WBP11 RNA-Seq in HepG2

General Information


RBP	WBP11
Cell_Line	HepG2
Method	CRISPR
Exp_Name	WBP11-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR393ZEG
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR484QEX
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	WBP11-BGHcLV22-63
Rep2	WBP11-BGHcLV22-64
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	56.1
Rep2_WB	64.4
Antibody Cat#	A304-855A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB949LDW
Status	Released
Project	ENCODE4
ID	50

Experiment Information (Status: Released)

	BGHcLV22-63	BGHcLV22-64
idx	656	657
TRCN#_or_BGC#	BGC#0000557	BGC#0000557
shRNA_or_gRNA_sequence	GAGTCGTAGAATACGTTCAA	GAGTCGTAGAATACGTTCAA
PAM	AGG	AGG
Name	WBP11_95	WBP11_95
Sample_ID	BGHcLV22-63	BGHcLV22-64
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	WBP11	WBP11
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	TGAACAGAAGAGGGCTCAACTT
RT-qPCR_primer-R	TGGCAAAGGAATACTCTCCACT
protein_conc	3461	2589
WB_result	56.1	64.4
Ave_WB	60.3
WB_DONE_date	9/17/20	JESS
MW	70kDa
IP	Rabbit / I
antibody_Cat#	A304-855A	LOT# 1
Antibody DCC ID	ENCAB949LDW
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	6811	6812

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
WBP11	Product_ID: A304-855A Lot_ID: 1 Source: Bethyl Labs Target Name: WBP11-human

Experiment Status

	BGHcLV22-63	BGHcLV22-64
Sample_ID	BGHcLV22-63	BGHcLV22-64
Sample Name
Sample Name	WBP11-BGHcLV22-63	WBP11-BGHcLV22-64
RBP	WBP11	WBP11
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7393	7394

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-63	BGHcLV22-64
Sample #	29	30
Sample Name	WBP11-BGHcLV22-63	WBP11-BGHcLV22-64
Sample_Name_Alias
Index Well Position	E04	F04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	295	284
Peak_Molarity	128.00	56.30
libSampleQC_DNA_Well	DNA_Library_set46/set1/E4.png	DNA_Library_set46/set1/F4.png
RIN	9.7	9.1
libSample_RNA_Well	RNA_Library_set46/set1/E12.png	RNA_Library_set46/set1/F12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-63	BGHcLV22-64
RBP	WBP11	WBP11
Batch_ID	BGHcLV22	BGHcLV22
WB_result	56.100	64.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1404	1405

Sequencing Information

	BGHcLV22-63	BGHcLV22-64
Sample_ID	BGHcLV22-63	BGHcLV22-64
Sample Name	WBP11-BGHcLV22-63	WBP11-BGHcLV22-64
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	225,288,912	167,426,464
total_aligned_reads	202,828,758	147,985,512
unique_aligned_reads	188,924,492	137,761,130
percent_uniqueAligned	0.83859	0.82282
correlation_replicates	0.993800	0.993800
spikein_reads	86,468	50,866
percent_spikeins	0.00038	0.00030
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	510	511

Data Submission Information

	BGHcLV22-63	BGHcLV22-63	BGHcLV22-63	BGHcLV22-63	BGHcLV22-63	BGHcLV22-63	BGHcLV22-64	BGHcLV22-64	BGHcLV22-64	BGHcLV22-64
ENCODE_alias	brenton-graveley:WBP11-BGHcLV22	brenton-graveley:WBP11-BGHcLV22-63	brenton-graveley:L-WBP11-BGHcLV22-63	brenton-graveley:WBP11-BGHcLV22-63_CCGTGAAG+ATCCACTG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:WBP11-BGHcLV22-63_CCGTGAAG+ATCCACTG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:WBP11-BGHcLV22-HepG2	brenton-graveley:WBP11-BGHcLV22-64	brenton-graveley:L-WBP11-BGHcLV22-64	brenton-graveley:WBP11-BGHcLV22-64_TTACAGGA+GCTTGTCA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:WBP11-BGHcLV22-64_TTACAGGA+GCTTGTCA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR484QEX	ENCBS287XWT	ENCLB148DMT	ENCFF385OVT	ENCFF025QPX	ENCSR393ZEG	ENCBS613BKP	ENCLB683OOU	ENCFF057IWI	ENCFF822HGU
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	BGHcLV22-63	BGHcLV22-63	BGHcLV22-63	BGHcLV22-63	BGHcLV22-63	BGHcLV22-63	BGHcLV22-64	BGHcLV22-64	BGHcLV22-64	BGHcLV22-64
Sample Name	WBP11-BGHcLV22-63	WBP11-BGHcLV22-63	WBP11-BGHcLV22-63	WBP11-BGHcLV22-63	WBP11-BGHcLV22-63	WBP11-BGHcLV22-63	WBP11-BGHcLV22-64	WBP11-BGHcLV22-64	WBP11-BGHcLV22-64	WBP11-BGHcLV22-64
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		WBP11-BGHcLV22-63.pdf	L-WBP11-BGHcLV22-63.pdf				WBP11-BGHcLV22-64.pdf	L-WBP11-BGHcLV22-64.pdf
ID	2409	2455	2519	2583	2613	7349	2456	2520	2584	2614

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
WBP11-BGHcLV22-63_CCGTGAAG+ATCCACTG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	510	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1376
WBP11-BGHcLV22-63_CCGTGAAG+ATCCACTG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	510	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1440
WBP11-BGHcLV22-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	510					GRCh38	V40	WBP11-BGHcLV22-63_CCGTGAAG+ATCCACTG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP11-BGHcLV22-63_CCGTGAAG+ATCCACTG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25279
WBP11-BGHcLV22-63_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	510					GRCh38	V40	WBP11-BGHcLV22-63_CCGTGAAG+ATCCACTG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP11-BGHcLV22-63_CCGTGAAG+ATCCACTG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25377
WBP11-BGHcLV22-63_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	510					GRCh38	V40	WBP11-BGHcLV22-63/Aligned.sortedByCoord.out.bam		ENCORE2	26027
WBP11-BGHcLV22-63_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	510					GRCh38	V40	WBP11-BGHcLV22-63/Aligned.sortedByCoord.out.bam		ENCORE2	26057
WBP11-BGHcLV22-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	510					GRCh38	V40	WBP11-BGHcLV22-63/Aligned.sortedByCoord.out.bam		ENCORE2	26087
WBP11-BGHcLV22-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	510					GRCh38	V40	WBP11-BGHcLV22-63/Aligned.sortedByCoord.out.bam		ENCORE2	26117
WBP11-BGHcLV22-64_TTACAGGA+GCTTGTCA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	511	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1377
WBP11-BGHcLV22-64_TTACAGGA+GCTTGTCA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	511	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1441
WBP11-BGHcLV22-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	511					GRCh38	V40	WBP11-BGHcLV22-64_TTACAGGA+GCTTGTCA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP11-BGHcLV22-64_TTACAGGA+GCTTGTCA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25280
WBP11-BGHcLV22-64_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	511					GRCh38	V40	WBP11-BGHcLV22-64_TTACAGGA+GCTTGTCA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,WBP11-BGHcLV22-64_TTACAGGA+GCTTGTCA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25378
WBP11-BGHcLV22-64_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	511					GRCh38	V40	WBP11-BGHcLV22-64/Aligned.sortedByCoord.out.bam		ENCORE2	26028
WBP11-BGHcLV22-64_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	511					GRCh38	V40	WBP11-BGHcLV22-64/Aligned.sortedByCoord.out.bam		ENCORE2	26058
WBP11-BGHcLV22-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	511					GRCh38	V40	WBP11-BGHcLV22-64/Aligned.sortedByCoord.out.bam		ENCORE2	26088
WBP11-BGHcLV22-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	511					GRCh38	V40	WBP11-BGHcLV22-64/Aligned.sortedByCoord.out.bam		ENCORE2	26118