PHF6      shRNA in HepG2      Control: NT_BGHLV18

General Information
RBPPHF6
Cell_LineHepG2
MethodshRNA
Exp_NamePHF6-BGHLV18-HepG2
ENCODE_series_IDENCSR633ZZV
Batch_IDBGHLV18
Pool IDPool-141010
Local_Set_Nameset18
ENCODE_KD_Exp_IDENCSR681SMT
ENCODE_CN_Exp_IDENCSR674KEK
Rep1PHF6_BGHLV18_39
Rep2PHF6_BGHLV18_40
CN1NT_BGHLV18_1
CN2NT_BGHLV18_2
Rep1_qPCR72.5
Rep2_qPCR80.0
Rep1_WB79.3
Rep2_WB67.6
Antibody Cat#A301-450A
Antibody Lot#A301-450A
Antibody DCC IDENCAB411AGR
StatusReleased
ProjectENCODE3
ID454




Experiment Information (Status: Released)
BGHLV18-39BGHLV18-40
idx339340
TRCN#_or_BGC#TRCN0000020121TRCN0000020121
shRNA_or_gRNA_sequenceCCACTGTGCATTGCATGATAACCACTGTGCATTGCATGATAA
PAM
NamePHF6PHF6
Sample_IDBGHLV18-39BGHLV18-40
transduction_Date8/28/20148/28/2014
days
RBP_namePHF6PHF6
qPCR_result72.580.0
Ave_qPCR76.3
RT-qPCR_primer-Faccactgtgcattgcatgat
RT-qPCR_primer-Rtcagcttcggagttatgtgc
protein_conc48444869
WB_result79.367.6
Ave_WB73.5
WB_DONE_date3/31/2015
MW41kDa
IP11
antibody_Cat#A301-450AA301-450A
Antibody DCC IDENCAB411AGRENCAB411AGR
submitted_to_DCC_date4/2/2015
Rep1_TPM3.10
Rep2_TPM3.10
Action
Library_start_date10/2/201410/2/2014
repeat_library
Note
ID24042405




Western Blot
RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
PHF6Product_ID: A301-450A
Lot_ID: 1
Source: Bethyl Labs
Target Name: PHF6-human
HepG2_Bethyl_A301-450A_1_PHF6.png<br>Caption: IP-Western Blot analysis of HepG2 whole cell lysate using PHF6 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-PHF6 antibody (lanes under 'PHF6').
PHF6_Secondary_Western.png<br>Caption: Western blot following shRNA against PHF6 in K562 and HepG2 whole cell lysate using PHF6 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against PHF6. Lanes 5-8 follow the same pattern, but in HepG2. PHF6 protein appears as the green band, Tubulin serves as a control and appears in red.
K562_Bethyl_A301-450A_1_PHF6.png<br>Caption: IP-Western Blot analysis of K562 whole cell lysate using PHF6 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-PHF6 antibody (lanes under 'PHF6').
PHF6_Secondary_Western.png<br>Caption: Western blot following shRNA against PHF6 in K562 and HepG2 whole cell lysate using PHF6 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different shRNAs against PHF6. Lanes 5-8 follow the same pattern, but in HepG2. PHF6 protein appears as the green band, Tubulin serves as a control and appears in red.




Experiment Status
BGHLV18-39BGHLV18-40
Sample_IDBGHLV18-39BGHLV18-40
Sample NamePHF6_BGHLV18_39PHF6_BGHLV18_40
Sample NamePHF6_BGHLV18_39PHF6_BGHLV18_40
RBPPHF6PHF6
Cell_LineHepG2HepG2
Exp UID
StatusReleasedReleased
Status_date2014-12-112014-12-11
ProjectENCODE3ENCODE3
Note
ID638639




Library-Prep Information
BGHLV18-39BGHLV18-40
Sample #
Sample NamePHF6-BGHLV18-39PHF6-BGHLV18-40
Sample_Name_AliasPHF6_BGHLV18_39PHF6_BGHLV18_40
Index Well PositionS25S27
Index_tableIDT_TruSeqSingleIndex_24IDT_TruSeqSingleIndex_24
LibPrep_date2014-10-022014-10-02
Lib_IDLib-141002Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_WellDNA_Library_LV18-19/set1/G3.pngDNA_Library_LV18-19/set1/H3.png
RIN9.29.2
libSample_RNA_WellRNA_Library_LV18-19/set1/E10.pngRNA_Library_LV18-19/set1/F10.png
SampleQC_method
SampleQC_date
Sample_IDBGHLV18-39BGHLV18-40
RBPPHF6PHF6
Batch_IDBGHLV18BGHLV18
WB_result79.30067.600
Library DescriptionTruSeq mRNATruSeq mRNA
Repeat_Library_Suffix
Lib_StatusSendToSequenceSendToSequence
ProjectENCODE3ENCODE3
ID23222323




Sequencing Information
BGHLV18-39BGHLV18-40
Sample_IDBGHLV18-39BGHLV18-40
Sample NamePHF6_BGHLV18_39PHF6_BGHLV18_40
Pool IDPool-141010Pool-141010
LocalServer_folderset18set18
total_reads55,830,00044,640,000
total_aligned_reads50,400,65039,545,260
unique_aligned_reads47,584,05437,314,016
percent_uniqueAligned0.852300.83589
correlation_replicates0.9956620.995662
spikein_reads134,002153,488
percent_spikeins0.002400.00344
original_ReadLength100100
QC_StatusSubmittedSubmitted
ID964965




Data Submission Information
BGHLV18-39BGHLV18-39
ENCODE_aliasbrenton-graveley:PHF6_BGHLV18brenton-graveley:PHF6-BGHLV18-HepG2
ENCODE_accessionENCSR681SMTENCSR633ZZV
object_typeexperimentgene_silencing_series
assay_typeknockdown followed by RNA-seqknockdown followed by RNA-seq
Sample_IDBGHLV18-39BGHLV18-39
Sample NamePHF6_BGHLV18_39PHF6_BGHLV18_39
SelectedYesYes
StatusReleasedReleased
Status_Date2014-12-082022-03-01
ProjectENCODE3ENCODE3
protocol_URL
ID28366855




File Information
file_namefile_pathfile_formatoutput_typeassay_typelabSample IDplatformread_lengthrun_typepaired_endassemblygenome_annotationderived_fromcontrolled_byProjectNoteFILE_ID
PHF6_BGHLV18_39_ACTGAT_L003_R1_001.fastq.gzENCODE_DATA/set18/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab964HiSeq2000100paired-ended1NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gzENCODE314812
PHF6_BGHLV18_39_ACTGAT_L003_R2_001.fastq.gzENCODE_DATA/set18/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab964HiSeq2000100paired-ended2NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gzENCODE314850
PHF6_BGHLV18_39_Aligned.sortedByCoord.out.bamENCODE_DATA/set18/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab964GRCh38V40PHF6_BGHLV18_39_ACTGAT_L003_R1_001.fastq.gz,PHF6_BGHLV18_39_ACTGAT_L003_R2_001.fastq.gzENCORE214888
PHF6_BGHLV18_39_Signal.Unique.strand+.bwENCODE_DATA/set18/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab964GRCh38V40PHF6_BGHLV18_39/Aligned.sortedByCoord.out.bamENCORE214926
PHF6_BGHLV18_39_Signal.Unique.strand-.bwENCODE_DATA/set18/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab964GRCh38V40PHF6_BGHLV18_39/Aligned.sortedByCoord.out.bamENCORE214964
PHF6_BGHLV18_39_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set18/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab964GRCh38V40PHF6_BGHLV18_39/Aligned.sortedByCoord.out.bamENCORE215002
PHF6_BGHLV18_39_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set18/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab964GRCh38V40PHF6_BGHLV18_39/Aligned.sortedByCoord.out.bamENCORE215040
PHF6_BGHLV18_39_quant.sfENCODE_DATA/set18/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab964GRCh38V40PHF6_BGHLV18_39_ACTGAT_L003_R1_001.fastq.gz,PHF6_BGHLV18_39_ACTGAT_L003_R2_001.fastq.gzENCORE215078
PHF6_BGHLV18_40_ATTCCT_L003_R1_001.fastq.gzENCODE_DATA/set18/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab965HiSeq2000100paired-ended1NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gzENCODE314813
PHF6_BGHLV18_40_ATTCCT_L003_R2_001.fastq.gzENCODE_DATA/set18/fastqfastqreadsknockdown followed by RNA-seqGraveley Lab965HiSeq2000100paired-ended2NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gzENCODE314851
PHF6_BGHLV18_40_Aligned.sortedByCoord.out.bamENCODE_DATA/set18/STAR_ENCORE2_file_linksbamalignmentsknockdown followed by RNA-seqGraveley Lab965GRCh38V40PHF6_BGHLV18_40_ATTCCT_L003_R1_001.fastq.gz,PHF6_BGHLV18_40_ATTCCT_L003_R2_001.fastq.gzENCORE214889
PHF6_BGHLV18_40_Signal.Unique.strand+.bwENCODE_DATA/set18/STAR_ENCORE2_file_linksbigWig+uniqueplus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab965GRCh38V40PHF6_BGHLV18_40/Aligned.sortedByCoord.out.bamENCORE214927
PHF6_BGHLV18_40_Signal.Unique.strand-.bwENCODE_DATA/set18/STAR_ENCORE2_file_linksbigWig-uniqueminus strand signal of unique readsknockdown followed by RNA-seqGraveley Lab965GRCh38V40PHF6_BGHLV18_40/Aligned.sortedByCoord.out.bamENCORE214965
PHF6_BGHLV18_40_Signal.UniqueMultiple.strand+.bwENCODE_DATA/set18/STAR_ENCORE2_file_linksbigWig+allplus strand signal of all readsknockdown followed by RNA-seqGraveley Lab965GRCh38V40PHF6_BGHLV18_40/Aligned.sortedByCoord.out.bamENCORE215003
PHF6_BGHLV18_40_Signal.UniqueMultiple.strand-.bwENCODE_DATA/set18/STAR_ENCORE2_file_linksbigWig-allminus strand signal of all readsknockdown followed by RNA-seqGraveley Lab965GRCh38V40PHF6_BGHLV18_40/Aligned.sortedByCoord.out.bamENCORE215041
PHF6_BGHLV18_40_quant.sfENCODE_DATA/set18/salmon_ENCORE2transcript_quantificationtranscript quantificationsknockdown followed by RNA-seqGraveley Lab965GRCh38V40PHF6_BGHLV18_40_ATTCCT_L003_R1_001.fastq.gz,PHF6_BGHLV18_40_ATTCCT_L003_R2_001.fastq.gzENCORE215079