QKI RNA-Seq in K562

General Information


RBP	QKI
Cell_Line	K562
Method	shRNA
Exp_Name	QKI-BGKLV08-K562
ENCODE_series_ID	ENCSR436LAN
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR256PLH
ENCODE_CN_Exp_ID	ENCSR344XID
Rep1	QKI-LV08-39
Rep2	QKI-LV08-40
CN1	Nontarget-LV08-1_00003531
CN2	nontarget-LV08-2_00003531
Rep1_qPCR	61.6
Rep2_qPCR	50.2
Rep1_WB	46.5
Rep2_WB	56.1
Antibody Cat#	A300-183A
Antibody Lot#	A300-183A
Antibody DCC ID	ENCAB494QSS
Status	Released
Project	ENCODE3
ID	296

Experiment Information (Status: Released)

	BGKLV08-39	BGKLV08-39	BGKLV08-40	BGKLV08-40
idx	40	40	41	41
TRCN#_or_BGC#	TRCN0000015184	TRCN0000015184	TRCN0000015184	TRCN0000015184
shRNA_or_gRNA_sequence	CCCTACCATAATGCCTTTGAT	CCCTACCATAATGCCTTTGAT	CCCTACCATAATGCCTTTGAT	CCCTACCATAATGCCTTTGAT
PAM
Name	QKI	QKI	QKI	QKI
Sample_ID	BGKLV08-39	BGKLV08-39	BGKLV08-40	BGKLV08-40
transduction_Date	4/4/2014	4/4/2014	4/4/2014	4/4/2014
days
RBP_name	QKI	QKI	QKI	QKI
qPCR_result	61.6	61.6	50.2	50.2
Ave_qPCR	55.9	55.9
RT-qPCR_primer-F	ACGATATGCGTGTCCATCCT	ACGATATGCGTGTCCATCCT
RT-qPCR_primer-R	GGGTGAAGAGTTCAGAGGTCA	GGGTGAAGAGTTCAGAGGTCA
protein_conc	2518	2518	2731	2731
WB_result	46.5	75.8	56.1	60.4
Ave_WB	51.3	68.1
WB_DONE_date	7/27/2015	6/13/23
MW	39kDa	39kDa
IP	1		1
antibody_Cat#	A300-183A	23065S	A300-183A	LOT# 1
Antibody DCC ID	ENCAB494QSS		ENCAB494QSS
submitted_to_DCC_date	8/6/2015	1/8/2024
Rep1_TPM	13.2686119	0	0	0
Rep2_TPM	11.5909523	0	0	0
Action	Ready		Ready
Library_start_date	5/9/2014		5/9/2014
repeat_library
Note
ID	41	43	42	44

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
QKI	Product_ID: A300-183A Lot_ID: 2 Source: Bethyl Labs Target Name: QKI-human
QKI	Product_ID: 23065S Lot_ID: 1 Source: Cell Signaling Technology Target Name: QKI-human

Experiment Status

	BGKLV08-39	BGKLV08-40
Sample_ID	BGKLV08-39	BGKLV08-40
Sample Name	QKI-LV08-39	QKI-LV08-40
Sample Name	QKI-LV08-39	QKI-LV08-40
RBP	QKI	QKI
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	304	305

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-39	BGKLV08-40
Sample #
Sample Name	QKI-BGKLV08-39	QKI-BGKLV08-40
Sample_Name_Alias	QKI-LV08-39	QKI-LV08-40
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-08	2014-05-08
Lib_ID	Lib-140508	Lib-140508
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set4/F1.png	DNA_Library_LV08/set4/G1.png
RIN	9.3	9.3
libSample_RNA_Well	RNA_Library_LV08/set3/G1.png	RNA_Library_LV08/set3/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-39	BGKLV08-40
RBP	QKI	QKI
Batch_ID	BGKLV08	BGKLV08
WB_result	46.500	56.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1924	1925

Sequencing Information

	BGKLV08-39	BGKLV08-40
Sample_ID	BGKLV08-39	BGKLV08-40
Sample Name	QKI-LV08-39	QKI-LV08-40
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	53,110,000	51,640,000
total_aligned_reads	47,375,808	45,936,798
unique_aligned_reads	43,308,442	41,742,332
percent_uniqueAligned	0.81545	0.80833
correlation_replicates	0.995792	0.995792
spikein_reads	404,486	278,622
percent_spikeins	0.00762	0.00540
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	624	625

Data Submission Information

	BGKLV08-39	BGKLV08-39
ENCODE_alias	brenton-graveley:QKI-LV08	brenton-graveley:QKI-BGKLV08-K562
ENCODE_accession	ENCSR256PLH	ENCSR436LAN
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-39	BGKLV08-39
Sample Name	QKI-LV08-39	QKI-LV08-39
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2701	6886

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
QKI-LV08-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	624					GRCh38	V40	QKI-LV08-39_AGTCAA_L006_R1_001.fastq.gz,QKI-LV08-39_AGTCAA_L006_R2_001.fastq.gz		ENCORE2	12011
QKI-LV08-39_AGTCAA_L006_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	624	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12067
QKI-LV08-39_AGTCAA_L006_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	624	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12123
QKI-LV08-39_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	624					GRCh38	V40	QKI-LV08-39/Aligned.sortedByCoord.out.bam		ENCORE2	12179
QKI-LV08-39_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	624					GRCh38	V40	QKI-LV08-39/Aligned.sortedByCoord.out.bam		ENCORE2	12235
QKI-LV08-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	624					GRCh38	V40	QKI-LV08-39/Aligned.sortedByCoord.out.bam		ENCORE2	12291
QKI-LV08-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	624					GRCh38	V40	QKI-LV08-39/Aligned.sortedByCoord.out.bam		ENCORE2	12347
QKI-LV08-39_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	624					GRCh38	V40	QKI-LV08-39_AGTCAA_L006_R1_001.fastq.gz,QKI-LV08-39_AGTCAA_L006_R2_001.fastq.gz		ENCORE2	13346
QKI-LV08-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	625					GRCh38	V40	QKI-LV08-40_AGTTCC_L006_R1_001.fastq.gz,QKI-LV08-40_AGTTCC_L006_R2_001.fastq.gz		ENCORE2	12012
QKI-LV08-40_AGTTCC_L006_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	625	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003531_GATCAG_L005_R1_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R1_001.fastq.gz	ENCODE3	12068
QKI-LV08-40_AGTTCC_L006_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	625	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003531_GATCAG_L005_R2_001.fastq.gz,nontarget-LV08-2_00003531_TAGCTT_L005_R2_001.fastq.gz	ENCODE3	12124
QKI-LV08-40_Signal.Unique.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	625					GRCh38	V40	QKI-LV08-40/Aligned.sortedByCoord.out.bam		ENCORE2	12180
QKI-LV08-40_Signal.Unique.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	625					GRCh38	V40	QKI-LV08-40/Aligned.sortedByCoord.out.bam		ENCORE2	12236
QKI-LV08-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	625					GRCh38	V40	QKI-LV08-40/Aligned.sortedByCoord.out.bam		ENCORE2	12292
QKI-LV08-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	625					GRCh38	V40	QKI-LV08-40/Aligned.sortedByCoord.out.bam		ENCORE2	12348
QKI-LV08-40_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	625					GRCh38	V40	QKI-LV08-40_AGTTCC_L006_R1_001.fastq.gz,QKI-LV08-40_AGTTCC_L006_R2_001.fastq.gz		ENCORE2	13347