FMR1      shRNA in HepG2      Control: non-target-BGHLV23

General Information
RBPFMR1
Cell_LineHepG2
MethodshRNA
Exp_NameFMR1-BGHLV23-HepG2
ENCODE_series_IDENCSR560IJH
Batch_IDBGHLV23
Pool IDPool-150701
Local_Set_Nameset23
ENCODE_KD_Exp_IDENCSR905HID
ENCODE_CN_Exp_IDENCSR042QTH
Rep1FMR1-BGHLV23-17
Rep2FMR1-BGHLV23-18
CN1non-target-BGHLV23-1
CN2non-target-BGHLV23-2
Rep1_qPCR67.5
Rep2_qPCR73.2
Rep1_WB83.7
Rep2_WB84.5
Antibody Cat#RN016P
Antibody Lot#RN016P
Antibody DCC IDENCAB000BFK
StatusReleased
ProjectENCODE3
ID543




Experiment Information (Status: Released)
BGHLV23-17BGHLV23-17BGHLV23-18BGHLV23-18
idx509509510510
TRCN#_or_BGC#TRCN0000059758TRCN0000059758TRCN0000059758TRCN0000059758
shRNA_or_gRNA_sequenceGCCAGAAGACTTACGGCAAATGCCAGAAGACTTACGGCAAATGCCAGAAGACTTACGGCAAATGCCAGAAGACTTACGGCAAAT
PAM
NameFMR1FMRP/FMR1FMR1FMRP/FMR1
Sample_IDBGHLV23-17BGHLV23-17BGHLV23-18BGHLV23-18
transduction_Date10/29/201410/29/201410/29/201410/29/2014
days
RBP_nameFMR1FMR1FMR1FMR1
qPCR_result67.567.573.273.2
Ave_qPCR70.470.4
RT-qPCR_primer-Fctgcgcactaagttgtctctgctgcgcactaagttgtctctg
RT-qPCR_primer-Rcatgaaatctcgaggcaagccatgaaatctcgaggcaagc
protein_conc5588558852035203
WB_result83.795.684.595.2
Ave_WB84.195.4
WB_DONE_date2/15/20161/14/2021
MW71kDa71kDaWES
IP11
antibody_Cat#RN016PPA5-34584RN016PTK2671134
Antibody DCC IDENCAB000BFKENCAB650WPE11/24/20
submitted_to_DCC_date3/8/2016
Rep1_TPM53.5000
Rep2_TPM42.8000
Action
Library_start_date6/10/20156/10/2015
repeat_library
Note
ID2586258825872589




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
FMR1Product_ID: RN016P
Lot_ID: 1
Source: MBLI
Target Name: FMR1-human		 FMR1-HEPG2.png<br>Caption: Western blot following shRNA against FMR1 in HepG2 whole cell lysate using FMR1 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against FMR1. FMR1 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
 K562_MBLI_RN016P_001_FMR1.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using FMR1 specific antibody. Lane 1 is 1% of twenty million whole cell lysate input and lane 2 is 25% of IP enrichment using rabbit normal IgG (lanes under 'IgG'). Lane 3 is 1% of twenty million whole cell lysate input and lane 4 is 10% IP enrichment using rabbit polyclonal anti-FMR1 antibody (lanes under 'FMR1').
 FMR1-K562.png<br>Caption: Western blot following shRNA against FMR1 in k562 whole cell lysate using FMR1 specific antibody. Lane 1 is a ladder, lane 2 is k562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against FMR1. FMR1 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
FMR1Product_ID: PA5-34584
Lot_ID: TK2671134
Source: Thermo Fisher
Target Name: FMR1-human		 FMR1-HEPG2-PA5-34584.png<br>Caption: Western blot following shRNA against FMR1 in HepG2 whole cell lysate using FMR1 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different shRNA against FMR1. FMR1 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 ThermoFisher_PA5-34584_TK2671134_FMRP.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the FMR1 specific antibody, PA5-34584. Lanes 1 and 3 are 2.5% of five million whole cell lysate input. Lanes 2 and 4 are 50% of IP enrichment from five million whole cell lysate using normal IgG antibody and the FMR1-specific antibody, PA5-34584. The same antibody was used to detect protein levels via Western blot. This antibody passes preliminary validation and will be further pursued for secondary validation. *NOTE* Protein sizes are taken from Genecards.org and are only estimates based on sequence. Actual protein size may differ based on protein characteristics and electrophoresis method used.




Experiment Status
BGHLV23-17BGHLV23-18
Sample_IDBGHLV23-17BGHLV23-18
Sample NameFMR1-BGHLV23-17FMR1-BGHLV23-18
Sample NameFMR1-BGHLV23-17FMR1-BGHLV23-18
RBPFMR1FMR1
Cell_LineHepG2HepG2
Exp UID
StatusReleasedReleased
Status_date2015-08-132015-08-13
ProjectENCODE3ENCODE3
Note
ID822823




Library-Prep Information
BGHLV23-17BGHLV23-18
Sample #
Sample NameFMR1-BGHLV23-17FMR1-BGHLV23-18
Sample_Name_AliasFMR1-BGHLV23-17FMR1-BGHLV23-18
Index Well PositionS05S06
Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
LibPrep_date2015-06-102015-06-10
Lib_IDLib-150610Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_WellDNA_Library_LV20-22-23/set1/E12.pngDNA_Library_LV20-22-23/set1/F12.png
RIN9.69.6
libSample_RNA_WellRNA_Library_LV19-21-24/set2/G5.pngRNA_Library_LV19-21-24/set2/H5.png
SampleQC_method
SampleQC_date
Sample_IDBGHLV23-17BGHLV23-18
RBPFMR1FMR1
Batch_IDBGHLV23BGHLV23
WB_result83.70084.500
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE3ENCODE3
ID25102511




Sequencing Information
BGHLV23-17BGHLV23-18
Sample_IDBGHLV23-17BGHLV23-18
Sample NameFMR1-BGHLV23-17FMR1-BGHLV23-18
Pool IDPool-150701Pool-150701
LocalServer_folderset23set23
total_reads47,420,00059,690,000
total_aligned_reads42,306,87653,817,438
unique_aligned_reads39,876,87850,811,210
percent_uniqueAligned0.840930.85125
correlation_replicates0.9832360.983236
spikein_reads285,894343,634
percent_spikeins0.006030.00576
original_ReadLength100100
QC_StatusSubmittedSubmitted
ID11321133




Data Submission Information
BGHLV23-17BGHLV23-17
ENCODE_aliasbrenton-graveley:FMR1-BGHLV23brenton-graveley:FMR1-BGHLV23-HepG2
ENCODE_accessionENCSR905HIDENCSR560IJH
object_typeexperimentgene_silencing_series
assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seq
Sample_IDBGHLV23-17BGHLV23-17
Sample NameFMR1-BGHLV23-17FMR1-BGHLV23-17
SelectedYesYes
StatusReleasedReleased
Status_Date2015-08-112022-03-01
ProjectENCODE3ENCODE3
protocol_URL
ID29436715




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
FMR1-BGHLV23-17_ACAGTG_L005_R1_001.fastq.gzENCODE_DATA/set23/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1132HiSeq2000100paired-ended1non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gzENCODE316660
FMR1-BGHLV23-17_ACAGTG_L005_R2_001.fastq.gzENCODE_DATA/set23/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1132HiSeq2000100paired-ended2non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gzENCODE316698
FMR1-BGHLV23-17_Aligned.sortedByCoord.out.bamENCODE_DATA/set23/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1132GRCh38V40FMR1-BGHLV23-17_ACAGTG_L005_R1_001.fastq.gz,FMR1-BGHLV23-17_ACAGTG_L005_R2_001.fastq.gzENCORE216736
FMR1-BGHLV23-17_Signal.Unique.strand+.bwENCODE_DATA/set23/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1132GRCh38V40FMR1-BGHLV23-17/Aligned.sortedByCoord.out.bamENCORE216774
FMR1-BGHLV23-17_Signal.Unique.strand-.bwENCODE_DATA/set23/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1132GRCh38V40FMR1-BGHLV23-17/Aligned.sortedByCoord.out.bamENCORE216812
FMR1-BGHLV23-17_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set23/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1132GRCh38V40FMR1-BGHLV23-17/Aligned.sortedByCoord.out.bamENCORE216850
FMR1-BGHLV23-17_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set23/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1132GRCh38V40FMR1-BGHLV23-17/Aligned.sortedByCoord.out.bamENCORE216888
FMR1-BGHLV23-17_quant.sfENCODE_DATA/set23/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1132GRCh38V40FMR1-BGHLV23-17_ACAGTG_L005_R1_001.fastq.gz,FMR1-BGHLV23-17_ACAGTG_L005_R2_001.fastq.gzENCORE216926
FMR1-BGHLV23-18_GCCAAT_L005_R1_001.fastq.gzENCODE_DATA/set23/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1133HiSeq2000100paired-ended1non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gzENCODE316661
FMR1-BGHLV23-18_GCCAAT_L005_R2_001.fastq.gzENCODE_DATA/set23/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab1133HiSeq2000100paired-ended2non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gzENCODE316699
FMR1-BGHLV23-18_Aligned.sortedByCoord.out.bamENCODE_DATA/set23/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab1133GRCh38V40FMR1-BGHLV23-18_GCCAAT_L005_R1_001.fastq.gz,FMR1-BGHLV23-18_GCCAAT_L005_R2_001.fastq.gzENCORE216737
FMR1-BGHLV23-18_Signal.Unique.strand+.bwENCODE_DATA/set23/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1133GRCh38V40FMR1-BGHLV23-18/Aligned.sortedByCoord.out.bamENCORE216775
FMR1-BGHLV23-18_Signal.Unique.strand-.bwENCODE_DATA/set23/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab1133GRCh38V40FMR1-BGHLV23-18/Aligned.sortedByCoord.out.bamENCORE216813
FMR1-BGHLV23-18_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set23/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1133GRCh38V40FMR1-BGHLV23-18/Aligned.sortedByCoord.out.bamENCORE216851
FMR1-BGHLV23-18_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set23/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab1133GRCh38V40FMR1-BGHLV23-18/Aligned.sortedByCoord.out.bamENCORE216889
FMR1-BGHLV23-18_quant.sfENCODE_DATA/set23/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab1133GRCh38V40FMR1-BGHLV23-18_GCCAAT_L005_R1_001.fastq.gz,FMR1-BGHLV23-18_GCCAAT_L005_R2_001.fastq.gzENCORE216927