NCBP1 RNA-Seq in K562

General Information


RBP	NCBP1
Cell_Line	K562
Method	CRISPR
Exp_Name	NCBP1-BGKcLV11-K562
ENCODE_series_ID	ENCSR123SFA
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR090SBZ
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	NCBP1-BGKcLV11-61
Rep2	NCBP1-BGKcLV11-62
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	63.4
Rep2_qPCR	49.6
Rep1_WB	64.6
Rep2_WB	66.5
Antibody Cat#	RN103PW
Antibody Lot#
Antibody DCC ID	ENCAB987FLC
Status	Released
Project	ENCODE4
ID	179

Experiment Information (Status: Released)

	BGKcLV11-61	BGKcLV11-61	BGKcLV11-62	BGKcLV11-62
idx	377	0	378	0
TRCN#_or_BGC#	BGC#0000233	BGC#0000233	BGC#0000233	BGC#0000233
shRNA_or_gRNA_sequence	GCAGTCCATACCTGTAACAT	GCAGTCCATACCTGTAACAT	GCAGTCCATACCTGTAACAT	GCAGTCCATACCTGTAACAT
PAM
Name	NCBP1_51-F	NCBP1_51-F	NCBP1_51-F	NCBP1_51-F
Sample_ID	BGKcLV11-61	BGKcLV11-61	BGKcLV11-62	BGKcLV11-62
transduction_Date	8/3/18	8/3/18	8/3/18	8/3/18
days	Day 6	Day 6	Day 6	Day 6
RBP_name	NCBP1	NCBP1	NCBP1	NCBP1
qPCR_result	63.4	63.4	49.6	49.6
Ave_qPCR	56.5	56.5
RT-qPCR_primer-F	TTCTGTCATCTTTGCCCTGG	TTCTGTCATCTTTGCCCTGG
RT-qPCR_primer-R	TGGGACTTAATGATGCAGTGAA	TGGGACTTAATGATGCAGTGAA
protein_conc	3041	3041	2714	2714
WB_result	64.6	80.8	66.5	62.9
Ave_WB	65.5
WB_DONE_date	8/14/18	2/6/24	wes
MW	92kd	92kd
IP
antibody_Cat#	RN103PW	24964S		LOT# 1
Antibody DCC ID	ENCAB987FLC
submitted_to_DCC_date	2/22/19
Rep1_TPM	40.6	0	0	0
Rep2_TPM	43.8	0	0	0
Action	Ready		Ready
Library_start_date	03/13/19		03/13/19
repeat_library
Note
ID	4477	4479	4478	4480

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

	BGKcLV11-61	BGKcLV11-62
Sample_ID	BGKcLV11-61	BGKcLV11-62
Sample Name	NCBP1-BGKcLV11-61	NCBP1-BGKcLV11-62
Sample Name	NCBP1-BGKcLV11-61	NCBP1-BGKcLV11-62
RBP	NCBP1	NCBP1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2681	2682

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-61	BGKcLV11-62
Sample #	9	10
Sample Name	NCBP1-BGKcLV11-61	NCBP1-BGKcLV11-62
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	1-A2	1-B2
Tecan	35.89	53.93
Tecan_date	2019-03-13	2019-03-13
Size_bp	294	293
Peak_Molarity	50.50	133.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/A2.png	DNA_Library_set42/set1/B2.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_set42/set1/A2.png	RNA_Library_set42/set1/B2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-61	BGKcLV11-62
RBP	NCBP1	NCBP1
Batch_ID	BGKcLV11	BGKcLV11
WB_result	64.600	66.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	9	10

Sequencing Information

	BGKcLV11-61	BGKcLV11-62
Sample_ID	BGKcLV11-61	BGKcLV11-62
Sample Name	NCBP1-BGKcLV11-61	NCBP1-BGKcLV11-62
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	44,939,212	44,562,016
total_aligned_reads	42,925,748	43,070,330
unique_aligned_reads	39,291,786	39,276,312
percent_uniqueAligned	0.87433	0.88139
correlation_replicates	0.989086	0.989086
spikein_reads	83,236	31,088
percent_spikeins	0.00185	0.00070
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	37	38

Data Submission Information

	BGKcLV11-61	BGKcLV11-61	BGKcLV11-61	BGKcLV11-61	BGKcLV11-61	BGKcLV11-61	BGKcLV11-62	BGKcLV11-62	BGKcLV11-62	BGKcLV11-62
ENCODE_alias	brenton-graveley:NCBP1-BGKcLV11	brenton-graveley:NCBP1-BGKcLV11-61	brenton-graveley:L-NCBP1-BGKcLV11-61	brenton-graveley:NCBP1-BGKcLV11-61_AGTTCAGG+CCAACAGA_HK3H2DSXX_S9_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NCBP1-BGKcLV11-61_AGTTCAGG+CCAACAGA_HK3H2DSXX_S9_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NCBP1-BGKcLV11-K562	brenton-graveley:NCBP1-BGKcLV11-62	brenton-graveley:L-NCBP1-BGKcLV11-62	brenton-graveley:NCBP1-BGKcLV11-62_GACCTGAA+TTGGTGAG_HK3H2DSXX_S10_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:NCBP1-BGKcLV11-62_GACCTGAA+TTGGTGAG_HK3H2DSXX_S10_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR090SBZ	ENCBS192AQT	ENCLB426ZQB	ENCFF206UDF	ENCFF405LQL	ENCSR123SFA	ENCBS674NPD	ENCLB801CZM	ENCFF105BJJ	ENCFF700HOG
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	BGKcLV11-61	BGKcLV11-61	BGKcLV11-61	BGKcLV11-61	BGKcLV11-61	BGKcLV11-61	BGKcLV11-62	BGKcLV11-62	BGKcLV11-62	BGKcLV11-62
Sample Name	NCBP1-BGKcLV11-61	NCBP1-BGKcLV11-61	NCBP1-BGKcLV11-61	NCBP1-BGKcLV11-61	NCBP1-BGKcLV11-61	NCBP1-BGKcLV11-61	NCBP1-BGKcLV11-62	NCBP1-BGKcLV11-62	NCBP1-BGKcLV11-62	NCBP1-BGKcLV11-62
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		NCBP1-BGKcLV11-61.pdf	L-NCBP1-BGKcLV11-61.pdf				NCBP1-BGKcLV11-62.pdf	L-NCBP1-BGKcLV11-62.pdf
ID	764	823	905	987	1069	7262	824	906	988	1070

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
NCBP1-BGKcLV11-61_AGTTCAGG+CCAACAGA_HK3H2DSXX_S9_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	37	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	369
NCBP1-BGKcLV11-61_AGTTCAGG+CCAACAGA_HK3H2DSXX_S9_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	37	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	451
NCBP1-BGKcLV11-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	37					GRCh38	V40	NCBP1-BGKcLV11-61_AGTTCAGG+CCAACAGA_HK3H2DSXX_S9_L004_R1_001.filtered.trimmed.paired.fastq.gz,NCBP1-BGKcLV11-61_AGTTCAGG+CCAACAGA_HK3H2DSXX_S9_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23708
NCBP1-BGKcLV11-61_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	37					GRCh38	V40	NCBP1-BGKcLV11-61/Aligned.sortedByCoord.out.bam		ENCORE2	23790
NCBP1-BGKcLV11-61_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	37					GRCh38	V40	NCBP1-BGKcLV11-61/Aligned.sortedByCoord.out.bam		ENCORE2	23872
NCBP1-BGKcLV11-61_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	37					GRCh38	V40	NCBP1-BGKcLV11-61/Aligned.sortedByCoord.out.bam		ENCORE2	23954
NCBP1-BGKcLV11-61_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	37					GRCh38	V40	NCBP1-BGKcLV11-61/Aligned.sortedByCoord.out.bam		ENCORE2	24036
NCBP1-BGKcLV11-61_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	37					GRCh38	V40	NCBP1-BGKcLV11-61_AGTTCAGG+CCAACAGA_HK3H2DSXX_S9_L004_R1_001.filtered.trimmed.paired.fastq.gz,NCBP1-BGKcLV11-61_AGTTCAGG+CCAACAGA_HK3H2DSXX_S9_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24118
NCBP1-BGKcLV11-62_GACCTGAA+TTGGTGAG_HK3H2DSXX_S10_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	38	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	370
NCBP1-BGKcLV11-62_GACCTGAA+TTGGTGAG_HK3H2DSXX_S10_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	38	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	452
NCBP1-BGKcLV11-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	38					GRCh38	V40	NCBP1-BGKcLV11-62_GACCTGAA+TTGGTGAG_HK3H2DSXX_S10_L004_R1_001.filtered.trimmed.paired.fastq.gz,NCBP1-BGKcLV11-62_GACCTGAA+TTGGTGAG_HK3H2DSXX_S10_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23709
NCBP1-BGKcLV11-62_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	38					GRCh38	V40	NCBP1-BGKcLV11-62/Aligned.sortedByCoord.out.bam		ENCORE2	23791
NCBP1-BGKcLV11-62_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	38					GRCh38	V40	NCBP1-BGKcLV11-62/Aligned.sortedByCoord.out.bam		ENCORE2	23873
NCBP1-BGKcLV11-62_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	38					GRCh38	V40	NCBP1-BGKcLV11-62/Aligned.sortedByCoord.out.bam		ENCORE2	23955
NCBP1-BGKcLV11-62_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	38					GRCh38	V40	NCBP1-BGKcLV11-62/Aligned.sortedByCoord.out.bam		ENCORE2	24037
NCBP1-BGKcLV11-62_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	38					GRCh38	V40	NCBP1-BGKcLV11-62_GACCTGAA+TTGGTGAG_HK3H2DSXX_S10_L004_R1_001.filtered.trimmed.paired.fastq.gz,NCBP1-BGKcLV11-62_GACCTGAA+TTGGTGAG_HK3H2DSXX_S10_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24119