WDR43 RNA-Seq in K562

General Information


RBP	WDR43
Cell_Line	K562
Method	shRNA
Exp_Name	WDR43-BGKLV34-K562
ENCODE_series_ID	ENCSR064IQS
Batch_ID	BGKLV34
Pool ID	Pool-160912
Local_Set_Name	set34
ENCODE_KD_Exp_ID	ENCSR341PZW
ENCODE_CN_Exp_ID	ENCSR174OYC
Rep1	WDR43_BGKLV34-51
Rep2	WDR43_BGKLV34-52
CN1	NT_BGKLV34-1
CN2	NT_BGKLV34-2
Rep1_qPCR	80.5
Rep2_qPCR	84.5
Rep1_WB	85.9
Rep2_WB	89.0
Antibody Cat#	A302-478A
Antibody Lot#	A302-478A
Antibody DCC ID	ENCAB350LKS
Status	Released
Project	ENCODE3
ID	729

Experiment Information (Status: Released)

	BGKLV34-51	BGKLV34-52
idx	714	715
TRCN#_or_BGC#	TRCN0000253868	TRCN0000253868
shRNA_or_gRNA_sequence	ACCGATGAACCTGTCTATATT	ACCGATGAACCTGTCTATATT
PAM
Name	WDR43	WDR43
Sample_ID	BGKLV34-51	BGKLV34-52
transduction_Date	11/4/2015	11/4/2015
days
RBP_name	WDR43	WDR43
qPCR_result	80.5	84.5
Ave_qPCR	82.5
RT-qPCR_primer-F	ggtccgatcagaaaacaaaga
RT-qPCR_primer-R	gccaacttgacaggctcttc
protein_conc	2647	3042
WB_result	85.9	89.0
Ave_WB	87.5
WB_DONE_date	2/22/2016	WES
MW	75kDa
IP	1	1
antibody_Cat#	A302-478A	A302-478A
Antibody DCC ID	ENCAB350LKS	ENCAB350LKS
submitted_to_DCC_date	3/8/2016
Rep1_TPM	32.96016323	0
Rep2_TPM	16.77997444	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	803	804

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
WDR43	Product_ID: A302-478A Lot_ID: 1 Source: Bethyl Labs Target Name: WDR43-human

Experiment Status

	BGKLV34-51	BGKLV34-52
Sample_ID	BGKLV34-51	BGKLV34-52
Sample Name	WDR43_BGKLV34-51	WDR43_BGKLV34-52
Sample Name	WDR43_BGKLV34-51	WDR43_BGKLV34-52
RBP	WDR43	WDR43
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1247	1248

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-51	BGKLV34-52
Sample #
Sample Name	WDR43-BGKLV34-51	WDR43-BGKLV34-52
Sample_Name_Alias	WDR43_BGKLV34-51	WDR43_BGKLV34-52
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/G4.png	DNA_Library_LV34_2-28/set2/C1.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/E6.png	RNA_Library_LV32-33-34/set1/F6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV34-51	BGKLV34-52
RBP	WDR43	WDR43
Batch_ID	BGKLV34	BGKLV34
WB_result	85.900	89.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2932	2933

Sequencing Information

	BGKLV34-51	BGKLV34-52
Sample_ID	BGKLV34-51	BGKLV34-52
Sample Name	WDR43_BGKLV34-51	WDR43_BGKLV34-52
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set34	set34
total_reads	71,492,280	68,986,086
total_aligned_reads	62,712,040	57,656,438
unique_aligned_reads	57,271,800	52,596,682
percent_uniqueAligned	0.80109	0.76242
correlation_replicates	0.998773	0.998773
spikein_reads	161,786	160,172
percent_spikeins	0.00226	0.00232
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1581	1582

Data Submission Information

	BGKLV34-51	BGKLV34-51
ENCODE_alias	brenton-graveley:WDR43_BGKLV34	brenton-graveley:WDR43-BGKLV34-K562
ENCODE_accession	ENCSR341PZW	ENCSR064IQS
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV34-51	BGKLV34-51
Sample Name	WDR43_BGKLV34-51	WDR43_BGKLV34-51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3163	7039

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
WDR43_BGKLV34-51_ATGTCA_L004_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1581	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21540
WDR43_BGKLV34-51_ATGTCA_L004_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1581	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21560
WDR43_BGKLV34-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1581					GRCh38	V40	WDR43_BGKLV34-51_ATGTCA_L004_001.R1.fastq.gz,WDR43_BGKLV34-51_ATGTCA_L004_001.R2.fastq.gz		ENCORE2	21580
WDR43_BGKLV34-51_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1581					GRCh38	V40	WDR43_BGKLV34-51/Aligned.sortedByCoord.out.bam		ENCORE2	21600
WDR43_BGKLV34-51_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1581					GRCh38	V40	WDR43_BGKLV34-51/Aligned.sortedByCoord.out.bam		ENCORE2	21620
WDR43_BGKLV34-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1581					GRCh38	V40	WDR43_BGKLV34-51/Aligned.sortedByCoord.out.bam		ENCORE2	21640
WDR43_BGKLV34-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1581					GRCh38	V40	WDR43_BGKLV34-51/Aligned.sortedByCoord.out.bam		ENCORE2	21660
WDR43_BGKLV34-51_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1581					GRCh38	V40	WDR43_BGKLV34-51_ATGTCA_L004_001.R1.fastq.gz,WDR43_BGKLV34-51_ATGTCA_L004_001.R2.fastq.gz		ENCORE2	21680
WDR43_BGKLV34-52_CCGTCC_L004_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1582	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21541
WDR43_BGKLV34-52_CCGTCC_L004_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1582	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21561
WDR43_BGKLV34-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1582					GRCh38	V40	WDR43_BGKLV34-52_CCGTCC_L004_001.R1.fastq.gz,WDR43_BGKLV34-52_CCGTCC_L004_001.R2.fastq.gz		ENCORE2	21581
WDR43_BGKLV34-52_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1582					GRCh38	V40	WDR43_BGKLV34-52/Aligned.sortedByCoord.out.bam		ENCORE2	21601
WDR43_BGKLV34-52_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1582					GRCh38	V40	WDR43_BGKLV34-52/Aligned.sortedByCoord.out.bam		ENCORE2	21621
WDR43_BGKLV34-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1582					GRCh38	V40	WDR43_BGKLV34-52/Aligned.sortedByCoord.out.bam		ENCORE2	21641
WDR43_BGKLV34-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1582					GRCh38	V40	WDR43_BGKLV34-52/Aligned.sortedByCoord.out.bam		ENCORE2	21661
WDR43_BGKLV34-52_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1582					GRCh38	V40	WDR43_BGKLV34-52_CCGTCC_L004_001.R1.fastq.gz,WDR43_BGKLV34-52_CCGTCC_L004_001.R2.fastq.gz		ENCORE2	21681