NUSAP1 RNA-Seq in K562

General Information


RBP	NUSAP1
Cell_Line	K562
Method	shRNA
Exp_Name	NUSAP1-BGKLV21-K562
ENCODE_series_ID	ENCSR483BZO
Batch_ID	BGKLV21
Pool ID	Pool-150615
Local_Set_Name	set21
ENCODE_KD_Exp_ID	ENCSR927XBT
ENCODE_CN_Exp_ID	ENCSR572FFX
Rep1	NUSAP1_BGKLV21_37_17578
Rep2	NUSAP1_BGKLV21_38_17579
CN1	non-target_BGKLV21_1
CN2	non-target_BGKLV21_2
Rep1_qPCR	80.6
Rep2_qPCR	83.2
Rep1_WB	68.9
Rep2_WB	68.4
Antibody Cat#	A302-596A
Antibody Lot#	A302-596A
Antibody DCC ID	ENCAB751SQO
Status	Released
Project	ENCODE3
ID	515

Experiment Information (Status: Released)

	BGKLV21-37	BGKLV21-38
idx	308	309
TRCN#_or_BGC#	TRCN0000137707	TRCN0000137707
shRNA_or_gRNA_sequence	GCATAAGCGTTCACTGACCAA	GCATAAGCGTTCACTGACCAA
PAM
Name	NUSAP1	NUSAP1
Sample_ID	BGKLV21-37	BGKLV21-38
transduction_Date	10/9/2014	10/9/2014
days
RBP_name	NUSAP1	NUSAP1
qPCR_result	80.6	83.2
Ave_qPCR	81.9
RT-qPCR_primer-F	gtgtggaccctgactcacag
RT-qPCR_primer-R	ctgagatcctggctttcctg
protein_conc	2978	3084
WB_result	68.9	68.4
Ave_WB	68.7
WB_DONE_date	3/30/2015
MW
IP	1	1
antibody_Cat#	A302-596A	A302-596A
Antibody DCC ID	ENCAB751SQO	ENCAB751SQO
submitted_to_DCC_date	5/4/2015
Rep1_TPM	35.6045895	0
Rep2_TPM	30.8924781	0
Action
Library_start_date	5/19/2015	5/19/2015
repeat_library
Note
ID	343	344

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NUSAP1	Product_ID: A302-596A Lot_ID: 1 Source: Bethyl Labs Target Name: NUSAP1-human

Experiment Status

	BGKLV21-37	BGKLV21-38
Sample_ID	BGKLV21-37	BGKLV21-38
Sample Name	NUSAP1_BGKLV21_37_17578	NUSAP1_BGKLV21_38_17579
Sample Name	NUSAP1_BGKLV21_37_17578	NUSAP1_BGKLV21_38_17579
RBP	NUSAP1	NUSAP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-08-14	2015-08-14
Project	ENCODE3	ENCODE3
Note
ID	764	765

Library-Prep
Sequencing

Library-Prep Information

	BGKLV21-37	BGKLV21-38
Sample #
Sample Name	NUSAP1-BGKLV21-37	NUSAP1-BGKLV21-38
Sample_Name_Alias	NUSAP1_BGKLV21_37_17578	NUSAP1_BGKLV21_38_17579
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-05-19	2015-05-19
Lib_ID	Lib-150519	Lib-150519
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV21-24/set1/E7.png	DNA_Library_LV21-24/set1/F7.png
RIN	9.5	9.1
libSample_RNA_Well	RNA_Library_LV19-21-24/set1/C10.png	RNA_Library_LV19-21-24/set1/D10.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV21-37	BGKLV21-38
RBP	NUSAP1	NUSAP1
Batch_ID	BGKLV21	BGKLV21
WB_result	68.900	68.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2450	2451

Sequencing Information

	BGKLV21-37	BGKLV21-38	BGKLV21-38
Sample_ID	BGKLV21-37	BGKLV21-38	BGKLV21-38
Sample Name	NUSAP1_BGKLV21_37_17578	NUSAP1_BGKLV21_38_17579	NUSAP1_BGKLV21_38_17579
Pool ID	Pool-150615	Pool-150615	Pool-151215B
LocalServer_folder	set21	set21	set21
total_reads	32,950,000	22,360,000	50,643,374
total_aligned_reads	30,744,782	20,752,250	47,435,832
unique_aligned_reads	28,268,730	19,020,294	43,286,106
percent_uniqueAligned	0.85793	0.85064	0.85472
correlation_replicates	0.988202	0.988202
spikein_reads	167,788	125,842	278,752
percent_spikeins	0.00509	0.00563	0.00550
original_ReadLength	100	100	100
QC_Status	Submitted	Submitted	Submitted
ID	1056	1057	1380

Data Submission Information

	BGKLV21-37	BGKLV21-37
ENCODE_alias	brenton-graveley:NUSAP1_BGKLV21	brenton-graveley:NUSAP1-BGKLV21-K562
ENCODE_accession	ENCSR927XBT	ENCSR483BZO
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV21-37	BGKLV21-37
Sample Name	NUSAP1_BGKLV21_37_17578	NUSAP1_BGKLV21_37_17578
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-13	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2968	6838

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
NUSAP1_BGKLV21_37_17578_CGTACG_L003_R1_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1056	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15946
NUSAP1_BGKLV21_37_17578_CGTACG_L003_R2_001.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1056	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15990
NUSAP1_BGKLV21_37_17578_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1056					GRCh38	V40	NUSAP1_BGKLV21_37_17578_CGTACG_L003_R1_001.fastq.gz,NUSAP1_BGKLV21_37_17578_CGTACG_L003_R2_001.fastq.gz		ENCORE2	16034
NUSAP1_BGKLV21_37_17578_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1056					GRCh38	V40	NUSAP1_BGKLV21_37_17578/Aligned.sortedByCoord.out.bam		ENCORE2	16078
NUSAP1_BGKLV21_37_17578_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1056					GRCh38	V40	NUSAP1_BGKLV21_37_17578/Aligned.sortedByCoord.out.bam		ENCORE2	16122
NUSAP1_BGKLV21_37_17578_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1056					GRCh38	V40	NUSAP1_BGKLV21_37_17578/Aligned.sortedByCoord.out.bam		ENCORE2	16166
NUSAP1_BGKLV21_37_17578_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1056					GRCh38	V40	NUSAP1_BGKLV21_37_17578/Aligned.sortedByCoord.out.bam		ENCORE2	16210
NUSAP1_BGKLV21_37_17578_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1056					GRCh38	V40	NUSAP1_BGKLV21_37_17578_CGTACG_L003_R1_001.fastq.gz,NUSAP1_BGKLV21_37_17578_CGTACG_L003_R2_001.fastq.gz		ENCORE2	16254
NUSAP1_BGKLV21_38_17579_GAGTGG_L003_R1_001.merged.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1057	HiSeq2000	100	paired-ended	1				non-target_BGKLV21_1_ATCACG_R1_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R1_001.fastq.gz	ENCODE3	15947
NUSAP1_BGKLV21_38_17579_GAGTGG_L003_R2_001.merged.fastq.gz	ENCODE_DATA/set21/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1057	HiSeq2000	100	paired-ended	2				non-target_BGKLV21_1_ATCACG_R2_001.fastq.gz,non-target_BGKLV21_2_CGATGT_R2_001.fastq.gz	ENCODE3	15991
NUSAP1_BGKLV21_38_17579_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1057					GRCh38	V40	NUSAP1_BGKLV21_38_17579_GAGTGG_L003_R1_001.merged.fastq.gz,NUSAP1_BGKLV21_38_17579_GAGTGG_L003_R2_001.merged.fastq.gz		ENCORE2	16035
NUSAP1_BGKLV21_38_17579_Signal.Unique.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1057					GRCh38	V40	NUSAP1_BGKLV21_38_17579/Aligned.sortedByCoord.out.bam		ENCORE2	16079
NUSAP1_BGKLV21_38_17579_Signal.Unique.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1057					GRCh38	V40	NUSAP1_BGKLV21_38_17579/Aligned.sortedByCoord.out.bam		ENCORE2	16123
NUSAP1_BGKLV21_38_17579_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1057					GRCh38	V40	NUSAP1_BGKLV21_38_17579/Aligned.sortedByCoord.out.bam		ENCORE2	16167
NUSAP1_BGKLV21_38_17579_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set21/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1057					GRCh38	V40	NUSAP1_BGKLV21_38_17579/Aligned.sortedByCoord.out.bam		ENCORE2	16211
NUSAP1_BGKLV21_38_17579_quant.sf	ENCODE_DATA/set21/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1057					GRCh38	V40	NUSAP1_BGKLV21_38_17579_GAGTGG_L003_R1_001.merged.fastq.gz,NUSAP1_BGKLV21_38_17579_GAGTGG_L003_R2_001.merged.fastq.gz		ENCORE2	16255