, less than 400 ng DNA was subjected to bisulfite conversion using the MethylCode Bisulfite Conversion Kit (Invitrogen, Cat# MECOV-50). PfuTurbo Cx Hotstart DNA polymerase (Agilent, Cat# 600414) and the following PCR conditions were used for amplification: 95°C for 2 minutes; 9 cycles of 98°C for 15 seconds, 60°C for 30 seconds and 72°C for 4 minutes; and 72°C for 10 minutes. The resulting libraries were quantified, pooled and sequenced using HiSeq 2000 with the 101-cycle single-end sequencing mode (Illumina). For all the remaining MethylC-seq libraries (Table S4), the sonicated and purified genomic DNA fragments were repaired using the End-It DNA End-It DNA End-Repair Kit (Epicentre, Cat# ER81050), and the DNA fragments were purified using Sera-Mag Magnetic SpeedBeads. The purified DNAs were adenylated at the 3? end using the polymerase activity of Klenow Fragment (3?"5? exo-) (New England Biolabs, Cat# M0212), followed by purification using Sera-Mag Magnetic SpeedBeads. The methylated adapters in the NEXTflex Bisulfite-Seq Barcodes Kit (BIOO Scientific, Cat# 511911) were ligated to the DNA fragments using T4 DNA Ligase (New England Biolabs, Cat# M0202). After purification using Sera-Mag Magnetic SpeedBeads, the DNA was subjected to bisulfite conversion using the MethylCode Bisulfite Conversion Kit (Invitrogen, Cat# MECOV-50). KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (KAPA Biosystems, Cat# KK2801) and the following PCR conditions were used for amplification: 95°C for 2 minutes; 98°C for 30 seconds; 4 cycles of 98°C for 15 seconds, 60°C for 30 seconds and 72°C for 4 minutes; and 72°C for 10 minutes. After purification using Sera-Mag Magnetic SpeedBeads, the libraries were quantified, pooled and sequenced at single-end 50 base-pair using the Illumina HiSeq 2500 v4 at the Salk NGS Core. Raw sequencing data was de-multiplexed and converted into FASTQ files using CASAVA (v1.8.2)

tag: ecotype

value: Columbia

tag: tissue

value: ten-day-old seedlings

tag: genotype/variation


title: DRSC_plate2_day2_G5_DRSCNA_NA_NA

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: 2day RNAi incubation

library_source: transcriptomic

data_processing:
Base calling was done with Illumina CASAVA 1.8.2 (Illumina, San Diego, CA).
We aligned short reads from RNA-Seq to Drosophila reference genome release 6 from Flybase (http://flybase.org, McQuilton et al., 2012. PMID:22127867) with ERCC spike-in sequences (Jiang et al., 2011. PMID: 21816910).  We used TopHat 2.0.10 aligner in doing that (Trapnell et al., 2009. PMID: 19289445) with -g 1 and -G parameters.  We used Flybase gene model version 6.06 with only major chromosome arms.
We counted gene level mapped reads using HTSeq (Anders et al., 2014. PMID: 25260700) with strand-specific, otherwise default parameters.  We also measured transcript abundance in FPKMs (rapnell et al., 2009. PMID: 19289445) using Cufflinks 2.2.1 (Trapnell et al., 2010. PMID: 20436464).  We have used -G, -b, and -u parameters.
Genome_build: BDGP release 6 (from FlyBase (http://www.flybase.org)
Supplementary_files_format_and_content: We provide tab delimited text files that were generated from HTseq and Cufflink. HTseq results have information on read counts. Cufflinks results contain gene level FPKM values.

molecule: polyA RNA

organism: Drosophila melanogaster

growth_protocol: We used protocols (Ramadan et al., 2007. PubMed ID: 17853882) from the Harvard Drosophila RNAi Screening Center (Boston, MA) to culture Drosophila S2R+ cells (http://www.flyrnai.org/DRSC-PRC.html ).

extract_protocol:
We used RNeasy 96 kits (Qiagen, Valencia, CA) according to the product manual (Protocol for Isolation of Total RNA from Animal Cells using spin technology, Cat#19504) to isolate total RNA from the RNAi-treated cells
Strand-specific RNA-Seq libraries were prepared as in our previous study (Lee et al., 2016, PMID:27599372) with the following exceptions. 1) We used 1ug of total RNA as an input, 2) we purified results from reverse transcription, second strand synthesis, end-repair, and A-tailing with 1.6 volume of MagNA beads (Rohland et al., 2012. PMID:22267522) instead of 1.9 volume, and 3) We ran 13 cycles of PCR amplification instead of 14 cycles. Briefly, we selected polyA+ RNA from total isolated RNA using Dynabeads Oligo(dT)25 (Life Technologies, Grand Island, NY).  Purified polyA+ RNA was fragmented with spike-in RNA from External RNA Control Consortium Standard Reference Material 2374 ( Zook et al., 2012. PMID:22859977).  We used pool 78A (Lee et al., 2016.  PMID:27512518).  We performed strand specific reverse transcription from the fragmented RNA by adding dUTP in the second strand synthesis.  We ligated 24 differently indexed adaptors from TruSeq v2 kit (Illumina, San Diego, CA) to the end-repaired, and 3’ adenylated DNA.  We removed dUTP-incorporated strands using DNA glycoxylase before PCR amplification of libraries.  Our libraries were sequenced on Illumina HiSeq 2500 (76 bp read-length, single-end. Illumina, San Diego, CA).

treatment_protocol: 2.7 ug of dsRNA in 27ul were pre-plated to 96-well plates before adding cells.  We removed serum-containing media from confluent S2R+ cells by centrifugation.  We re-suspended cells in serum-free media to have 100,000 cells per ml.  53 ul of cell suspension was transferred to each well of the dsRNA-containing plates.  We incubated cells for 30 minute, and added 160 ul serum-containing media (10% FBS).   We incubated cells in humidified chamber at 25C for 24, 48, and 72 hours.  After incubation, we removed media with 12-well vacuum wands, and lysed cells with 150 ul of RLT lysis buffer (Qiagen, Valencia, CA, Cat. No. 79216).  We stored lysed cells at -80C until RNA isolation.

tag: cell type

value: S2R+ cells

tag: RNAi target gene id (flybase)

tag: RNAi target gene name

tag: RNAi reagent from harvard drosophila rnai screening center

value: DRSCNA

tag: time point

value: 2day RNAi incubation


title: DRSC_plate2_day2_G4_DRSC30099_FBgn0000611_exd

description: 2day RNAi incubation

value: exd


title: DRSC_plate2_day2_G2_DRSC30105_FBgn0052296_Mrtf

description: 2day RNAi incubation

value: Mrtf


title: DRSC_plate2_day2_G3_DRSC26006_FBgn0261239_Hr39

description: 2day RNAi incubation


title: Sample 3_YJ_mbd7-4_r1 MethylC-seq

source_name: YJ_mbd7-4_r1 MethylC-seq


title: Sample 2_YJ_lil-1_r1 MethylC-seq

source_name: YJ_lil-1_r1 MethylC-seq


title: DRSC_plate2_day2_G1_DRSC32517_FBgn0016694_Pdp1

description: 2day RNAi incubation


title: Sample 1_YJ_r1 MethylC-seq

source_name: YJ_r1 MethylC-seq


title: CS-6

city: Melbourne

first: Cyril

last: Seillet

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

data_processing:
Base calling and quality scoring: Real-Time Analysis v1.12.4.2
FASTQ file generation and de-multiplexing: CASAVA pipeline version 1.8.2
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.16.1) using the in-built mm10 annotation.
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise generalised linear models (McCarthy et al NAR 2012) were fitted to summarise the values from replicates samples using functionality from the edgeR package (version 3.22.0, Smyth, 2005).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: total RNA

organism: Mus musculus

source_name: ILC2 progenitor

extract_protocol:
RNA was harvested using RNeasy Micro Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 100ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Bone marrow cells were flushed and single cell suspension were stained with appropriate antibodies. Cells were FACS-sorted

tag: strain

value: Bone marrow


title: ILC2P-1_CS-5


title: DRSC_plate2_day2_G12_DRSC34905_FBgn0013799_Deaf1

description: 2day RNAi incubation


title: U266_WCE

city: Boston

first: Nikhil

middle: C

last: Munshi

state: MA

address: 450 Brookline Avenue

department: Hematologic Oncology

institute: Dana-Farber Cancer Institute

description: ChIP-Seq whole cell extract (WCE) input control in U266 cells

data_processing:
Sequenced reads were aligned to HG19 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

organism: Homo sapiens

source_name: Multiple Myeloma

growth_protocol: All MM cell lines were cultured in RPMI–1640 media containing 10% fetal bovine serum (FBS, GIBCO, Life technologies, Carlsbad, CA, United States), 2 mmol/L L-glutamine, 100 U/mL penicillin, and 100 mg/mL streptomycin (GIBCO, Life technologies, Carlsbad, CA, United States).

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatin-DNA complexes were isolated with antibody.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.

tag: cell line

tag: input

tag: treatment

tag: barcode

tag: antibody

tag: antibody maker

tag: antibody catalog number


title: ChIP-seq Input for Pax7-ChIP in iPax7 myogenic progenitors -dox 3d

city: New York

first: Karin

last: Lilja

state: New York

address: 522 First Avenue, Smilow Research Building, 1106

department: Cancer Institute

institute: New York University School of Medicine

description: Processed data file: Pax7_plusDox_All_no-chrM.bed.gz (see GSM2394784)

data_processing:
[ATAC-seq] Raw reads were aligned to the Mus musculus mm9 reference genome with Bowtie2 version 2.2.6 using the options ‘--local --dovetail --minins 38 --maxins 2000 --no-mixed --no-discordant’. PCR and optical duplicates were removed with Picard. Prior to downstream analysis, mitochondrial reads were removed and the coordinates of the remaining reads were corrected to account for the 9 bp insert introduced by the Tn5 transposase by offsetting the 5' ends by either +4 (for plus strand reads) or -5 (for minus strand reads) as described (Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods, 10(12), 1213-1218. doi:10.1038/nmeth.2688)
[ATAC-seq] Replicate experiments were merged or kept individual depending on downstream analysis.
[ATAC-seq] For data visualization reads at each locus was normalized per million total reads for each respective individual replicate experiment or merged experiment, and the resulting data were visualized in Integrative Genomics Viewer (IGV) (Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616. Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013). Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform, 14(2), 178-192. doi:10.1093/bib/bbs017.)
[ATAC-seq] Transposase-accessible regions for either individual replicates or merged replicates were identified using the callpeak command of MACS2 version 2.0.10 with options ‘--nomodel --nolambda --keep-dup all --call-summits --f BAM --g mm’ as described (Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., . . . Greenleaf, W. J. (2015). Single-cell chromatin accessibility reveals principles of regulatory variation. Nature, 523(7561), 486-490. doi:10.1038/nature14590)
[RNA-seq] Raw reads were first trimmed of the first 6 bp using Trimmomatic v0.32 (Bolger, Lohse, & Usadel, 2014) and filtered through Bowtie2 v2.2 using default options to remove ribosomal RNAs.
[RNA-seq] The remaining reads were aligned to known Mus musculus mm9 RefSeq genes with the TopHat2 v2.0 and Bowtie2 v2.2 tools (Kim et al., 2013) using options ‘--no-coverage-search --prefilter-multihits --no-discordant --no-mixed -N 0 --b2-very-sensitive,’.
[RNA-seq] Reads were counted across each gene with HTSeq v0.6 (Anders, Pyl, & Huber, 2015) using the default options for non-stranded, paired-end reads.
[RNA-seq] For data visualization reads at each locus was normalized per million total reads for each respective individual replicate experiment or merged experiment, and the resulting data were visualized in Integrative Genomics Viewer (IGV) (Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616. Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013). Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform, 14(2), 178-192. doi:10.1093/bib/bbs017.)
[ChIP-seq] Raw reads were aligned to the Mus musculus reference genome (mm9 assembly), and non-duplicate, uniquely mapped reads were selected for downstream processing as previously described (Bowman et al., 2014; Cheng et al., 2014).
[ChIP-seq] Peak-calling was performed using Qeseq (Micsinai, M., Parisi, F., Strino, F., Asp, P., Dynlacht, B. D., & Kluger, Y. (2012). Picking ChIP-seq peak detectors for analyzing chromatin modification experiments. Nucleic Acids Res, 40(9), e70. doi:10.1093/nar/gks048) with a default p-value of 0.05.  For each histone mark, duplicate reads were removed, replicates were merged, and peaks were called from merged data.  The bed output from Qeseq for ChIP-seq only gave positional information.
[ChIP-seq] For data visualization, (1) each read was extended in the 3' direction by the average DNA fragment length, (2) the number of reads at each locus was normalized per million total reads for each respective experiment, and (3) the resulting data were visualized in Integrative Genomics Viewer (IGV) (Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616. Thorvaldsdottir, H., Robinson, J. T., & Mesirov, J. P. (2013). Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform, 14(2), 178-192. doi:10.1093/bib/bbs017.)
[ChIP-seq] Fragment lengths were 150 bp (histone marks in iPax7 +Dox and iPax7 -Dox cells), 200 bp (myotubes differentiated from iPax7 cells), 230 bp (C2C12 myoblasts over-expressing Flag control or Pax7-Flag protein), and 250 bp (Pax7 ChIP in iPax7 cells).
[ChIP-seq] For Pax7 ChIP-seq, each replicate was used to generate peaks for each condition (+Dox and –Dox). The final list of Pax7-bound sites was generated by retaining peaks that were (1) found in two or more +Dox-treated samples and (2) removing peaks that were found in any replicate without Dox treatment.
Genome_build: mm9
Supplementary_files_format_and_content: [ATAC-seq] bigwig and bed (narrowPeak) files
Supplementary_files_format_and_content: [RNA-seq] bigwig for replicates and merged samples and HTseq counts for replicates
Supplementary_files_format_and_content: [ChIP-seq] bigwig and bed files

source_name: iPax7 myogenic progenitors -dox 3d

growth_protocol:
[iPax7 +dox] iPax7 cells were grown on 0.1% gelatin-coated culture plates in GlutaMAX supplemented IMDM (Gibco) with 15% stem cell qualified fetal bovine serum (Gemini), 200 mg/ml bovine holo-transferrin (Sigma), 10 mg/ml ascorbic acid, 4.5 mM 1-thioglycerol, 100 IU penicillin, and 100 mg/ml streptomycin. Media was changed every two days with the addition of 5 ng/ml recombinant mouse FGF basic protein (R&D systems), and 0.75 mg/ml doxycycline (Dox) for the expression of Pax7.
[iPax7 -dox] iPax7 cells were grown on 0.1% gelatin-coated culture plates and plated in GlutaMAX supplemented IMDM (Gibco) with 15% stem cell qualified fetal bovine serum (Gemini), 200 mg/ml bovine holo-transferrin (Sigma), 10 mg/ml ascorbic acid, 4.5 mM 1-thioglycerol, 100 IU penicillin, and 100 mg/ml streptomycin. Media was changed every two days with the addition of 5 ng/ml recombinant mouse FGF basic protein (R&D systems), and 0.75 mg/ml doxycycline (Dox) for the expression of Pax7. Upon start of -dox time point cells were washed with PBS and cells were now grown in the above mentioned media supplemented with only 5 ng/ml FGF protein and media for mentioned time points for each sample.
[iPax7 myotubes "HS"] iPax7 cells were grown on 0.1% gelatin-coated culture plates in GlutaMAX supplemented IMDM (Gibco) with 15% stem cell qualified fetal bovine serum (Gemini), 200 mg/ml bovine holo-transferrin (Sigma), 10 mg/ml ascorbic acid, 4.5 mM 1-thioglycerol, 100 IU penicillin, and 100 mg/ml streptomycin. Media was changed every two days with the addition of 5 ng/ml recombinant mouse FGF basic protein (R&D systems), and 0.75 mg/ml doxycycline (Dox) for the expression of Pax7. Cells were grown to confluence upon which cells were washed with PBS and differentiated into myotubes in DMEM (Corning) supplemented with 2% horse serum, 2 mM L-Glutamine, 100 IU penicillin, and 100 mg/ml streptomycin ("2% HS medium").
[C2C12 myoblasts] C2C12 myoblast cells were grown in DMEM (Corning) supplemented with 10% Fetal Bovine Serum (FBS), 2 mM L-Glutamine, 100 IU penicillin, and 100 mg/ml streptomycin ("C2C12 growing media").
[C2C12 myotubes "HS"] C2C12 cells were plated in "C2C12 growing media" and grown to confluence upon which cells were washed with PBS and differentiated into myotubes in "2% HS medium".

extract_protocol:
[ATAC-seq] Cells were harvested by trypsinization and resuspended in appropriate media. 500,000 cells were subsequently used for nuclear extraction, except for satellite cells (described separately) and myotubes where 100,000 cells were used to adjust for their multinucleated nature. Cells were washed with 500 µl cold PBS and resuspended in 500 µl cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), and spun at 500g for 10 minutes at 4°C. Supernatant was discarded and the nuclear pellet was resuspended in nuclease-free water and 50,000 cells (10,000 cells for myotubes) in 22.5 µl nuclease free water was mixed with 25 µl TD Buffer and 2.5 µl Tn5 Transposase (Illumina cat #FC-121-130). 50,000 freshly sorted satellite cells from Pax7-ZsGreen mice were washed with 200 µl of cold PBS then resuspended in 100 µl of cold lysis buffer, spun at 500 g for 10 minutes at 4°C and resuspended in 50 µl of the transposition reaction mix. Transposition occurred at 37°C for 30 minutes, after which transposed DNA was purified using a Qiagen MinElute Kit and eluted in 10 ml Elution Buffer. Transposed DNA fragments were mixed with 7 μl nuclease free H2O, 2.5 μl of each forward and reverse 25 µM stock of Nextera PCR primers, 3 μl of 1000x diluted stock of SYBR Green I (Invitrogen #S-7563), 25 μl NEBNext High-Fidelity 2x PCR Master Mix (New England BioLab #M0541). All samples were amplified for 5 cycles (as described in (Buenrostro et al., 2013)) after which 5 µl was aliquoted to determine optimal cycle numbers. 5 μl was mixed with 1.9 μl Nuclease Free H2O, 1.25 μl of each forward and reverse customized 5 μM stock of Nextera PCR primers, 0.6 µl of 1000x diluted stock of SYBR Green I, and 5 μl NEBNext High-Fidelity 2x PCR Master Mix. All samples were amplified for 20 cycles, and the number of additional cycles to the remaining transposed DNA was determined as described by (Buenrostro et al., 2013). Libraries were then purified with 1.2x vol AMPure (Beckman) beads. Tagmentation was confirmed via Tapestation.
[RNA-seq] Bioanalyzer RNA quality and quantity assay picochip was used to measure RNA concentrations for each of the collected samples and ca 1.5 ng/sample were used to generate RNA-seq libraries with SMARTer® Ultra® Low Input RNA for Illumina® Sequencing – HV (Clontech Laboratories) using the manufacturer’s instructions. Libraries were sequenced (51 bp, paired end) on an Illumina HiSeq 2500 machine with v4 chemistry. RNA-seq libraries were prepared with the manufacturer’s instructions.
[ChIP-seq] ChIP and ChIP-seq libraries were prepared as described (Asp, P., Blum, R., Vethantham, V., Parisi, F., Micsinai, M., Cheng, J., . . . Dynlacht, B. D. (2011). Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci U S A, 108(22), E149-158. doi:10.1073/pnas.1102223108) and sequenced (51 bp, single reads) using an Illumina HiSeq 2500 machine.

value: minusdox 3d iPax7 media

tag: chip antibody


title: DRSC_plate2_day2_F8_DRSC23558_FBgn0265784_CrebB

description: 2day RNAi incubation

value: CrebB


title: DRSC_plate2_day2_F9_DRSCNA_NA_NA

description: 2day RNAi incubation


title: DRSC_plate2_day2_G11_DRSC29174_FBgn0000520_dwg

description: 2day RNAi incubation

value: dwg


title: ChIP-seq Input histone marks in iPax7 myogenic progenitors +dox

source_name: iPax7 myogenic progenitors +dox

value: 0.75ug/ml dox in iPax7 media


title: ChIP-seq Input histone marks in iPax7 myogenic progenitors -dox 3d


title: ChIP-seq Input for Pax7-ChIP in iPax7 myogenic progenitors +dox


title: Sample 4_YJ_mbd7-3_r1 MethylC-seq

source_name: YJ_mbd7-3_r1 MethylC-seq

tag: ecotype


title: DRSC_plate2_day2_F5_DRSC30106_FBgn0001168_h

description: 2day RNAi incubation

value: h


title: SAM24327527 anti.ngf.dmso

city: South San Francisco

first: Kevin

last: Huang

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

data_processing: Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from primary DRG neurons grown for 4 days in vitro

extract_protocol: RNA was isolated from primary DRGs (ca 400,000 cells/well) treated with NGF, anti-NGF, and 4 individual wells for ISRIB/anti-NGF and DLKi/anti-NGF using RNeasy Plus Mini Kit (Qiagen).  Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.

tag: tissue

value: dorsal root ganglion neurons


title: SAM24327532 anti.ngf.isrib


title: SAM24327520 ngf.dmso


title: DRSC_plate2_day2_F7_DRSC20260_FBgn0002914_Myb

description: 2day RNAi incubation

value: Myb


title: SAM24327521 ngf.dmso


title: DRSC_plate2_day2_F4_DRSC27700_FBgn0001222_Hsf

description: 2day RNAi incubation

value: Hsf


title: DRSC_plate2_day2_F3_DRSC25984_FBgn0013799_Deaf1

description: 2day RNAi incubation


title: SAM24327533 anti.ngf.isrib


title: SAM24327534 anti.ngf.DLKi


title: DRSC_plate2_day2_F1_DRSC37618_FBgn0039044_p53

description: 2day RNAi incubation


title: DRSC_plate2_day2_F2_DRSC25100_FBgn0004198_ct

description: 2day RNAi incubation

value: ct


title: SAM24327530 anti.ngf.isrib


title: SAM24327535 anti.ngf.DLKi


title: DRSC_plate2_day2_G10_DRSC40910_FBgn0003117_pnr

description: 2day RNAi incubation

value: pnr


title: SAM24327524 ngf.dmso


title: DRSC_plate2_day2_F11_DRSC28794_FBgn0266411_sima

description: 2day RNAi incubation

value: sima


title: DRSC_plate2_day2_F6_DRSC37640_FBgn0003345_sd

description: 2day RNAi incubation

value: S2R+ cells

value: sd


title: DRSC_plate2_day2_F10_DRSC26054_FBgn0016076_vri

description: 2day RNAi incubation

value: vri

value: 2day RNAi incubation


title: DRSC_plate2_day2_E8_DRSC27606_FBgn0001291_Jra

description: 2day RNAi incubation

value: Jra


title: DRSC_plate2_day2_E9_DRSC29930_FBgn0264075_tgo

description: 2day RNAi incubation

value: tgo


title: DRSC_plate2_day2_E7_DRSC24447_FBgn0003964_usp

description: 2day RNAi incubation

value: usp


title: SAM24327528 anti.ngf.dmso


title: DRSC_plate2_day2_E6_DRSC23134_FBgn0004050_z

description: 2day RNAi incubation

value: z


title: SAM24327523 ngf.dmso


title: SAM24327525 anti.ngf.dmso


title: SAM24327526 anti.ngf.dmso


title: SAM24327531 anti.ngf.isrib


title: SAM24327536 anti.ngf.DLKi


title: SAM24327537 anti.ngf.DLKi


title: DRSC_plate2_day2_E3_DRSC40784_FBgn0267821_da

description: 2day RNAi incubation

value: da


title: DRSC_plate2_day2_E4_DRSC37563_FBgn0261283_SREBP

description: 2day RNAi incubation

value: SREBP


title: SAM24327529 anti.ngf.dmso


title: DRSC_plate2_day2_E5_DRSC16977_FBgn0001297_kay

description: 2day RNAi incubation

value: kay


title: DRSC_plate2_day2_F12_DRSC31100_FBgn0002914_Myb

description: 2day RNAi incubation


title: SAM24327522 ngf.dmso

value: dorsal root ganglion neurons


title: DRSC_plate2_day2_E2_DRSCNA_NA_NA

description: 2day RNAi incubation

value: DRSCNA


title: DRSC_plate2_day2_E12_DRSC37262_FBgn0264075_tgo

description: 2day RNAi incubation


title: DRSC_plate2_day2_E11_DRSC18766_FBgn0000520_dwg

description: 2day RNAi incubation

value: dwg


title: DRSC_plate2_day2_E1_DRSC34559_FBgn0001222_Hsf

description: 2day RNAi incubation

value: Hsf


title: DRSC_plate2_day2_E10_DRSC39162_FBgn0000097_aop

description: 2day RNAi incubation

value: aop


title: delchd1_RNA_R2

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description:
Both mRNA and introns were features of interest.
processed data file (mRNA): delChd1_mrna_yae2.txt
processed data file (intron): delChd1_mrna_yae2_int.txt

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were aligned to the sacCer3 genome assembly using TopHat with default options
Genome_build: sacCer3
Supplementary_files_format_and_content: TXT file, including five columns: i) Name, ii) Name, iii) Transcript length, iv) Raw counts of sequencing redads for the features of interest, v) Normalized abundance measurements

organism: Saccharomyces cerevisiae

source_name: yeast cells_CHD1_deletion

growth_protocol: Growth conditions were 30°C in YPD media with shaking at 250 rpm. Yeast cells were grown to mid-log phase (O.D 600 nm of 0.6 to 0.8).

extract_protocol:
Hot acid phenol extraction method
The NEBNext Multiplex Small RNA-Seq Library preparation set for Illumina (New England BioLabs, cat.# E7300L) was used to sequence the samples using Illumina HiSeq 2500.

tag: strain background

tag: genotype

value: CHD1 deletion


title: DRSC_plate2_day2_D9_DRSC25045_FBgn0013263_Trl

description: 2day RNAi incubation

tag: cell type

value: S2R+ cells

tag: RNAi target gene id (flybase)

value: Trl


title: DRSC_plate2_day2_D8_DRSC22973_FBgn0016694_Pdp1

description: 2day RNAi incubation

tag: RNAi target gene name

tag: RNAi reagent from harvard drosophila rnai screening center


title: delchd1_RNA_R1

description:
Both mRNA and introns were features of interest.
processed data file (mRNA): delChd1_mrna_yae1.txt
processed data file (intron): delChd1_mrna_yae1_int.txt


title: WT_RNA_R1

description:
Both mRNA and introns were features of interest.
processed data file (mRNA): wt_mrna_yn1.txt
processed data file (intron): wt_mrna_yn1_int.txt

source_name: yeast cells_wildtype

value: wildtype


title: WT_RNA_R2

description:
Both mRNA and introns were features of interest.
processed data file (mRNA): wt_mrna_yn2.txt
processed data file (intron): wt_mrna_yn2_int.txt


title: DRSC_plate2_day2_D5_DRSC27078_FBgn0003870_ttk

description: 2day RNAi incubation

value: ttk

tag: time point

value: 2day RNAi incubation


title: DRSC_plate2_day2_D7_DRSC11122_FBgn0004396_CrebA

description: 2day RNAi incubation

value: CrebA


title: Mock_R3

description: replicate3, Mock_ChIP

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the sacCer3 genome assembly using BWA with default options
Genome_build: sacCer3
Supplementary_files_format_and_content: Wig format

source_name: yeast cells_wildtype_mock

growth_protocol: Growth conditions were 30°C in YPD media with shaking at 250 rpm. Yeast cells were grown to mid-log phase (O.D 600 nm of 0.6 to 0.8), and fixed with formaldehyde.

extract_protocol:
Cross-linked chromatins were sheared using a sonicator, and immunoprecipitated using the following beads or anti-bodies: anti-Myc conjugated agarose bead (Sigma Aldrich, cat.# E6654) to pull-down Chd1 in the Chd1-13XMyc strains (WT and ten elongation factor mutants), and H3K4me3 antibody (EMD Millipore, cat.# 07-473) and H3K36me3 antibody (Abcam, cat.# ab9050) to pull-down H3K4me3/H3K36me3, respectively, in WT and CHD1 deletion mutant.
The NEBNext ChIP-Seq Library Preparation Master Mix Set for Illumina (New England BioLabs, cat.# E6240L) was used to sequence the samples using Illumina HiSeq 2500.

tag: background strains


title: Mock_R2

description: replicate2, Mock_ChIP


title: DRSC_plate2_day2_D6_DRSC29336_FBgn0003507_srp

description: 2day RNAi incubation

value: srp


title: DRSC_plate2_day2_D3_DRSC21341_FBgn0040305_MTF-1

description: 2day RNAi incubation


title: DRSC_plate2_day2_D2_DRSC08706_FBgn0025725_alphaCOP

description: 2day RNAi incubation

value: alphaCOP


title: Mock_R1

description: replicate1, Mock_ChIP


title: delchd1_H3K36me3_R1

source_name: yeast cells_CHD1_deletion_H3K36me3_ChIP

value: H3K36me3 antibody (Abcam, cat.# ab9050)


title: delchd1_H3K36me3_R2


title: DRSC_plate2_day2_D1_DRSC30999_FBgn0011766_E2f1

description: 2day RNAi incubation


title: WT_H3K36me3 R2

source_name: yeast cells_wildtype_H3K36me3_ChIP


title: delchd1_H3K4me3_R1

source_name: yeast cells_CHD1_deletion_H3K4me3_ChIP

value: H3K4me3 antibody (EMD Millipore, cat.# 07-473)


title: DRSC_plate2_day2_D10_DRSC27330_FBgn0001133_grau

description: 2day RNAi incubation

value: grau


title: DRSC_plate2_day2_D12_DRSC32152_FBgn0033846_mip120

description: 2day RNAi incubation


title: DRSC_plate2_day2_D11_DRSC29572_FBgn0011766_E2f1

description: 2day RNAi incubation


title: WT_H3K36me3 R1


title: DRSC_plate2_day2_C9_DRSC40777_FBgn0039044_p53

description: 2day RNAi incubation


title: WT_H3K4me3 R2

source_name: yeast cells_wildtype_H3K4me3_ChIP


title: WT_H3K4me3 R1


title: DRSC_plate2_day2_C8_DRSC29182_FBgn0033846_mip120

description: 2day RNAi incubation


title: delspt4_CHD1-MYC

source_name: yeast cells_SPT4_deletion_CHD1_ChIP

value: SPT4 deletion

value: anti-Myc conjugated agarose bead (Sigma Aldrich, cat.# E6654)


title: DRSC_plate2_day2_C6_DRSC26931_FBgn0004606_zfh1

description: 2day RNAi incubation


title: DRSC_plate2_day2_C7_DRSCNA_FBgn0260635_NA

description: 2day RNAi incubation

value: DRSCNA


title: DRSC_plate2_day2_C5_DRSC25347_FBgn0003117_pnr

description: 2day RNAi incubation

value: pnr


title: DRSC_plate2_day2_D4_DRSC25219_FBgn0259938_cwo

description: 2day RNAi incubation

value: cwo


title: DRSC_plate2_day2_C4_DRSC41279_FBgn0000611_exd

description: 2day RNAi incubation

value: exd


title: delset1_CHD1-MYC

source_name: yeast cells_SET1_deletion_CHD1_ChIP

value: SET1 deletion


title: delset2_CHD1-MYC

source_name: yeast cells_SET2_deletion_CHD1_ChIP

value: SET2 deletion


title: delrco1_CHD1-MYC

source_name: yeast cells_RCO1_deletion_CHD1_ChIP

value: RCO1 deletion


title: DRSC_plate2_day2_C3_DRSC04917_FBgn0267978_ap

description: 2day RNAi incubation

value: S2R+ cells

value: ap


title: delrtf1_CHD1-MYC

source_name: yeast cells_RTF1_deletion_CHD1_ChIP

value: RTF1 deletion


title: delchd1_H3K4me3_R2

value: CHD1 deletion


title: DRSC_plate2_day2_C2_DRSC40819_FBgn0011763_Dp

description: 2day RNAi incubation

value: Dp

value: 2day RNAi incubation


title: delhtz1_CHD1-MYC

source_name: yeast cells_HTZ1_deletion_CHD1_ChIP

value: HTZ1 deletion


title: DRSC_plate2_day2_C1_DRSC34422_FBgn0004396_CrebA

description: 2day RNAi incubation

value: CrebA


title: DRSC_plate2_day2_C12_DRSC37320_FBgn0265784_CrebB

description: 2day RNAi incubation

value: CrebB


title: DRSC_plate2_day2_C11_DRSCNA_NA_NA

description: 2day RNAi incubation


title: delleo1_CHD1-MYC

source_name: yeast cells_LEO1_deletion_CHD1_ChIP

value: LEO1 deletion

value: anti-Myc conjugated agarose bead (Sigma Aldrich, cat.# E6654)


title: delcdc73_CHD1-MYC

source_name: yeast cells_CDC73_deletion_CHD1_ChIP

value: CDC73 deletion


title: delctr9_CHD1-MYC

source_name: yeast cells_CTR9_deletion_CHD1_ChIP

value: CTR9 deletion


title: DRSC_plate2_day2_C10_DRSC37552_FBgn0001078_ftz-f1

description: 2day RNAi incubation


title: delpaf1_CHD1-MYC

source_name: yeast cells_paf1_deletion_CHD1_ChIP

value: PAF1 deletion


title: DRSC_plate2_day2_B9_DRSC03740_FBgn0003866_tsh

description: 2day RNAi incubation

value: tsh


title: WT_CHD1-MYC_R2

source_name: yeast cells_wildtype_CHD1_ChIP

value: wildtype


title: DRSC_plate2_day2_B8_DRSC03346_FBgn0261239_Hr39

description: 2day RNAi incubation


title: DRSC_plate2_day2_B7_DRSC35831_FBgn0034534_maf-S

description: 2day RNAi incubation

value: maf-S


title: WT_CHD1-MYC_R1


title: DRSC_plate2_day2_H11_DRSC35845_FBgn0011656_Mef2

description: 2day RNAi incubation

value: S2R+ cells


title: DRSC_plate2_day2_B6_DRSC29116_FBgn0003118_pnt

description: 2day RNAi incubation

value: pnt


title: DRSC_plate2_day2_B5_DRSC23794_FBgn0000567_Eip74EF

description: 2day RNAi incubation


title: human pluripotent stem cells, naïve, shNANOG, 2-1

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

data_processing:
Quality cotrol were performed on the raw sequencing data usinf FastQC. Law quality bases were trimmed using Trimmomatic (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25)
Trimmed RNA-seq reads were aligned to the human reference genome (hg19) using TopHat (-read-mismatches 2 --read-gap-length 2 --max-insertion-length 3 --max-deletion-length 3)
Partek Genomics Suite 6.6 was used to produce gene RPKM counts from allinged data
Genome_build: hg19
Supplementary_files_format_and_content: txt file; gene RPKM values

growth_protocol: Human induced pluripotent stem cells were cultured on Matrigel [BD Biosciences] in MEF conditioned medium (MEF-CM) supplemented with 8 ng/ml bFGF [Invitrogen] or maintained on irradiated feeder MEFs (iMEFs) with hPSC medium (DMEM/F12 [Gibco] with 20% Knockout Serum Replacement [Gibco], 100 mM b-mercaptoethanol, 100 mM nonessential amino acid [Gibco], 1 mM L-glutamine [Gibco], and 10 ng/ml bFGF, as previously described (Werbowetski-Ogilvie et al., 2009). Cells were routinely passaged every 5-7 days by mechanical transfer using 1 mg/ml Collagenase IV [Invitrogen]. For the derivation of naïve hPSCs, cells in primed pluripotent states were switched into hPSC medium supplemented with 1 mM MEK inhibitor PD0325901, 3 mM GSK3 inhibitor CHIR99021, and 10 ng/ml LIF (abbreviated LIF/2i) as previously reported (Buecker et al., 2010; Hanna et al., 2010; Li et al., 2009) or de novo reprogramming of somatic cells in naïve conditions. We also established naïve hPSCs using 10 ng/ml LIF and a combination of inhibitors for MEK/ERK (1 mM PD0325901), GSK3 (0.3 mM CHIR99021), LCF/SRC (1 mM WH-4-023), BRAF (0.5 mM SB590885) and ROCK (10 mM Y-27632) (5i)(Theunissen et al., 2014). Emerging colonies with a mESC-like morphology (appeared after 10-20 days of culture) were individually picked and subcultured by trypsinization or mechanical passaging onto feeder-free Matrigel or iMEFs with LIF/2i

extract_protocol:
Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.
Library preparation was achieved from poly-A enriched mRNA, using NEBNext Ultra Directional RNA Library Prep Kit for Illumina, according to the manufacturer's instructions.

value: Human pluripotent stem cells (hPSCs)

tag: cell status

value: naïve

tag: transduced with

value: shNANOG shRNA lentiviruses


title: human pluripotent stem cells, naïve, shNANOG, 2-2


title: human pluripotent stem cells, naïve, shNANOG, 1-2


title: DRSC_plate2_day2_B4_DRSCNA_NA_NA

description: 2day RNAi incubation

value: DRSCNA

value: 2day RNAi incubation


title: NE_3

city: Salt Lake City

first: Melinda

middle: L.

last: Angus-Hill

state: UT

address: 2000 Circle of Hope

department: Medicine

institute: University of Utah

data_processing:
The RNA-Seq reads were aligned to the UCSC mouse reference genome (mm10) plus all possible splice junctions (Ensembl build 73) using Novoalign V2.08.01.
The USeq (v8.7.8) RNASeq application was used to convert splice junction alignments back to genomic space, generate per gene read counts and to call DESeq (v1.14.0) for differential expression analysis. (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing gene identifiers, log2 fold change (DESeq), FDR (DESeq) and per gene read counts (USeq)

source_name: distal colon of Tcf4Het/+ ApcMin/+ animals

growth_protocol: Animals were raised in NE (conventional housing) or EE (enriched housing) conditions for 4 months

extract_protocol:
RNA was isolated using Ambion RNAqueous Kit.
RNA was amplified using Illumina TruSeq Stranded RNA Kit w/ Ribo-Zero Gold, and sequencing was performed on Illumina HiSeq using 50 single-cycle end read. negative binomial distribution (Love et al., 2014). All analyses were quality controlled and coordinated via USeq, an open-source suite of sequencing tools developed by the University of Utah’s Bioinformatics Shared Resource (http://useq.sourceforge.net; (Nix et al., 2008)).

value: distal colon

tag: mouse environmental conditions (ne-non enriched, ee-environmentally enriched)

value: Non-enriched (NE)


title: NE_2


title: NE_4


title: human pluripotent stem cells, naïve, shPOU5F1, 2-2

value: shPOU5F1 shRNA lentiviruses


title: NE_1


title: DRSC_plate2_day2_B2_DRSC03320_FBgn0024371_E2f2

description: 2day RNAi incubation


title: DRSC_plate2_day2_B1_DRSC31026_FBgn0004606_zfh1

description: 2day RNAi incubation


title: EE_4

value: Environmentally Enriched (EE)


title: EE_3


title: DRSC_plate2_day2_B12_DRSC31967_FBgn0040305_MTF-1

description: 2day RNAi incubation


title: DRSC_plate2_day2_B3_DRSC03462_FBgn0010287_Trf

description: 2day RNAi incubation

value: Trf


title: human pluripotent stem cells, naïve, shPOU5F1, 2-1


title: EE_1


title: human pluripotent stem cells, naïve, control, 2-1


title: DRSC_plate2_day2_B10_DRSC25554_FBgn0011656_Mef2

description: 2day RNAi incubation


title: human pluripotent stem cells, naïve, control, 1-2


title: DRSC_plate2_day2_A8_DRSC31684_FBgn0013263_Trl

description: 2day RNAi incubation

value: Trl


title: human pluripotent stem cells, naïve, control, 2-2


title: ChIP-seq Input Myoblasts Pax7-flag C2C12 cells

source_name: Myoblasts Pax7-flag C2C12 cells

tag: treatment

value: 10 % FBS growth media


title: DRSC_plate2_day2_B11_DRSC26287_FBgn0032940_Mondo

description: 2day RNAi incubation

value: Mondo


title: human pluripotent stem cells, naïve, control, 1-1


title: human pluripotent stem cells, naïve, shNANOG, 1-1


title: DRSC_plate2_day2_A7_DRSC31022_FBgn0001297_kay

description: 2day RNAi incubation

value: kay


title: DRSC_plate2_day2_A9_DRSC34303_FBgn0003507_srp

description: 2day RNAi incubation

value: srp


title: ChIP-seq H3K4me3 Myoblasts Pax7-flag C2C12 cells

value: H3K4me3 (Active Motif 39159, 2.5 ug for ChIP)


title: ChIP-seq H3K27me3 Myoblasts Pax7-flag C2C12 cells

value: H3K27me3 (Millipore 07-449, 2.5 ug for ChIP)


title: human pluripotent stem cells, naïve, shPOU5F1, 1-2

value: Human pluripotent stem cells (hPSCs)


title: human pluripotent stem cells, primed, control, 2-2

value: primed


title: human pluripotent stem cells, primed, control, 2-1


title: DRSC_plate2_day2_A5_DRSC35830_FBgn0034534_maf-S

description: 2day RNAi incubation

value: S2R+ cells

value: maf-S


title: ChIP-seq H3K4me1 Myoblasts Pax7-flag C2C12 cells

value: H3K4me1 (Abcam ab8895, 2.5 ug for ChIP)


title: ChIP-seq H3K27Ac Myoblasts Pax7-flag C2C12 cells

value: H3K27Ac (Abcam ab4729, 2.5 ug for ChIP)


title: DRSC_plate2_day2_A6_DRSC41069_FBgn0032940_Mondo

description: 2day RNAi incubation

value: 2day RNAi incubation


title: DRSC_plate2_day2_A4_DRSC33100_FBgn0266411_sima

description: 2day RNAi incubation

value: sima


title: EE_2

value: distal colon

value: Environmentally Enriched (EE)


title: ChIP-seq Input Myoblasts flag control C2C12 cells

source_name: Myoblasts flag control C2C12 cells


title: human pluripotent stem cells, naïve, shPOU5F1, 1-1

value: naïve

value: shPOU5F1 shRNA lentiviruses


title: DRSC_plate2_day2_A3_DRSC31698_FBgn0016076_vri

description: 2day RNAi incubation

value: vri


title: human pluripotent stem cells, primed, control, 1-1


title: human pluripotent stem cells, primed, control, 1-2


title: ChIP-seq H3K27me3 Myoblasts flag control C2C12 cells

value: 10 % FBS growth media


title: ChIP-seq H3K4me3 Myoblasts flag control C2C12 cells


title: DRSC_plate2_day2_A2_DRSC30795_FBgn0001291_Jra

description: 2day RNAi incubation

value: Jra


title: ChIP-seq H3K4me1 Myoblasts flag control C2C12 cells


title: DRSC_plate2_day2_A12_DRSC37538_FBgn0024371_E2f2

description: 2day RNAi incubation


title: ChIP-seq H3K27Ac Myoblasts flag control C2C12 cells


title: ChIP-seq H3K27me3 2% HS from iPax7 myogenic progenitors

source_name: 2% HS from iPax7 myogenic progenitors

value: 2 percent horse serum media


title: ChIP-seq Input 2% HS from iPax7 myogenic progenitors


title: DRSC_plate1_day1_H9_DRSC31627_FBgn0261283_SREBP

description: 1day RNAi incubation

value: SREBP

value: 1day RNAi incubation


title: DRSC_plate2_day2_A11_DRSC40711_FBgn0000567_Eip74EF

description: 2day RNAi incubation


title: DRSC_plate2_day2_A10_DRSC36079_FBgn0003964_usp

description: 2day RNAi incubation

value: usp


title: ChIP-seq H3K4me3 2% HS from iPax7 myogenic progenitors

value: H3K4me3 (Active Motif 39159, 2.5 ug for ChIP)


title: ChIP-seq H3K4me1 2% HS from iPax7 myogenic progenitors


title: DRSC_plate1_day1_H6_DRSC40439_FBgn0003870_ttk

description: 1day RNAi incubation

value: S2R+ cells

value: ttk


title: DRSC_plate1_day1_H8_DRSC37675_FBgn0003866_tsh

description: 1day RNAi incubation

value: tsh


title: ChIP-seq H3K27Ac 2% HS from iPax7 myogenic progenitors

value: H3K27Ac (Abcam ab4729, 2.5 ug for ChIP)


title: ChIP-seq H3K27me3 in iPax7 myogenic progenitors -dox 3d

source_name: iPax7 myogenic progenitors -dox 3d

value: minusdox 3d iPax7 media

value: H3K27me3 (Millipore 07-449, 2.5 ug for ChIP)


title: DRSC_plate1_day1_H7_DRSC37439_FBgn0259938_cwo

description: 1day RNAi incubation

value: cwo


title: DRSC_plate1_day1_H4_DRSC32506_FBgn0052296_Mrtf

description: 1day RNAi incubation

value: Mrtf


title: DRSC_plate1_day1_H5_DRSC35747_FBgn0001078_ftz-f1

description: 1day RNAi incubation


title: ChIP-seq H3K4me3 in iPax7 myogenic progenitors -dox 3d


title: ChIP-seq H3K4me3 in iPax7 myogenic progenitors +dox

source_name: iPax7 myogenic progenitors +dox

value: 0.75ug/ml dox in iPax7 media


title: DRSC_plate1_day1_H2_DRSC37384_FBgn0267978_ap

description: 1day RNAi incubation

value: ap


title: DRSC_plate1_day1_H1_DRSC40479_FBgn0003345_sd

description: 1day RNAi incubation

value: sd


title: DRSC_plate2_day2_A1_DRSC37534_FBgn0011763_Dp

description: 2day RNAi incubation

value: Dp

value: 2day RNAi incubation


title: ChIP-seq H3K4me1 in iPax7 myogenic progenitors -dox 3d

value: H3K4me1 (Abcam ab8895, 2.5 ug for ChIP)


title: DRSC_plate1_day1_H11_DRSC35845_FBgn0011656_Mef2

description: 1day RNAi incubation

value: 1day RNAi incubation


title: ChIP-seq H3K4me1 in iPax7 myogenic progenitors +dox


title: ChIP-seq Pax7 in iPax7 myogenic progenitors +dox

source_name: Pax7 in iPax7 myogenic progenitors +dox

value: Pax7 (DSHB, 3 ug for ChIP)


title: DRSC_plate1_day1_G9_DRSC32788_FBgn0000097_aop

description: 1day RNAi incubation

value: aop


title: DRSC_plate1_day1_G8_DRSC31645_FBgn0003118_pnt

description: 1day RNAi incubation

value: S2R+ cells

value: pnt


title: ChIP-seq Pax7 in iPax7 myogenic progenitors -dox 3d


title: DRSC_plate1_day1_G7_DRSC37681_FBgn0004050_z

description: 1day RNAi incubation

value: z


title: ChIP-seq H3K27me3 in iPax7 myogenic progenitors +dox


title: RNA-seq Satellite cells

source_name: Satellite cells

value: in vivo


title: RNA-seq +dox iPax7 myogenic progenitors

source_name: plusdox iPax7 myogenic progenitors


title: RNA-seq -dox 3d iPax7 myogenic progenitors

source_name: -dox 3d iPax7 myogenic progenitors

value: minusdox 3d iPax7 media


title: DRSC_plate1_day1_G6_DRSC37529_FBgn0267821_da

description: 1day RNAi incubation

value: da


title: DRSC_plate1_day1_G5_DRSCNA_NA_NA

description: 1day RNAi incubation

value: DRSCNA


title: DRSC_plate1_day1_G4_DRSC30099_FBgn0000611_exd

description: 1day RNAi incubation

value: exd


title: DRSC_plate1_day1_G3_DRSC26006_FBgn0261239_Hr39

description: 1day RNAi incubation


title: DRSC_plate1_day1_H3_DRSC31616_FBgn0001168_h

description: 1day RNAi incubation

value: h


title: DRSC_plate1_day1_H12_DRSC40438_FBgn0004198_ct

description: 1day RNAi incubation

value: ct


title: ATAC-seq Myoblasts from C2C12 cells

source_name: Myoblasts from C2C12 cells

value: 10 % FBS growth media


title: ChIP-seq H3K27Ac in iPax7 myogenic progenitors -dox 3d

value: H3K27Ac (Abcam ab4729, 2.5 ug for ChIP)


title: ChIP-seq H3K27Ac in iPax7 myogenic progenitors +dox

value: 0.75ug/ml dox in iPax7 media


title: ATAC-seq Myotubes from C2C12 cells

source_name: Myotubes from C2C12 cells

value: 2 percent horse serum media


title: DRSC_plate1_day1_G11_DRSC29174_FBgn0000520_dwg

description: 1day RNAi incubation

value: dwg

value: 1day RNAi incubation


title: DRSC_plate1_day1_G1_DRSC32517_FBgn0016694_Pdp1

description: 1day RNAi incubation


title: ATAC-seq Myotubes from iPax7 myogenic progenitors


title: ATAC-seq Myoblasts Pax7-flag from C2C12 cells

source_name: Myoblasts Pax7-flag from C2C12 cells


title: ATAC-seq iPax7 myogenic progenitors -dox 3d


title: DRSC_plate1_day1_G10_DRSC40910_FBgn0003117_pnr

description: 1day RNAi incubation

value: pnr


title: DRSC_plate1_day1_G2_DRSC30105_FBgn0052296_Mrtf

description: 1day RNAi incubation

value: S2R+ cells

value: Mrtf


title: DRSC_plate1_day1_H10_DRSC32737_FBgn0001133_grau

description: 1day RNAi incubation

value: grau


title: DRSC_plate1_day1_F9_DRSCNA_NA_NA

description: 1day RNAi incubation


title: DRSC_plate1_day1_F8_DRSC23558_FBgn0265784_CrebB

description: 1day RNAi incubation

value: CrebB


title: ATAC-seq iPax7 myogenic progenitors +dox

source_name: iPax7 myogenic progenitors


title: ATAC-seq Satellite cells

value: in vivo


title: ATAC-seq iPax7 myogenic progenitors -dox 12h

source_name: iPax7 myogenic progenitors -dox 12h

value: minusdox 12h iPax7 media


title: DRSC_plate1_day1_F7_DRSC20260_FBgn0002914_Myb

description: 1day RNAi incubation

value: Myb


title: DRSC_plate1_day1_F6_DRSC37640_FBgn0003345_sd

description: 1day RNAi incubation

value: sd


title: DRSC_plate1_day1_F5_DRSC30106_FBgn0001168_h

description: 1day RNAi incubation

value: h


title: DRSC_plate1_day1_F3_DRSC25984_FBgn0013799_Deaf1

description: 1day RNAi incubation


title: 11178X41

description: Microbiome Genomic DNA from Mouse stool

data_processing:
Library strategy: Microbiome sequencing
Sequenced reads were analyzed using Quantitative Insights Into Microbial Ecology (QIIME) tools and MacQIIME software package version 1.9.1 (compiled by Werner Lab, SUNY, http://www.wernerlab.org/software/macqiime/citations). De-multiplexed fastq files from the MiSeq were assembled using the fastq-join method and all unassembled sequences were discarded. Analysis was performed following de-novo OUT picking protocol. Sequences were binned into a single fasta file by sampleID, and sequences with 97% or greater similarity were grouped into Open Taxonomic Units (OTUs) with Uclust (Edgar, 2010). Representative sequences were then aligned against the Greengenes core set (version 13_8) using PyNAST using the default of minimum sequence length of 150 and minimum percent id of 75% (Caporaso et al., 2010a; DeSantis et al., 2006). Uclust consensus taxonomy assigner was then used to assign taxonomy (Caporaso et al., 2010b; Edgar, 2010). For alpha- diversity analyses, all samples were rarefied to 20,000 OTUs to remove sequencing-depth variation bias. All other taxonomy summaries were calculated in terms of relative abundance using QIIME’s summarize taxa script (http://qiime.org/scripts/summarize_taxa.html).
Genome_build: metagenome
Supplementary_files_format_and_content: tab-delimited text files listing Taxonomic rank, bacteria name, average relative abundance of that bacteria for each condition, standard error of the mean for each condition, number of samples in each condition and a p-value generated using a two-sample t-test with Welch correction

organism: mouse gut metagenome

source_name: Stool isolated from male mice

growth_protocol: Animals were grown in EE and NE conditions and stool was collected when animals were 4 months of age.

extract_protocol:
Great care was taken to avoid microbial variability that is independent of experimental design.  Since the microbiome is transmitted from the dam, female C57BL/6J mice were newly purchased from Jackson labs as dams of all animals in the experiment, Further, animals from each genotype were housed together until weaning, then placed within their respective environment, to avoid non-genetic or environmental effects (Moon et al., 2015). Given the possible confounding effects of coprophagia, each cage contained similar numbers of animals from all 4 genotypes: wild-type, Tcf4Het/+ Apc+/+, Tcf4+/+ ApcMin/+, and Tcf4Het/+ ApcMin/+. Stool was collected from all mice at time of sacrifice from colon during dissection. Genomic DNA was isolated from control and enriched mouse stool samples using QIAamp DNA Stool Minikit (QIAGEN, 51504) following manufacturer’s instructions for stool pathogen detection protocol.
Primers were designed to selectively amplify the V1-V3 bacterial genomic 16S rRNA regions and include adapter sequences compatible with the Nextera XT 96 Index Kit by Illumina. The two primer sequences chosen have been published previously as Bosshard forward and 533 reverse (Table S5; (Bosshard et al., 2002; Chen et al., 2012). Samples were amplified using 2x KAPA HiFi HotStart Ready Mix (KAPA Biosystems, KK2601) with primers at a final working concentration of 1 µM, purified using Agencourt AMPure XP beads (Beckman Coulter Genomics, A63880), and indexed using Nextera XT 96 Index Kit (Illumina, FC-131-1002). Final samples were re-purified using Agencourt AMPure XP beads (Beckman Coulter Genomics, A63880), resuspended in 10 mM Tris, pH 8.5, and pooled at a final concentration of 4 nM.

tag: mouse genotype

value: WT

value: Non-enriched (NE)

tag: barcode sequence

value: GGACTCCTAGAGTAGA

tag: linker primer sequence

value: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG


title: DRSC_plate1_day1_F2_DRSC25100_FBgn0004198_ct

description: 1day RNAi incubation

value: ct


title: DRSC_plate1_day1_G12_DRSC34905_FBgn0013799_Deaf1

description: 1day RNAi incubation


title: 11178X40

description: Microbiome Genomic DNA from Mouse stool

value: TCCTGAGCAGAGTAGA


title: ATAC-seq Myoblasts flag control from C2C12 cells

source_name: Myoblasts flag control from C2C12 cells

value: 10 % FBS growth media


title: DRSC_plate1_day1_F1_DRSC37618_FBgn0039044_p53

description: 1day RNAi incubation

value: 1day RNAi incubation


title: 11178X35

description: Microbiome Genomic DNA from Mouse stool

value: AAGAGGCATATCCTCT


title: 11178X38

description: Microbiome Genomic DNA from Mouse stool

value: CGTACTAGAGAGTAGA


title: 11178X36

description: Microbiome Genomic DNA from Mouse stool

value: GTAGAGGATATCCTCT


title: 11178X37

description: Microbiome Genomic DNA from Mouse stool

value: TAAGGCGAAGAGTAGA


title: 11178X39

description: Microbiome Genomic DNA from Mouse stool

value: AGGCAGAAAGAGTAGA


title: 11178X31

description: Microbiome Genomic DNA from Mouse stool

value: Tcf4Het ApcMin

value: CTCTCTACTATCCTCT


title: DRSC_plate1_day1_E7_DRSC24447_FBgn0003964_usp

description: 1day RNAi incubation

value: S2R+ cells

value: usp


title: 11178X33

description: Microbiome Genomic DNA from Mouse stool

value: GCTACGCTTATCCTCT


title: DRSC_plate1_day1_F12_DRSC31100_FBgn0002914_Myb

description: 1day RNAi incubation

value: Myb


title: DRSC_plate1_day1_F10_DRSC26054_FBgn0016076_vri

description: 1day RNAi incubation

value: vri


title: 11178X34

description: Microbiome Genomic DNA from Mouse stool

value: Non-enriched (NE)

value: CGAGGCTGTATCCTCT

value: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG


title: DRSC_plate1_day1_E5_DRSC16977_FBgn0001297_kay

description: 1day RNAi incubation

value: kay


title: ATAC-seq iPax7 myogenic progenitors -dox 24h

source_name: iPax7 myogenic progenitors -dox 24h

value: minusdox 24h iPax7 media


title: DRSC_plate1_day1_E6_DRSC23134_FBgn0004050_z

description: 1day RNAi incubation

value: z

value: 1day RNAi incubation


title: 11178X30

description: Microbiome Genomic DNA from Mouse stool

value: TAGGCATGTATCCTCT


title: DRSC_plate1_day1_E3_DRSC40784_FBgn0267821_da

description: 1day RNAi incubation

value: da


title: DRSC_plate1_day1_E2_DRSCNA_NA_NA

description: 1day RNAi incubation

value: DRSCNA


title: DRSC_plate1_day1_E9_DRSC29930_FBgn0264075_tgo

description: 1day RNAi incubation

value: tgo


title: DRSC_plate1_day1_F11_DRSC28794_FBgn0266411_sima

description: 1day RNAi incubation

value: sima


title: 11178X28

description: Microbiome Genomic DNA from Mouse stool

value: ApcMin

value: TCCTGAGCTATCCTCT


title: 11178X26

description: Microbiome Genomic DNA from Mouse stool

value: CGTACTAGTATCCTCT


title: 11178X27

description: Microbiome Genomic DNA from Mouse stool

value: AGGCAGAATATCCTCT


title: DRSC_plate1_day1_F4_DRSC27700_FBgn0001222_Hsf

description: 1day RNAi incubation

value: S2R+ cells

value: Hsf


title: DRSC_plate1_day1_E12_DRSC37262_FBgn0264075_tgo

description: 1day RNAi incubation


title: 11178X29

description: Microbiome Genomic DNA from Mouse stool

value: Non-enriched (NE)

value: GGACTCCTTATCCTCT


title: DRSC_plate1_day1_E8_DRSC27606_FBgn0001291_Jra

description: 1day RNAi incubation

value: Jra


title: 11178X32

description: Microbiome Genomic DNA from Mouse stool

value: Tcf4Het ApcMin

value: CAGAGAGGTATCCTCT

value: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG


title: DRSC_plate1_day1_E4_DRSC37563_FBgn0261283_SREBP

description: 1day RNAi incubation

value: SREBP

value: 1day RNAi incubation


title: DRSC_plate1_day1_E11_DRSC18766_FBgn0000520_dwg

description: 1day RNAi incubation

value: dwg


title: 11178X25

description: Microbiome Genomic DNA from Mouse stool

value: WT

value: Environmentally Enriched (EE)

value: TAAGGCGATATCCTCT


title: 11178X24

description: Microbiome Genomic DNA from Mouse stool

value: GTAGAGGACTCTCTAT


title: 11178X23

description: Microbiome Genomic DNA from Mouse stool

value: AAGAGGCACTCTCTAT


title: DRSC_plate1_day1_E1_DRSC34559_FBgn0001222_Hsf

description: 1day RNAi incubation


title: 11178X22

description: Microbiome Genomic DNA from Mouse stool

value: CGAGGCTGCTCTCTAT


title: DRSC_plate1_day1_E10_DRSC39162_FBgn0000097_aop

description: 1day RNAi incubation

value: S2R+ cells

value: aop


title: DRSC_plate1_day1_D8_DRSC22973_FBgn0016694_Pdp1

description: 1day RNAi incubation


title: 11178X21

description: Microbiome Genomic DNA from Mouse stool

value: GCTACGCTCTCTCTAT


title: 11178X19

description: Microbiome Genomic DNA from Mouse stool

value: CTCTCTACCTCTCTAT


title: DRSC_plate1_day1_D4_DRSC25219_FBgn0259938_cwo

description: 1day RNAi incubation

value: cwo


title: DRSC_plate1_day1_D3_DRSC21341_FBgn0040305_MTF-1

description: 1day RNAi incubation


title: DRSC_plate1_day1_D6_DRSC29336_FBgn0003507_srp

description: 1day RNAi incubation

value: srp


title: 11178X20

description: Microbiome Genomic DNA from Mouse stool

value: CAGAGAGGCTCTCTAT


title: DRSC_plate1_day1_D9_DRSC25045_FBgn0013263_Trl

description: 1day RNAi incubation

value: Trl


title: DRSC_plate1_day1_D5_DRSC27078_FBgn0003870_ttk

description: 1day RNAi incubation

value: ttk


title: 11178X16

description: Microbiome Genomic DNA from Mouse stool

value: TCCTGAGCCTCTCTAT

value: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG


title: DRSC_plate1_day1_D12_DRSC32152_FBgn0033846_mip120

description: 1day RNAi incubation

value: 1day RNAi incubation


title: 11178X18

description: Microbiome Genomic DNA from Mouse stool

value: Environmentally Enriched (EE)

value: TAGGCATGCTCTCTAT


title: DRSC_plate1_day1_D7_DRSC11122_FBgn0004396_CrebA

description: 1day RNAi incubation

value: CrebA


title: DRSC_plate1_day1_D1_DRSC30999_FBgn0011766_E2f1

description: 1day RNAi incubation


title: 11178X15

description: Microbiome Genomic DNA from Mouse stool

value: AGGCAGAACTCTCTAT


title: DRSC_plate1_day1_D2_DRSC08706_FBgn0025725_alphaCOP

description: 1day RNAi incubation

value: alphaCOP


title: DRSC_plate1_day1_D11_DRSC29572_FBgn0011766_E2f1

description: 1day RNAi incubation

value: S2R+ cells


title: 11178X13

description: Microbiome Genomic DNA from Mouse stool

value: Tcf4Het ApcMin

value: TAAGGCGACTCTCTAT


title: 11178X14

description: Microbiome Genomic DNA from Mouse stool

value: CGTACTAGCTCTCTAT


title: 11178X12

description: Microbiome Genomic DNA from Mouse stool

value: GTAGAGGAGCGTAAGA


title: DRSC_plate1_day1_D10_DRSC27330_FBgn0001133_grau

description: 1day RNAi incubation

value: grau


title: 11178X11

description: Microbiome Genomic DNA from Mouse stool

value: AAGAGGCAGCGTAAGA


title: DRSC_plate1_day1_C9_DRSC40777_FBgn0039044_p53

description: 1day RNAi incubation


title: 11178X17

description: Microbiome Genomic DNA from Mouse stool

value: GGACTCCTCTCTCTAT


title: 11178X10

description: Microbiome Genomic DNA from Mouse stool

value: CGAGGCTGGCGTAAGA


title: 11178X9

description: Microbiome Genomic DNA from Mouse stool

value: GCTACGCTGCGTAAGA


title: DRSC_plate1_day1_C7_DRSCNA_FBgn0260635_NA

description: 1day RNAi incubation

value: DRSCNA


title: 11178X8

description: Microbiome Genomic DNA from Mouse stool

value: ApcMin

value: CAGAGAGGGCGTAAGA

value: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG


title: DRSC_plate1_day1_C4_DRSC41279_FBgn0000611_exd

description: 1day RNAi incubation

value: exd

value: 1day RNAi incubation


title: 11178X7

description: Microbiome Genomic DNA from Mouse stool

value: Environmentally Enriched (EE)

value: CTCTCTACGCGTAAGA


title: DRSC_plate1_day1_C5_DRSC25347_FBgn0003117_pnr

description: 1day RNAi incubation

value: S2R+ cells

value: pnr


title: 11178X3

description: Microbiome Genomic DNA from Mouse stool

value: AGGCAGAAGCGTAAGA


title: 11178X2

description: Microbiome Genomic DNA from Mouse stool

value: CGTACTAGGCGTAAGA


title: DRSC_plate1_day1_C2_DRSC40819_FBgn0011763_Dp

description: 1day RNAi incubation

value: Dp


title: DRSC_plate1_day1_C12_DRSC37320_FBgn0265784_CrebB

description: 1day RNAi incubation

value: CrebB


title: DRSC_plate1_day1_C3_DRSC04917_FBgn0267978_ap

description: 1day RNAi incubation

value: ap


title: 11178X5

description: Microbiome Genomic DNA from Mouse stool

value: GGACTCCTGCGTAAGA


title: 11178X1

description: Microbiome Genomic DNA from Mouse stool

value: TAAGGCGAGCGTAAGA


title: 11178X4

description: Microbiome Genomic DNA from Mouse stool

value: TCCTGAGCGCGTAAGA


title: DRSC_plate1_day1_C1_DRSC34422_FBgn0004396_CrebA

description: 1day RNAi incubation

value: CrebA


title: 11178X6

description: Microbiome Genomic DNA from Mouse stool

value: ApcMin

value: TAGGCATGGCGTAAGA


title: Drought treatment: Treat_3_Seogwang9

city: Daegu

first: Sang-Uk

last: Lee

address: 80 Daehakro, Bukgu

country: South Korea

institute: Kyungpook National University

data_processing:
Sequencing quality assessment with RSeQC and FastQC
Read alignment with TopHat
Transcript quantification with Cufflinks
https://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html
Genome_build: Populus trichocarpa genome: http://plants.ensembl.org/Populus_trichocarpa/Location/Genome?db=;g=POPTR_0001s00200;r=1:12436-13808;t=POPTR_0001s00200.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Populus davidiana

source_name: Leaf

growth_protocol: The saplings of P. davidiana sensitive and tolerant cultivars were re-propagated on MS [4.4 g MS, 3% Sucrose, 0.27% Gelrite at a final pH 5.8, supplemented with 0.5ppm Naphthalene acetic acid (NAA)] by internode culture for organogenesis and kept at 23◦C (16 h light/ 8 h dark cycle)

extract_protocol:
RNA was extracted from triplicate leaf samples of treated and control plants using RNeasy® Plant Mini Kit (Qiagen) according to standard protocol provided by the manufacturer.
RNA was purified using miRNeasy Kit (Qiagen), following the manufacturer’s instructions. Quality of RNA was analyzed by Agilent 2100 Bioanalyzer QC and samples with RIN(RNA Integrity Number) 7 ≥ and 28s/18s ratio 1.0 ≥ were used for c DNA synthesis. Library was prepared using TruSeq RNA library prep kit (Illumina) for 100bp paired-end sequencing.  Briefly, poly A tailed transcript RNA was isolated using oligo(dT) selection from 2µg total RNA and ramdomly fragmented by Mg 2+  ion treatment. The fragmented mRNA was subjected to cDNA synthesis through random hexamer priming. End-repair, A-tailing and Adapter ligation was conducted for Blunt-end producing and Adapter genernation. After that c DNA was amplified by PCRcDNA libraries were quantified by KAPA library quantification kit (Illumina). Samples were sequenced using Hiseq-2500 sequencer (Illumina)

treatment_protocol: About six week old plants were used for drought stress treatment. To have a robust change in gene expression plants were carefully up-rooted from the medium, washed carefully with sterile distilled water and left in open air for about 10 minutes to induced drought stress.

tag: drought sensitivity

value: tolerant

tag: developmental stage

value: Seedling

tag: cultivar

value: leaf


title: DRSC_plate1_day1_C11_DRSCNA_NA_NA

description: 1day RNAi incubation

value: DRSCNA

value: 1day RNAi incubation


title: DRSC_plate1_day1_C10_DRSC37552_FBgn0001078_ftz-f1

description: 1day RNAi incubation

value: S2R+ cells


title: Drought treatment: Treat_1_Seogwang9

tag: tissue


title: DRSC_plate1_day1_B9_DRSC03740_FBgn0003866_tsh

description: 1day RNAi incubation

tag: cell type

value: tsh


title: DRSC_plate1_day1_B7_DRSC35831_FBgn0034534_maf-S

description: 1day RNAi incubation

tag: RNAi target gene id (flybase)

value: maf-S


title: Drought treatment: Treat_2_Seogwang9


title: Drought treatment: Control_3_Seogwang9


title: DRSC_plate1_day1_B8_DRSC03346_FBgn0261239_Hr39

description: 1day RNAi incubation

tag: RNAi target gene name


title: DRSC_plate1_day1_C6_DRSC26931_FBgn0004606_zfh1

description: 1day RNAi incubation

tag: RNAi reagent from harvard drosophila rnai screening center


title: DRSC_plate1_day1_C8_DRSC29182_FBgn0033846_mip120

description: 1day RNAi incubation

tag: time point


title: Drought treatment: Control_2_Seogwang9


title: Drought treatment: Control_1_Seogwang9


title: DRSC_plate1_day1_B4_DRSCNA_NA_NA

description: 1day RNAi incubation


title: DRSC_plate1_day1_B5_DRSC23794_FBgn0000567_Eip74EF

description: 1day RNAi incubation


title: DRSC_plate1_day1_B6_DRSC29116_FBgn0003118_pnt

description: 1day RNAi incubation

value: pnt


title: DRSC_plate1_day1_B2_DRSC03320_FBgn0024371_E2f2

description: 1day RNAi incubation


title: DRSC_plate1_day1_B3_DRSC03462_FBgn0010287_Trf

description: 1day RNAi incubation

value: Trf


title: DRSC_plate1_day1_B1_DRSC31026_FBgn0004606_zfh1

description: 1day RNAi incubation


title: Drought treatment: Treat_1_Seogwang15

value: sensitive


title: Drought treatment: Treat_2_Seogwang15


title: P5-dcKO-TazYap-2

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
RNA-seq: Reads mapped to mm10 whole genome by Tophat with default options
ChIP-seq: Reads mapped to rn5 whole genome by Bowtie2 with default options
RNA-seq: Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file.
ChIP-seq: Peak calling was performed using MACS1.4 with a default p value cut off.
Genome_build: mm10
Genome_build: rn5
Supplementary_files_format_and_content: format:fpkm_traking ; Contain the estimated expression values produced by Cufflinks.
Supplementary_files_format_and_content: wig files were generated by MACS14

source_name: sciatic nerve

growth_protocol: Rat Schwann cells from sciatic nerves of newborn rats (1–2 days-old) were isolated. Schwann cells were grown routinely in DMEM/10% FBS (Life Technologies), supplemented with 10 ng/ml Neuregulin 1 (Nrg1; R&D Systems), and 5 μM forskolin (Sigma), plus L-glutamine and penicillin/streptomycin, hereafter denoted as SC proliferation medium. Cells between passages 2 and 6 were used in all experiments. >95% SC purity was achieved, assessed by positive SOX10 and S100β immunoreactivity.

extract_protocol:
RNA from control and Gnas or TazYap mutant cerebella were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
Purified rat SCs (∼20 million cells) were fixed for 10 min at room temperature with 1% formaldehyde-containing medium. Nuclei were isolated and sonicated in sonication buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA, and protease inhibitor cocktail). Sonicated chromatin (∼300 μg) was used for immunoprecipitation by incubation with rabbit IgG oranti-Taz, anti-H3K27ac antibody (4 μg) overnight at 4°C.
RNA-seq libraries were prepared using Illumina RNA-Seq Preparation Kit.
The ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB catalogue number E6240L) and then run on the Illumina sequencer HiSeq 2000.

tag: sample type

value: Mutant

tag: passage

tag: genotype/variation

value: Tazfl/fl;Yapfl/fl;Dhh-cre


title: Drought treatment: Treat_3_Seogwang15


title: Drought treatment: Control_3_Seogwang15


title: DRSC_plate1_day1_B12_DRSC31967_FBgn0040305_MTF-1

description: 1day RNAi incubation


title: Drought treatment: Treat_3_Palgong2


title: P5-cKOTaz-HetYap-2

value: Tazfl/fl;Yapfl/+;Dhh-cre


title: Drought treatment: Control_2_Seogwang15


title: Drought treatment: Control_1_Seogwang15


title: P5-cKOTaz-HetYap-1


title: DRSC_plate1_day1_A9_DRSC34303_FBgn0003507_srp

description: 1day RNAi incubation

value: srp


title: P5-Ctr-TazYap-2

value: Control

value: Tazfl/fl;Yapfl/fl


title: Drought treatment: Treat_1_Palgong2

value: tolerant


title: DRSC_plate1_day1_A8_DRSC31684_FBgn0013263_Trl

description: 1day RNAi incubation

value: Trl


title: DRSC_plate1_day1_A7_DRSC31022_FBgn0001297_kay

description: 1day RNAi incubation

value: kay


title: Drought treatment: Control_3_Palgong2

value: Seedling

value: leaf


title: P5_Ctr-TazYap-1


title: P5_Cko-Gnas

value: Gnasfl/fl;Dhh-Cre


title: Drought treatment: Control_2_Palgong2


title: P5_Ctr-Gnas

value: Gnasfl/fl


title: P5-dcKO-TazYap-1


title: DRSC_plate1_day1_A6_DRSC41069_FBgn0032940_Mondo

description: 1day RNAi incubation

value: S2R+ cells

value: Mondo

value: 1day RNAi incubation


title: DRSC_plate1_day1_A5_DRSC35830_FBgn0034534_maf-S

description: 1day RNAi incubation

value: maf-S


title: Drought treatment: Control_1_Palgong2


title: total RNA from human fetal brain_CaptureSeq [s_7]

city: Copenhagen N

first: Niels

last: Tommerup

state: Copenhagen

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine (ICMM)

country: Denmark

institute: Wilhelm Johannsen Centre for Functional Genome Research

data_processing:
Library strategy: CaptureSeq
Sequence reads were trimmed for adapters (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG followed by any number of A’s at the 3’ end) and low quality ends (Phred33<30) and trimmed reads shorter than 40 nt were discarded with cutadapt v1.8.3. Then reads were aligned to human genome assembly hg38 using STAR 2.5.2a with default parameters and alignments of at most 2 mismatches were reported (--outFilterMismatchNoverLmax 0.03). We applied the following strategy to define read islands, their read counts and the significance of RNA probe assigned read islands (on-targets): (1) filter uniquely mapped reads and remove simple repeats (>=50% overlap); (2) extend reads to 150 nucleotides in reading direction (unified reads) and define the region of overlapping unified reads as a read island; (4) count the reads inside a read island: (4) intersect read islands with RNA probes (overlap >=1 nucleotide); (5) calculate empirical P-value for read counts of RNA probe assigned read islands. The empirical P-value is based on the read count distribution of off-targets (read islands that are not assigned to an RNA probe) and we selected P<0.1 for expressed RNA probes.

source_name: Human fetal brain

extract_protocol:
Total RNA from human fetal brain (Clontech) was DNAseI treated (Invitrogen), and rRNA was depleted using RiboMinus (Invitrogen) according to the manufacturer’s recommendations. Following depletion of rRNA, samples were cleaned on Microcon YM-30 columns (Millipore).
RNA was then chemically fragmented and cleaned on Microcon YM-10 columns (Millipore). Fragmented RNA was reverse transcribed using a random hexamer oligo with an attached adaptor. Immediately following reverse transcription, second strand synthesis was performed followed by blunt ending and adaptor ligation. The library was size-selected on an agarose gel, where fragments of 100-200bp were excised from the gel and cleaned. The excised fragments were enriched by 18 cycles of PCR and cleaned (Qiagen). An aliquot was run on a gel to ensure that the average length of fragments was 100-150bp, with visible smear in the range of approximately 75-500 bases. The amount of amplified material was quantified. The library was split into two equally sized sub-libraries for investigating two different annealing temperatures to optimize the hybridization step of potentially self-folded RNA probes that target highly structured RNA molecules. The dried library was mixed with hybridization buffer and heated to 100 degrees to denature. The denatured sample was immediately loaded onto the pre-warmed custom chip (NimbleGen) and incubated isothermally at 70 degrees for 3 days (sample s_6). Following incubation, the slide was eluted according to the manufacturer’s protocol (NimbleGen Arrays User’s Guide, Sequence Capture Array Delivery, Version 3.2). Following elution, the samples were subjected to a final enrichment by 19 cycles of PCR and cleaned (Qiagen). The chip was stripped and rehybridized with the second half of the library at 42 degrees for 3 days (sample s_7). The eluate was washed and enriched as described above.

tag: tissue source

value: Human fetal brain


title: DRSC_plate1_day1_B11_DRSC26287_FBgn0032940_Mondo

description: 1day RNAi incubation


title: total RNA from human fetal brain_CaptureSeq [s_6]

value: Total RNA from human fetal brain (Clontech)


title: Drought treatment: Treat_3_Palgong1

value: sensitive


title: DRSC_plate1_day1_B10_DRSC25554_FBgn0011656_Mef2

description: 1day RNAi incubation


title: DRSC_plate1_day1_A4_DRSC33100_FBgn0266411_sima

description: 1day RNAi incubation

value: sima


title: Drought treatment: Treat_2_Palgong2


title: Drought treatment: Treat_1_Palgong1


title: DRSC_plate1_day1_A1_DRSC37534_FBgn0011763_Dp

description: 1day RNAi incubation

value: Dp


title: Drought treatment: Treat_2_Palgong1


title: DRSC_plate1_day1_A3_DRSC31698_FBgn0016076_vri

description: 1day RNAi incubation

value: vri


title: DRSC_plate1_day1_A12_DRSC37538_FBgn0024371_E2f2

description: 1day RNAi incubation


title: EC18_CK

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: EC18_CK:  Bacillus mycoides EC18 added with 10% of MQ water as the control.

data_processing:
mapping of reads was done using: bowtie2  -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Bacillus mycoides strain ATCC 6462, complete genome | VERSION     NZ_CP009692.1  GI:754380545 | 19-AUG-2015
Supplementary_files_format_and_content: Processed_data_rpkm.txt reports normalized RPKMs

organism: Bacillus mycoides

source_name: Cell culture

growth_protocol: Cells were grown in LB at 30C, 200rpm.

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation kit for IonProton

treatment_protocol: 10% potato root exudates was added to the experimental group, and deionized water added to the control group.

tag: strain

value: ATCC 6462

tag: accession

tag: isolate

value: endosphere isolate EC18

tag: treatment

value: control

value: soil

value: the Netherlands


title: SB_8_CK

description: SB_8_CK:  Bacillus mycoides SB8 added with 10% of potato root exudates.

value: soil isolate SB8

value: 10% potato root exudates


title: SB_8_RE

description: SB_8_RE:  Bacillus mycoides SB8 added with 10% of MQ water as the control.


title: EC18_RE

description: EC18_RE:  Bacillus mycoides EC18 added with 10% of potato root exudates.


title: Drought treatment: Control_1_Palgong1

tag: drought sensitivity

value: Seedling

value: leaf


title: Drought treatment: Control_2_Palgong1

tag: developmental stage


title: DRSC_plate1_day1_A10_DRSC36079_FBgn0003964_usp

description: 1day RNAi incubation

value: S2R+ cells

value: usp

value: 1day RNAi incubation


title: DRSC_plate1_day1_A11_DRSC40711_FBgn0000567_Eip74EF

description: 1day RNAi incubation


title: extracellular, replicate 3

city: Vienna

first: Lena

last: König

address: Althanstrasse 14

country: Austria

institute: University of Vienna

data_processing:
Filtering and trimming (in order shown): removal of first 13 bases (PRINSEQ-lite), quality trimming (mothur), removal of reads containing >2 ambiguous bases (PRINSEQ-lite), removal of poly-A tails (PRINSEQ-lite), clipping of remaining adapter sequences (Biopieces), removal of reads <25 bases;
Reads were mapped to the P. amoebophila genome using BWA (default settings). For the mapping to the A. castellanii genome TopHat was used (default settings, with the options fr-firststrand and -G gff.file).
Strand-specific reads per predicted gene were counted via HTSeq (union mode).
Normalized gene expression values and differential gene expression were determined using edgeR.
Genome_build: Protochlamydia amoebophila UWE25 (Accession number: BX908798)
Genome_build: Acanthamoeba castellanii Neff (Accession number: AHJI00000000)
Supplementary_files_format_and_content: log2RPKM values by gene (rows) and time point (columns)

organism:
Acanthamoeba castellanii
Candidatus Protochlamydia amoebophila

source_name: extracellular endosymbionts

growth_protocol: Amoebae with and without the endosymbiont were maintained at 20°C in PYG (20 g/l proteose peptone, 100 mM glucose, 2 g/l yeast extract, 1 g/l sodium citrate dihydrate, 4 mM MgSO4*7H2O, 1.32 mM Na2HPO4*2H2O, 2.5 mM KH2PO4, 0.05 mM Fe(NH4)2(SO4)2*6H2O; pH 6.5). For infection, uninfected amoebae were seeded at low density 3 days prior to infection and were then allowed to grow as above, before purified, extracellular endosymbionts were added. Two hours after infection cultures were washed 3x and infected cultures were harvested or further incubated at 20°C in PYG for 48 and 96 hours. Purified, extracellular endosymbionts were obtained from amoeba-endosymbiont cultures that were grown at the same conditions, and extracellular endosymbionts were harvested from the medium supernatant after one week of incubation.

extract_protocol:
After collection of cells pellets were immediately resuspended in TRIzol reagent, followed by bead-beating (30s, 4.5 m/s, lysing matrix A tubes, MP Biomedicals). Subsequent RNA extraction was performed according to the TRIzol guidelines. Residual DNA was removed using the Turbo DNA-free Kit (Thermo Fisher Scientific).
Ribosomal RNA was removed using the RiboZero Magnetic kit (Illumina) for Gram-positive bacteria as recommended by the manufacturer. To enrich for mRNA from symbiont-free amoebae, the RNA was additionally treated with Dynabeads mRNA Purification Kit (Thermo Fisher Scientific). For strand-specific cDNA library preparation, the NEBNext Ultra Directional RNA Library Prep Kit for Illumina in combination with the NEBNext Multiplex Oligos (New England Biolabs) was used.

treatment_protocol: At respective time points post infection infected amoebae were harvested, resuspended in sucrose buffer (35 mM Tris-HCl, 250 mM sucrose, 25 mM KCl, 10 mM MgCl2) supplemented with 50 µg/ml Rifampicin, amoebae were disrupted by 1 min vortexing in the presence of glass beads, suspensions were filtered through 5 µm filters, and bacteria were collected by 2 min high-speed centrifugation. Extracellular bacteria were pelleted, resuspended in sucrose buffer and treated like the time points. Uninfected amoebae were harvested with the 2 hpi samples.

tag: a. castellanii strain

value: Neff

tag: p. amoebophila strain

tag: developmental stage of endosymbiont

value: extracellular forms

tag: multiplicity of infection


title: Drought treatment: Treat_3_Odae19

value: tolerant

tag: cultivar

tag: tissue


title: Drought treatment: Treat_1_Odae19


title: Drought treatment: Treat_2_Odae19


title: Drought treatment: Control_3_Odae19


title: extracellular, replicate 1


title: extracellular, replicate 2


title: DRSC_plate1_day1_A2_DRSC30795_FBgn0001291_Jra

description: 1day RNAi incubation

tag: cell type

tag: RNAi target gene id (flybase)

tag: RNAi target gene name

value: Jra

tag: RNAi reagent from harvard drosophila rnai screening center

tag: time point


title: 96 hpi, replicate 3

description:
UWE25_log2rpkm.txt
Neff_log2rpkm.txt

source_name: amoeba cells infected with endosymbionts

value: 96 hours post infection


title: Drought treatment: Control_3_Palgong1

value: sensitive


title: 96 hpi, replicate 2

description:
UWE25_log2rpkm.txt
Neff_log2rpkm.txt


title: Drought treatment: Control_2_Odae19


title: 48 hpi, replicate 3

description:
UWE25_log2rpkm.txt
Neff_log2rpkm.txt

value: 48 hours post infection


title: Drought treatment: Control_1_Odae19


title: Drought treatment: Treat_3_Junguk6-2

tag: developemental stage


title: 96 hpi, replicate 1

description:
UWE25_log2rpkm.txt
Neff_log2rpkm.txt


title: Drought treatment: Treat_2_Junguk6-2


title: Drought treatment: Treat_1_Junguk6-2


title: 48 hpi, replicate 1

description:
UWE25_log2rpkm.txt
Neff_log2rpkm.txt


title: 2 hpi, replicate 2

description:
UWE25_log2rpkm.txt
Neff_log2rpkm.txt

value: 2 hours post infection


title: uninfected

organism: Acanthamoeba castellanii

source_name: uninfected amoeba cells


title: 48 hpi, replicate 2

description:
UWE25_log2rpkm.txt
Neff_log2rpkm.txt


title: 2 hpi, replicate 3

description:
UWE25_log2rpkm.txt
Neff_log2rpkm.txt


title: Grass_J86-T01-I_good.Seq

city: Kunming

first: Jing

last: Chen

address: No. 727 South Jingming Road

country: China

institute: Kunming University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: T01.isoforms.results.txt: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: Grass.Unigene.fa: FASTA file

organism: Gerbera delavayi

source_name: Leaf tissue

extract_protocol:
Fresh leaves of Gerbera delavayi were picked from a healthy plant, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: disease state

value: healthy


title: Drought treatment: Control_3_Junguk6-2


title: Drought treatment: Control_2_Junguk6-2


title: 2 hpi, replicate 1

description:
UWE25_log2rpkm.txt
Neff_log2rpkm.txt


title: Met/PIK3CA Shp2ΔH(3d)-3

status: Public on Apr 25 2017

first: Jijun

last: Liu

address: Rm1220 Bay-C, Biomedical Research Facility II, 9500 Gilman Drive

department: Pathology

institute: UC San Diego

data_processing:
Sequenced reads were de-multiplexed
Sequenced reads were mapped to GRCm38 genome using STAR with parameters --runThreadN 16 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Mapped SAM files were then compressed and sorted using samtools view, sort and index
Find significant changes in gene expression using Cuffdiff
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample as well as fold changes and q value between two groups.

source_name: Liver

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Oncogene and sleeping beauty plasmids dissolved in PBS solution (Met/?-Catenin: 5?g/10g Body Weight each oncogene; Met/PIK3CA: 10ug/10g BW each oncogene) were hydrodynamically injected into Shp2F/F and Shp2?H (Shp2F/F:Alb-cre) mice. Liver tissue collected 3 days after hydrodynamic injection.

tag: strain

value: Liver

tag: genotype

value: Shp2 KO in hepatocytes


title: Met/PIK3CA Shp2ΔH(3d)-2


title: Met/PIK3CA Shp2ΔH(3d)-1


title: Met/PIK3CA Shp2F/F(3d)-3


title: Met/PIK3CA Shp2F/F(3d)-2


title: Met/PIK3CA Shp2F/F(3d)-1


title: Met/β-Catenin Shp2ΔH(3d)-3


title: Met/β-Catenin Shp2F/F(3d)-2


title: Met/β-Catenin Shp2F/F(3d)-3


title: Met/β-Catenin Shp2ΔH(3d)-1


title: Met/β-Catenin Shp2F/F(3d)-1


title: Met/β-Catenin Shp2ΔH(3d)-2


title: Shp2ΔH control-3


title: Shp2F/F control-2


title: Shp2F/F control-3


title: Shp2F/F control-1


title: Shp2ΔH control-1


title: RC2-wt grown in 2%YPD replicate 1

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

data_processing:
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cryptococcus_neoformans reference build Ensembl_R23 with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.  Transcript counts were produced by Sailfish version 0.6.3.  All gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR  and TMM normalized to adjust for differences in library size.  Genes or transcripts not expressed in any sample were excluded from further analysis.
Genome_build: Cryptococcus_neoformans reference build Ensembl_R23
http://www.ncbi.nlm.nih.gov/assembly/GCF_000149245.1
Supplementary_files_format_and_content:
tab-delimited text files include read count values for each or all samples.
gene_counts_*.txt: abundance measurements at gene level
transcript_counts_all.txt: abundance measurements at transcript level

organism: Cryptococcus neoformans

source_name: RC2 RM-wt_whole cell

growth_protocol: Comparable number of wt or sir2mutant yeast cells (background strain H99 or RC2) were grown in yeast extract peptone with 2% or 0.05% glucose for 16 hours at 37degCelsius with agitation at 150rpm

extract_protocol:
Total RNA was extracted using a QIAGEN RNeasy kit per manufacturer's instructions
The library preparation protocol was oligo-d(T)-priming based Clontech SMARTer Ultra Low RNA Kit for Illumina® Sequencing from Clontech (a Takara Bio Company, hereafter labeled as “ClonTech”).  A starting amount of 10 ng RNAs was processed in ClonTech assays, amplified cDNA was sheared using a Covaris E210 instrument. cDNA was then end repaired, A tailed, and standard Illumina adapters were ligated on. Libraries were then amplified with primers to incorporate a unique index to each sample.  In pooling of multiple libraries for running on 2 lanes of 50bp single reads, equal amount of library mass was determined by Qubit reading and Bioanalyzer for the 24 RNA libraries.  Lastly, pooled libraries were amplified with Illumina® TruSeq™ Cluster kits and sequenced with Illumina® sequencing primers on Illumina® HiSeq2500™ next-generation sequencing system as a high output single read 50 cycle run.

tag: genotype/variation

value: wild type

tag: growth condition

value: rich media; 2% glucose

value: TCAACTG


title: RC2-sir2mutant grown in 0.05%YPD replicate 3

source_name: RC2 CR-mutant_whole cell

value: SIR2 mutant

value: calorie-restricted media; 0.05% glucose

value: TCCCAGC


title: H99-wt grown in 2%YPD replicate 3

source_name: H99 RM-wt_whole cell

value: TTTTGTC


title: H99-sir2mutant grown in 0.05%YPD replicate 3

source_name: H99 CR-mutant_whole cell

value: TGTTTGT


title: RC2-wt grown in 2%YPD replicate 3

value: TTTAACT


title: RC2-sir2mutant grown in 2%YPD replicate 3

source_name: RC2 RM-mutant_whole cell

value: GGGTCAA


title: H99-wt grown in 0.05%YPD replicate 3

source_name: H99 CR-wt_whole cell

value: GTCGATA


title: H99-wt grown in 2%YPD replicate 2

value: GTCTGAT


title: H99-sir2mutant grown in 0.05%YPD replicate 2

value: GGTCCTC


title: H99-wt grown in 0.05%YPD replicate 2

value: GCTTAGA


title: Shp2ΔH control-2


title: H99-sir2mutant grown in 2% YPD replicate 3

source_name: H99 RM-mutant_whole cell

value: GCAGGGG


title: RC2-wt grown in 0.05%YPD replicate 3

source_name: RC2 CR-wt_whole cell

value: GCAACGC


title: H99-wt grown in 2%YPD replicate 1

value: GAGGCGT


title: RC2-wt grown in 0.05%YPD replicate 2

value: wild type

value: CTCCCGA


title: RC2-wt grown in 2%YPD replicate 2

value: rich media; 2% glucose

value: TGAGGTT


title: H99-sir2mutant grown in 0.05%YPD replicate 1

value: SIR2 mutant

value: calorie-restricted media; 0.05% glucose

value: CGTCGCT


title: RC2-sir2mutant grown in 2%YPD replicate 2

value: CAATATC


title: H99-sir2mutant grown in 2% YPD replicate 2

value: CAAGCCG


title: RC2-wt grown in 0.05%YPD replicate 1

value: CCGGACC


title: Drought treatment: Control_1_Junguk6-2

source_name: Leaf

tag: drought sensitivity

value: sensitive

value: Seedling

value: leaf


title: H99-wt grown in 0.05%YPD replicate 1

value: AGATACT


title: H99-sir2mutant grown in 2% YPD replicate 1

value: ACGTCTG


title: RC2-sir2mutant grown in 0.05%YPD replicate 1

value: ATGACAG


title: RC2-mutant grown in 2%YPD replicate 1

value: ACCCACT


title: RC2-sir2mutant grown in 0.05%YPD replicate 2

value: TACAGAC


title: T 15Gy 4w-2

city: Milwaukee

first: Meetha

last: Medhora

state: Wisconsin

address: 8701 Watertown Plank Rd

department: Radiation oncology

institute: Medical College of Wisconsin

data_processing:
Data QC and trim with trim_galore version 0.2.5
read alignment with bowtie version 1.1.1
microRNA identification with miRanalyzer version 0.3
Genome_build: rn4
Supplementary_files_format_and_content: microRNA read counts

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
Lungs were removed, blood were collected from heart, and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012,RS-200-0024,RS-200-0036) was used with 1 ug of total RNA for the construction of sequencing libraries.
MicroRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Un-anesthetized 9- to 10-week-old female WAG/RijCmcr rats weighing approximately 140 g were immobilized in a plastic jig and irradiated with 320-kVp orthovoltage system X-rays, with a half-value layer (HVL) of 1.4 mm Cu. Rats were treated with a single dose of 15 Gy to the whole thorax at dose rate of 1.43 Gy/min.  The radiation dose was delivered by two equally-weighted lateral beams to improve uniformity. The whole lung, heart and a small amount of liver were in the field. One group of age-matched rats was not irradiated (non-irradiated controls or 0 Gy group) but maintained under identical conditions.

tag: Sex

value: female

value: WAG/RijCmcr

value: Lung

tag: treatment

value: 15Gy X-ray radiation to the whole thorax

value: 4 week after radiation


title: T 15Gy 4w-3


title: T 15Gy 3w-3

value: 3 week after radiation


title: T 15Gy 2w-2

value: 2 week after radiation


title: T 15Gy 3w-1


title: T 15Gy 2w-1


title: T 15Gy 3w-2


title: T 15Gy 1w-2

value: 1 week after radiation


title: T 15Gy 2w-3


title: T 15Gy 1w-3


title: T 15Gy 1w-1


title: T 0Gy 4w-3

value: age matched non-radiation control


title: T 0Gy 1w-2


title: T 0Gy 4w-2


title: T 0Gy 4w-1


title: T 0Gy 1w-1


title: B 15Gy 4w-2

source_name: Blood

value: Blood


title: B 15Gy 4w-3


title: T 0Gy 1w-3


title: B 15Gy 4w-1


title: B 15Gy 2w-3


title: B 15Gy 3w-2


title: B 15Gy 3w-1


title: B 15Gy 1w-3


title: T 15Gy 4w-1


title: B 15Gy 2w-2


title: B 15Gy 2w-1


title: B 15Gy 1w-2


title: B 15Gy 1w-1


title: B 0Gy 4w-3


title: B 0Gy 4w-2


title: B 0Gy 4w-1


title: B 0Gy 1w-3


title: B 0Gy 1w-2


title: B 0Gy 1w-1


title: BJ Old MYOD WT DM Rep2

city: Cambridge

first: Alessandra

last: Dall'Agnese

address: 455 Main Street

institute: Whitehead Institute

data_processing:
BJ: Reads were mapped using TopHat2.1.1 with option -p 8 -g 1 -segment-length 12 -library-type fr-unstranded to homo sapiens hg19 genome, HTSeq-0.6.1p1 with option "stranded=no" was used to assign mapped reads ro H. sapiens GRCh37.75 genes. Differential gene expression analysis was performed using DESEq2.
Genome_build: hg19
Supplementary_files_format_and_content: Differential gene expression

source_name: BJ

growth_protocol: BJ cells were cultured in DMEM supplemented with 10% FBS, nonessential amino acids

extract_protocol:
For RNASeq: cells were lyzed with Trizol and RNA was extracted following manufacturer's instruction.
BJ: Illumina kits.

treatment_protocol: BJ cells were infected with Adeno Track or Adenovirus containing MYOD WT or MYOD Y30F, cells were induced to differentiate in DMEM supplemented with 2% horse serum (DM)

value: Skin fibroblasts

tag: ectopic gene expression

value: MYOD WT

tag: passage from isolation

value: passage High 45


title: BJ Young MYOD Y30F DM Rep2

value: MYOD Y30F

value: passage Low 12


title: BJ Old TRACK DM Rep2

value: EMPTY VECTOR


title: BJ Old TRACK DM Rep1


title: BJ Young TRACK DM Rep2


title: Bj Old MYOD Y30F DM Rep1


title: BJ Young MYOD WT DM Rep2


title: Bj Old MYOD Y30F DM Rep2


title: BJ Young MYOD Y30F DM Rep1


title: B 15Gy 3w-3

tag: tissue


title: BJ Old MYOD WT DM Rep1

tag: cell type


title: BJ Young TRACK DM Rep1


title: miR873Mut_Con_3

city: Brisbane

first: Sarah

middle: Marguerite

last: Williams

state: QLD

address: QBI Building 79, University of Queensland, St Lucia

department: Queensland Brain Institute

institute: University of Queensland

description: Mutant miR-873-5p transfection rep 3 control transcriptome

data_processing:
Illumina adaptor sequences were removed and reads quality trimmed with Trimmomatic.
Sequences were aligned to the human GRCh38 Ensembl release 83 transcriptome with TopHat2
Gene-level counts were generated from paired reads in HTseq-count (Parameters: -s reverse -m union).
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts of sequence fragments aligned to each gene.

source_name: SH-SY5Y cell line

extract_protocol:
RNA was purified with RNAeasy columns (QiAGEN).
Sequencing libraries prepared from 100 ng input RNA with Illumina TruSeq Stranded mRNA kit.

treatment_protocol: Control 'Con' samples are whole transcriptome. Pulldown 'PD' samples are matched sample subjected to tagged-microRNA mRNA capture.

tag: microrna

tag: replicate

value: Con - control transcriptome