title: Hmel-shPTEN-H4TETRAAC

description: processed data file: Hmel-shPTEN_45_dense.bed

source_name: Hmel-shPTEN

value: HMEL

value: Hmel-shPTEN

value: tumorigenic variant

value: Active Motif-39179


title: RNA sequencing of High Worms biological replicate 1

status: Public on Apr 24 2017

type: SRA

city: Boulder

first: Eduard

last: Casas

state: Colorado

address: Porter Biosciences, CU Campus

department: MCDB

country: USA

institute: CU Boulder

description:
F0
Worms grown continuously at 25C
WH01_12374_CGATGT

library_source: transcriptomic

data_processing:
Sequence mapping to the transcriptome using tophat v2.1.0 --no-coverage-search -i 10 -I 40000 -g 20
Assigning reads to genes using featureCounts v1.5.1 -s 2 -B -p -M --fraction -t exon -g gene_name -O
Count normalization was done using DESeq2 v1.8.1.
Genome_build: C. elegans genome assembly WS215 from WormBase and annotation from Ensembl release 70
Supplementary_files_format_and_content: Matrix of raw number of reads mapping to each gene

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole multiple worms_25C_F0

growth_protocol: To prepare samples for sequencing N2 worms grown continuously ( > 20 generations) at 20 °C were shifted to 25 °C as L4 larvae and grown at that temperature for five generations. At the fifth generation, synchronized gravid adult worms were collected and RNA extracted. To obtain synchronized gravid F0 animals we bleached the previous generation to obtain the eggs, plated 1500 eggs per plate and grew for 54 - 56 hours at 25 °C.  These constituted the F0 ancestral population. Before reaching adulthood, at L4 stage, a fraction of these animals were transferred to 20 °C and propagated for 3 more generation at that temperature. To obtain synchronized gravid F3 animals we bleached the previous generation to obtain the eggs, plated 1500 eggs per plate and grew for 72 - 76 hours at 20 °C. A control population was processed in parallel, starting from L4 animals grown continuously at 20 °C. We used 3 plates for each replicate and three replicates for each condition. We monitored the cultures to ensure that they did no starve at any point. Animals were collected in M9 and RNA extracted using TRIzol® extraction protocol.

extract_protocol:
RNA was extracted using TRIzol® extraction protocol (Portman, D.S. (2006). Profiling C. elegans gene expression with DNA microarrays. WormBook : the online review of C elegans biology, 1-11.)
Libraries for RNA-seq were prepared from 400 ng total RNA using the TruSeq Stranded Total RNA Library Prep Kit (ref. RS-122-2201, Illumina) using the included RiboZero reagents to deplete ribosomal RNAs according to manufacturer's instructions. The poly(A)-mRNA selection step was not carried out. Samples were sequenced with 2x50 bp paired-end reads using Illumina HiSeq v4 sequencing chemistry.
paired-end mRNA-Seq

tag: strain

tag: strain background

value: wild-type

tag: developmental stage

value: gravid adult


title: Pmel-shGFP-H3K36ME1

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: processed data file: Pmel-shGFP_45_dense.bed

library_source: genomic

data_processing:
ChIP-Seq reads were aligned using Bowtie (version 1.0.0) to human genome assembly NCBI Build 37 (UCSC hg19) with the following parameters: -n 1 -m 1 --best –strata (uniquely mapped reads with one mismatch were retained).
We used the ChromHMM method with default parameters to derive genome-wide chromatin state maps for all cell types. Sequencing reads that map to the same genomic location and strand were counted once in the input data in order to avoid biases due to PCR artifacts. This number of states was chosen, because it was the minimum number required to separate bivalent and poised states from active states. The 45 state model was learned jointly on all chromatin marks from H and Hmp. The chromatin state segmentation of Hmel-shGFP, Hmel-shPTEN, Pmel-shGFP and Pmel-shPTEN was produced subsequently by applying this model to the chromatin data from these cell types. Prior to that, we normalized each chromatin mark in Pmel-shGFP and Pmel-shPTEN to have the same number of binary calls across these two cell types in the binarization procedure of ChromHMM.
Genome_build: hg19
Supplementary_files_format_and_content: Gnome segmentation files generated for each cell type by ChromHMM.
Supplementary_files_format_and_content: *18_dense.bed files contain 18 state chromatin model data based on ChIP-Seq dataset for each individual cell line.

molecule: genomic DNA

organism: Homo sapiens

source_name: Pmel-shGFP

growth_protocol: Cells were maintained in standard tissue culture conditions (5% CO2 , 37oC) in DMEM medium supplemented with 10%FBS and Pen-Strep.

extract_protocol:
Cells (5 million per antibody) were crosslinked using 1% paraformaldehyde for 10mins at 37 degrees. Reaction was quenched by 0.125M glycine for 5mins, cells washed with PBS and stored at -80oC. Next day cells were thawed on ice and lysed with RIPA buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 140mM NaCl, 1% Triton x-100, 0.2%SDS, 0.1% DOC) for 10min on ice. Sonication was performed using Branson Sonifier 250 to achieve shear length of 200-500bp. Antibodies were bound to dynabeads for 1 hr at 4oC. Extracts were then incubated overnight with antibody-dynabead mixture Immunecomplexes were then washed 5 times with RIPA buffer, once with RIPA-500 (RIPA with 500mM NaCl) and once with LiCl wash buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). Elution and decrosslinking was performed in direct elution buffer (10mM Tris-Cl pH 8.0, 5mM EDTA, 300mM NaCl, 0.5% SDS) by incubating immunecomplxes at 65oC for 4-16hrs. Proteinase K (20mg/ml) and RNaseA treatment was performed and DNA cleaned up using SPRI beads (Beckman-Coulter).
Libraries were prepared using NEB reagents as described earlier (Garber et al 2012). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~300-500 bp (insert plus adaptor and PCR primer sequences) were size selected by SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: Cells were infected with mko-shGFP or mko-shPTEN lentiviruses. Two hundred million cells were harvested for ChIP.

tag: partially transformed melanocytic line

value: PMEL

tag: clone subtype

value: Pmel-shGFP

tag: cell phentype

value: non-tumorigenic variant

tag: chip antibody

tag: chip antibody vendor-cat.#


title: RNA sequencing of set25 mutant worms biological replicate 1

description:
set25
RNA sequencing of set25 mutant worms grown at a reference temperature of 20 degrees
SL31_16181_ATCACG

source_name: whole multiple worms_20C_set25

growth_protocol: To prepare samples for sequencing worms were grown continuously ( > 20 generations) at 20 °C. Synchronized gravid adult worms were collected and RNA extracted. To obtain synchronized gravid animals we bleached the previous generation to obtain the eggs, plated 1500 eggs per plate and grew for 72 - 76 hours at 20 °C. We used 3 plates for each replicate and three replicates for each condition. We monitored the cultures to ensure that they did no starve at any point. Animals were collected in M9 and RNA extracted using TRIzol® extraction protocol.

extract_protocol:
RNA was extracted using TRIzol® extraction protocol (Portman, D.S. (2006). Profiling C. elegans gene expression with DNA microarrays. WormBook : the online review of C elegans biology, 1-11.)
Libraries for RNA-seq were prepared from 400 ng total RNA using the TruSeq Stranded Total RNA Library Prep Kit (ref. RS-122-2201, Illumina) using the included RiboZero reagents to deplete ribosomal RNAs according to manufacturer's instructions. The poly(A)-mRNA selection step was not carried out. Samples were sequenced with 2x50 bp paired-end reads using Illumina HiSeq v4 sequencing chemistry.


title: U6_6899_SR50

city: Worcester

first: Edith

last: Pfister

state: MASSACHUSETTS

address: 368 Plantation St, ASC4-2007

department: Medicine

institute: UMass Medical School

description: protocol: Cell. 2009 May 1;137(3):509-21. doi: 10.1016/j.cell.2009.04.027. Epub 2009 Apr 23.

data_processing:
Reads were trimmed using trimmomatic v. 0.32 (Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.)
Alignment with TopHat v2.0.12
Differential expression calculated with DESeq2
genome build: mm10
processed data files format and content: Table containing raw counts. Tab separated. *_t1.txt: Columns: start pos on 5p arm (major species), 5p arm counts, start position on 3p arm (major species), 3p counts , # 5p species, total 5p counts, total 3p counts. *_t2.txt: Columns: hairpin name, 5p or 3p arm, start position, counts.

organism: Mus musculus

source_name: brain-striatum_Yac128 mouse

extract_protocol: The striatum was dissected out, quickly homogenized in RNA lysis buffer and RNA was extracted using the MirVana RNA isolation kit total RNA protocol.

tag: tissue

value: brain

tag: tissue compartment

value: striatum

tag: treatment

tag: barcode

value: CGATGT


title: Pmel-shGFP-H3K27ME1


title: Pmel-shGFP-H3K27ME3


title: Pmel-shGFP-H2AK5AC


title: Hmel-shPTEN-IgG

value: IgG

value: Rabbit IgG (Millipore)


title: U6_6900_SR50


title: Hmel-shPTEN-H4K91AC


title: Hmel-shPTEN-H4K8AC


title: U6_6898_SR50


title: PBS_7353_SR50

value: PBS

value: ATCACG


title: Hmel-shPTEN-H4K5AC


title: PBS_7258_SR50

value: ACAGTG


title: CBA_6965ni_SR50

value: TTAGGC


title: RNA sequencing of High Worms F3 biological replicate 1

description:
F3
Worms grown at 25C and then transferred to 20C for three generations
WH31_12377_CAGATC

source_name: whole multiple worms_transferred to 20C_F3


title: RNA sequencing of High Worms F3 biological replicate 3

description:
F3
Worms grown at 25C and then transferred to 20C for three generations
WH33_12379_CCGTCC


title: CBAni_6906ni_SR50


title: Pmel-shGFP-H2BK120AC

value: Active Motif-39119


title: CBA_7427_SR50

value: GCCAAT


title: RNA sequencing of High Worms biological replicate 2

description:
F0
Worms grown continuously at 25C
WH02_12375_TTAGGC


title: CBA_6906_SR50


title: CBA_6905_SR50


title: Hmel-shPTEN-H4K12AC

value: HMEL

value: Hmel-shPTEN

value: tumorigenic variant

value: Active Motif-39165


title: Hmel-shPTEN-H4


title: rluc_8712

description: protocol: Silence. 2012 Dec 28;3(1):9. doi: 10.1186/1758-907X-3-9.

data_processing:
Reads were trimmed using trimmomatic v. 0.32 (Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.)
Alignment with TopHat v2.0.12
Differential expression calculated with DESeq2
genome build: mm10
processed data files format and content: text file containing gene counts (1 per sample)


title: Hmel-shPTEN-H3K9ME3


title: empty_8711


title: empty_8563


title: rluc_8569

value: TGACCA


title: Hmel-shPTEN-H3K9AC


title: Hmel-shPTEN-H3K9ME1


title: Hmel-shPTEN-H3K79ME2


title: U6_8444


title: empty_8567


title: Hmel-shPTEN-H3K79ME1


title: rluc_8568


title: Hmel-shPTEN-H3K79ME3


title: CBA_8442


title: Hmel-shPTEN-H3K4ME3


title: Hmel-shPTEN-H4K20ME2

value: Active Motif-39173


title: Hmel-shPTEN-H4K20ME3


title: Hmel-shPTEN-H4K20ME1


title: CBA_8441

value: brain


title: Hmel-shPTEN-H4K16AC


title: CBA_8439

value: striatum


title: Hmel-shPTEN-H3K4ME1


title: Hmel-shPTEN-H3K4ME2


title: naïve_8436

value: ACTTGA


title: Hmel-shPTEN-H3K36ME3


title: Hmel-shPTEN-H3K4AC


title: U6_8440


title: U6_8347


title: Hmel-shPTEN-H3K36ME2


title: Hmel-shPTEN-H3K36ME1


title: Hmel-shPTEN-H3K36AC

value: Active Motif-39379


title: Hmel-shPTEN-H3K27ME3


title: Tissue_resident_1 (RNA-Seq)

city: Saint Louis

first: Mei San

last: Tang

state: MO

address: 660 S Euclid, Campus Box 8118

department: Pathology & Immunology

institute: Washington University in St Louis

data_processing:
Raw reads aligned to the reference mouse genome Grcm38 and the Ensembl reference transcriptome Grcm38.84.gtf using Tophat (version 2.1.0) with default settings.
Reads with mappability score (MAPQ) <30, as well as reads mapping to mitochondrial DNA and chromosome Y, were removed.
The number of filtered reads were subsequently counted for each gene using htseq-count, with the parameters --mode=union and --stranded=no.
Genome_build: Grcm38
Supplementary_files_format_and_content: 2-column HTSeq count files specific to each sample, where Column 1 is the Ensembl Gene ID and Column 2 is its corresponding absolute count.

source_name: Peritoneal macrophages

growth_protocol: Cx3cr1creER-YFP/+R26tdTomato/+ were bred in specific-pathogen free animal facility in NYU.

extract_protocol:
RNA was extracted from FACS-sorted macrophages using the Rneasy Mini kit or the Rneasy Micro Kit where cell numbers were less than 5x10^5 cells, as recommended by the manufacturer.
Library was constructed using a low input protocol with TotalScript RNA-Seq kit

treatment_protocol: 4 days prior to peritoneal cells harvest, all mice were treated with intra-peritoneal injection of IL-4 complexes  (i.e. 5μg of IL-4 and 25μg of anti-IL4) every other day, in addition to the group-specific treatment as detailed in the Samples Section above.

tag: cell type

value: Peritoneal macrophages

tag: genotype


title: Tissue_converted_3 (RNA-Seq)

description: Group-specific treatment protocol: Mice treated with 2ml Thioglycollate and kept on continuous tamoxifen diet for 10 weeks before peritoneal cells harvest.


title: Hmel-shPTEN-H3K18AC


title: Tissue_converted_1 (RNA-Seq)


title: Hmel-shPTEN-H3K14AC


title: Monocyte_derived_3 (RNA-Seq)

description: Group-specific treatment protocol: Mice treated with 2ml Thioglycollate on Day 0 and peritoneal cells harvested on Day 4.


title: Hmel-shPTEN-H3


title: Monocyte_derived_2 (RNA-Seq)


title: Monocyte_derived_1 (RNA-Seq)


title: Hmel-shPTEN-H2BK15AC


title: Tissue_resident_3 (RNA-Seq)


title: Hmel-shPTEN-H2BK5AC

value: Active Motif-39123


title: Tissue_resident_3 (ATAC-Seq)

description:
-
processed data: tissue_nonconv_merged_pval0.00001_sorted.bed

data_processing:
Raw reads aligned to the reference mouse genome mm10 using bowtie2 (v2.2.9), with the parameters --maxin 2000 and --local, while keeping all other parameters at default settings.
Reads with mappability score (MAPQ) <30 and duplicate reads, as well as reads mapping to mitochondrial DNA and chromosome Y, were removed.
Filtered reads were merged across all replicates from the same group. Peak calling was done on the merged reads for each group using PeaKDeck v1.1 (McCarthy and O'Callaghan, Bioinformatics 2014), using the parameters: central bin (-bin) 75bp, background bin (-back) 10000bp and step size (-STEP) of 25. Background probability distribution was generated using 100000 randomly selected sites (-npBack). Significance was defined using a p-value of less than 0.00001.
Genome_build: Grcm38
Supplementary_files_format_and_content: 6-column BED files of the peaks called for each group (i.e. Monocyte-derived, tissue converted and tissue resident peritoneal macrophages, respectively). The 5th column corresponds to the p-value of the peak called.

extract_protocol:
ATACSeq was performed as described in Buenrostro et al (Nature Methods 2013). FACS-purified cells were spinned down at 1500rpm for 5 min at 4 degree Celsius and washed once with 50ul cold PBS. Cells were then lysed with 50ul lysis buffer (10 mM Tris-HCl, pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and the nuclei were immediately spinned down at 1500rpm for 10 min at 4 degree Celsius. The isolated cell nuclei were then incubated with 50ul of transposase reaction (25ul TD buffer, 2.5ul Tn5 enzyme, 22.5ul nuclease-free water)for 30 mins at 37 degree Celcius. Transposed DNA was purified using the QIAgen MinElute PCR Purification Kit following manufacturer's guide. TD buffer and Tn5 enzyme are from the Nextera DNA Sample Preparation kit (Illumina Cat #FC-121-1030).
Tranposed DNA was amplified using a low-cycle number PCR protocol and custom primers designed for multiplexing based on Buenrostro et al (Nature Methods 2013). Each sample underwent … cycles of PCR amplification. Amplified libraries of transposed DNA were purified with the QIAgen MinElute Kit and sequenced on the HiSeq 2000.


title: Hmel-shPTEN-H2AK5AC


title: naïve_8433

value: CAGATC


title: Tissue_resident_2 (ATAC-Seq)


title: Hmel-shPTEN-H2BK120AC


title: Hmel-shGFP-H4K91AC

description: processed data file: Hmel-shGFP_45_dense.bed

source_name: Hmel-shGFP

value: Hmel-shGFP

value: non-tumorigenic variant


title: Tissue_resident_2 (RNA-Seq)


title: Hmel-shPTEN-H3K27ME1


title: Hmel-shPTEN-H3K27AC


title: Tissue_converted_3 (ATAC-Seq)

description:
Group-specific treatment protocol: Mice treated with 2ml Thioglycollate and kept on continuous tamoxifen diet for 8 weeks before peritoneal cells harvest.
processed data: tissue_conv_merged_pval0.00001_sorted.bed


title: Hmel-shGFP-H4K8AC


title: Tissue_resident_1 (ATAC-Seq)


title: Hmel-shGFP-H4K5AC


title: Hmel-shGFP-H4K20ME3


title: Tissue_converted_2 (RNA-Seq)


title: Tissue_converted_2 (ATAC-Seq)


title: Hmel-shGFP-H4K20ME1


title: Hmel-shPTEN-H3K23AC


title: Tissue_converted_1 (ATAC-Seq)


title: Hmel-shGFP-H4K20ME2


title: Hmel-shGFP-H4K12AC


title: Monocyte_derived_3 (ATAC-Seq)

description:
Group-specific treatment protocol: Mice treated with 2ml Thioglycollate on Day 0 and peritoneal cells harvested on Day 4.
processed data: monocyte_merged_pval0.00001_sorted.bed


title: Hmel-shGFP-IgG

value: IgG

value: Rabbit IgG (Millipore)


title: 2_MUT_h3.3kd

city: Dallas

first: Hume

last: Stroud

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
Initial data analysis was done at AITbiotech (Singapore), using tophat, cufflinks, cuffmerge and cuffdiff
Genome_build: TAIR9
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 10 day seedlings

growth_protocol: Sterilized seeds were grown on 1 x MS medium with glucose at long day conditions in a Percival incubator for 10 days.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen)
Libraries were prepared and sequenced at AITbiotech (Singapore)

tag: ecotype

value: Columbia

value: h3.3kd (htr4;htr8;amiRHTR5-II)


title: Monocyte_derived_1 (ATAC-Seq)


title: Hmel-shGFP-H4TETRAAC

value: HMEL

value: Active Motif-39179


title: mESC shScr

city: Dublin 2

first: Darren

middle: John

last: Fitzpatrick

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
ChIP-Seq reads were aligned to the mm10 reference genome using bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by first creating wig files using MACS 1.4 and converting them to bigwig files using the wigToBigWig utility from UCSC.

source_name: Embryonic stem cells

growth_protocol: mESCs E14 were cultivated on gelatinized culture dishes in GMEM (SIGMA) supplemented with 10% (v/v) mESC certified FBS (Gibco), 100 U/ml penicillin and 100 U/ml streptomycin (Gibco), 50 M -Mercaptoethanol (SIGMA), 1:100 GlutaMAX (Gibco), 1:100 non-essential amino acids (Gibco), 1 mM sodium pyruvate (Gibco) and 1000 U/ml  LIF (ESGRO). The cells were propagated every other day. NIH3T3 were grown in DMEM (Sigma) supplemented with 10% (v/v) FBS (Gibco), 100 U/ml penicillin and 100 U/ml streptomycin (Gibco).

extract_protocol:
For ChIP, cells were crosslinked in 1% Formaldehyde at room temperature at for 10 min before harvest. Chromatin was sheared to 300-500 bp and DNA-protein complexes were isolated with antibody. Precipitates were digested with RNaseA and Proteinase K and then Phenol-Chloroform purified.
For ChIP-Seq, DNA was quantified using the Qubit® dsDNA HS Assay Kit (Invitrogen). 1-5 ng DNA from ChIP experiments were used for library preparation using the Illumina ChIP-Seq sample prep kit (IP-102-1001) and multiplexing oligonucelotide kit (PE-400-1001). For DNA purification steps, DNA SPRI bead (Beckman) cleanup was performed. The quality of the DNA libraries was assessed using a high sensitivity Bioanalyzer Chip (Agilent). Libraries were used for cluster generation and sequencing using HiSeq 2000 (Illumina) with 50 bp read length.

treatment_protocol: Stable shRNA-mediated knockdown was achieved by lentiviral transduction of E14 mESCs with pLKO.1 targeting mouse Fam60a. Control cells were generated in parallel by transduction of non-targeting pLKO.1 shScrambled. Cells were incubated with virus particles in the presence of 10 ug/ml Polybrene (Sigma) for 24 hours. After a recovery phase of 12 hours, cells were selected for several days with 2 ug/ml puromycin.

tag: lentivirus transduction

value: non-targeting pLKO.1 shScrambled


title: mESC shFam60a

value: shRNA-mediated knockdown of E14 mESCs with pLKO.1 targeting mouse Fam60a


title: H33KD_H2AZ_#2

data_processing:
Reads were mapped to the TAIR10 genome by allowing up to 2 mismatches, and only retaining uniquely mapping reads using Bowtie (Langmead et al., 2009). Reads mapping to identical locations were collapsed in to one read.
Genome_build: TAIR10
Supplementary_files_format_and_content: Column 1 is chromosome. Column 2 is the genomic strand(+/-) the read mapped to. Column 3 is the genomic coordinate the read mapped to.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared for sequencing using standard Illumina protocols

value: H2A.Z (inhouse synthesized)


title: Hmel-shGFP-H3K79ME3


title: NIH3T3 Fam60a

tag: antibody


title: Hmel-shGFP-H3K79ME2


title: NIH3T3 Sin3a


title: WT_H3K4me3_#2

value: H3K4me3 (Abcam, ab8580)


title: mESC Fam60a


title: mESC Sin3a


title: WT_H2AZ_#2


title: Hmel-shGFP-H4K16AC


title: Hmel-shGFP-H3K79ME1


title: Control-3

city: New York

first: Sagar

last: Chhangawala

state: NY

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

description: scramble shRNA-1

data_processing:
Alignment: STAR (v2.3.0e_r291)
Read counting: htseq-count (v0.6.0, parameters –t exon)
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file with gene names and counts.

source_name: scramble shRNA-1

extract_protocol:
TRIZOL RNAeasy
RNA was denatured and 1st chain of cDNA was synthesized using oligo-dT primer containing illumina-compatible linker sequence. After removal of RNA 2nd cDNA chain was synthesized with random decamer containing another illumina-compatible linker sequence. Illumina compatible annealing sequences and external barcodes were introduced during amplification of the libraries.

treatment_protocol: murine MLL-AF9 leukemia cells tertiary transplanted were shRNA depleted for SYNCRIP or control scrambe assesed 4 days post transduction

tag: cell line

value: MLL-AF9 murine leukemia cell line

tag: genotype/variation

value: control


title: Hmel-shGFP-H3K4ME3


title: Hmel-shGFP-H3K9ME3


title: 1_WT_Col-0

value: wildtype


title: h3.3 kd rep1

data_processing:
Bisulfite-seq: Analyzed exactly as previously described (Stroud et al., 2013), by allowing up to 2 mismatches using BS seeker (Chen et al., 2010) except that reads were mapped to the TAIR10 genome.
Genome_build: TAIR10
Supplementary_files_format_and_content: Chromosome(1-5); genome coordinate; strand (+/-); cytosine context (CG, CHG, CHH); unconverted calls (C); converted calls (T)

source_name: Mature leaves

extract_protocol:
Tissue were collected and ground in liquid nitrogen to a fine powder. DNA was extracted using the DNeasy Plant Mini Kit (Qiagen) according to manufacturer’s instructions
Libraries were prepared using Truseq DNA LT sample kit (Illumina), and bisulfite conversion was performed using the Methylcode bisulfite conversion kit (Life technologies) and amplifid using KAPA HiFi HotStart Uracil+ Mix (Kapa Biosystems)

value: h3.3 kd


title: Hmel-shGFP-H3K4ME2


title: Hmel-shGFP-H3K4ME1


title: Control-2

description: scramble shRNA-1


title: D152V_Rescue_rep3

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

data_processing:
Basecalls were performed using bcl2fastq v2.17.1.14.
Low quality reads and adaptors were trimmed/removed using Trimmomatic v0.33
Illumina spike-in PhiX were removed using BBMap v34
Cleaned reads were aligned against Homo sapiens GRCh38 ensembl release 83 using Tophat2 v2.0.13 with ‘--library-type fr-firststrand --no-mixed --no-novel-juncs' as parameters
Differential expression was calculated using cufflinks v2.2.1 pipeline and viewed in cummeRbund v2.14 R package
Genome_build: GRCh38
Supplementary_files_format_and_content: Replicate FPKM table from cummeRbund

growth_protocol: K-562 cells were cultivated in IMDM (ThermoFisher Scientific) supplemented with 10% Fetal Bovine Serum and 1% Penicillin Streptamycin. For selection of stable cell lines, 200 µg/ml G418 was added to the cells

extract_protocol:
RNeasy Mini kit (Qiagen, 74104)
TruSeq stranded RNA library prep, poly(A) selection (Illumina)

value: human erythroleukemic cell line

tag: stably expressing

tag: sirna

value: si2992 (MYB knockdown)


title: Wild type

value: Wild type


title: Hmel-shGFP-H3K9AC

tag: partially transformed melanocytic line

tag: clone subtype

value: Hmel-shGFP

value: non-tumorigenic variant


title: Control-1

description: scramble shRNA-1


title: D152V_Rescue_rep1


title: D152V_Rescue_rep2


title: KD2-3

description: shRNA-2 depleted for SYNCRIP 4 days post transduction (REPLICATE 3)

value: SYNCRIP KD (shRNA-2)


title: Hmel-shGFP-H3K4AC

tag: cell phentype

tag: chip antibody


title: Hmel-shGFP-H3K36ME3

tag: chip antibody vendor-cat.#


title: MYB-WT_Rescue_rep2


title: Hmel-shGFP-H3K36AC

value: Active Motif-39379


title: KD1-2

description: shRNA-1 depleted for SYNCRIP 4 days post transduction (REPLICATE 2)

value: SYNCRIP KD (shRNA-1)


title: MYB-WT_Rescue_rep3


title: KD2-2

description: shRNA-2 depleted for SYNCRIP 4 days post transduction (REPLICATE 2)


title: KD1-1

description: shRNA-1 depleted for SYNCRIP 4 days post transduction (REPLICATE 1)


title: KD2-1

description: shRNA-2 depleted for SYNCRIP 4 days post transduction (REPLICATE 1)


title: KD1-3

description: shRNA-1 depleted for SYNCRIP 4 days post transduction (REPLICATE 3)


title: Hmel-shGFP-H3K36ME1

value: HMEL


title: MYB-WT_Rescue_rep1


title: MYB_KnockDown_rep2


title: Hmel-shGFP-H3K27ME1


title: MYB_KnockDown_rep3


title: Hmel-shGFP-H3K27ME3


title: Hmel-shGFP-H3K27AC


title: Hmel-shGFP-H3K23AC


title: MYB_KnockDown_rep1


title: Hmel-shGFP-H3K36ME2


title: Hmel-shGFP-H3K18AC


title: siRNA_Control_rep3

value: siGENOME non-targeting control siRNA


title: siRNA_Control_rep1


title: siRNA_Control_rep2


title: Hmel-shGFP-H3


title: Hmel-shGFP-H3K14AC


title: Hmel-shGFP-H2BK5AC

value: Active Motif-39123


title: 24hInd + 0.5mM PFA ORF59 ChIP (iSLK-Bac16WT cells)

city: Reno

first: Subhash

middle: C

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

description: ORF59 ChIP

data_processing:
The libraries were run on Illumina NextSeq500 instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Genomic Workbech 10.0.1 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the KSHV genome database to determine the DNA bound by specific targets
ChIP peaks were calculated using CLC workbench ChiP-peak tool using input as reference
Genome_build: NCBI genome build of KSHV sequence accession# NC_009333
Supplementary_files_format_and_content: ChIP peaks on the viral genomes are in wig file (CLC workbench)

organism: Human gammaherpesvirus 8

source_name: iSLK-Bac16WT cells

growth_protocol: iSLKBac16WT cells were grown in DMEM medium supplemented with 10%FBS 1ug/ml puromycin, 250 ug/ml G418, and 600 ug/ml hygromycin B

extract_protocol:
Latent and lytic cells were cross-linked using formaldehyde to fix the protein-DNA for ChIP assay
Chromatins were immunoprecipitated using specific listed antibody by following standard ChIP protocol
ChIP DNA was used for library prepartation for ChIP-seq analysis

treatment_protocol: Cells were induced for lytic reactivation by Doxycycline for  24h.

value: KSHV positive iSLK endothelial cells derived from gingival KS lesion

value: RTA protein is under tet-inducible promoter

value: induced with doxycycline for 24h to trigger lytic reactivation

tag: agent

value: PFA

value: ORF59 (Custom synthesized for our lab - anti-KSHV-ORF59 antibody from GenScript)


title: 24hInd Control IgG ChIP (iSLK-Bac16WT cells)

description: control IgG ChIP

tag: treatment

value: IgG (Cell Signaling Technology, catalog #2729, lot# 7)


title: Hmel-shGFP-H2BK15AC


title: Hmel-shGFP-H4


title: 24hInd ORF59 ChIP (iSLK-Bac16WT cells)

description: ORF59 ChIP


title: Hmel-shGFP-H2BK120AC

value: Active Motif-39119


title: 24hInd Input (iSLK-Bac16WT cells)

description: DNA extracted from the sonicated chromatin


title: Monocyte_derived_2 (ATAC-Seq)

value: Peritoneal macrophages


title: NY56_RNA

status: Public on Apr 23 2017

city: Irvine

first: Eddie

last: Park

state: CA

address: 2300 Biological Sciences 3

department: DevCell

institute: UCI

description: mock treatment

data_processing:
An initial set of sites were obtained using samtools (Li 2009) version 0.1.19 requiring variants to be seen in at least two RNA-seq replicates and a minimum editing rate of 5%. We also required the following for at least one replicate: a p-value less than 0.01 for the variant frequency between the ICE and RNA samples, less coverage in the ICE-seq than the RNA-seq, and a lower variant frequency in the ICE-seq than the RNA-seq. The Storer-Kim method was used to determine the p-value because it is considered one of the better statistical tests, in terms of power and Type I error, particularly for small and/or unequal sample sizes. We limited ourselves to A-to-G, T-to-C, G-to-A, and C-to-T variants because of the error bias in the NextSeq. The A-to-G and T-to-C variants represented our potential set of RNA editing sites (T-to-C variants were included because we used an unstranded library protocol). The G-to-A and C-to-T variants were used as a negative control because these types of variants had a comparable error profile and drosophila do not have C-to-U RNA editing. We computed the IDR for each site using the change in the number of G’s from RNA-seq to ICE-seq as the signal value. The sites were sorted by IDR and a 0.85 fraction of A-to-G/T-to-C sites were used to determine a cutoff threshold. Of the remaining sites, we removed sites outside gene boundaries, sites that were not A-to-G in the direction of transcription, and sites in repetitive regions. We sequenced two biological replicates of RNA-seq libraries derived from Drosophila melanogaster heads. The libraries were sequenced on a HiSeq 2500 and NextSeq 500. The resulting reads were normalized for read number and read length and mapped onto the dm3 assembly using tophat2 (Kim 2013) version 2.0.6. Variants were called using samtools mpileup with any at least 1 read supporting a variant. We reasoned that true biological variants and mapping errors were shared between the two sequencers while sequencing errors should be in the outersects. Variants that were sequencer specific were determined to be sequencing errors.   Gene ontology analysis was done using WebGestalt (Wang 2013). A significance level of 0.01 adjusted with the Benjamini-Hochberg procedure was used. A minimum of 5 genes per category was required.
Genome_build: dm3/droYak2
Supplementary_files_format_and_content: bed files containing RNA editing sites or other variants

organism: Drosophila yakuba

source_name: head

extract_protocol:
Total RNA was obtained from each Drosophila yakuba strain. Approximately 50 fly heads were used to obtain total RNA (5 µg) using TRIzol reagent (Life) as per manufacturer’s instruction. RNA integrity was evaluated on the BioAnalyzer (Aligent). Oligo(dT) selection was performed by using Dynal magnetic beads (Invitrogen) according to the manufacturer's protocol. The mRNA was fragmented by addition of 5x fragmentation buffer (200 mM Tris acetate, pH 8.2, 500 mM potassium acetate and 150 mM magnesium acetate), heated at 94 °C for 90 seconds, and then transferred to ice and run over a Sephadex-G50 column (USA Scientific) to remove the fragmentation ions.The fragmented mRNA was incubated in 38 µl CE solution (50% (v/v) ethanol, 1.1 M triethylammoniumacetate (pH 8.6)) with 1.6 M acrylonitrile at 70 °C for 1 hr (ICE treatment). A parallel mock treatment was preformed without 1.6 M acrylonitrile. The RNA was purified with ethanol precipitation and reverse transcribed with random hexamers, added to prime first-strand reverse transcription according to the manufacturer's protocol (Invitrogen cDNA synthesis kit). After the first strand was synthesized, a custom second-strand synthesis buffer (Illumina) was added, and dNTPs, RNase H and Escherichia coli polymerase I were added to nick translate the second-strand synthesis for 2.5 h at 16 °C. The reaction was then cleaned up on a QiaQuick PCR column (Qiagen) and eluted in 30 µl EB buffer (Qiagen).HiSeq reads were sequenced as single-ended 50-mers and NextSeq reads were sequenced as 86-mers. The reads were mapped onto the Drosophila melanogaster genome (BDGP R5/dm3) or Drosophila yakuba genome (WUGSC 7.1/droYak2) using TopHat version 2.0.6 (Kim 2013) / Bowtie version 2.0.2 (Langmead 2012) using the following options: --read-realign-edit-dist 0 --read-edit-dist 4 --read-mismatches 4 -G <gene annotation file> -x 1 -g 1. Unmapped reads were allowed to remap using bsmap version 2.74 (Xi 2009) using the following options: -v 3 -M GA.
The RNA was purified with ethanol precipitation and reverse transcribed with random hexamers, added to prime first-strand reverse transcription according to the manufacturer's protocol (Invitrogen cDNA synthesis kit). After the first strand was synthesized, a custom second-strand synthesis buffer (Illumina) was added, and dNTPs, RNase H and Escherichia coli polymerase I were added to nick translate the second-strand synthesis for 2.5 h at 16 °C. The reaction was then cleaned up on a QiaQuick PCR column (Qiagen) and eluted in 30 µl EB buffer (Qiagen)

tag: strain

tag: tissue

value: head

tag: developmental stage

value: adult


title: NY48_RNA

description: mock treatment


title: Hmel-shGFP-H3K9ME1

value: Hmel-shGFP

value: non-tumorigenic variant


title: CY21B3_RNA

description: mock treatment


title: NY66-2_ICE

description:
ICE treatment
protocol: ICE-Seq


title: NY56_ICE

description:
ICE treatment
protocol: ICE-Seq


title: NY81_ICE

description:
ICE treatment
protocol: ICE-Seq


title: NY48_ICE

description:
ICE treatment
protocol: ICE-Seq


title: CY21B3_ICE

description:
ICE treatment
protocol: ICE-Seq


title: CY08_ICE

description:
ICE treatment
protocol: ICE-Seq


title: Dmel_RNA_HiSeq_R2

description: mock treatment

organism: Drosophila melanogaster

value: y; cn, bw, sp


title: Dmel_RNA_HiSeq_R1

description: mock treatment


title: fCLIP_HEK293T_Replicate2

city: Seoul

first: Kyowon

last: Jeong

address: 1 Gwanak-ro

country: South Korea

institute: Seoul National University

description: A DROSHA fCLIP-seq sample from HEK293T

data_processing:
The base calling was done by RTA (Real Time Analysis. v1.18)
Using cutadapt (ver 1.8.1) 5p and 3p adapter sequences were removed with the following command : cutadapt -O 5 -g TACAGTCCGACGATC -A TGGAATTCTCGGGTGCCAAGG
The paired end reads were joined using pear (ver 0.9.0)  with the following command : pear -n 50
The processed reads were aligned using STAR (ver 2.3.0e Linux)  with the following command : STAR --outFilterMultimapNmax 5 --outFilterMismatchNmax 4
Per cell line, aligned BAM files were merged using samtools (ver 0.1.19, with the command : samtools merge), then merged file were used to find DROSHA cleavage sites using our in-house tool
Genome_build: hg38 for HEK293T and HeLa
Supplementary_files_format_and_content: tab-delimited tsv files including DROSHA cleavage sites for each cell line

source_name: HEK293T cells

extract_protocol:
HEK293T and HeLa cells grown on a 150 mm plate were rinsed twice with 18 ml of phosphate-buffered saline (PBS) solution and fixed with 18 ml of PBS-diluted 0.1% formaldehyde solution (Electron Microscopy Science) at room temperature (RT) for 10 min. For quenching of formaldehyde crosslinking, 2 ml of 1.5 M glycine solution was added to the plate at RT for 10 min. Fixed cells were harvested and resuspended in 550 μl of CLIP Wash buffer (1X PBS, 0.1% SDS, 0.5% deoxycholate, and 0.5% NP-40). After 10 min, lysate was sonicated by using bioruptor (COSMO BIO) and then treated with 20 μl of DNaseⅠ (Takara) at 37 ℃ for 10 min. The lysate was then centrifuged at 16,100 g for 10 min at 4 ℃, and supernatant was used in immunoprecipitation. For immunoprecipitation, 25 μl of protein A sepharose beads (GE healthcare, 17-5138-01) was prewashed three times with 1 ml of CLIP Wash buffer, and 20 μg of rabbit monoclonal DROSHA antibody (Cell Signaling, #3364) was attached to the washed beads in 400 μl of CLIP Wash buffer at 4 ℃ for 4 hr. The antibody-bound beads were then washed twice with CLIP Wash buffer, and incubated with the prepared lysate supernatant at 4 ℃ for 4 hr. After incubation, immunoprecipitates were washed six times with CLIP Wash buffer. The crosslinked DROSHA-RNA complexes were eluted from beads and antibodies by incubating the immunoprecipitates in 300 μl of PK-7M Urea buffer (200 mM Tris-HCl pH 7.4, 100 mM NaCl, 20 mM EDTA, 2% SDS, and 7 M Urea) at 25 ℃ for 2 hr with 950 rpm and taking ~300 μl of supernatant after brief spin down of the immunoprecipitates. The crosslinked RNAs were then separated from DROSHA proteins by treating additional 300 μl of 20 mg/ml Proteinase K (Roche) to the supernatant and incubating the solution at 65 ℃ for 12 hr with 1000 rpm. The RNAs were finally purified from the solution by phenol extraction.
Purified RNAs were sequentially treated with DNaseⅠ (Takara), alkaline phosphatase (Takara), and T4 polynucleotide kinase (PNK, Takara), and RNA products were purified from each treatment by phenol extraction. After PNK treatment, RNAs were run on 10% Urea-PAGE gel to obtain 25-160 nt RNA fragments and exclude remaining free ATPs. RNAs were purified from the excised gel, and the extracted RNAs were ligated to 3ʹ adapters by using T4 RNA ligase 2, truncated KQ (T4 Rnl2tr R55K, K227Q) (NEB). To exclude remaining free 3ʹ adapters, ligation products were run on 10% Urea-PAGE gel and purified from the excised gel. The 3ʹ adapter-ligated RNAs were ligated to 5ʹ adapters by T4 RNA ligase 1 (NEB) and then reverse transcribed by using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific) and RT primer. For Illumina sequencing, cDNA was amplified by PCR that utilized Phusion HF polymerase (Thermo Fisher Scientific), 5ʹ PCR primer, and 3ʹ PCR primer. Amplified cDNA library was purified from 6% acrylamide gel and sequenced on an Illumina HiSeq 2500 platform.

tag: cell type

value: human embryonic kidney cell line


title: fCLIP_HEK293T_Replicate1

description: A DROSHA fCLIP-seq sample from HEK293T


title: fCLIP_HeLa_Replicate1

description: A DROSHA fCLIP-seq sample from HeLa

source_name: HeLa cells

value: HeLa

value: human cervical cancer cell line


title: Dmel_RNA_NextSeq_R2

description: mock treatment


title: fCLIP_HeLa_Replicate2

description: A DROSHA fCLIP-seq sample from HeLa


title: Dmel_RNA_NextSeq_R1

description: mock treatment


title: Hmel-shGFP-H2AK5AC

value: HMEL


title: NY66-2_RNA

description: mock treatment


title: NY81_RNA

description: mock treatment


title: RNA-seq_siDROSHA_Rep3

description: rRNA-depleted RNA-seq

data_processing:
The base calling was done by CASAVA v1.8.2
Using cutadapt (ver 1.8.1) adapter sequences were removed with the following command : cutadapt -A GGAATTCTCGGGTGCCAAGG -g GTTCAGAGTTCTACAGTCCGACGATC for paired end libraries/ cutadapt -a TGGAATTCTCGGGTGCCAAGG for single end libraries
The processed reads were aligned using STAR (ver 2.3.0e Linux)  with the following command : STAR --outFilterMultimapNmax 5 --outFilterMismatchNmax 4
Per library, read count on each gene was calculated using our in-house tool. Then, the read fold changes between control and DROSHA/DICER KD samples were calculated.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited tsv files including DROSHA cleavage sites for each cell line

extract_protocol:
Total RNA was extracted from cells by using TRIzol reagent (Thermo Fisher Scientific) and treated with DNase I (Takara).
RNA-Seq Library-protocol

tag: condition

value: DROSHA siRNA treated


title: Dmel_RNA_R1

description: mock treatment


title: Dmel_RNA_R2

description: mock treatment


title: RNA-seq_siDICER_Rep3

description: rRNA-depleted RNA-seq

value: DICER siRNA treated


title: Dmel_ICE_R2

description:
ICE treatment
protocol: ICE-Seq


title: CY08_RNA

description: mock treatment


title: RNA-seq_siControl_Rep3

description: rRNA-depleted RNA-seq

value: Negative control siRNA treated


title: Dmel_ICE_R1

description:
ICE treatment
protocol: ICE-Seq


title: R_S432

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

data_processing:
The fastqs were aligned using STAR 2.5.2a and hg19
The aligned files were processed using PORT gene-based normalization ( https://github.com/itmat/Normalization )
The differential gene expression was done with limma
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts and normalized counts

source_name: PBMC

extract_protocol:
RNA was isolated using the Qiagen RNeasy micro kit (#74034) according to the manufacturer's protocol
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit for Pico Input Mammalian from Clonetech according to the manufacturer's protocol (#635007)
The libraries were sequenced on an Illumina NextSeq machine using a 300 cycle high output flow cell (#15057929)

tag: age

tag: Sex

value: female

value: Cycle3 treatment

value: peripheral blood mononuclear cell

tag: disease state

value: melanoma patient


title: R_S433

value: Cycle4 treatment


title: R_S430

value: Pre-treatment


title: R_S431

value: Cycle1 treatment


title: RNA-seq_siDROSHA_Rep2

description: rRNA-depleted RNA-seq

tag: cell line


title: RNA-seq_siDICER_Rep2

description: rRNA-depleted RNA-seq


title: R_S429


title: PD1-1 neurons

city: Boston

first: Ioannis

middle: S

last: Vlachos

state: MA

address: 330 Brookline Ave

department: Pathology

institute: Beth Israel Deaconess Medical Center

data_processing:
Raw RNA-Seq reads were quality checked using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Contaminants were detected and removed utilizing a combination of an in-house-developed algorithm and already available tools such as Minion, Reaper, Trimgalore and Trimmomatic
Following pre-processing, GSNAP spliced aligner was utilized to map the RNA-Seq reads against the reference genome (GRCh37/hg19 genome assembly). GSNAP has been appropriately parameterized in order to detect novel and known splice junctions
Read coverage of genes (read counts) was calculated with HT-Seq and R/Bioconductor.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Read counts (tsv format)

source_name: iPSC-derived neurons

growth_protocol: NPCs were dissociated with accutase and plated onto poly-L-ornithine (PLO; 20 µg/ml; Sigma-Aldrich)/ laminin (5 µg/ml; Sigma-Aldrich)-coated coverslips (Passage 1; P1) in Neurobasal/ B27/N2-medium supplemented with 200 ng/ml human recombinant sonic hedgehog (SHH, R&D Systems) and 100 ng/ml murine recombinant fibroblast growth factor 8b (FGF-8b, R&D Systems) for 8 DIV, followed by a cocktail consisting of 20 ng/ml brain-derived neurotrophic factor (BDNF, R&D Systems), 10 ng/ml glial cell-derived neurotrophic factor (GDNF, R&D Systems), 200 µM ascorbic acid (AA, Sigma-Aldrich) and 0.5 mM cyclic AMP (cAMP, Sigma-Aldrich) for at least 3 weeks. Half of the medium was replaced every other day. After 30-35 DIV of neuronal differentiation, corresponding to a total of 43-48 DIV,cells were harvested for RNA extraction.

extract_protocol:
Total RNA was extracted from cell pellets using the TRIzol® Reagent (Life Technologies).
Total cellular RNA was extracted from the following samples and sequenced on an Illumina HiSeq sequencer. RNA libraries were prepared with the TruSeq RNA Sample Preparation Kit V2 (Illumina).

value: neuron

tag: group

value: Parkinson's disease Patient

tag: clone


title: PD1-2 neurons


title: R_S426


title: R_S428


title: R_S420

value: male


title: RNA-seq_siControl_Rep2

description: rRNA-depleted RNA-seq

value: human embryonic kidney cell line


title: R_S419


title: C1-2 neurons

value: Control


title: R_S427


title: RNA-seq_siDROSHA_Rep1

description: rRNA-depleted RNA-seq


title: R_S418

value: Cycle2 treatment


title: R_S417


title: C1-1 neurons


title: R_S416


title: RNA-seq_siControl_Rep1

description: rRNA-depleted RNA-seq


title: RNA-seq_siDICER_Rep1

description: rRNA-depleted RNA-seq


title: HUES-neurons

source_name: HUES-derived neurons

value: Reference


title: DS2

status: Public on Apr 22 2017

city: changsha

first: chunsheng

last: gao

address: No.348 Xianjiahu West Rd

department: Institute of Bast Fiber Crops and Center of Southern Economic Crops

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Tag sequencing: The 3'-tag molecules were fixed onto the Illumina Sequencing Chip (flow cell). Each molecule grew into a single-molecule cluster sequencing template through in situ amplification. Four color-labeled nucleotides were added, and sequencing was performed with the method of sequencing by synthesis. Image analysis and base calling were performed using the Illumina Pipeline, and cDNA sequence tags were revealed after purity filtering. The tags passing initial quality tests were sorted and counted. Each tunnel generates millions of raw reads with sequencing length of 49 bp (target tags plus 3’adaptor). Each molecule in the library represented a single tag derived from a single transcript.
Filtering: low quality tags  such as tags containing ‘N’ and adaptor sequences were filtered
Gene annotation :“Clean Tags” were obtained by filtering off adaptor-only tags and low-quality tags (containing ambiguous bases). Comparison of the Clean Tags sequences with ramie transcriptome sequence (published in BMC genomics, Liu et al. 14:125) by BLASTN was carried out. All clean tags were annotated based on ramie reference genes. The number of annotated clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags)
Genome_build: Cannabis Transcriptome Shotgun Assembly (TSA) sequence database with accession numbers between [genbank:JP449145] - [genbank:JP482359]
Supplementary_files_format_and_content: the text file contain the tag sequence, copy number and TPM value

organism: Cannabis sativa

source_name: Yunma 1

extract_protocol:
After seven days the hemp suffering from drought stress, the whole plant excluding the CK and DS hemp tissues including leaf, root, stem bast, and stem shoot were individually collected. The sampled tissues were immediately frozen in liquid nitrogen and stored at -80° until use. Total RNA was extracted from the tissue of CK1, CK2, DS1 and DS2 using TRIzol reagent (Invitrogen, USA), and treated with DNase I (Fermentas, USA) according to the manufacturer’s protocol.
Equal amounts of total RNA from each sample were pooled together. Then, the poly(A)+ RNAs were purified from 20ug of total RNA by oligo(dT) Dynabeads.  To avoid priming bias when synthesizing cDNA, the purified mRNA was first fragmented into small pieces. First strand cDNAs were synthesized using random hexamers primer, then second strand cDNAs were synthesized using dNTPs, RNase H and DNA polymerase I. Double stranded cDNAs were purified by QIAquick PCR Purification Kit, repaired and added an adenine base to the 3’ end. Two different adapters were ligated to 5’ and 3’ ends, respectively. The ligated fragments were separated on gel and purfied. After amplification by PCR, the fragments were separated using electrophoresis and purified. The paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2000)

treatment_protocol: Watering was withheld after 30 days after sowing in the soil. CK was grown under well water condition, where DS was treated with drought stress by controlling the relative water content of soil no more than 20%. After seven days the hemp suffering from drought stress, the whole plant excluding the CK and DS hemp tissues including leaf, root, stem bast, and stem shoot were individually collected.

value: leaf, root, stem and shoot

value: drought stress


title: CK1

value: control


title: CK2


title: DS1


title: SSF1163_H9_ACY1215_1_KP2313_P3

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

data_processing:
Sequenced reads were mapped to the mouse genome (mm10) by Tophat
Estimated transcript counts were retrieved via the Cufflinks suite version 2.2.1.
Only single cell samples with at least 100.000 paired-end reads and a minimum of 20% aligning to the transcriptome were retained for further analysis.
Processed counts only show samples that passed the minimum reads and alignment criteria.
Genome_build: mm10
Supplementary_files_format_and_content: processed_counts.txt: txt file with processed counts after cufflinks

source_name: Lung tumor Macrophage ACY1215

growth_protocol: Genetically engineered mouse model (GEMM) of conditional activating mutation that harboring endogenous Kras (KrasLSL-G12D/+) were crossed with p53 conditional knockout Trp53fl/fl. CRE recombinase was induced through intranasal inhalation of 5x106 p.f.u. adeno-Cre (University of Iowa adenoviral core).

extract_protocol:
Viable CD45+CD3+ T cells  or CD45+CD11c+CD11blo macrophages were sorted from tumor cell suspensions into 2ul of Qiagen TCL buffer in 96-well plates
SmartSeq2 protocol with modifications (Trombetta et al., 2014)

treatment_protocol: Ricolinostat, 50 mg/kg, IP, QD

tag: position

value: Lung tumor

value: Mixed background

tag: gemm model

value: Macrophage


title: SSF1163_H9_Vehicle_1_KP2311_P3

source_name: Lung tumor Macrophage Vehicle

value: Vehicle


title: SSF1163_H7_ACY1215_1_KP2313_P3

source_name: Lung tumor Tcell ACY1215

value: Tcell


title: SSF1163_H7_Vehicle_1_KP2311_P3

source_name: Lung tumor Tcell Vehicle


title: SSF1163_H6_Vehicle_1_KP2311_P3


title: H33KD_H3K4me3_#2

tag: ecotype

value: Columbia

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: SSF1163_H6_ACY1215_1_KP2313_P3


title: male_119a_non-obese_t2d_1h

city: Gothenburg

first: Leif

last: Väremo

address: Kemivägen 10

department: Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

data_processing:
Basecalling, demultiplexing and conversion using CASAVA v1.8.2.
The reads were trimmed from adapter sequences and aligned to the human genome (Ensembl GRCh37.73, DNA primary assembly) using STAR 2.3.1u and the Homo_sapiens.GRCh37.73.gtf-file. The following additional flags were used: --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outStd SAM --outFilterType BySJout
Samtools 0.1.18 was used for indexing and sorting
Gene counts were calculated using HTSeq-count 0.5.4p3
Genome_build: Ensembl GRCh37.73
Supplementary_files_format_and_content: The count files contain the gene counts for each sample, as output by HTSeq-count.

molecule: polyA RNA

source_name: vastus lateralis muscle

growth_protocol: Muscle precursor cells (satellite cells) were isolated from human skeletal muscle biopsies obtained from the vastus lateralis muscle using a biopsy needle with suction (Bergström, 1975) as described in detail previously (Broholm et al., 2012). Isolated satellite cells were cultured in growth media 1 (HAM/F10 supplied with 20% Fetal Bovine Serum and 1% penicillin/streptomycin) and plated in 6-well plates. Upon 70-80% confluence, the media was changed to differentiation media 1 (DMEM 4.5 g/L glucose supplied with 10% FBS and 1% penicillin/streptomycin) for two-three days, until the myoblasts were completely confluent and had lined up. Hereafter, media was changed to differentiation media 2 (DMEM 4.5 g/L glucose supplied with 2% horse serum and 1% penicillin/streptomycin) thereby initiating fusion into myotubes. Cultures were fully differentiated by day 5 as determined by visual confirmation of myotube formation (>3 nuclei per myotube in ~70% of the cells). At day 5, media was changed to DMEM 1.0 g/L glucose without any supplements for two hours and the myotubes were subsequently stimulated with insulin (100nM). Cells were harvested before insulin stimulation, 30 minutes, one hour or two hours after insulin stimulation and total RNA was extracted using Trizol® (Life Sciences) according to the manufactures’ instructions.

extract_protocol:
Total RNA was extracted using Trizol® (Life Sciences) according to the manufactures’ instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq RNA kit

treatment_protocol: The myotubes were stimulated with insulin (100nM) before harvesting.

tag: sample id

tag: cell id

tag: disease

tag: weight

value: non-obese

tag: gender

tag: time after insulin, h

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_H5_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: female_79a_obese_ngt_0.5h

tag: sample id

tag: cell id

tag: disease

value: ngt

tag: weight

value: obese

tag: gender

value: female

tag: time after insulin, h

tag: age

tag: bmi


title: SSF1163_H5_Vehicle_1_KP2311_P3


title: female_79a_obese_ngt_0h

treatment_protocol: No treatment.

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l


title: SSF1163_H4_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_H4_ACY1215_1_KP2313_P3


title: SSF1163_H3_Vehicle_1_KP2311_P3


title: female_46a_obese_t2d_0h

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: gender

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_H3_ACY1215_1_KP2313_P3


title: female_2a_non-obese_ngt_2h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir


title: male_56a_obese_ngt_2h

value: male

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l


title: SSF1163_H2_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: female_8a_non-obese_t2d_1h

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: gender

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: female_8a_non-obese_t2d_0.5h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir


title: SSF1163_H2_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: female_8a_non-obese_t2d_0h

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: gender

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l


title: SSF1163_H8_Vehicle_1_KP2311_P3


title: SSF1163_H8_ACY1215_1_KP2313_P3


title: SSF1163_H12_ACY1215_1_KP2313_P3


title: male_27_obese_ngt_1h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: male_27_obese_ngt_0.5h

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir


title: male_20a_non-obese_t2d_1h

tag: sample id

tag: cell id

tag: disease


title: male_41a_obese_t2d_0.5h

tag: weight

tag: gender

tag: cholesterol (total), mmol/l


title: SSF1163_H11_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_H12_Vehicle_1_KP2311_P3


title: SSF1163_H11_Vehicle_1_KP2311_P3


title: SSF1163_H10_Vehicle_1_KP2311_P3


title: male_32a_non-obese_ngt_0.5h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l


title: SSF1163_H1_Vehicle_1_KP2311_P3


title: SSF1163_H10_ACY1215_1_KP2313_P3


title: male_63a_non-obese_t2d_2h

tag: sample id

tag: cell id

tag: disease

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: female_28a_obese_ngt_2h

tag: weight

tag: gender

tag: cholesterol (total), mmol/l


title: SSF1163_G9_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: female_28a_obese_ngt_1h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l


title: male_20a_non-obese_t2d_2h

tag: sample id

tag: cell id

tag: disease

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_G8_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_G9_ACY1215_1_KP2313_P3


title: male_119a_non-obese_t2d_2h

tag: weight

tag: gender

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (total), mmol/l


title: female_46a_obese_t2d_1h

tag: sample id

tag: cell id

tag: disease

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l


title: female_46a_obese_t2d_2h

tag: homa-ir

tag: free fatty acids (0h), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_G6_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_G7_Vehicle_1_KP2311_P3


title: male_63a_non-obese_t2d_0.5h

tag: weight

tag: gender

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (total), mmol/l


title: SSF1163_G7_ACY1215_1_KP2313_P3


title: h3.3 kd rep2

tag: ecotype

tag: genotype/variation

value: h3.3 kd


title: SSF1163_G8_ACY1215_1_KP2313_P3


title: SSF1163_G6_ACY1215_1_KP2313_P3


title: male_35a_non-obese_ngt_1h

tag: sample id

tag: cell id

tag: disease

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: SSF1163_G5_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_G5_ACY1215_1_KP2313_P3


title: female_124a_obese_t2d_2h

tag: weight

tag: gender

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (total), mmol/l

tag: free fatty acids (2h), mmol/l


title: male_35a_non-obese_ngt_0.5h

tag: sample id

tag: cell id

tag: disease

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l


title: male_32a_non-obese_ngt_1h

tag: weight

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: female_28a_obese_ngt_0.5h

tag: gender

tag: time after insulin, h

tag: age


title: SSF1163_G4_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_H1_ACY1215_1_KP2313_P3


title: SSF1163_G3_ACY1215_1_KP2313_P3


title: male_34a_non-obese_ngt_2h

tag: sample id

tag: cell id

tag: disease

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (total), mmol/l

tag: free fatty acids (2h), mmol/l


title: female_28a_obese_ngt_0h

tag: weight

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: male_96a_obese_t2d_0h

tag: gender

tag: time after insulin, h

tag: age


title: SSF1163_G4_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: female_85a_obese_t2d_0h

tag: sample id

tag: cell id

tag: disease

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (total), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_G2_ACY1215_1_KP2313_P3


title: male_20a_non-obese_t2d_0h

tag: weight

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (hdl), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: SSF1163_G2_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: male_63a_non-obese_t2d_0h

tag: sample id

tag: cell id

tag: disease

tag: gender

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l


title: SSF1163_G12_ACY1215_1_KP2313_P3


title: female_8a_non-obese_t2d_2h

tag: weight

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_G12_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: female_127a_non-obese_t2d_1h

tag: sample id

tag: cell id

tag: disease

tag: gender

tag: time after insulin, h

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: male_59a_obese_ngt_2h

tag: weight

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir


title: female_127a_non-obese_t2d_2h

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_G10_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_G10_ACY1215_1_KP2313_P3


title: male_59a_obese_ngt_0.5h

tag: sample id

tag: cell id

tag: disease

tag: gender

tag: time after insulin, h

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: male_59a_obese_ngt_1h

tag: weight

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir


title: SSF1163_G11_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_G1_ACY1215_1_KP2313_P3


title: male_56a_obese_ngt_0.5h

tag: sample id

tag: cell id

tag: disease

tag: gender

tag: time after insulin, h

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_G1_Vehicle_1_KP2311_P3


title: female_71a_obese_ngt_2h

tag: weight

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: SSF1163_G3_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: male_35a_non-obese_ngt_2h

tag: sample id

tag: cell id

tag: disease

tag: gender

tag: time after insulin, h

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir


title: SSF1163_F8_Vehicle_1_KP2311_P3


title: SSF1163_F7_ACY1215_1_KP2313_P3


title: SSF1163_F9_ACY1215_1_KP2313_P3


title: SSF1163_F9_Vehicle_1_KP2311_P3


title: SSF1163_G11_ACY1215_1_KP2313_P3


title: female_124a_obese_t2d_0h

tag: weight

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_F7_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: female_124a_obese_t2d_1h

tag: sample id

tag: cell id

tag: disease

tag: gender

tag: time after insulin, h

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: SSF1163_F6_Vehicle_1_KP2311_P3


title: SSF1163_F6_ACY1215_1_KP2313_P3


title: female_71a_obese_ngt_0.5h

tag: weight

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir


title: SSF1163_F5_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: male_27_obese_ngt_0h

tag: sample id

tag: cell id

tag: disease

tag: gender

tag: time after insulin, h

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: male_56a_obese_ngt_1h

tag: weight

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: female_2a_non-obese_ngt_1h

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir


title: female_79a_obese_ngt_1h

tag: sample id

tag: cell id

tag: disease


title: SSF1163_F3_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_F3_Vehicle_1_KP2311_P3


title: SSF1163_F5_Vehicle_1_KP2311_P3


title: female_13a_non-obese_ngt_2h

tag: weight

tag: gender

tag: time after insulin, h

tag: age

tag: bmi

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_F4_Vehicle_1_KP2311_P3


title: female_2a_non-obese_ngt_0.5h

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: male_32a_non-obese_ngt_2h

tag: sample id

tag: cell id

tag: disease


title: SSF1163_F8_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_F2_Vehicle_1_KP2311_P3


title: SSF1163_F12_ACY1215_1_KP2313_P3


title: female_124a_obese_t2d_0.5h

tag: weight

tag: gender

tag: time after insulin, h

tag: age

tag: bmi

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: male_20a_non-obese_t2d_0.5h

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: SSF1163_F12_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: female_109a_non-obese_t2d_1h

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: gender

tag: time after insulin, h

tag: age

tag: bmi


title: female_71a_obese_ngt_1h

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: female_79a_obese_ngt_2h

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: SSF1163_F11_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_F4_ACY1215_1_KP2313_P3


title: SSF1163_F11_Vehicle_1_KP2311_P3


title: female_109a_non-obese_t2d_0h

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: gender

tag: time after insulin, h

tag: age

tag: bmi


title: SSF1163_F10_Vehicle_1_KP2311_P3


title: female_13a_non-obese_ngt_0.5h

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: female_46a_obese_t2d_0.5h

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: SSF1163_F10_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: male_27_obese_ngt_2h

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: gender

tag: time after insulin, h

tag: age

tag: bmi


title: male_34a_non-obese_ngt_0.5h

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_F1_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: female_71a_obese_ngt_0h

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: gender

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: female_109a_non-obese_t2d_0.5h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir


title: SSF1163_F1_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: male_41a_obese_t2d_2h

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: gender

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: male_41a_obese_t2d_0h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: SSF1163_E9_Vehicle_1_KP2311_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_E9_ACY1215_1_KP2313_P3


title: male_41a_obese_t2d_1h

tag: sample id

tag: cell id

tag: disease

tag: weight

tag: gender

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir


title: SSF1163_E8_Vehicle_1_KP2311_P3


title: female_13a_non-obese_ngt_1h

tag: time after insulin, h

tag: age

tag: bmi

tag: fasting glucose (0h), mmol/l

tag: glucose (2h), mmol/l

tag: cholesterol (total), mmol/l

tag: cholesterol (hdl), mmol/l

tag: free fatty acids (2h), mmol/l


title: SSF1163_E8_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

tag: gemm model

tag: treatment


title: SSF1163_E7_ACY1215_1_KP2313_P3


title: SSF1163_F2_ACY1215_1_KP2313_P3


title: SSF1163_E7_Vehicle_1_KP2311_P3


title: MAGIC86_30C

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

institute: University of Utah

description:
WTCHG_37667_267
FPKMs.tsv.gz
RANKSUM.tsv.gz

data_processing:
Illumina sequencing was performed at the Oxford Genomics Centre (Oxford, UK) to produce 100 bp paired-end reads using a HiSeq 2000 instrument and the TruSeq V3 chemistry. Reads from each library were aligned to the TAIR10 reference genome using PALMapper v0.6512 following a variation-aware alignment approach. Genome variants collected from the 19 founder strains (Gan et al., 2011; PMID: 21874022) as well as variants reported for a diverse natural population (Long et al., 2013; PMID: 23793030) were integrated and provided to the aligner as a set of known variants. Briefly, the mapper used this set of variants in alignments to prevent reference biases in RNA-seq read mapping. To facilitate accurate alignments, we further provided splice junction information collected in an earlier study with the founder strains (Gan et al., 2011; PMID: 21874022) as well as junction information extracted from the TAIR10 genome annotation. The full alignment parameter set for PALMapper was: -M 3 -G 0 -E 3 -l 12 –L 14 -K 12 -C 14 -I 5000 -NI 1 -SA 5 -UA 50 -CT 50 -JA 15 -JI 1 -z 10 -S -seed-hit-truncate-threshold 100 -report-map-read -report-spliced-read -report-map region -report-splice-sites 0.9 -filter-max-mismatches 0 -filter-max-gaps 0 -filter-splice-region 5 -min-spliced-segment-len 1 -qpalma-use-map-max-len 10 -f bam -qpalma-prb-offset-fix -junction-remapping <junction_file> -score-annotated-splice-sites <junction_file> -max-dp-deletions 2 -use-variants-editop-filter -use-variants <variant_file> -filter-variants-minuse 1 –merge-variant-source-ids -use-iupac-snp-variants -filter-variants-map-window 20 -iupac-genome -filter-variants-maxlen 100 -index-precache.
From the aligned reads per sample, gene expression quantification was performed using custom Python scripts that counted the number of reads overlapping with at least one exonic position of an annotated gene feature. For each read only the best alignment as assessed with the PALMapper aligner was considered for counting. An alignment was excluded from being counted towards the expression of a gene if (i) at least one position in the alignment overlapped to an annotated intron, (ii) the alignment fell entirely into a region where two or more annotated genes overlap, and (iii) the alignment did not start at a position that is part of an exon in all annotated isoforms. For each gene feature the total number of reads passing these filters was used to calculate Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and RANKSUM expression values (briefly, for the latter a rank transformation was applied in which the gene expression levels were ranked across samples and then transformed values were sampled from an inverse Gaussian CDF based on the ranks). Genes included in the expression quantification were from the TAIR10 annotation and a set of novel genes reported in an earlier study (Gan et al., 2011; PMID: 21874022).
The 103 MAGIC lines included in this analysis are part of a larger set of nearly 500 lines for which the genomic intervals derived from the 19 founder accessions of the MAGIC cross were imputed using Illumina genomic sequencing of both the MAGIC founders and the derived lines. The imputed genomes of each MAGIC line as assessed from genomic DNA sequences are publically available at the respective genome project site (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/magic.html). An analogous imputation using variants inferred from the RNA-seq alignments gave similar imputations for most lines -- a prerequisite for using the RNA-seq data with the genomic imputations for genotype-phenotype studies -- with a small number of exceptions that included MAGIC lines 311, 423 and 432. In some of these cases, differences may reflect regions of lines that were not fixed by inbreeding (the seed stocks used in the current RNA-seq study were from a different batch than used for genomic DNA imputation), and the result should be factored into specific downstream analyses with this subset of lines.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM and RANKSUM normalized expression values as separate text files.

source_name: aerial seedling

growth_protocol: A subset of MAGIC lines were obtained from the Nottingham Arabidopsis Stock Centre (NASC). Briefly, 103 of the MAGIC lines were grown under long day conditions (16 hours light: 8 hours dark) at 20˚C followed by a 48 hour shift to 30°C in Percival environmental chambers (Perry, IA, USA) and total RNA was prepared as previously described for an earlier study with the MAGIC parental founders (twenty aerial rosettes from seedlings at the fourth true leaf stage were pooled per single biological replicate per line; Gan et al., 2011, PMID: 21874022).

extract_protocol:
Pools of 20 aerial seedlings per MAGIC line were ground in liquid nitrogen using a mortar and pestle and RNA was isolated using PureLink Plant RNA Reagent (#12322-012, Invitrogen, Carlsbad, CA, USA) following the manufacturers instructions. Precipitated RNA was resuspended in RNAsecure Resuspension Solution (#AM7010, Ambion; Life Technologies, Carlsbad, CA, USA) following manufacturers guidelines to prevent RNA degradation. Contaminating genomic DNA was removed by incubating samples with Turbo DNase (#AM2238, Ambion) for 15 min at 37°C. Finally, RNA was precipitated using 2.5 vol 100% ethanol, 0.1 volume 5M Ammonium Acetate and 1µl glycogen (5 mg/ml) and resuspended in RNase-free water.
Non-strand specific RNA-seq libraries were constructed using the Illumina method at the Oxford Genomics Centre (Oxford, UK). Poly-A selection was employed in the library construction.

tag: Stage

value: 4th true leaf stage

tag: accession

value: MAGIC Line 86

tag: growth temperature

value: 30°C for 48 hours (following growth at 20˚C)


title: MAGIC213_30C

description:
WTCHG_37667_269
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 213


title: SSF1163_E6_Vehicle_1_KP2311_P3

value: Lung tumor


title: MAGIC118_30C

description:
WTCHG_37667_268
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 118


title: SSF1163_E6_ACY1215_1_KP2313_P3

value: Mixed background


title: SSF1163_E5_Vehicle_1_KP2311_P3

value: Vehicle


title: MAGIC307_30C

description:
WTCHG_37667_262
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 307


title: MAGIC414_30C

description:
WTCHG_37667_232
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 414


title: MAGIC321_30C

description:
WTCHG_37667_231
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 321


title: SSF1163_E4_ACY1215_1_KP2313_P3

value: Tcell


title: SSF1163_E4_Vehicle_1_KP2311_P3


title: SSF1163_E3_ACY1215_1_KP2313_P3


title: SSF1163_E3_Vehicle_1_KP2311_P3


title: MAGIC261_30C

description:
WTCHG_37667_230
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 261


title: SSF1163_E2_ACY1215_1_KP2313_P3


title: SSF1163_E2_Vehicle_1_KP2311_P3


title: male_34a_non-obese_ngt_1h

tag: sample id

tag: cell id

tag: disease

value: ngt

tag: weight

value: non-obese

tag: gender

tag: insulin (0h), pmol/l

tag: insulin (2h), pmol/l

tag: homa-ir

tag: cholesterol (ldl), mmol/l

tag: triglycerides, mmol/l

tag: free fatty acids (0h), mmol/l


title: MAGIC490_30C

description:
WTCHG_37666_288
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 490


title: SSF1163_E12_ACY1215_1_KP2313_P3

tag: position

tag: tissue

tag: strain

value: Macrophage


title: MAGIC104_30C

description:
WTCHG_37667_228
FPKMs.tsv.gz
RANKSUM.tsv.gz

tag: Stage

value: 4th true leaf stage

value: MAGIC Line 104


title: MAGIC72_30C

description:
WTCHG_37667_227
FPKMs.tsv.gz
RANKSUM.tsv.gz

tag: accession

value: MAGIC Line 72

value: 30°C for 48 hours (following growth at 20˚C)


title: SSF1163_E12_Vehicle_1_KP2311_P3

value: Lung tumor

tag: gemm model

tag: treatment


title: SSF1163_E11_ACY1215_1_KP2313_P3


title: MAGIC434_30C

description:
WTCHG_37667_264
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 434

tag: growth temperature


title: MAGIC25_30C

description:
WTCHG_37667_265
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 25


title: MAGIC135_30C

description:
WTCHG_37666_284
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 135


title: MAGIC92_30C

description:
WTCHG_37666_283
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 92


title: MAGIC222_30C

description:
WTCHG_37666_285
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 222


title: SSF1163_E11_Vehicle_1_KP2311_P3

value: Mixed background

value: Vehicle


title: SSF1163_E5_ACY1215_1_KP2313_P3

value: Tcell


title: SSF1163_E10_ACY1215_1_KP2313_P3


title: MAGIC30_30C

description:
WTCHG_37666_281
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 30


title: SSF1163_E1_Vehicle_1_KP2311_P3


title: MAGIC328_30C

description:
WTCHG_37667_263
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 328


title: SSF1163_D9_ACY1215_1_KP2313_P3


title: MAGIC253_30C

description:
WTCHG_37666_214
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 253


title: MAGIC175_30C

description:
WTCHG_37666_213
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 175


title: SSF1163_E1_ACY1215_1_KP2313_P3


title: MAGIC11_30C

description:
WTCHG_37667_225
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: 4th true leaf stage

value: MAGIC Line 11


title: SSF1163_D9_Vehicle_1_KP2311_P3

value: Macrophage


title: SSF1163_D8_Vehicle_1_KP2311_P3


title: MAGIC66_30C

description:
WTCHG_37666_211
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 66

value: 30°C for 48 hours (following growth at 20˚C)


title: SSF1163_D8_ACY1215_1_KP2313_P3

value: Lung tumor


title: MAGIC35_30C

description:
WTCHG_37666_210
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 35


title: SSF1163_D7_ACY1215_1_KP2313_P3


title: MAGIC353_30C

description:
WTCHG_37666_287
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 353


title: SSF1163_D7_Vehicle_1_KP2311_P3


title: MAGIC6_30C

description:
WTCHG_37666_209
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 6


title: MAGIC432_30C

description:
WTCHG_37665_256
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 432


title: SSF1163_E10_Vehicle_1_KP2311_P3

value: Mixed background


title: MAGIC99_30C

description:
WTCHG_37666_212
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 99


title: SSF1163_D6_Vehicle_1_KP2311_P3

value: Tcell

value: Vehicle


title: MAGIC327_30C

description:
WTCHG_37665_255
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 327


title: MAGIC305_30C

description:
WTCHG_37665_254
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 305


title: SSF1163_D5_Vehicle_1_KP2311_P3


title: SSF1163_D5_ACY1215_1_KP2313_P3


title: MAGIC205_30C

description:
WTCHG_37665_253
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 205


title: MAGIC317_30C

description:
WTCHG_37666_215
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: 4th true leaf stage

value: MAGIC Line 317


title: SSF1163_D4_Vehicle_1_KP2311_P3


title: SSF1163_D6_ACY1215_1_KP2313_P3


title: MAGIC18_30C

description:
WTCHG_37665_249
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 18


title: MAGIC80_30C

description:
WTCHG_37665_251
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 80


title: MAGIC44_30C

description:
WTCHG_37665_250
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 44

value: 30°C for 48 hours (following growth at 20˚C)


title: MAGIC316_30C

description:
WTCHG_37665_207
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 316


title: MAGIC362_30C

description:
WTCHG_37665_208
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 362


title: SSF1163_D3_ACY1215_1_KP2313_P3

value: Lung tumor


title: SSF1163_D3_Vehicle_1_KP2311_P3


title: SSF1163_D2_ACY1215_1_KP2313_P3


title: SSF1163_D12_Vehicle_1_KP2311_P3

value: Macrophage


title: SSF1163_D12_ACY1215_1_KP2313_P3

value: Mixed background


title: SSF1163_D11_ACY1215_1_KP2313_P3


title: MAGIC62_30C

description:
WTCHG_37665_203
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 62


title: MAGIC96_30C

description:
WTCHG_37665_204
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 96


title: MAGIC236_30C

description:
WTCHG_37665_206
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 236


title: SSF1163_D2_Vehicle_1_KP2311_P3

value: Tcell

value: Vehicle


title: MAGIC212_30C

description:
WTCHG_37417_261
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 212


title: MAGIC4_30C

description:
WTCHG_37665_201
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: 4th true leaf stage

value: MAGIC Line 4


title: SSF1163_D11_Vehicle_1_KP2311_P3


title: SSF1163_D10_ACY1215_1_KP2313_P3


title: MAGIC116_30C

description:
WTCHG_37417_260
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 116


title: MAGIC45_30C

description:
WTCHG_37417_258
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 45


title: MAGIC505_30C

description:
WTCHG_37417_207
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 505


title: MAGIC21_30C

description:
WTCHG_37417_257
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 21

value: 30°C for 48 hours (following growth at 20˚C)


title: SSF1163_D1_ACY1215_1_KP2313_P3


title: SSF1163_D1_Vehicle_1_KP2311_P3


title: SSF1163_D4_ACY1215_1_KP2313_P3


title: SSF1163_C9_ACY1215_1_KP2313_P3


title: SSF1163_C9_Vehicle_1_KP2311_P3


title: MAGIC503_30C

description:
WTCHG_37417_206
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 503


title: MAGIC495_30C

description:
WTCHG_37417_203
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 495


title: SSF1163_C8_ACY1215_1_KP2313_P3

value: Lung tumor


title: MAGIC498_30C

description:
WTCHG_37417_204
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 498


title: MAGIC501_30C

description:
WTCHG_37417_205
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 501


title: SSF1163_C7_ACY1215_1_KP2313_P3

value: Mixed background


title: SSF1163_C8_Vehicle_1_KP2311_P3


title: MAGIC494_30C

description:
WTCHG_37417_202
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 494


title: SSF1163_C7_Vehicle_1_KP2311_P3

value: Tcell


title: MAGIC492_30C

description:
WTCHG_37417_201
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 492


title: MAGIC483_30C

description:
WTCHG_37416_272
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 483


title: SSF1163_C6_Vehicle_1_KP2311_P3

value: Vehicle


title: SSF1163_C5_ACY1215_1_KP2313_P3


title: MAGIC346_30C

description:
WTCHG_37416_271
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: 4th true leaf stage

value: MAGIC Line 346


title: MAGIC31_30C

description:
WTCHG_37416_289
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 31


title: SSF1163_C6_ACY1215_1_KP2313_P3


title: MAGIC83_30C

description:
WTCHG_37417_259
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 83


title: SSF1163_D10_Vehicle_1_KP2311_P3

value: Macrophage


title: SSF1163_C5_Vehicle_1_KP2311_P3


title: SSF1163_C4_ACY1215_1_KP2313_P3


title: MAGIC430_30C

description:
WTCHG_37416_248
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 430

value: 30°C for 48 hours (following growth at 20˚C)


title: SSF1163_C3_ACY1215_1_KP2313_P3


title: SSF1163_C3_Vehicle_1_KP2311_P3


title: SSF1163_C4_Vehicle_1_KP2311_P3


title: MAGIC324_30C

description:
WTCHG_37416_247
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 324


title: MAGIC297_30C

description:
WTCHG_37416_246
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 297


title: MAGIC198_30C

description:
WTCHG_37416_245
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 198


title: SSF1163_C12_ACY1215_1_KP2313_P3

value: Lung tumor


title: SSF1163_C2_Vehicle_1_KP2311_P3

value: Mixed background


title: MAGIC76_30C

description:
WTCHG_37416_243
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 76


title: MAGIC42_30C

description:
WTCHG_37416_242
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 42


title: SSF1163_C2_ACY1215_1_KP2313_P3

value: Tcell


title: MAGIC108_30C

description:
WTCHG_37416_244
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 108


title: SSF1163_C12_Vehicle_1_KP2311_P3

value: Vehicle


title: MAGIC16_30C

description:
WTCHG_37416_241
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: 4th true leaf stage

value: MAGIC Line 16


title: SSF1163_C11_ACY1215_1_KP2313_P3


title: MAGIC308_30C

description:
WTCHG_37416_270
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 308


title: SSF1163_C11_Vehicle_1_KP2311_P3


title: MAGIC351_30C

description:
WTCHG_37415_279
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 351


title: MAGIC366_30C

description:
WTCHG_37416_216
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 366


title: MAGIC311_30C

description:
WTCHG_37415_278
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 311


title: SSF1163_C1_ACY1215_1_KP2313_P3


title: SSF1163_C10_ACY1215_1_KP2313_P3

value: Macrophage


title: SSF1163_C1_Vehicle_1_KP2311_P3


title: MAGIC90_30C

description:
WTCHG_37415_275
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 90

value: 30°C for 48 hours (following growth at 20˚C)


title: SSF1163_C10_Vehicle_1_KP2311_P3


title: SSF1163_B9_ACY1215_1_KP2313_P3


title: MAGIC130_30C

description:
WTCHG_37415_276
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 130


title: MAGIC52_30C

description:
WTCHG_37415_274
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 52


title: SSF1163_B8_Vehicle_1_KP2311_P3

value: Lung tumor

value: Mixed background


title: SSF1163_B9_Vehicle_1_KP2311_P3


title: MAGIC196_30C

description:
WTCHG_37415_237
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 196


title: MAGIC322_30C

description:
WTCHG_37415_239
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 322


title: SSF1163_B7_ACY1215_1_KP2313_P3

value: Tcell


title: MAGIC423_30C

description:
WTCHG_37415_240
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 423


title: SSF1163_B7_Vehicle_1_KP2311_P3

value: Vehicle


title: SSF1163_B8_ACY1215_1_KP2313_P3


title: SSF1163_B6_Vehicle_1_KP2311_P3


title: MAGIC74_30C

description:
WTCHG_37415_235
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: 4th true leaf stage

value: MAGIC Line 74


title: SSF1163_B5_ACY1215_1_KP2313_P3


title: MAGIC491_30C

description:
WTCHG_37414_296
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 491


title: SSF1163_B6_ACY1215_1_KP2313_P3


title: MAGIC41_30C

description:
WTCHG_37415_234
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 41


title: MAGIC14_30C

description:
WTCHG_37415_233
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 14


title: MAGIC312_30C

description:
WTCHG_37414_286
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 312


title: SSF1163_B5_Vehicle_1_KP2311_P3


title: MAGIC220_30C

description:
WTCHG_37415_277
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 220


title: MAGIC55_30C

description:
WTCHG_37414_282
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 55

value: 30°C for 48 hours (following growth at 20˚C)


title: SSF1163_B4_Vehicle_1_KP2311_P3


title: SSF1163_B4_ACY1215_1_KP2313_P3


title: SSF1163_B3_ACY1215_1_KP2313_P3


title: MAGIC50_30C

description:
WTCHG_37414_266
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 50


title: SSF1163_B3_Vehicle_1_KP2311_P3

value: Lung tumor


title: MAGIC114_30C

description:
WTCHG_37414_252
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 114


title: SSF1163_B2_ACY1215_1_KP2313_P3

value: Mixed background


title: MAGIC26_30C

description:
WTCHG_37414_273
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 26


title: MAGIC194_30C

description:
WTCHG_37414_229
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 194


title: SSF1163_B2_Vehicle_1_KP2311_P3

value: Tcell


title: SSF1163_B12_ACY1215_1_KP2313_P3

value: Macrophage


title: MAGIC266_30C

description:
WTCHG_37414_238
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: 4th true leaf stage

value: MAGIC Line 266


title: MAGIC106_30C

description:
WTCHG_37415_236
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 106


title: MAGIC319_30C

description:
WTCHG_37414_223
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 319


title: SSF1163_B11_Vehicle_1_KP2311_P3

value: Vehicle


title: MAGIC39_30C

description:
WTCHG_37414_226
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 39


title: SSF1163_B12_Vehicle_1_KP2311_P3


title: SSF1163_B10_Vehicle_1_KP2311_P3


title: MAGIC255_30C

description:
WTCHG_37414_222
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 255


title: MAGIC34_30C

description:
WTCHG_37414_202
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 34


title: MAGIC361_30C

description:
WTCHG_36988_295
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 361

value: 30°C for 48 hours (following growth at 20˚C)


title: SSF1163_B1_Vehicle_1_KP2311_P3

value: Lung tumor


title: MAGIC314_30C

description:
WTCHG_36988_294
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 314


title: MAGIC161_30C

description:
WTCHG_36988_292
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 161


title: MAGIC226_30C

description:
WTCHG_36988_293
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 226


title: MAGIC94_30C

description:
WTCHG_36988_291
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 94


title: SSF1163_A9_Vehicle_1_KP2311_P3

value: Mixed background


title: SSF1163_A9_ACY1215_1_KP2313_P3

value: Macrophage


title: SSF1163_B1_ACY1215_1_KP2313_P3

value: Tcell


title: SSF1163_A8_Vehicle_1_KP2311_P3


title: MAGIC60_30C

description:
WTCHG_36988_290
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: 4th true leaf stage

value: MAGIC Line 60


title: SSF1163_A7_ACY1215_1_KP2313_P3


title: MAGIC388_30C

description:
WTCHG_36988_224
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 388


title: MAGIC485_30C

description:
WTCHG_36988_280
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 485


title: MAGIC180_30C

description:
WTCHG_36988_221
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 180


title: MAGIC101_30C

description:
WTCHG_36988_220
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 101


title: SSF1163_A8_ACY1215_1_KP2313_P3


title: SSF1163_A6_Vehicle_1_KP2311_P3

value: Vehicle


title: SSF1163_B11_ACY1215_1_KP2313_P3


title: SSF1163_A7_Vehicle_1_KP2311_P3


title: MAGIC170_30C

description:
WTCHG_37414_205
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 170


title: SSF1163_A6_ACY1215_1_KP2313_P3


title: MAGIC70_30C

description:
WTCHG_36988_219
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 70

value: 30°C for 48 hours (following growth at 20˚C)


title: MAGIC37_30C

description:
WTCHG_36988_218
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 37


title: SSF1163_B10_ACY1215_1_KP2313_P3

value: Lung tumor


title: SSF1163_A5_Vehicle_1_KP2311_P3


title: SSF1163_A5_ACY1215_1_KP2313_P3


title: MAGIC9_30C

description:
WTCHG_36988_217
FPKMs.tsv.gz
RANKSUM.tsv.gz

value: MAGIC Line 9


title: SSF1163_A4_Vehicle_1_KP2311_P3


title: SSF1163_A4_ACY1215_1_KP2313_P3


title: SSF1163_A3_ACY1215_1_KP2313_P3


title: embryo_18_24_hr_mRNA

first: Eric

last: Lai

state: New York

address: 430 E 67th Street

department: Department of Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Read processing. Fastq files for six embryo timepoints were adapter trimmed and demultiplexed with a custom pipeline using Flexbar (https://github.com/seqan/flexbar), and pyBarcodeFilter.py from the pyCRAC software suite, respectively. PCR duplicates in the dataset were removed and the read headers were then altered to be compatible with the CIMS software package using methods previously described in Linder et al. 2014. Paired-end RNA-seq data from control mRNA and miCLIP for six embryo developmental timepoints were mapped to the Drosophila reference genome sequence (version r5.45) with Subread-align package from the Subread software suite. Read counts for each gene was extracted from the RNA-seq bam files using featureCounts package from the Subread software. The read counts per gene were then normalized to obtain FPKM values using DEseq package from R Bioconductor.
miCLIP analysis and mutation calling. The reads were mapped to the Drosophila reference genome sequence (version r5.45) with Novoalign (Novocraft) or the Subread-align package from the Subread software suite. For the Novoalign alignment, a maximum alignment score of 85 was allowed and the parameters were adjusted to map short reads. For alignment using the subread-align, the alignment was performed using default parameters for mapping paired-end RNA sequence data. Positions of C to T transitions from the mapped data were identified using the CIMS software package as described in Linder et al. 2014.
Genome_build: r5.45
Supplementary_files_format_and_content: bigWig, matrix.txt: FPKM

source_name: embryo

growth_protocol: We mass-collected Canton S embryos across these developmental timepoints: 0-45', 45-90', 1.5-6 hr, 6-12 hr, 12-18 hr and 18-24 hr. In principle, zygotic transcription does not initiate until ~2 hr. However, due to variability in time of egg laying after fertilization, it can be difficult for early timepoints to be staged precisely. Therefore, we changed egg laying plates frequently when collecting the earliest timepoints, and split these into two stages that should both reflect the maternal transcriptome.

extract_protocol:
Linder et al. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. 2015. Nature Methods 12:767-772.
miCLIP: Reads were sequenced in paired-end mode with 50 bases. All samples were sequenced together on one flowcell lane. Sequencing was performed on an Illumina HiSeq 2500 instrument at Weill Cornell Medicine Epigenomics Core
mRNA: RNA samples were subjected to Illumina mRNA TruSeq Stranded library Prep and sequenced on HiSeq 2500, 2x50, High Output at the New York Genome Center.

tag: developmental stage

tag: tissue type

value: embryo

value: yw

tag: antibody

tag: iclip barcode


title: SSF1163_A3_Vehicle_1_KP2311_P3

value: Mixed background


title: SSF1163_A2_ACY1215_1_KP2313_P3

value: Tcell


title: SSF1163_A2_Vehicle_1_KP2311_P3


title: embryo_12_18_hr_mRNA


title: embryo_6_12_hr_mRNA


title: SSF1163_A12_ACY1215_1_KP2313_P3

value: Macrophage


title: embryo_45_90_min_mRNA


title: embryo_0_45_min_mRNA


title: SSF1163_A12_Vehicle_1_KP2311_P3


title: embryo_18_24_hr_miCLIP

value: Abcam anti-m6A (ab151230)

value: NNNAACC


title: embryo_6_12_hr_miCLIP

value: NNNTGGC


title: SSF1163_A11_ACY1215_1_KP2313_P3


title: SSF1163_A11_Vehicle_1_KP2311_P3


title: SSF1163_A10_ACY1215_1_KP2313_P3


title: embryo_1.5_6_hr_miCLIP

value: NNNAATG