{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["DCC modENCODE"],"study_type":["RNA-seq of coding RNA"],"organism":["Drosophila melanogaster"],"species":["Drosophila melanogaster"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-37291"],"description":["modENCODE_submission_4771 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: S3; Tissue: embryo-derived cell-line; Replicate type: biological; Developmental Stage: late embryonic stage; Sex: Unknown;  EXPERIMENTAL FACTORS: Cell Line S3"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Protocol for isolation of total RNA from cell cultures, which retains short RNAs. mRNAs were purified from total RNA extracts, using standard Illumina protocol. Briefly, 10ug total RNA was bound to oligo(dT) beads, washed twice, and eluted with 10mM Tris-HCl, using Ambion kit. [A] Gel purification of RNA sample. 1. Spike 50 ug of total RNA with 32P-labeled 19bp and 24bp oligos (~10,000 counts per second) and load the sample in a 15% polyacrylamide/urea gel (Sequagel, National Diagnostics). Run the gel in 1x TBE at constant 10W for 1-2 hours. Expose the gel for 10 minutes in Phosphoimager. 2. Excise the band corresponding to the desired size of small RNA (~19-24 nt) into Eppendorf tubes, including the radio-labeled oligos. Add 400uL of 0.4M NaCl. Freeze rapidly in dry ice. Incubate (thaw) for 16 hours at room temperature with agitation to maximize RNA elution. 3. Spin down gel slice homogenate through micropore filter (Ultrafree-MC, 0.22um, Millipore) for 1 minute at room temperature. Add 20ug of glycogen and 2 volumes of 100% Ethanol (RNase-free). Incubate at -20oC for 4 hours. 4. Spin the sample at 4oC for 30 minutes. Wash the pellet with 70% EtOH, air dry for 2 min and resuspend in DEPC MQ water and proceed to section B. [B] 3'-linker ligation and gel purification of the ligated RNA product. 5. Ligate 50 pmol of Modban oligo (IDT:miRNA cloning linker 1) to the 3' terminus of the purified RNA sample in 1X ATP-free T4 RNA ligase buffer (50mM Tris-HCl (pH 7.5-7.6), 10mM MgCl2, 10mM DTT, 60ug/mL BSA) and 10% DMSO, with 5-10 pmol of T4 RNA ligase 2 Rnl2(1-249) (Ho et al, 2004). Incubate at room temperature for 1 hour 30 min. 6. Load the sample on a 15% polyacrylamide/urea gel as described above and expose the gel for 30 minutes. 7. Excise the band corresponding to the desired size of small RNA (~36-41 nt) into Eppendorf tubes, including the ligated radio-labeled oligos. 8. Proceed again with overnight elution and precipitation as in steps 2-4. [C] 5'-linker ligation and gel purification of the ligated RNA product. 9. Ligate 50 pmol of Solexa linker to the 5' terminus of the RNA sample in 1XT4 RNA ligase buffer (Ambion) and 10% DMSO with 5-10 Units of T4 RNA ligase (Ambion). Incubate at 37oC for 1 hour 30 min. 10. Load the sample on a 15% polyacrylamide/urea gel as described above and expose the gel for 1 hour. 11. Excise the band corresponding to the desired size of small RNA (~68-73 nt) into Eppendorf tubes, including the ligated radio-labeled oligos. 12. Proceed again with overnight elution and precipitation as in steps 2-4. [D] Reverse transcription and cDNA amplification. 13. Reverse-transcribe the ligated RNA product by using 21 pmol of BanOne primer and 1 ul Superscript III Reverse Transcriptase (Invitrogen), for 1 hour at 50oC in 20 ul of reaction. Then, amplify 5 ul of the cDNA product with 100 pmol of primers Sol_5_SBS3 and Sol_3_Modban, and 5 Units of Taq Polymerase (New England Biolabs): [94oC 15 sec; 54oC 30 sec; 72oC 30 sec] x 5 cycles and [94oC 15 sec; 60oC 30 sec; 72oC 30 sec] x 17 cycles. 14. Clean up the PCR product with phenol:chloroform and chloroform. Precipitate the amplified cDNA with Ethanol 100%. [E] Digestion of the spikes and gel-purification of the amplified cDNA. 15. Perform PmeI (New England Biolabs) digestion of radiolabeled oligos (spikes) for 3-4 hours at 37oC and purify the amplified cDNA in a 2% low-melt agarose gel (SeaKem). 16. Excise the ~ 120 bp DNA band and proceed to hot-phenol-based gel purification. Transfer aqueous phase to a new eppendorf tube and clean up with phenol:chloroform and chloroform. Precipitate the DNA with Ethanol 100% and resuspend it in 20uL water. 17. Perform Agilent test and dilute the sample to 10nM for Solexa sequencing. 1. cluster generation2. the length of short reads, i.e., the number of sequencing cycles, should list here. in this protocol, it is 35 cycles of sequencing.3. after each cycle, a CCD camera will scan the cells to make a image.","Growth Protocol - Summary of conditions used to produce cell lines for transcriptomics group, excluding W1-Cl.8+, Kc167, S2-DRSC and DmBG3-c2, each of which have their own protocols. For details see relevant pages at the DGRC Cell Lines page (http://dgrc.cgb.indiana.edu/cells)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Eric Lai","DCC modENCODE"],"data_protocol":["Feature Extraction - sequence analysis protocol. 1. 3' adapter sequences starting with 'CTGTAGG' were trimmed with fastx_clipper (fastx_toolkit: http://hannonlab.cshl.edu/fastx_toolkit/). Only reads with recognized 3' adapter and longer than 18 bases were considered in further analysis.2. The trimmed sequences were mapped to genome with Bowtie. only sequences can perfectly match to genome were acceptable. Processed data are obtained using following parameters: genome version is 5"],"additional_accession":[]},"is_claimable":false,"name":"Lai_S3cell_V074/BS23","description":"modENCODE_submission_4771 This submission comes from a modENCODE project of Eric Lai. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We plan to generate a comprehensive catalog of expressed and functional microRNAs, and generate biological evidence for their regulatory activity. We plan also to delineate the primary transcription units of microRNA genes. Finally, we plan to annotate other classes of non-miRNA expressed small RNAs, as least some of which may define novel classes of small RNA genes. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: RNA-seq. BIOLOGICAL SOURCE: Cell Line: S3; Tissue: embryo-derived cell-line; Replicate type: biological; Developmental Stage: late embryonic stage; Sex: Unknown;  EXPERIMENTAL FACTORS: Cell Line S3","dates":{"release":"2012-04-18T00:00:00Z","modification":"2023-08-23T08:57:43.241Z","creation":"2022-03-09T02:23:35.8Z"},"accession":"E-GEOD-37291","cross_references":{"ENA":["SRP012303"],"EFO":["EFO_0003738"]}}