PHF6 RNA-Seq in K562

General Information


RBP	PHF6
Cell_Line	K562
Method	shRNA
Exp_Name	PHF6-BGKLV21-K562
ENCODE_series_ID	ENCSR408GKZ
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR322XVS
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	PHF6_BGKLV21_39_17580
Rep2	PHF6_BGKLV21_40_17581
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	65.6
Rep2_qPCR	81.0
Rep1_WB	62.2
Rep2_WB	62.0
Antibody Cat#	A301-450A
Antibody Lot#	A301-450A
Antibody DCC ID	ENCAB411AGR
Status	Released
Project	ENCODE3
ID	516

Experiment Information (Status: Released)

	BGKLV21-39	BGKLV21-40
idx	310	311
TRCN#_or_BGC#	TRCN0000020121	TRCN0000020121
shRNA_or_gRNA_sequence	CCACTGTGCATTGCATGATAA	CCACTGTGCATTGCATGATAA
PAM
Name	PHF6	PHF6
Sample_ID	BGKLV21-39	BGKLV21-40
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	PHF6	PHF6
qPCR_result	65.6	81.0
Ave_qPCR	73.3
RT-qPCR_primer-F	accactgtgcattgcatgat
RT-qPCR_primer-R	tcagcttcggagttatgtgc
protein_conc	2976	2760
WB_result	62.2	62.0
Ave_WB	62.1
WB_DONE_date	3/31/2015
MW
IP	1	1
antibody_Cat#	A301-450A	A301-450A
Antibody DCC ID	ENCAB411AGR	ENCAB411AGR
submitted_to_DCC_date	5/4/2015
Rep1_TPM	20.0762225	0
Rep2_TPM	14.5508431	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	345	346

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PHF6	Product_ID: A301-450A Lot_ID: 1 Source: Bethyl Labs Target Name: PHF6-human

Experiment Status

	BGKLV21-39	BGKLV21-40
Sample_ID	BGKLV21-39	BGKLV21-40
Sample Name	PHF6_BGKLV21_39_17580	PHF6_BGKLV21_40_17581
Sample Name	PHF6_BGKLV21_39_17580	PHF6_BGKLV21_40_17581
RBP	PHF6	PHF6
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	766	767

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-39	BGKLV21-40
Sample #
Sample Name	PHF6-BGKLV21-39	PHF6-BGKLV21-40
Sample_Name_Alias	PHF6_BGKLV21_39_17580	PHF6_BGKLV21_40_17581
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/G7.png	DNA_Library_LV21-24/set1/H7.png
RIN	9.6	9.3
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/E10.png	RNA_Library_LV19-21-24/set1/F10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-39	BGKLV21-40
RBP	PHF6	PHF6
Batch_ID	BGKLV21	BGKLV21
WB_result	62.200	62.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2452	2453

Sequencing Information

	BGKLV21-39	BGKLV21-40
Sample_ID	BGKLV21-39	BGKLV21-40
Sample Name	PHF6_BGKLV21_39_17580	PHF6_BGKLV21_40_17581
Pool ID	Pool-150615	Pool-150615
LocalServer_folder	set21	set21
total_reads	69,910,000	35,280,000
total_aligned_reads	64,861,370	32,777,092
unique_aligned_reads	59,510,422	30,047,876
percent_uniqueAligned	0.85124	0.85170
correlation_replicates	0.997582	0.997582
spikein_reads	387,138	201,100
percent_spikeins	0.00554	0.00570
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1058	1059

Data Submission Information

	BGKLV21-39	BGKLV21-39
ENCODE_alias	brenton-graveley:PHF6_BGKLV21	brenton-graveley:PHF6-BGKLV21-K562
ENCODE_accession	ENCSR322XVS	ENCSR408GKZ
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-39	BGKLV21-39
Sample Name	PHF6_BGKLV21_39_17580	PHF6_BGKLV21_39_17580
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2969	6856

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
PHF6_BGKLV21_39_17580_ACTGAT_L003_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1058	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15948
PHF6_BGKLV21_39_17580_ACTGAT_L003_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1058	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15992
PHF6_BGKLV21_39_17580_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1058					GRCh38	V40	PHF6_BGKLV21_39_17580_ACTGAT_L003_R1_001.fastq.gz,PHF6_BGKLV21_39_17580_ACTGAT_L003_R2_001.fastq.gz		ENCORE2	16036
PHF6_BGKLV21_39_17580_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1058					GRCh38	V40	PHF6_BGKLV21_39_17580/Aligned.sortedByCoord.out.bam		ENCORE2	16080
PHF6_BGKLV21_39_17580_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1058					GRCh38	V40	PHF6_BGKLV21_39_17580/Aligned.sortedByCoord.out.bam		ENCORE2	16124
PHF6_BGKLV21_39_17580_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1058					GRCh38	V40	PHF6_BGKLV21_39_17580/Aligned.sortedByCoord.out.bam		ENCORE2	16168
PHF6_BGKLV21_39_17580_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1058					GRCh38	V40	PHF6_BGKLV21_39_17580/Aligned.sortedByCoord.out.bam		ENCORE2	16212
PHF6_BGKLV21_39_17580_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1058					GRCh38	V40	PHF6_BGKLV21_39_17580_ACTGAT_L003_R1_001.fastq.gz,PHF6_BGKLV21_39_17580_ACTGAT_L003_R2_001.fastq.gz		ENCORE2	16256
PHF6_BGKLV21_40_17581_ATTCCT_L003_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1059	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15949
PHF6_BGKLV21_40_17581_ATTCCT_L003_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1059	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15993
PHF6_BGKLV21_40_17581_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1059					GRCh38	V40	PHF6_BGKLV21_40_17581_ATTCCT_L003_R1_001.fastq.gz,PHF6_BGKLV21_40_17581_ATTCCT_L003_R2_001.fastq.gz		ENCORE2	16037
PHF6_BGKLV21_40_17581_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1059					GRCh38	V40	PHF6_BGKLV21_40_17581/Aligned.sortedByCoord.out.bam		ENCORE2	16081
PHF6_BGKLV21_40_17581_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1059					GRCh38	V40	PHF6_BGKLV21_40_17581/Aligned.sortedByCoord.out.bam		ENCORE2	16125
PHF6_BGKLV21_40_17581_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1059					GRCh38	V40	PHF6_BGKLV21_40_17581/Aligned.sortedByCoord.out.bam		ENCORE2	16169
PHF6_BGKLV21_40_17581_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1059					GRCh38	V40	PHF6_BGKLV21_40_17581/Aligned.sortedByCoord.out.bam		ENCORE2	16213
PHF6_BGKLV21_40_17581_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1059					GRCh38	V40	PHF6_BGKLV21_40_17581_ATTCCT_L003_R1_001.fastq.gz,PHF6_BGKLV21_40_17581_ATTCCT_L003_R2_001.fastq.gz		ENCORE2	16257