NCBP2 RNA-Seq in HepG2

General Information


RBP	NCBP2
Cell_Line	HepG2
Method	shRNA
Exp_Name	NCBP2-BGHLV12-HepG2
ENCODE_series_ID	ENCSR087ZNB
Batch_ID	BGHLV12
Pool ID	Pool-140701A
Local_Set_Name	set12
ENCODE_KD_Exp_ID	ENCSR030ARO
ENCODE_CN_Exp_ID	ENCSR603TCV
Rep1	NCBP2-BGHLV12-51
Rep2	NCBP2-BGHLV12-52
CN1	NT-BGHLV12-93
CN2	NT-BGHLV12-94
Rep1_qPCR	66.8
Rep2_qPCR	69.1
Rep1_WB	55.4
Rep2_WB	41.5
Antibody Cat#	A302-553A
Antibody Lot#	A302-553A
Antibody DCC ID	ENCAB039KCI
Status	Released
Project	ENCODE3
ID	346

Experiment Information (Status: Released)

	BGHLV12-51	BGHLV12-52
idx	51	52
TRCN#_or_BGC#	TRCN0000059994	TRCN0000059994
shRNA_or_gRNA_sequence	GTGACAATGAAGAACAAGAAA	GTGACAATGAAGAACAAGAAA
PAM
Name	NCBP2	NCBP2
Sample_ID	BGHLV12-51	BGHLV12-52
transduction_Date	5/15/2014	5/15/2014
days
RBP_name	NCBP2	NCBP2
qPCR_result	66.8	69.1
Ave_qPCR	68.0
RT-qPCR_primer-F	TTTAAGGAGGGCAGGCAATA
RT-qPCR_primer-R	CTCCTCTCCCAGCATCGTAG
protein_conc	2822	2407
WB_result	55.4	41.5
Ave_WB	48.4
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	67.5	0
Rep2_TPM	63	0
Action
Library_start_date	6/12/2014	6/12/2014
repeat_library
Note
ID	2098	2099

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

	BGHLV12-51	BGHLV12-52
Sample_ID	BGHLV12-51	BGHLV12-52
Sample Name	NCBP2-BGHLV12-51	NCBP2-BGHLV12-52
Sample Name	NCBP2-BGHLV12-51	NCBP2-BGHLV12-52
RBP	NCBP2	NCBP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-09-25	2014-09-25
Project	ENCODE3	ENCODE3
Note
ID	406	407

Library-Prep
Sequencing

Library-Prep Information

	BGHLV12-51	BGHLV12-52
Sample #
Sample Name	NCBP2-BGHLV12-51	NCBP2-BGHLV12-52
Sample_Name_Alias	NCBP2-BGHLV12-51	NCBP2-BGHLV12-52
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-06-12	2014-06-12
Lib_ID	Lib-140612	Lib-140612
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV12/set3/G1.png	DNA_Library_LV12/set3/H1.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_LV12/set1/G5.png	RNA_Library_LV12/set1/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date
Sample_ID	BGHLV12-51	BGHLV12-52
RBP	NCBP2	NCBP2
Batch_ID	BGHLV12	BGHLV12
WB_result	55.400	41.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2030	2031

Sequencing Information

	BGHLV12-51	BGHLV12-52
Sample_ID	BGHLV12-51	BGHLV12-52
Sample Name	NCBP2-BGHLV12-51	NCBP2-BGHLV12-52
Pool ID	Pool-140701A	Pool-140701A
LocalServer_folder	set12	set12
total_reads	71,190,000	64,990,000
total_aligned_reads	65,244,850	59,503,912
unique_aligned_reads	61,717,832	56,253,150
percent_uniqueAligned	0.86695	0.86557
correlation_replicates	0.997409	0.997409
spikein_reads	297,424	406,972
percent_spikeins	0.00418	0.00626
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	730	731

Data Submission Information

	BGHLV12-51	BGHLV12-51
ENCODE_alias	brenton-graveley:NCBP2-BGHLV12	brenton-graveley:NCBP2-BGHLV12-HepG2
ENCODE_accession	ENCSR030ARO	ENCSR087ZNB
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV12-51	BGHLV12-51
Sample Name	NCBP2-BGHLV12-51	NCBP2-BGHLV12-51
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-09-24	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2752	6818

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-BGHLV12-51_ATGTCA_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	730	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12787
NCBP2-BGHLV12-51_ATGTCA_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	730	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12856
NCBP2-BGHLV12-51_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	730					GRCh38	V40	NCBP2-BGHLV12-51_ATGTCA_L006_R1_001.fastq.gz,NCBP2-BGHLV12-51_ATGTCA_L006_R2_001.fastq.gz		ENCORE2	12926
NCBP2-BGHLV12-51_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	730					GRCh38	V40	NCBP2-BGHLV12-51/Aligned.sortedByCoord.out.bam		ENCORE2	12996
NCBP2-BGHLV12-51_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	730					GRCh38	V40	NCBP2-BGHLV12-51/Aligned.sortedByCoord.out.bam		ENCORE2	13066
NCBP2-BGHLV12-51_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	730					GRCh38	V40	NCBP2-BGHLV12-51/Aligned.sortedByCoord.out.bam		ENCORE2	13136
NCBP2-BGHLV12-51_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	730					GRCh38	V40	NCBP2-BGHLV12-51/Aligned.sortedByCoord.out.bam		ENCORE2	13206
NCBP2-BGHLV12-51_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	730					GRCh38	V40	NCBP2-BGHLV12-51_ATGTCA_L006_R1_001.fastq.gz,NCBP2-BGHLV12-51_ATGTCA_L006_R2_001.fastq.gz		ENCORE2	13276
NCBP2-BGHLV12-52_CCGTCC_L006_R1_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	731	HiSeq2000	100	paired-ended	1				NT-BGHLV12-01_ATCACG_L001_R1_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R1_001.fastq.gz	ENCODE3	12788
NCBP2-BGHLV12-52_CCGTCC_L006_R2_001.fastq.gz	ENCODE_DATA/set12/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	731	HiSeq2000	100	paired-ended	2				NT-BGHLV12-01_ATCACG_L001_R2_001.fastq.gz,NT-BGHLV12-02_CGATGT_L001_R2_001.fastq.gz	ENCODE3	12857
NCBP2-BGHLV12-52_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	731					GRCh38	V40	NCBP2-BGHLV12-52_CCGTCC_L006_R1_001.fastq.gz,NCBP2-BGHLV12-52_CCGTCC_L006_R2_001.fastq.gz		ENCORE2	12927
NCBP2-BGHLV12-52_Signal.Unique.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	731					GRCh38	V40	NCBP2-BGHLV12-52/Aligned.sortedByCoord.out.bam		ENCORE2	12997
NCBP2-BGHLV12-52_Signal.Unique.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	731					GRCh38	V40	NCBP2-BGHLV12-52/Aligned.sortedByCoord.out.bam		ENCORE2	13067
NCBP2-BGHLV12-52_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	731					GRCh38	V40	NCBP2-BGHLV12-52/Aligned.sortedByCoord.out.bam		ENCORE2	13137
NCBP2-BGHLV12-52_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set12/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	731					GRCh38	V40	NCBP2-BGHLV12-52/Aligned.sortedByCoord.out.bam		ENCORE2	13207
NCBP2-BGHLV12-52_quant.sf	ENCODE_DATA/set12/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	731					GRCh38	V40	NCBP2-BGHLV12-52_CCGTCC_L006_R1_001.fastq.gz,NCBP2-BGHLV12-52_CCGTCC_L006_R2_001.fastq.gz		ENCORE2	13277