NUSAP1 RNA-Seq in HepG2

General Information


RBP	NUSAP1
Cell_Line	HepG2
Method	shRNA
Exp_Name	NUSAP1-BGHLV18-HepG2
ENCODE_series_ID	ENCSR222VTT
Batch_ID	BGHLV18
Pool ID	Pool-141010
Local_Set_Name	set18
ENCODE_KD_Exp_ID	ENCSR180XTP
ENCODE_CN_Exp_ID	ENCSR674KEK
Rep1	NUSAP1_BGHLV18_37
Rep2	NUSAP1_BGHLV18_38
CN1	NT_BGHLV18_1
CN2	NT_BGHLV18_2
Rep1_qPCR	77.3
Rep2_qPCR	76.9
Rep1_WB	86.7
Rep2_WB	60.8
Antibody Cat#	A302-596A
Antibody Lot#	A302-596A
Antibody DCC ID	ENCAB751SQO
Status	Released
Project	ENCODE3
ID	453

Experiment Information (Status: Released)

	BGHLV18-37	BGHLV18-38
idx	337	338
TRCN#_or_BGC#	TRCN0000137707	TRCN0000137707
shRNA_or_gRNA_sequence	GCATAAGCGTTCACTGACCAA	GCATAAGCGTTCACTGACCAA
PAM
Name	NUSAP1	NUSAP1
Sample_ID	BGHLV18-37	BGHLV18-38
transduction_Date	8/28/2014	8/28/2014
days
RBP_name	NUSAP1	NUSAP1
qPCR_result	77.3	76.9
Ave_qPCR	77.1
RT-qPCR_primer-F	gtgtggaccctgactcacag
RT-qPCR_primer-R	ctgagatcctggctttcctg
protein_conc	4026	4042
WB_result	86.7	60.8
Ave_WB	73.7
WB_DONE_date	4/6/2015
MW	49kDa
IP	1	1
antibody_Cat#	A302-596A	A302-596A
Antibody DCC ID	ENCAB751SQO	ENCAB751SQO
submitted_to_DCC_date	5/6/2015
Rep1_TPM	8.5	0
Rep2_TPM	4	0
Action
Library_start_date	10/2/2014	10/2/2014
repeat_library
Note
ID	2402	2403

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

	BGHLV18-37	BGHLV18-38
Sample_ID	BGHLV18-37	BGHLV18-38
Sample Name	NUSAP1_BGHLV18_37	NUSAP1_BGHLV18_38
Sample Name	NUSAP1_BGHLV18_37	NUSAP1_BGHLV18_38
RBP	NUSAP1	NUSAP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	636	637

Library-Prep
Sequencing

Library-Prep Information

	BGHLV18-37	BGHLV18-38
Sample #
Sample Name	NUSAP1-BGHLV18-37	NUSAP1-BGHLV18-38
Sample_Name_Alias	NUSAP1_BGHLV18_37	NUSAP1_BGHLV18_38
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-10-02	2014-10-02
Lib_ID	Lib-141002	Lib-141002
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV18-19/set1/E3.png	DNA_Library_LV18-19/set1/F3.png
RIN	9.2	9.3
libSample_RNA_Well	RNA_Library_LV18-19/set1/C10.png	RNA_Library_LV18-19/set1/D10.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV18-37	BGHLV18-38
RBP	NUSAP1	NUSAP1
Batch_ID	BGHLV18	BGHLV18
WB_result	86.700	60.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2320	2321

Sequencing Information

	BGHLV18-37	BGHLV18-38
Sample_ID	BGHLV18-37	BGHLV18-38
Sample Name	NUSAP1_BGHLV18_37	NUSAP1_BGHLV18_38
Pool ID	Pool-141010	Pool-141010
LocalServer_folder	set18	set18
total_reads	48,480,000	54,000,000
total_aligned_reads	43,758,358	47,481,594
unique_aligned_reads	41,281,546	44,777,104
percent_uniqueAligned	0.85152	0.82921
correlation_replicates	0.995891	0.995891
spikein_reads	213,406	175,398
percent_spikeins	0.00440	0.00325
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	962	963

Data Submission Information

	BGHLV18-37	BGHLV18-37
ENCODE_alias	brenton-graveley:NUSAP1_BGHLV18	brenton-graveley:NUSAP1-BGHLV18-HepG2
ENCODE_accession	ENCSR180XTP	ENCSR222VTT
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV18-37	BGHLV18-37
Sample Name	NUSAP1_BGHLV18_37	NUSAP1_BGHLV18_37
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2835	6837

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_BGHLV18_37_CGTACG_L003_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	962	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14810
NUSAP1_BGHLV18_37_CGTACG_L003_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	962	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14848
NUSAP1_BGHLV18_37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	962					GRCh38	V40	NUSAP1_BGHLV18_37_CGTACG_L003_R1_001.fastq.gz,NUSAP1_BGHLV18_37_CGTACG_L003_R2_001.fastq.gz		ENCORE2	14886
NUSAP1_BGHLV18_37_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	962					GRCh38	V40	NUSAP1_BGHLV18_37/Aligned.sortedByCoord.out.bam		ENCORE2	14924
NUSAP1_BGHLV18_37_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	962					GRCh38	V40	NUSAP1_BGHLV18_37/Aligned.sortedByCoord.out.bam		ENCORE2	14962
NUSAP1_BGHLV18_37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	962					GRCh38	V40	NUSAP1_BGHLV18_37/Aligned.sortedByCoord.out.bam		ENCORE2	15000
NUSAP1_BGHLV18_37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	962					GRCh38	V40	NUSAP1_BGHLV18_37/Aligned.sortedByCoord.out.bam		ENCORE2	15038
NUSAP1_BGHLV18_37_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	962					GRCh38	V40	NUSAP1_BGHLV18_37_CGTACG_L003_R1_001.fastq.gz,NUSAP1_BGHLV18_37_CGTACG_L003_R2_001.fastq.gz		ENCORE2	15076
NUSAP1_BGHLV18_38_GAGTGG_L003_R1_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	963	HiSeq2000	100	paired-ended	1				NT_BGHLV18_1_ATCACG_L008_R1_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R1_001.fastq.gz	ENCODE3	14811
NUSAP1_BGHLV18_38_GAGTGG_L003_R2_001.fastq.gz	ENCODE_DATA/set18/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	963	HiSeq2000	100	paired-ended	2				NT_BGHLV18_1_ATCACG_L008_R2_001.fastq.gz,NT_BGHLV18_2_CGATGT_L008_R2_001.fastq.gz	ENCODE3	14849
NUSAP1_BGHLV18_38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	963					GRCh38	V40	NUSAP1_BGHLV18_38_GAGTGG_L003_R1_001.fastq.gz,NUSAP1_BGHLV18_38_GAGTGG_L003_R2_001.fastq.gz		ENCORE2	14887
NUSAP1_BGHLV18_38_Signal.Unique.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	963					GRCh38	V40	NUSAP1_BGHLV18_38/Aligned.sortedByCoord.out.bam		ENCORE2	14925
NUSAP1_BGHLV18_38_Signal.Unique.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	963					GRCh38	V40	NUSAP1_BGHLV18_38/Aligned.sortedByCoord.out.bam		ENCORE2	14963
NUSAP1_BGHLV18_38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	963					GRCh38	V40	NUSAP1_BGHLV18_38/Aligned.sortedByCoord.out.bam		ENCORE2	15001
NUSAP1_BGHLV18_38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set18/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	963					GRCh38	V40	NUSAP1_BGHLV18_38/Aligned.sortedByCoord.out.bam		ENCORE2	15039
NUSAP1_BGHLV18_38_quant.sf	ENCODE_DATA/set18/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	963					GRCh38	V40	NUSAP1_BGHLV18_38_GAGTGG_L003_R1_001.fastq.gz,NUSAP1_BGHLV18_38_GAGTGG_L003_R2_001.fastq.gz		ENCORE2	15077