FXR1      shRNA in K562      Control: Nontarget-LV08-3527

General Information
RBPFXR1
Cell_LineK562
MethodshRNA
Exp_NameFXR1-BGKLV08-K562
ENCODE_series_IDENCSR196OST
Batch_IDBGKLV08
Pool IDPool-140601
Local_Set_Nameset10
ENCODE_KD_Exp_IDENCSR780YFF
ENCODE_CN_Exp_IDENCSR913CAE
Rep1FXR1-LV08-29
Rep2FXR1-LV08-30
CN1Nontarget-LV08-1_00003527
CN2nontarget-LV08-2_00003527
Rep1_qPCR67.5
Rep2_qPCR67.2
Rep1_WB96.1
Rep2_WB74.5
Antibody Cat#A303-892A
Antibody Lot#A303-892A
Antibody DCC IDENCAB712TFO
StatusReleased
ProjectENCODE3
ID291




Experiment Information (Status: Released)
BGKLV08-29BGKLV08-29BGKLV08-30BGKLV08-30
idx300310
TRCN#_or_BGC#TRCN0000159153TRCN0000159153TRCN0000159153TRCN0000159153
shRNA_or_gRNA_sequenceGACGCTACTTACAATGAAATAGACGCTACTTACAATGAAATAGACGCTACTTACAATGAAATAGACGCTACTTACAATGAAATA
PAM
NameFXR1FXR1FXR1FXR1
Sample_IDBGKLV08-29BGKLV08-29BGKLV08-30BGKLV08-30
transduction_Date4/4/20144/4/20144/4/20144/4/2014
days
RBP_nameFXR1FXR1FXR1FXR1
qPCR_result67.567.567.267.2
Ave_qPCR67.467.4
RT-qPCR_primer-FGTCGAGGTCGTGGTGGACGTCGAGGTCGTGGTGGAC
RT-qPCR_primer-RCAAGTAAGCTGTATGGATTGCTGCAAGTAAGCTGTATGGATTGCTG
protein_conc1289128913671367
WB_result96.160.574.564.3
Ave_WB85.362.4
WB_DONE_date6/30/20143/14/2019wes
MW70kDa70kDa
IP11
antibody_Cat#A303-892A702410A303-892ALOT# 2038609
Antibody DCC IDENCAB712TFOENCAB076XDIENCAB712TFO
submitted_to_DCC_date8/6/20153/11/2019
Rep1_TPM63.589305563.589305500
Rep2_TPM81.023242881.023242800
ActionReadyReadyReadyReady
Library_start_date5/5/20145/5/20145/5/20145/5/2014
repeat_library
Note
ID29313032




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
FXR1Product_ID: 702410
Lot_ID: 2038609
Source: Thermo Fisher
Target Name: FXR1-human		 ThermoFisher_702410_2038609_FXR1.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the FXR1 specific antibody, 702410. 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 FXR1-specific antibody, 702410. 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.
 FXR1-K562-702410.png<br>Caption: Western blot following shRNA against FXR1 in K562 whole cell lysate using FXR1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNA against FXR1. FXR1 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
FXR1Product_ID: A303-892A
Lot_ID: 1
Source: Bethyl Labs
Target Name: FXR1-human		 HepG2_Bethyl_A303-892A_1_FXR1.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using FXR1specific antibody. Lane 1 is 1% of twenty million whole cell lysate input and lane 2 is 10% 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-FXR1 antibody (lanes under 'FXR1').
 K562_Bethyl_A303-892A_1_FXR1.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using FXR1 specific antibody. Lane 1 is 1% of twenty million whole cell lysate input and lane 2 is 10% 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-FXR1 antibody (lanes under 'FXR1').
 FXR1_Secondary_Western.png<br>Caption: Western blot following shRNA against FXR1 in K562 whole cell lysate using FXR1 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against FXR1. FXR1 protein appears as the green band, Tubulin serves as a control and appears in red.




Experiment Status
BGKLV08-29BGKLV08-30
Sample_IDBGKLV08-29BGKLV08-30
Sample NameFXR1-LV08-29FXR1-LV08-30
Sample NameFXR1-LV08-29FXR1-LV08-30
RBPFXR1FXR1
Cell_LineK562K562
Exp UID
StatusReleasedReleased
Status_date2014-09-162014-09-16
ProjectENCODE3ENCODE3
Note
ID290291




Library-Prep Information
BGKLV08-29BGKLV08-30
Sample #
Sample NameFXR1-BGKLV08-29FXR1-BGKLV08-30
Sample_Name_AliasFXR1-LV08-29FXR1-LV08-30
Index Well PositionS01S02
Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
LibPrep_date2014-05-052014-05-05
Lib_IDLib-140505Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_WellDNA_Library_LV08/set2/C2.pngDNA_Library_LV08/set2/D2.png
RIN8.99.0
libSample_RNA_WellRNA_Library_LV08/set2/E2.pngRNA_Library_LV08/set2/F2.png
SampleQC_methodTapeStationTapeStation
SampleQC_date
Sample_IDBGKLV08-29BGKLV08-30
RBPFXR1FXR1
Batch_IDBGKLV08BGKLV08
WB_result96.10074.500
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE3ENCODE3
ID19121913




Sequencing Information
BGKLV08-29BGKLV08-30
Sample_IDBGKLV08-29BGKLV08-30
Sample NameFXR1-LV08-29FXR1-LV08-30
Pool IDPool-140601Pool-140601
LocalServer_folderset10set10
total_reads52,750,00051,300,000
total_aligned_reads45,743,41844,250,350
unique_aligned_reads41,977,63640,682,012
percent_uniqueAligned0.795780.79302
correlation_replicates0.9936200.993620
spikein_reads400,146531,150
percent_spikeins0.007590.01035
original_ReadLength100100
QC_StatusSubmittedSubmitted
ID612613




Data Submission Information
BGKLV08-29BGKLV08-29
ENCODE_aliasbrenton-graveley:FXR1-LV08brenton-graveley:FXR1-BGKLV08-K562
ENCODE_accessionENCSR780YFFENCSR196OST
object_typeexperimentgene_silencing_series
assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seq
Sample_IDBGKLV08-29BGKLV08-29
Sample NameFXR1-LV08-29FXR1-LV08-29
SelectedYesYes
StatusReleasedReleased
Status_Date2014-08-132022-03-01
ProjectENCODE3ENCODE3
protocol_URL
ID26946724




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
FXR1-LV08-29_Aligned.sortedByCoord.out.bamENCODE_DATA/set10/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab612GRCh38V40FXR1-LV08-29_ATCACG_L004_R1_001.fastq.gz,FXR1-LV08-29_ATCACG_L004_R2_001.fastq.gzENCORE211997
FXR1-LV08-29_ATCACG_L004_R1_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab612HiSeq2000100paired-ended1Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gzENCODE312053
FXR1-LV08-29_ATCACG_L004_R2_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab612HiSeq2000100paired-ended2Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gzENCODE312109
FXR1-LV08-29_Signal.Unique.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab612GRCh38V40FXR1-LV08-29/Aligned.sortedByCoord.out.bamENCORE212165
FXR1-LV08-29_Signal.Unique.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab612GRCh38V40FXR1-LV08-29/Aligned.sortedByCoord.out.bamENCORE212221
FXR1-LV08-29_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab612GRCh38V40FXR1-LV08-29/Aligned.sortedByCoord.out.bamENCORE212277
FXR1-LV08-29_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab612GRCh38V40FXR1-LV08-29/Aligned.sortedByCoord.out.bamENCORE212333
FXR1-LV08-29_quant.sfENCODE_DATA/set10/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab612GRCh38V40FXR1-LV08-29_ATCACG_L004_R1_001.fastq.gz,FXR1-LV08-29_ATCACG_L004_R2_001.fastq.gzENCORE213332
FXR1-LV08-30_Aligned.sortedByCoord.out.bamENCODE_DATA/set10/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab613GRCh38V40FXR1-LV08-30_CGATGT_L004_R1_001.fastq.gz,FXR1-LV08-30_CGATGT_L004_R2_001.fastq.gzENCORE211998
FXR1-LV08-30_CGATGT_L004_R1_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab613HiSeq2000100paired-ended1Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gzENCODE312054
FXR1-LV08-30_CGATGT_L004_R2_001.fastq.gzENCODE_DATA/set10/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab613HiSeq2000100paired-ended2Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gzENCODE312110
FXR1-LV08-30_Signal.Unique.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab613GRCh38V40FXR1-LV08-30/Aligned.sortedByCoord.out.bamENCORE212166
FXR1-LV08-30_Signal.Unique.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab613GRCh38V40FXR1-LV08-30/Aligned.sortedByCoord.out.bamENCORE212222
FXR1-LV08-30_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab613GRCh38V40FXR1-LV08-30/Aligned.sortedByCoord.out.bamENCORE212278
FXR1-LV08-30_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set10/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab613GRCh38V40FXR1-LV08-30/Aligned.sortedByCoord.out.bamENCORE212334
FXR1-LV08-30_quant.sfENCODE_DATA/set10/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab613GRCh38V40FXR1-LV08-30_CGATGT_L004_R1_001.fastq.gz,FXR1-LV08-30_CGATGT_L004_R2_001.fastq.gzENCORE213333