KHSRP RNA-Seq in K562

General Information


RBP	KHSRP
Cell_Line	K562
Method	shRNA
Exp_Name	KHSRP-BGKLV11-K562
ENCODE_series_ID	ENCSR535RFH
Batch_ID	BGKLV11
Pool ID	Pool-140701
Local_Set_Name	set11
ENCODE_KD_Exp_ID	ENCSR561CBC
ENCODE_CN_Exp_ID	ENCSR129RWD
Rep1	KHSRP-LV11-23
Rep2	KHSRP-LV11-24
CN1	Nontarget-LV11-1
CN2	nontarget-LV11-2
Rep1_qPCR	82.3
Rep2_qPCR	79.3
Rep1_WB	92.0
Rep2_WB	90.2
Antibody Cat#	RN065PW
Antibody Lot#	RN065PW
Antibody DCC ID	ENCAB531WWS
Status	Released
Project	ENCODE3
ID	313

Experiment Information (Status: Released)

	BGKLV11-23	BGKLV11-23	BGKLV11-24	BGKLV11-24
idx	92	92	93	93
TRCN#_or_BGC#	TRCN0000013254	TRCN0000013254	TRCN0000013254	TRCN0000013254
shRNA_or_gRNA_sequence	CCCGAGAAGATTGCTCATATA	CCCGAGAAGATTGCTCATATA	CCCGAGAAGATTGCTCATATA	CCCGAGAAGATTGCTCATATA
PAM
Name	KHSRP	KHSRP	KHSRP	KHSRP
Sample_ID	BGKLV11-23	BGKLV11-23	BGKLV11-24	BGKLV11-24
transduction_Date	5/1/2014	5/1/2014	5/1/2014	5/1/2014
days
RBP_name	KHSRP	KHSRP	KHSRP	KHSRP
qPCR_result	82.3	82.3	79.3	79.3
Ave_qPCR	80.8	80.8
RT-qPCR_primer-F	aatccgcaaggacgcttt	aatccgcaaggacgcttt
RT-qPCR_primer-R	tattcactgtcgtggcagcat	tattcactgtcgtggcagcat
protein_conc	1964	1964	1891	1891
WB_result	92.0	92.3	90.2	90.9
Ave_WB	91.1	91.6
WB_DONE_date		6/14/2023
MW	73kDa	73kDa
IP	1		1
antibody_Cat#	RN065PW	13398S	RN065PW	LOT # 1
Antibody DCC ID	ENCAB531WWS		ENCAB531WWS
submitted_to_DCC_date	4/2/2015	1/8/2024
Rep1_TPM	82.4121147	0	0	0
Rep2_TPM	76.7348064	0	0	0
Action	Ready		Ready
Library_start_date	5/19/2014		5/19/2014
repeat_library
Note
ID	103	105	104	106

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
KHSRP	Product_ID: RN065PW Lot_ID: 1 Source: MBLI Target Name: KHSRP-human
KHSRP	Product_ID: 13398S Lot_ID: 1 Source: Cell Signaling Technology Target Name: KHSRP-human

Experiment Status

	BGKLV11-23	BGKLV11-24
Sample_ID	BGKLV11-23	BGKLV11-24
Sample Name	KHSRP-LV11-23	KHSRP-LV11-24
Sample Name	KHSRP-LV11-23	KHSRP-LV11-24
RBP	KHSRP	KHSRP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-17	2014-09-17
Project	ENCODE3	ENCODE3
Note
ID	338	339

Library-Prep
Sequencing

Library-Prep Information

	BGKLV11-23	BGKLV11-24
Sample #
Sample Name	KHSRP-BGKLV11-23	KHSRP-BGKLV11-24
Sample_Name_Alias	KHSRP-LV11-23	KHSRP-LV11-24
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-19	2014-05-19
Lib_ID	Lib-140519	Lib-140519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV11/set2/C1.png	DNA_Library_LV11/set2/D1.png
RIN	8.9	9.1
libSample_RNA_Well	RNA_Library_LV11/set1/A3.png	RNA_Library_LV11/set1/B3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV11-23	BGKLV11-24
RBP	KHSRP	KHSRP
Batch_ID	BGKLV11	BGKLV11
WB_result	92.000	90.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1960	1961

Sequencing Information

	BGKLV11-23	BGKLV11-24
Sample_ID	BGKLV11-23	BGKLV11-24
Sample Name	KHSRP-LV11-23	KHSRP-LV11-24
Pool ID	Pool-140701	Pool-140701
LocalServer_folder	set11	set11
total_reads	56,210,000	68,100,000
total_aligned_reads	46,319,768	54,347,488
unique_aligned_reads	42,209,338	49,728,800
percent_uniqueAligned	0.75092	0.73023
correlation_replicates	0.992652	0.992652
spikein_reads	423,362	363,492
percent_spikeins	0.00753	0.00534
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	660	661

Data Submission Information

	BGKLV11-23	BGKLV11-23
ENCODE_alias	brenton-graveley:KHSRP-LV11	brenton-graveley:KHSRP-BGKLV11-K562
ENCODE_accession	ENCSR561CBC	ENCSR535RFH
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV11-23	BGKLV11-23
Sample Name	KHSRP-LV11-23	KHSRP-LV11-23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2718	6790

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
KHSRP-LV11-23_GTCCGC_L003_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	660	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12381
KHSRP-LV11-23_GTCCGC_L003_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	660	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12429
KHSRP-LV11-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	660					GRCh38	V40	KHSRP-LV11-23_GTCCGC_L003_R1_001.fastq.gz,KHSRP-LV11-23_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	12477
KHSRP-LV11-23_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	660					GRCh38	V40	KHSRP-LV11-23/Aligned.sortedByCoord.out.bam		ENCORE2	12525
KHSRP-LV11-23_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	660					GRCh38	V40	KHSRP-LV11-23/Aligned.sortedByCoord.out.bam		ENCORE2	12573
KHSRP-LV11-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	660					GRCh38	V40	KHSRP-LV11-23/Aligned.sortedByCoord.out.bam		ENCORE2	12621
KHSRP-LV11-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	660					GRCh38	V40	KHSRP-LV11-23/Aligned.sortedByCoord.out.bam		ENCORE2	12669
KHSRP-LV11-23_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	660					GRCh38	V40	KHSRP-LV11-23_GTCCGC_L003_R1_001.fastq.gz,KHSRP-LV11-23_GTCCGC_L003_R2_001.fastq.gz		ENCORE2	12717
KHSRP-LV11-24_GTGAAA_L003_R1_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	661	HiSeq2000	100	paired-ended	1				Nontarget-LV11-1_ATCACG_L001_R1_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12382
KHSRP-LV11-24_GTGAAA_L003_R2_001.fastq.gz	ENCODE_DATA/set11/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	661	HiSeq2000	100	paired-ended	2				Nontarget-LV11-1_ATCACG_L001_R2_001.fastq.gz,nontarget-LV11-2_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12430
KHSRP-LV11-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	661					GRCh38	V40	KHSRP-LV11-24_GTGAAA_L003_R1_001.fastq.gz,KHSRP-LV11-24_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	12478
KHSRP-LV11-24_Signal.Unique.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	661					GRCh38	V40	KHSRP-LV11-24/Aligned.sortedByCoord.out.bam		ENCORE2	12526
KHSRP-LV11-24_Signal.Unique.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	661					GRCh38	V40	KHSRP-LV11-24/Aligned.sortedByCoord.out.bam		ENCORE2	12574
KHSRP-LV11-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	661					GRCh38	V40	KHSRP-LV11-24/Aligned.sortedByCoord.out.bam		ENCORE2	12622
KHSRP-LV11-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set11/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	661					GRCh38	V40	KHSRP-LV11-24/Aligned.sortedByCoord.out.bam		ENCORE2	12670
KHSRP-LV11-24_quant.sf	ENCODE_DATA/set11/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	661					GRCh38	V40	KHSRP-LV11-24_GTGAAA_L003_R1_001.fastq.gz,KHSRP-LV11-24_GTGAAA_L003_R2_001.fastq.gz		ENCORE2	12718