NCBP2 RNA-Seq in K562

General Information


RBP	NCBP2
Cell_Line	K562
Method	shRNA
Exp_Name	NCBP2-BGKLV08-K562
ENCODE_series_ID	ENCSR249VBV
Batch_ID	BGKLV08
Pool ID	Pool-140601
Local_Set_Name	set10
ENCODE_KD_Exp_ID	ENCSR361LBE
ENCODE_CN_Exp_ID	ENCSR913CAE
Rep1	NCBP2-LV08-35
Rep2	NCBP2-LV08-36
CN1	Nontarget-LV08-1_00003527
CN2	nontarget-LV08-2_00003527
Rep1_qPCR	47.4
Rep2_qPCR	65.6
Rep1_WB	43.9
Rep2_WB	46.0
Antibody Cat#	A302-553A
Antibody Lot#	A302-553A
Antibody DCC ID	ENCAB039KCI
Status	Released
Project	ENCODE3
ID	293

Experiment Information (Status: Released)

	BGKLV08-35	BGKLV08-36
idx	36	37
TRCN#_or_BGC#	TRCN0000059994	TRCN0000059994
shRNA_or_gRNA_sequence	GTGACAATGAAGAACAAGAAA	GTGACAATGAAGAACAAGAAA
PAM
Name	NCBP2	NCBP2
Sample_ID	BGKLV08-35	BGKLV08-36
transduction_Date	4/4/2014	4/4/2014
days
RBP_name	NCBP2	NCBP2
qPCR_result	47.4	65.6
Ave_qPCR	56.5
RT-qPCR_primer-F	TTTAAGGAGGGCAGGCAATA
RT-qPCR_primer-R	CTCCTCTCCCAGCATCGTAG
protein_conc	2534	2571
WB_result	43.9	46.0
Ave_WB	45.0
WB_DONE_date	6/12/2014
MW	18kDa
IP	1	1
antibody_Cat#	A302-553A	A302-553A
Antibody DCC ID	ENCAB039KCI	ENCAB039KCI
submitted_to_DCC_date	4/2/2015
Rep1_TPM	30.9900941	0
Rep2_TPM	22.8450236	0
Action	Ready	Ready
Library_start_date	5/9/2014	5/9/2014
repeat_library
Note
ID	37	38

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NCBP2	Product_ID: A302-553A Lot_ID: 1 Source: Bethyl Labs Target Name: NCBP2-human

Experiment Status

	BGKLV08-35	BGKLV08-36
Sample_ID	BGKLV08-35	BGKLV08-36
Sample Name	NCBP2-LV08-35	NCBP2-LV08-36
Sample Name	NCBP2-LV08-35	NCBP2-LV08-36
RBP	NCBP2	NCBP2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2014-09-16	2014-09-16
Project	ENCODE3	ENCODE3
Note
ID	296	297

Library-Prep
Sequencing

Library-Prep Information

	BGKLV08-35	BGKLV08-36
Sample #
Sample Name	NCBP2-BGKLV08-35	NCBP2-BGKLV08-36
Sample_Name_Alias	NCBP2-LV08-35	NCBP2-LV08-36
Index Well Position	S07	S08
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-05-05	2014-05-05
Lib_ID	Lib-140505	Lib-140505
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV08/set3/B1.png	DNA_Library_LV08/set3/C1.png
RIN	9.3	9.2
libSample_RNA_Well	RNA_Library_LV08/set3/C1.png	RNA_Library_LV08/set3/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGKLV08-35	BGKLV08-36
RBP	NCBP2	NCBP2
Batch_ID	BGKLV08	BGKLV08
WB_result	43.900	46.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	1916	1917

Sequencing Information

	BGKLV08-35	BGKLV08-36
Sample_ID	BGKLV08-35	BGKLV08-36
Sample Name	NCBP2-LV08-35	NCBP2-LV08-36
Pool ID	Pool-140601	Pool-140601
LocalServer_folder	set10	set10
total_reads	50,500,000	50,590,000
total_aligned_reads	44,051,108	44,556,742
unique_aligned_reads	40,334,466	40,900,248
percent_uniqueAligned	0.79870	0.80847
correlation_replicates	0.997497	0.997497
spikein_reads	290,420	544,442
percent_spikeins	0.00575	0.01076
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	616	617

Data Submission Information

	BGKLV08-35	BGKLV08-35
ENCODE_alias	brenton-graveley:NCBP2-LV08	brenton-graveley:NCBP2-BGKLV08-K562
ENCODE_accession	ENCSR361LBE	ENCSR249VBV
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV08-35	BGKLV08-35
Sample Name	NCBP2-LV08-35	NCBP2-LV08-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2697	6819

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
NCBP2-LV08-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	616					GRCh38	V40	NCBP2-LV08-35_CAGATC_L005_R1_001.fastq.gz,NCBP2-LV08-35_CAGATC_L005_R2_001.fastq.gz		ENCORE2	12003
NCBP2-LV08-35_CAGATC_L005_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	616	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12059
NCBP2-LV08-35_CAGATC_L005_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	616	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12115
NCBP2-LV08-35_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	616					GRCh38	V40	NCBP2-LV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	12171
NCBP2-LV08-35_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	616					GRCh38	V40	NCBP2-LV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	12227
NCBP2-LV08-35_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	616					GRCh38	V40	NCBP2-LV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	12283
NCBP2-LV08-35_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	616					GRCh38	V40	NCBP2-LV08-35/Aligned.sortedByCoord.out.bam		ENCORE2	12339
NCBP2-LV08-35_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	616					GRCh38	V40	NCBP2-LV08-35_CAGATC_L005_R1_001.fastq.gz,NCBP2-LV08-35_CAGATC_L005_R2_001.fastq.gz		ENCORE2	13338
NCBP2-LV08-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set10/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	617					GRCh38	V40	NCBP2-LV08-36_ACTTGA_L005_R1_001.fastq.gz,NCBP2-LV08-36_ACTTGA_L005_R2_001.fastq.gz		ENCORE2	12004
NCBP2-LV08-36_ACTTGA_L005_R1_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	617	HiSeq2000	100	paired-ended	1				Nontarget-LV08-1_00003527_ATCACG_L001_R1_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12060
NCBP2-LV08-36_ACTTGA_L005_R2_001.fastq.gz	ENCODE_DATA/set10/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	617	HiSeq2000	100	paired-ended	2				Nontarget-LV08-1_00003527_ATCACG_L001_R2_001.fastq.gz,nontarget-LV08-2_00003527_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12116
NCBP2-LV08-36_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	617					GRCh38	V40	NCBP2-LV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	12172
NCBP2-LV08-36_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	617					GRCh38	V40	NCBP2-LV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	12228
NCBP2-LV08-36_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	617					GRCh38	V40	NCBP2-LV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	12284
NCBP2-LV08-36_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	617					GRCh38	V40	NCBP2-LV08-36/Aligned.sortedByCoord.out.bam		ENCORE2	12340
NCBP2-LV08-36_quant.sf	ENCODE_DATA/set10/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	617					GRCh38	V40	NCBP2-LV08-36_ACTTGA_L005_R1_001.fastq.gz,NCBP2-LV08-36_ACTTGA_L005_R2_001.fastq.gz		ENCORE2	13339