NCBP1 RNA-Seq in HepG2

General Information


RBP	NCBP1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	NCBP1-BGHcLV10-HepG2
ENCODE_series_ID	ENCSR418VOT
Batch_ID	BGHcLV10
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR324GSI
ENCODE_CN_Exp_ID	ENCSR775ZWO
Rep1	NCBP1-BGHcLV10-25
Rep2	NCBP1-BGHcLV10-26
CN1	NT-BGHcLV10-1
CN2	NT-BGHcLV10-2
Rep1_qPCR	23.9
Rep2_qPCR	25.4
Rep1_WB	60.2
Rep2_WB	54.4
Antibody Cat#	RN103PW
Antibody Lot#
Antibody DCC ID	ENCAB987FLC
Status	Released
Project	ENCODE4
ID	224

Experiment Information (Status: Released)

	BGHcLV10-25	BGHcLV10-26
idx	222	223
TRCN#_or_BGC#	BGC#0000232	BGC#0000232
shRNA_or_gRNA_sequence	GCAGTCCATACCTGTAACAT	GCAGTCCATACCTGTAACAT
PAM
Name	NCBP1_51	NCBP1_51
Sample_ID	BGHcLV10-25	BGHcLV10-26
transduction_Date	4/27/18	4/27/18
days	D6	D6
RBP_name	NCBP1	NCBP1
qPCR_result	23.9	25.4
Ave_qPCR	24.7
RT-qPCR_primer-F	TTCTGTCATCTTTGCCCTGG
RT-qPCR_primer-R	TGGGACTTAATGATGCAGTGAA
protein_conc	2300	2175
WB_result	60.2	54.4
Ave_WB	57.3
WB_DONE_date	5/7/18	WES
MW	92kd
IP
antibody_Cat#	RN103PW
Antibody DCC ID	ENCAB987FLC
submitted_to_DCC_date	9/6/18
Rep1_TPM	22	0
Rep2_TPM	30	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6365	6366

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
NCBP1	Product_ID: RN103PW Lot_ID: 1 Source: MBLI Target Name: NCBP1-human

Experiment Status

	BGHcLV10-25	BGHcLV10-26
Sample_ID	BGHcLV10-25	BGHcLV10-26
Sample Name
Sample Name	NCBP1-BGHcLV10-25	NCBP1-BGHcLV10-26
RBP	NCBP1	NCBP1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6299	6300

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV10-25	BGHcLV10-26
Sample #	59	60
Sample Name	NCBP1-BGHcLV10-25	NCBP1-BGHcLV10-26
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	279	275
Peak_Molarity	68.10	49.50
libSampleQC_DNA_Well	DNA_Library_set41/set5/G8.png	DNA_Library_set41/set5/H8.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set41/set1/C8.png	RNA_Library_set41/set1/D8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV10-25	BGHcLV10-26
RBP	NCBP1	NCBP1
Batch_ID	BGHcLV10	BGHcLV10
WB_result	60.200	54.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	909	910

Sequencing Information

	BGHcLV10-25	BGHcLV10-26
Sample_ID	BGHcLV10-25	BGHcLV10-26
Sample Name	NCBP1-BGHcLV10-25	NCBP1-BGHcLV10-26
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	127,718,842	86,845,406
total_aligned_reads	121,916,186	83,630,186
unique_aligned_reads	113,963,062	78,126,964
percent_uniqueAligned	0.89230	0.89961
correlation_replicates	0.992689	0.992689
spikein_reads	347,854	148,814
percent_spikeins	0.00272	0.00171
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	315	316

Data Submission Information

	BGHcLV10-25	BGHcLV10-25	BGHcLV10-25	BGHcLV10-25	BGHcLV10-25	BGHcLV10-25	BGHcLV10-26	BGHcLV10-26	BGHcLV10-26	BGHcLV10-26
ENCODE_alias	brenton-graveley:NCBP1-BGHcLV10	brenton-graveley:NCBP1-BGHcLV10-25	brenton-graveley:L-NCBP1-BGHcLV10-25	brenton-graveley:NCBP1-BGHcLV10-25_TTGCCTAG+ACCACTTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NCBP1-BGHcLV10-25_TTGCCTAG+ACCACTTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NCBP1-BGHcLV10-HepG2	brenton-graveley:NCBP1-BGHcLV10-26	brenton-graveley:L-NCBP1-BGHcLV10-26	brenton-graveley:NCBP1-BGHcLV10-26_CCATTCGA+GTTGTCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NCBP1-BGHcLV10-26_CCATTCGA+GTTGTCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR324GSI	ENCBS460XAH	ENCLB339PUP	ENCFF492NKK	ENCFF662UHG	ENCSR418VOT	ENCBS798CLM	ENCLB085WTZ	ENCFF259XTY	ENCFF697DQP
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV10-25	BGHcLV10-25	BGHcLV10-25	BGHcLV10-25	BGHcLV10-25	BGHcLV10-25	BGHcLV10-26	BGHcLV10-26	BGHcLV10-26	BGHcLV10-26
Sample Name	NCBP1-BGHcLV10-25	NCBP1-BGHcLV10-25	NCBP1-BGHcLV10-25	NCBP1-BGHcLV10-25	NCBP1-BGHcLV10-25	NCBP1-BGHcLV10-25	NCBP1-BGHcLV10-26	NCBP1-BGHcLV10-26	NCBP1-BGHcLV10-26	NCBP1-BGHcLV10-26
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		NCBP1-BGHcLV10-25.pdf	L-NCBP1-BGHcLV10-25.pdf				NCBP1-BGHcLV10-26.pdf	L-NCBP1-BGHcLV10-26.pdf
ID	1129	1178	1248	1318	1388	7261	1179	1249	1319	1389

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
NCBP1-BGHcLV10-25_TTGCCTAG+ACCACTTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	315				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	525
NCBP1-BGHcLV10-25_TTGCCTAG+ACCACTTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	315				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	595
NCBP1-BGHcLV10-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	315	GRCh38	V40	NCBP1-BGHcLV10-25_TTGCCTAG+ACCACTTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NCBP1-BGHcLV10-25_TTGCCTAG+ACCACTTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26763
NCBP1-BGHcLV10-25_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	315	GRCh38	V40	NCBP1-BGHcLV10-25/Aligned.sortedByCoord.out.bam		ENCORE2	26833
NCBP1-BGHcLV10-25_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	315	GRCh38	V40	NCBP1-BGHcLV10-25/Aligned.sortedByCoord.out.bam		ENCORE2	26903
NCBP1-BGHcLV10-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	315	GRCh38	V40	NCBP1-BGHcLV10-25/Aligned.sortedByCoord.out.bam		ENCORE2	26973
NCBP1-BGHcLV10-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	315	GRCh38	V40	NCBP1-BGHcLV10-25/Aligned.sortedByCoord.out.bam		ENCORE2	27043
NCBP1-BGHcLV10-25_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	315	GRCh38	V40	NCBP1-BGHcLV10-25_TTGCCTAG+ACCACTTA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NCBP1-BGHcLV10-25_TTGCCTAG+ACCACTTA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27113
NCBP1-BGHcLV10-26_CCATTCGA+GTTGTCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	316				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	526
NCBP1-BGHcLV10-26_CCATTCGA+GTTGTCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	316				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	596
NCBP1-BGHcLV10-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	316	GRCh38	V40	NCBP1-BGHcLV10-26_CCATTCGA+GTTGTCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NCBP1-BGHcLV10-26_CCATTCGA+GTTGTCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26764
NCBP1-BGHcLV10-26_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	316	GRCh38	V40	NCBP1-BGHcLV10-26/Aligned.sortedByCoord.out.bam		ENCORE2	26834
NCBP1-BGHcLV10-26_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	316	GRCh38	V40	NCBP1-BGHcLV10-26/Aligned.sortedByCoord.out.bam		ENCORE2	26904
NCBP1-BGHcLV10-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	316	GRCh38	V40	NCBP1-BGHcLV10-26/Aligned.sortedByCoord.out.bam		ENCORE2	26974
NCBP1-BGHcLV10-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	316	GRCh38	V40	NCBP1-BGHcLV10-26/Aligned.sortedByCoord.out.bam		ENCORE2	27044
NCBP1-BGHcLV10-26_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	316	GRCh38	V40	NCBP1-BGHcLV10-26_CCATTCGA+GTTGTCCG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NCBP1-BGHcLV10-26_CCATTCGA+GTTGTCCG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27114