KPNB1 RNA-Seq in HepG2

General Information


RBP	KPNB1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	KPNB1-BGHcLV14-HepG2
ENCODE_series_ID	ENCSR994VHG
Batch_ID	BGHcLV14
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR977NJB
ENCODE_CN_Exp_ID	ENCSR750CPT
Rep1	KPNB1-BGHcLV14-47
Rep2	KPNB1-BGHcLV14-48
CN1	NT-BGHcLV14-1
CN2	NT-BGHcLV14-2
Rep1_qPCR	43.1
Rep2_qPCR	43.4
Rep1_WB	77.4
Rep2_WB	70.8
Antibody Cat#	MA3-070
Antibody Lot#	LOT# SL259850
Antibody DCC ID	ENCAB340RAJ
Status	Released
Project	ENCODE4
ID	176

Experiment Information (Status: Released)

	BGHcLV14-47	BGHcLV14-48
idx	402	403
TRCN#_or_BGC#	BGC#0000326	BGC#0000326
shRNA_or_gRNA_sequence	GCACATGAAGGAGTCGACAT	GCACATGAAGGAGTCGACAT
PAM	tgg	tgg
Name	KPNB1_93	KPNB1_93
Sample_ID	BGHcLV14-47	BGHcLV14-48
transduction_Date	12/5/18	12/5/18
days	D6	D6
RBP_name	KPNB1	KPNB1
qPCR_result	43.1	43.4
Ave_qPCR	43.3
RT-qPCR_primer-F	tgcactcctgaactcattgg
RT-qPCR_primer-R	tctggacactgtgtggcttc
protein_conc	3429	3026
WB_result	77.4	70.8
Ave_WB	74.1
WB_DONE_date	1/10/19	wes
MW	91KD
IP	Rabbit
antibody_Cat#	MA3-070	LOT# SL259850
Antibody DCC ID	ENCAB340RAJ
submitted_to_DCC_date	3/11/19
Rep1_TPM	325	0
Rep2_TPM	397	0
Action	Ready	Ready
Library_start_date	03/18/19	03/18/19
repeat_library
Note
ID	6547	6548

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
KPNB1	Product_ID: MA3-070 Lot_ID: SJ259850 Source: Thermo Fisher Target Name: KPNB1-human

Experiment Status

	BGHcLV14-47	BGHcLV14-48
Sample_ID	BGHcLV14-47	BGHcLV14-48
Sample Name	KPNB1-BGHcLV14-47	KPNB1-BGHcLV14-48
Sample Name	KPNB1-BGHcLV14-47	KPNB1-BGHcLV14-48
RBP	KPNB1	KPNB1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2985	2986

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV14-47	BGHcLV14-48
Sample #	79	80
Sample Name	KPNB1-BGHcLV14-47	KPNB1-BGHcLV14-48
Sample_Name_Alias
Index Well Position	G10	H10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	2-G2	2-H2
Tecan	51.29	42.98
Tecan_date	2019-03-18	2019-03-18
Size_bp	284	282
Peak_Molarity	50.60	37.80
libSampleQC_DNA_Well	DNA_Library_set42/set1/G10.png	DNA_Library_set42/set1/H10.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set42/set1/G10.png	RNA_Library_set42/set1/H10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGHcLV14-47	BGHcLV14-48
RBP	KPNB1	KPNB1
Batch_ID	BGHcLV14	BGHcLV14
WB_result	77.400	70.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	79	80

Sequencing Information

	BGHcLV14-47	BGHcLV14-48
Sample_ID	BGHcLV14-47	BGHcLV14-48
Sample Name	KPNB1-BGHcLV14-47	KPNB1-BGHcLV14-48
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	59,195,660	69,703,528
total_aligned_reads	55,603,522	65,712,870
unique_aligned_reads	52,383,488	61,883,336
percent_uniqueAligned	0.88492	0.88781
correlation_replicates	0.997713	0.997713
spikein_reads	39,978	56,284
percent_spikeins	0.00068	0.00081
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	31	32

Data Submission Information

	BGHcLV14-47	BGHcLV14-47	BGHcLV14-47	BGHcLV14-47	BGHcLV14-47	BGHcLV14-47	BGHcLV14-48	BGHcLV14-48	BGHcLV14-48	BGHcLV14-48
ENCODE_alias	brenton-graveley:KPNB1-BGHcLV14	brenton-graveley:KPNB1-BGHcLV14-47	brenton-graveley:L-KPNB1-BGHcLV14-47	brenton-graveley:KPNB1-BGHcLV14-47_ACAGGCGC+CTCTGCCT_HK3H2DSXX_S79_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:KPNB1-BGHcLV14-47_ACAGGCGC+CTCTGCCT_HK3H2DSXX_S79_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:KPNB1-BGHcLV14-HepG2	brenton-graveley:KPNB1-BGHcLV14-48	brenton-graveley:L-KPNB1-BGHcLV14-48	brenton-graveley:KPNB1-BGHcLV14-48_GTGAATAT+TCTCATTC_HK3H2DSXX_S80_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:KPNB1-BGHcLV14-48_GTGAATAT+TCTCATTC_HK3H2DSXX_S80_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR977NJB	ENCBS503VAO	ENCLB771WLV	ENCFF448AHS	ENCFF865PCG	ENCSR994VHG	ENCBS796JCM	ENCLB012EEU	ENCFF537DVA	ENCFF028SSM
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	BGHcLV14-47	BGHcLV14-47	BGHcLV14-47	BGHcLV14-47	BGHcLV14-47	BGHcLV14-47	BGHcLV14-48	BGHcLV14-48	BGHcLV14-48	BGHcLV14-48
Sample Name	KPNB1-BGHcLV14-47	KPNB1-BGHcLV14-47	KPNB1-BGHcLV14-47	KPNB1-BGHcLV14-47	KPNB1-BGHcLV14-47	KPNB1-BGHcLV14-47	KPNB1-BGHcLV14-48	KPNB1-BGHcLV14-48	KPNB1-BGHcLV14-48	KPNB1-BGHcLV14-48
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
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		KPNB1-BGHcLV14-47.pdf	L-KPNB1-BGHcLV14-47.pdf				KPNB1-BGHcLV14-48.pdf	L-KPNB1-BGHcLV14-48.pdf
ID	758	811	893	981	1063	7244	812	894	982	1064

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
KPNB1-BGHcLV14-47_ACAGGCGC+CTCTGCCT_HK3H2DSXX_S79_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	31	NovaSeq6000	100	paired-ended	1				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	363
KPNB1-BGHcLV14-47_ACAGGCGC+CTCTGCCT_HK3H2DSXX_S79_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	31	NovaSeq6000	100	paired-ended	2				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	445
KPNB1-BGHcLV14-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	31					GRCh38	V40	KPNB1-BGHcLV14-47_ACAGGCGC+CTCTGCCT_HK3H2DSXX_S79_L004_R1_001.filtered.trimmed.paired.fastq.gz,KPNB1-BGHcLV14-47_ACAGGCGC+CTCTGCCT_HK3H2DSXX_S79_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23702
KPNB1-BGHcLV14-47_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	31					GRCh38	V40	KPNB1-BGHcLV14-47/Aligned.sortedByCoord.out.bam		ENCORE2	23784
KPNB1-BGHcLV14-47_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	31					GRCh38	V40	KPNB1-BGHcLV14-47/Aligned.sortedByCoord.out.bam		ENCORE2	23866
KPNB1-BGHcLV14-47_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	31					GRCh38	V40	KPNB1-BGHcLV14-47/Aligned.sortedByCoord.out.bam		ENCORE2	23948
KPNB1-BGHcLV14-47_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	31					GRCh38	V40	KPNB1-BGHcLV14-47/Aligned.sortedByCoord.out.bam		ENCORE2	24030
KPNB1-BGHcLV14-47_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	31					GRCh38	V40	KPNB1-BGHcLV14-47_ACAGGCGC+CTCTGCCT_HK3H2DSXX_S79_L004_R1_001.filtered.trimmed.paired.fastq.gz,KPNB1-BGHcLV14-47_ACAGGCGC+CTCTGCCT_HK3H2DSXX_S79_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24112
KPNB1-BGHcLV14-48_GTGAATAT+TCTCATTC_HK3H2DSXX_S80_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	32	NovaSeq6000	100	paired-ended	1				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	364
KPNB1-BGHcLV14-48_GTGAATAT+TCTCATTC_HK3H2DSXX_S80_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	32	NovaSeq6000	100	paired-ended	2				NT-BGHcLV14-1_ACTCGTGT+ATTGGAAC_HK3H2DSXX_S71_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV14-2_GTCTACAC+GCCAAGGT_HK3H2DSXX_S72_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	446
KPNB1-BGHcLV14-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	32					GRCh38	V40	KPNB1-BGHcLV14-48_GTGAATAT+TCTCATTC_HK3H2DSXX_S80_L004_R1_001.filtered.trimmed.paired.fastq.gz,KPNB1-BGHcLV14-48_GTGAATAT+TCTCATTC_HK3H2DSXX_S80_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23703
KPNB1-BGHcLV14-48_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	32					GRCh38	V40	KPNB1-BGHcLV14-48/Aligned.sortedByCoord.out.bam		ENCORE2	23785
KPNB1-BGHcLV14-48_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	32					GRCh38	V40	KPNB1-BGHcLV14-48/Aligned.sortedByCoord.out.bam		ENCORE2	23867
KPNB1-BGHcLV14-48_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	32					GRCh38	V40	KPNB1-BGHcLV14-48/Aligned.sortedByCoord.out.bam		ENCORE2	23949
KPNB1-BGHcLV14-48_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	32					GRCh38	V40	KPNB1-BGHcLV14-48/Aligned.sortedByCoord.out.bam		ENCORE2	24031
KPNB1-BGHcLV14-48_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	32					GRCh38	V40	KPNB1-BGHcLV14-48_GTGAATAT+TCTCATTC_HK3H2DSXX_S80_L004_R1_001.filtered.trimmed.paired.fastq.gz,KPNB1-BGHcLV14-48_GTGAATAT+TCTCATTC_HK3H2DSXX_S80_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24113