MAGOH      shRNA in HepG2      Control: NT-BGHLV12-93-94

General Information
RBPMAGOH
Cell_LineHepG2
MethodshRNA
Exp_NameMAGOH-BGHLV12-HepG2
ENCODE_series_IDENCSR453OOG
Batch_IDBGHLV12
Pool IDPool-140701A
Local_Set_Nameset12
ENCODE_KD_Exp_IDENCSR746EKS
ENCODE_CN_Exp_IDENCSR603TCV
Rep1MAGOH-BGHLV12-47
Rep2MAGOH-BGHLV12-48
CN1NT-BGHLV12-93
CN2NT-BGHLV12-94
Rep1_qPCR69.8
Rep2_qPCR83.4
Rep1_WB80.9
Rep2_WB74.5
Antibody Cat#RN089PW
Antibody Lot#RN089PW
Antibody DCC IDENCAB122RRN
StatusReleased
ProjectENCODE3
ID344




Experiment Information (Status: Released)
BGHLV12-47BGHLV12-48
idx4748
TRCN#_or_BGC#TRCN0000006614TRCN0000006614
shRNA_or_gRNA_sequenceCCAGAAGGCTTACGAGTATTTCCAGAAGGCTTACGAGTATTT
PAM
NameMAGOHMAGOH
Sample_IDBGHLV12-47BGHLV12-48
transduction_Date5/15/20145/15/2014
days
RBP_nameMAGOHMAGOH
qPCR_result69.883.4
Ave_qPCR76.6
RT-qPCR_primer-FCAAAAATTGGTTCCCTTATTGA
RT-qPCR_primer-RAACACTTCAGGTCCTGGACAA
protein_conc13781580
WB_result80.974.5
Ave_WB77.7
WB_DONE_date6/19/2014
MW17kDa
IP11
antibody_Cat#RN089PWRN089PW
Antibody DCC IDENCAB122RRNENCAB122RRN
submitted_to_DCC_date4/2/2015
Rep1_TPM51.40
Rep2_TPM36.80
Action
Library_start_date6/12/20146/12/2014
repeat_library
Note
ID20942095




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
MAGOHProduct_ID: RN089PW
Lot_ID: 1
Source: MBLI
Target Name: MAGOH-human
MAGOH_Secondary_Western.png<br>Caption: Western blot following shRNA against MAGOH in K562 and HepG2 whole cell lysate using MAGOH specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 2 and 3 are two different shRNAs against MAGOH. Lanes 5-7 follow the same pattern, but in HepG2. MAGOH protein appears as the green band, GAPDH serves as a control and appears in red.
MAGOH_Secondary_Western.png<br>Caption: Western blot following shRNA against MAGOH in K562 and HepG2 whole cell lysate using MAGOH specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 2 and 3 are two different shRNAs against MAGOH. Lanes 5-7 follow the same pattern, but in HepG2. MAGOH protein appears as the green band, GAPDH serves as a control and appears in red.




Experiment Status
BGHLV12-47BGHLV12-48
Sample_IDBGHLV12-47BGHLV12-48
Sample NameMAGOH-BGHLV12-47MAGOH-BGHLV12-48
Sample NameMAGOH-BGHLV12-47MAGOH-BGHLV12-48
RBPMAGOHMAGOH
Cell_LineHepG2HepG2
Exp UID
StatusReleasedReleased
Status_date2014-09-252014-09-25
ProjectENCODE3ENCODE3
Note
ID402403




Library-Prep Information
BGHLV12-47BGHLV12-48
Sample #
Sample NameMAGOH-BGHLV12-47MAGOH-BGHLV12-48
Sample_Name_AliasMAGOH-BGHLV12-47MAGOH-BGHLV12-48
Index Well PositionS11S12
Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
LibPrep_date2014-06-122014-06-12
Lib_IDLib-140612Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_WellDNA_Library_LV12/set3/C1.pngDNA_Library_LV12/set3/D1.png
RIN9.49.4
libSample_RNA_WellRNA_Library_LV12/set1/C5.pngRNA_Library_LV12/set1/D5.png
SampleQC_methodTapeStationTapeStation
SampleQC_date
Sample_IDBGHLV12-47BGHLV12-48
RBPMAGOHMAGOH
Batch_IDBGHLV12BGHLV12
WB_result80.90074.500
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE3ENCODE3
ID20262027




Sequencing Information
BGHLV12-47BGHLV12-48
Sample_IDBGHLV12-47BGHLV12-48
Sample NameMAGOH-BGHLV12-47MAGOH-BGHLV12-48
Pool IDPool-140701APool-140701A
LocalServer_folderset12set12
total_reads73,950,00063,500,000
total_aligned_reads66,318,52058,556,314
unique_aligned_reads62,772,61455,459,628
percent_uniqueAligned0.848850.87338
correlation_replicates0.9969120.996912
spikein_reads298,838330,548
percent_spikeins0.004040.00521
original_ReadLength100100
QC_StatusSubmittedSubmitted
ID726727




Data Submission Information
BGHLV12-47BGHLV12-47
ENCODE_aliasbrenton-graveley:MAGOH-BGHLV12brenton-graveley:MAGOH-BGHLV12-HepG2
ENCODE_accessionENCSR746EKSENCSR453OOG
object_typeexperimentgene_silencing_series
assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seq
Sample_IDBGHLV12-47BGHLV12-47
Sample NameMAGOH-BGHLV12-47MAGOH-BGHLV12-47
SelectedYesYes
StatusReleasedReleased
Status_Date2014-09-242022-03-01
ProjectENCODE3ENCODE3
protocol_URL
ID27506803




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
MAGOH-BGHLV12-47_GGCTAC_L005_R1_001.fastq.gzENCODE_DATA/set12/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab726HiSeq2000100paired-ended1NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gzENCODE312783
MAGOH-BGHLV12-47_GGCTAC_L005_R2_001.fastq.gzENCODE_DATA/set12/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab726HiSeq2000100paired-ended2NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gzENCODE312852
MAGOH-BGHLV12-47_Aligned.sortedByCoord.out.bamENCODE_DATA/set12/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab726GRCh38V40MAGOH-BGHLV12-47_GGCTAC_L005_R1_001.fastq.gz,MAGOH-BGHLV12-47_GGCTAC_L005_R2_001.fastq.gzENCORE212922
MAGOH-BGHLV12-47_Signal.Unique.strand+.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab726GRCh38V40MAGOH-BGHLV12-47/Aligned.sortedByCoord.out.bamENCORE212992
MAGOH-BGHLV12-47_Signal.Unique.strand-.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab726GRCh38V40MAGOH-BGHLV12-47/Aligned.sortedByCoord.out.bamENCORE213062
MAGOH-BGHLV12-47_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab726GRCh38V40MAGOH-BGHLV12-47/Aligned.sortedByCoord.out.bamENCORE213132
MAGOH-BGHLV12-47_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab726GRCh38V40MAGOH-BGHLV12-47/Aligned.sortedByCoord.out.bamENCORE213202
MAGOH-BGHLV12-47_quant.sfENCODE_DATA/set12/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab726GRCh38V40MAGOH-BGHLV12-47_GGCTAC_L005_R1_001.fastq.gz,MAGOH-BGHLV12-47_GGCTAC_L005_R2_001.fastq.gzENCORE213272
MAGOH-BGHLV12-48_CTTGTA_L006_R1_001.fastq.gzENCODE_DATA/set12/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab727HiSeq2000100paired-ended1NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gzENCODE312784
MAGOH-BGHLV12-48_CTTGTA_L006_R2_001.fastq.gzENCODE_DATA/set12/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab727HiSeq2000100paired-ended2NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gzENCODE312853
MAGOH-BGHLV12-48_Aligned.sortedByCoord.out.bamENCODE_DATA/set12/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab727GRCh38V40MAGOH-BGHLV12-48_CTTGTA_L006_R1_001.fastq.gz,MAGOH-BGHLV12-48_CTTGTA_L006_R2_001.fastq.gzENCORE212923
MAGOH-BGHLV12-48_Signal.Unique.strand+.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab727GRCh38V40MAGOH-BGHLV12-48/Aligned.sortedByCoord.out.bamENCORE212993
MAGOH-BGHLV12-48_Signal.Unique.strand-.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab727GRCh38V40MAGOH-BGHLV12-48/Aligned.sortedByCoord.out.bamENCORE213063
MAGOH-BGHLV12-48_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab727GRCh38V40MAGOH-BGHLV12-48/Aligned.sortedByCoord.out.bamENCORE213133
MAGOH-BGHLV12-48_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set12/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab727GRCh38V40MAGOH-BGHLV12-48/Aligned.sortedByCoord.out.bamENCORE213203
MAGOH-BGHLV12-48_quant.sfENCODE_DATA/set12/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab727GRCh38V40MAGOH-BGHLV12-48_CTTGTA_L006_R1_001.fastq.gz,MAGOH-BGHLV12-48_CTTGTA_L006_R2_001.fastq.gzENCORE213273