GPKOW RNA-Seq in K562

General Information


RBP	GPKOW
Cell_Line	K562
Method	shRNA
Exp_Name	GPKOW-BGKLV36-K562
ENCODE_series_ID	ENCSR888VLT
Batch_ID	BGKLV36
Pool ID	Pool-161129
Local_Set_Name	set36
ENCODE_KD_Exp_ID	ENCSR967QNT
ENCODE_CN_Exp_ID	ENCSR424QCW
Rep1	GPKOW_BGKLV36-27
Rep2	GPKOW_BGKLV36-28
CN1	NT_BGKLV36-1
CN2	NT_BGKLV36-2
Rep1_qPCR	54.3
Rep2_qPCR	47.2
Rep1_WB	50.0
Rep2_WB	57.0
Antibody Cat#	GTX117716
Antibody Lot#	GTX117716
Antibody DCC ID	ENCAB445RKH
Status	Released
Project	ENCODE3
ID	746

Experiment Information (Status: Released)

	BGKLV36-27	BGKLV36-28
idx	750	751
TRCN#_or_BGC#	TRCN0000130596	TRCN0000130596
shRNA_or_gRNA_sequence	CGGAGGAGAAGGATTTCTTGA	CGGAGGAGAAGGATTTCTTGA
PAM
Name	GPKOW	GPKOW
Sample_ID	BGKLV36-27	BGKLV36-28
transduction_Date	5/19/2016	5/19/2016
days
RBP_name	GPKOW	GPKOW
qPCR_result	54.3	47.2
Ave_qPCR	50.8
RT-qPCR_primer-F	TGAAGATGTCCTAAGCCCAGA
RT-qPCR_primer-R	GAACCAGGGTCTCCAGCA
protein_conc	4402	4329
WB_result	50.0	57.0
Ave_WB	53.5
WB_DONE_date	6/8/16	wes
MW	52kDa
IP	1MB	1MB
antibody_Cat#	GTX117716	GTX117716
Antibody DCC ID	ENCAB445RKH
submitted_to_DCC_date	11/16/17
Rep1_TPM	26.2	0
Rep2_TPM	36.9	0
Action
Library_start_date	07/28/16	07/28/16
repeat_library
Note
ID	841	842

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
GPKOW	Product_ID: GTX117716 Lot_ID: 40289 Source: GeneTex Target Name: GPKOW-human

Experiment Status

	BGKLV36-27	BGKLV36-28
Sample_ID	BGKLV36-27	BGKLV36-28
Sample Name	GPKOW_BGKLV36-27	GPKOW_BGKLV36-28
Sample Name	GPKOW_BGKLV36-27	GPKOW_BGKLV36-28
RBP	GPKOW	GPKOW
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-12-12	2016-12-12
Project	ENCODE3	ENCODE3
Note
ID	1285	1286

Library-Prep
Sequencing

Library-Prep Information

	BGKLV36-27	BGKLV36-28
Sample #
Sample Name	GPKOW-BGKLV36-27	GPKOW-BGKLV36-28
Sample_Name_Alias	GPKOW_BGKLV36-27	GPKOW_BGKLV36-28
Index Well Position	S20	S21
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-07-28	2016-07-28
Lib_ID	Lib-160728	Lib-160728
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV36/set1/C2.png	DNA_Library_LV36/set1/D2.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV35_LV36/set1/E5.png	RNA_Library_LV35_LV36/set1/F5.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV36-27	BGKLV36-28
RBP	GPKOW	GPKOW
Batch_ID	BGKLV36	BGKLV36
WB_result	50.000	57.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2970	2971

Sequencing Information

	BGKLV36-27	BGKLV36-28
Sample_ID	BGKLV36-27	BGKLV36-28
Sample Name	GPKOW_BGKLV36-27	GPKOW_BGKLV36-28
Pool ID	Pool-161129	Pool-161129
LocalServer_folder	set36	set36
total_reads	65,455,828	61,878,766
total_aligned_reads	56,801,586	53,845,426
unique_aligned_reads	51,906,990	49,291,658
percent_uniqueAligned	0.79301	0.79658
correlation_replicates	0.997620	0.997620
spikein_reads	118,230	140,202
percent_spikeins	0.00181	0.00227
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1619	1620

Data Submission Information

	BGKLV36-27	BGKLV36-27
ENCODE_alias	brenton-graveley:GPKOW_BGKLV36	brenton-graveley:GPKOW-BGKLV36-K562
ENCODE_accession	ENCSR967QNT	ENCSR888VLT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV36-27	BGKLV36-27
Sample Name	GPKOW_BGKLV36-27	GPKOW_BGKLV36-27
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3182	6736

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
GPKOW_BGKLV36-27_GTGGCC_L001_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1619	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21898
GPKOW_BGKLV36-27_GTGGCC_L001_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1619	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21916
GPKOW_BGKLV36-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1619					GRCh38	V40	GPKOW_BGKLV36-27_GTGGCC_L001_001.R1.fastq.gz,GPKOW_BGKLV36-27_GTGGCC_L001_001.R2.fastq.gz		ENCORE2	21934
GPKOW_BGKLV36-27_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1619					GRCh38	V40	GPKOW_BGKLV36-27/Aligned.sortedByCoord.out.bam		ENCORE2	21952
GPKOW_BGKLV36-27_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1619					GRCh38	V40	GPKOW_BGKLV36-27/Aligned.sortedByCoord.out.bam		ENCORE2	21970
GPKOW_BGKLV36-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1619					GRCh38	V40	GPKOW_BGKLV36-27/Aligned.sortedByCoord.out.bam		ENCORE2	21988
GPKOW_BGKLV36-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1619					GRCh38	V40	GPKOW_BGKLV36-27/Aligned.sortedByCoord.out.bam		ENCORE2	22006
GPKOW_BGKLV36-27_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1619					GRCh38	V40	GPKOW_BGKLV36-27_GTGGCC_L001_001.R1.fastq.gz,GPKOW_BGKLV36-27_GTGGCC_L001_001.R2.fastq.gz		ENCORE2	22024
GPKOW_BGKLV36-28_GTTTCG_L001_001.R1.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1620	HiSeq2500	100	paired-ended	1				NT_BGKLV36-1_GATCAG_L008_001.R1.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R1.fastq.gz	ENCODE3	21899
GPKOW_BGKLV36-28_GTTTCG_L001_001.R2.fastq.gz	ENCODE_DATA/set36/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1620	HiSeq2500	100	paired-ended	2				NT_BGKLV36-1_GATCAG_L008_001.R2.fastq.gz,NT_BGKLV36-2_TAGCTT_L008_001.R2.fastq.gz	ENCODE3	21917
GPKOW_BGKLV36-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1620					GRCh38	V40	GPKOW_BGKLV36-28_GTTTCG_L001_001.R1.fastq.gz,GPKOW_BGKLV36-28_GTTTCG_L001_001.R2.fastq.gz		ENCORE2	21935
GPKOW_BGKLV36-28_Signal.Unique.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1620					GRCh38	V40	GPKOW_BGKLV36-28/Aligned.sortedByCoord.out.bam		ENCORE2	21953
GPKOW_BGKLV36-28_Signal.Unique.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1620					GRCh38	V40	GPKOW_BGKLV36-28/Aligned.sortedByCoord.out.bam		ENCORE2	21971
GPKOW_BGKLV36-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1620					GRCh38	V40	GPKOW_BGKLV36-28/Aligned.sortedByCoord.out.bam		ENCORE2	21989
GPKOW_BGKLV36-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set36/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1620					GRCh38	V40	GPKOW_BGKLV36-28/Aligned.sortedByCoord.out.bam		ENCORE2	22007
GPKOW_BGKLV36-28_quant.sf	ENCODE_DATA/set36/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1620					GRCh38	V40	GPKOW_BGKLV36-28_GTTTCG_L001_001.R1.fastq.gz,GPKOW_BGKLV36-28_GTTTCG_L001_001.R2.fastq.gz		ENCORE2	22025