KPNB1 RNA-Seq in K562

General Information


RBP	KPNB1
Cell_Line	K562
Method	CRISPR
Exp_Name	KPNB1-BGKcLV13-K562
ENCODE_series_ID	ENCSR916AEX
Batch_ID	BGKcLV13
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR667FZF
ENCODE_CN_Exp_ID	ENCSR712CQC
Rep1	KPNB1-BGKcLV13-45
Rep2	KPNB1-BGKcLV13-46
CN1	NT-BGKcLV13-1
CN2	NT-BGKcLV13-2
Rep1_qPCR	71.4
Rep2_qPCR	61.4
Rep1_WB	82.4
Rep2_WB	84.8
Antibody Cat#	MA3-070
Antibody Lot#	LOT# SL259850
Antibody DCC ID	ENCAB340RAJ
Status	Released
Project	ENCODE4
ID	177

Experiment Information (Status: Released)

	BGKcLV13-45	BGKcLV13-45	BGKcLV13-45	BGKcLV13-46	BGKcLV13-46	BGKcLV13-46
idx	490	490	0	491	491	0
TRCN#_or_BGC#	BGC#0000325	BGC#0000325	BGC#0000325	BGC#0000325	BGC#0000325	BGC#0000325
shRNA_or_gRNA_sequence	ATCTTGGCAAATATAACCGA	ATCTTGGCAAATATAACCGA	ATCTTGGCAAATATAACCGA	ATCTTGGCAAATATAACCGA	ATCTTGGCAAATATAACCGA	ATCTTGGCAAATATAACCGA
PAM	tgg	tgg	tgg	tgg	tgg	tgg
Name	KPNB1_84	KPNB1_84	KPNB1_84	KPNB1_84	KPNB1_84	KPNB1_84
Sample_ID	BGKcLV13-45	BGKcLV13-45	BGKcLV13-45	BGKcLV13-46	BGKcLV13-46	BGKcLV13-46
transduction_Date	11/28/18	11/28/18	11/28/18	11/28/18	11/28/18	11/28/18
days	Day 6	Day 6	Day 6	Day 6	Day 6	Day 6
RBP_name	KPNB1	KPNB1	KPNB1	KPNB1	KPNB1	KPNB1
qPCR_result	71.4	71.4	71.4	61.4	61.4	61.4
Ave_qPCR	66.4	66.4	66.4
RT-qPCR_primer-F	tgcactcctgaactcattgg	tgcactcctgaactcattgg	tgcactcctgaactcattgg
RT-qPCR_primer-R	tctggacactgtgtggcttc	tctggacactgtgtggcttc	tctggacactgtgtggcttc
protein_conc	4381	4381	4381	3873	3873	3873
WB_result	82.4	71.7	67.5	84.8	60.71	62.6309
Ave_WB	83.6	66.2
WB_DONE_date	12/17/18	6/27/23	2/2/24	wes
MW	91KD	91KD	91KD
IP	Rabbit
antibody_Cat#	MA3-070	60769S	51186S	LOT# SL259850	LOT # 1	LOT # 1
Antibody DCC ID	ENCAB340RAJ
submitted_to_DCC_date	3/11/19	1/8/24
Rep1_TPM	382.1	0	0	0	0	0
Rep2_TPM	347.2	0	0	0	0	0
Action	Ready			Ready
Library_start_date	03/18/19			03/18/19
repeat_library
Note
ID	4594	4596	4598	4595	4597	4599

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
KPNB1	Product_ID: 60769S Lot_ID: 1 Source: Cell Signaling Technology Target Name: KPNB1-human

Experiment Status

	BGKcLV13-45	BGKcLV13-46
Sample_ID	BGKcLV13-45	BGKcLV13-46
Sample Name	KPNB1-BGKcLV13-45	KPNB1-BGKcLV13-46
Sample Name	KPNB1-BGKcLV13-45	KPNB1-BGKcLV13-46
RBP	KPNB1	KPNB1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2905	2906

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV13-45	BGKcLV13-46
Sample #	59	60
Sample Name	KPNB1-BGKcLV13-45	KPNB1-BGKcLV13-46
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	1-C2	1-D2
Tecan	43.16	56.02
Tecan_date	2019-03-18	2019-03-18
Size_bp	286	285
Peak_Molarity	37.90	47.10
libSampleQC_DNA_Well	DNA_Library_set42/set1/C8.png	DNA_Library_set42/set1/D8.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set42/set1/C8.png	RNA_Library_set42/set1/D8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGKcLV13-45	BGKcLV13-46
RBP	KPNB1	KPNB1
Batch_ID	BGKcLV13	BGKcLV13
WB_result	82.400	84.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	59	60

Sequencing Information

	BGKcLV13-45	BGKcLV13-46
Sample_ID	BGKcLV13-45	BGKcLV13-46
Sample Name	KPNB1-BGKcLV13-45	KPNB1-BGKcLV13-46
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	76,136,022	51,118,228
total_aligned_reads	74,170,560	48,961,456
unique_aligned_reads	67,286,940	44,387,276
percent_uniqueAligned	0.88377	0.86833
correlation_replicates	0.997957	0.997957
spikein_reads	88,104	57,906
percent_spikeins	0.00116	0.00113
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	33	34

Data Submission Information

	BGKcLV13-45	BGKcLV13-45	BGKcLV13-45	BGKcLV13-45	BGKcLV13-45	BGKcLV13-45	BGKcLV13-46	BGKcLV13-46	BGKcLV13-46	BGKcLV13-46
ENCODE_alias	brenton-graveley:KPNB1-BGKcLV13	brenton-graveley:KPNB1-BGKcLV13-45	brenton-graveley:L-KPNB1-BGKcLV13-45	brenton-graveley:KPNB1-BGKcLV13-45_GATCTATC+ATGAGGCT_HK3H2DSXX_S59_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:KPNB1-BGKcLV13-45_GATCTATC+ATGAGGCT_HK3H2DSXX_S59_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:KPNB1-BGKcLV13-K562	brenton-graveley:KPNB1-BGKcLV13-46	brenton-graveley:L-KPNB1-BGKcLV13-46	brenton-graveley:KPNB1-BGKcLV13-46_AGCTCGCT+GCAGAATC_HK3H2DSXX_S60_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:KPNB1-BGKcLV13-46_AGCTCGCT+GCAGAATC_HK3H2DSXX_S60_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR667FZF	ENCBS488XRL	ENCLB876JWM	ENCFF304BOT	ENCFF400GAJ	ENCSR916AEX	ENCBS352MSE	ENCLB938DOP	ENCFF625XBT	ENCFF937GQM
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	BGKcLV13-45	BGKcLV13-45	BGKcLV13-45	BGKcLV13-45	BGKcLV13-45	BGKcLV13-45	BGKcLV13-46	BGKcLV13-46	BGKcLV13-46	BGKcLV13-46
Sample Name	KPNB1-BGKcLV13-45	KPNB1-BGKcLV13-45	KPNB1-BGKcLV13-45	KPNB1-BGKcLV13-45	KPNB1-BGKcLV13-45	KPNB1-BGKcLV13-45	KPNB1-BGKcLV13-46	KPNB1-BGKcLV13-46	KPNB1-BGKcLV13-46	KPNB1-BGKcLV13-46
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-BGKcLV13-45.pdf	L-KPNB1-BGKcLV13-45.pdf				KPNB1-BGKcLV13-46.pdf	L-KPNB1-BGKcLV13-46.pdf
ID	780	855	937	983	1065	7245	856	938	984	1066

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-BGKcLV13-45_GATCTATC+ATGAGGCT_HK3H2DSXX_S59_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	33	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	365
KPNB1-BGKcLV13-45_GATCTATC+ATGAGGCT_HK3H2DSXX_S59_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	33	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	447
KPNB1-BGKcLV13-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	33					GRCh38	V40	KPNB1-BGKcLV13-45_GATCTATC+ATGAGGCT_HK3H2DSXX_S59_L004_R1_001.filtered.trimmed.paired.fastq.gz,KPNB1-BGKcLV13-45_GATCTATC+ATGAGGCT_HK3H2DSXX_S59_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23704
KPNB1-BGKcLV13-45_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	33					GRCh38	V40	KPNB1-BGKcLV13-45/Aligned.sortedByCoord.out.bam		ENCORE2	23786
KPNB1-BGKcLV13-45_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	33					GRCh38	V40	KPNB1-BGKcLV13-45/Aligned.sortedByCoord.out.bam		ENCORE2	23868
KPNB1-BGKcLV13-45_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	33					GRCh38	V40	KPNB1-BGKcLV13-45/Aligned.sortedByCoord.out.bam		ENCORE2	23950
KPNB1-BGKcLV13-45_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	33					GRCh38	V40	KPNB1-BGKcLV13-45/Aligned.sortedByCoord.out.bam		ENCORE2	24032
KPNB1-BGKcLV13-45_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	33					GRCh38	V40	KPNB1-BGKcLV13-45_GATCTATC+ATGAGGCT_HK3H2DSXX_S59_L004_R1_001.filtered.trimmed.paired.fastq.gz,KPNB1-BGKcLV13-45_GATCTATC+ATGAGGCT_HK3H2DSXX_S59_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24114
KPNB1-BGKcLV13-46_AGCTCGCT+GCAGAATC_HK3H2DSXX_S60_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	34	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	366
KPNB1-BGKcLV13-46_AGCTCGCT+GCAGAATC_HK3H2DSXX_S60_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	34	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	448
KPNB1-BGKcLV13-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	34					GRCh38	V40	KPNB1-BGKcLV13-46_AGCTCGCT+GCAGAATC_HK3H2DSXX_S60_L004_R1_001.filtered.trimmed.paired.fastq.gz,KPNB1-BGKcLV13-46_AGCTCGCT+GCAGAATC_HK3H2DSXX_S60_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23705
KPNB1-BGKcLV13-46_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	34					GRCh38	V40	KPNB1-BGKcLV13-46/Aligned.sortedByCoord.out.bam		ENCORE2	23787
KPNB1-BGKcLV13-46_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	34					GRCh38	V40	KPNB1-BGKcLV13-46/Aligned.sortedByCoord.out.bam		ENCORE2	23869
KPNB1-BGKcLV13-46_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	34					GRCh38	V40	KPNB1-BGKcLV13-46/Aligned.sortedByCoord.out.bam		ENCORE2	23951
KPNB1-BGKcLV13-46_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	34					GRCh38	V40	KPNB1-BGKcLV13-46/Aligned.sortedByCoord.out.bam		ENCORE2	24033
KPNB1-BGKcLV13-46_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	34					GRCh38	V40	KPNB1-BGKcLV13-46_AGCTCGCT+GCAGAATC_HK3H2DSXX_S60_L004_R1_001.filtered.trimmed.paired.fastq.gz,KPNB1-BGKcLV13-46_AGCTCGCT+GCAGAATC_HK3H2DSXX_S60_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24115