C1QBP RNA-Seq in HepG2

General Information


RBP	C1QBP
Cell_Line	HepG2
Method	CRISPR
Exp_Name	C1QBP-BGHcLV27-HepG2
ENCODE_series_ID	ENCSR015QNL
Batch_ID	BGHcLV27
Pool ID	Pool-210908
Local_Set_Name	set48_H
ENCODE_KD_Exp_ID	ENCSR944KLG
ENCODE_CN_Exp_ID	ENCSR650TTU
Rep1	C1QBP-BGHcLV27-31
Rep2	C1QBP-BGHcLV27-32
CN1	NT-BGHcLV27-1
CN2	NT-BGHcLV27-2
Rep1_qPCR	48.5
Rep2_qPCR	48.2
Rep1_WB	56.2
Rep2_WB	56.2
Antibody Cat#	A302-861A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB868FMO
Status	Released
Project	ENCODE4
ID	812

Experiment Information (Status: Released)

	BGHcLV27-31	BGHcLV27-31	BGHcLV27-32	BGHcLV27-32
idx	797	797	798	798
TRCN#_or_BGC#	BGC#0000655	BGC#0000655	BGC#0000655	BGC#0000655
shRNA_or_gRNA_sequence	CTTCCATTCAGACTCGCCAG	CTTCCATTCAGACTCGCCAG	CTTCCATTCAGACTCGCCAG	CTTCCATTCAGACTCGCCAG
PAM	TGG	TGG	TGG	TGG
Name	C1QBP_89	C1QBP_89	C1QBP_89	C1QBP_89
Sample_ID	BGHcLV27-31	BGHcLV27-31	BGHcLV27-32	BGHcLV27-32
transduction_Date	5/18/21	5/18/21	5/18/21	5/18/21
days	D6	D6	D6	D6
RBP_name	C1QBP	C1QBP	C1QBP	C1QBP
qPCR_result	48.5	48.5	48.2	48.2
Ave_qPCR	48.4	48.4
RT-qPCR_primer-F	cccaatttcgtggttgaagt	cccaatttcgtggttgaagt
RT-qPCR_primer-R	gcctcgtcttcttgtccaac	gcctcgtcttcttgtccaac
protein_conc	3348	3348	3032	3032
WB_result	56.2	54.1	56.2	60.7
Ave_WB	56.2	57.4
WB_DONE_date	6/1/21	2/22/22
MW	31kDa	31kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A302-861A	A302-862A	LOT# 1	LOT# 1
Antibody DCC ID	ENCAB868FMO	ENCAB952HPS	10/22/21	7/31/24
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/03/21		09/03/21
repeat_library
Note
ID	6962	6964	6963	6965

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
C1QBP	Product_ID: A302-861A Lot_ID: 1 Source: Bethyl Labs Target Name: C1QBP-human
C1QBP	Product_ID: A302-862A Lot_ID: 1 Source: Bethyl Labs Target Name: C1QBP-human

Experiment Status

	BGHcLV27-31	BGHcLV27-32
Sample_ID	BGHcLV27-31	BGHcLV27-32
Sample Name
Sample Name	C1QBP-BGHcLV27-31	C1QBP-BGHcLV27-32
RBP	C1QBP	C1QBP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9687	9688

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV27-31	BGHcLV27-32
Sample #	91	92
Sample Name	C1QBP-BGHcLV27-31	C1QBP-BGHcLV27-32
Sample_Name_Alias
Index Well Position	G09	H09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-02	2021-09-02
Lib_ID	Lib-210902	Lib-210902
Tecan_Location
Tecan
Tecan_date
Size_bp	310	289
Peak_Molarity	132.00	148.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set2/G8.png	DNA_Library_set48-49/set2/H8.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set48-49/set1/A9.png	RNA_Library_set48-49/set1/B9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-08	2021-09-08
Sample_ID	BGHcLV27-31	BGHcLV27-32
RBP	C1QBP	C1QBP
Batch_ID	BGHcLV27	BGHcLV27
WB_result	56.200	56.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1650	1651

Sequencing Information

	BGHcLV27-31	BGHcLV27-32
Sample_ID	BGHcLV27-31	BGHcLV27-32
Sample Name	C1QBP-BGHcLV27-31	C1QBP-BGHcLV27-32
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_H	set48_H
total_reads	85,633,648	47,091,036
total_aligned_reads	75,203,140	40,194,928
unique_aligned_reads	70,722,724	37,853,024
percent_uniqueAligned	0.82588	0.80383
correlation_replicates	0.991432	0.991432
spikein_reads	20,206	9,032
percent_spikeins	0.00024	0.00019
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1801	1802

Data Submission Information

	BGHcLV27-31	BGHcLV27-31	BGHcLV27-31	BGHcLV27-31	BGHcLV27-31	BGHcLV27-31	BGHcLV27-32	BGHcLV27-32	BGHcLV27-32	BGHcLV27-32
ENCODE_alias	brenton-graveley:C1QBP-BGHcLV27	brenton-graveley:C1QBP-BGHcLV27-31	brenton-graveley:L-C1QBP-BGHcLV27-31	brenton-graveley:C1QBP-BGHcLV27-31_S71_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:C1QBP-BGHcLV27-31_S71_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:C1QBP-BGHcLV27-HepG2	brenton-graveley:C1QBP-BGHcLV27-32	brenton-graveley:L-C1QBP-BGHcLV27-32	brenton-graveley:C1QBP-BGHcLV27-32_S72_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:C1QBP-BGHcLV27-32_S72_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR944KLG	ENCBS097DNB	ENCLB144NTT	ENCFF356MZB	ENCFF986JMB	ENCSR015QNL	ENCBS530FWA	ENCLB455OAS	ENCFF992JQB	ENCFF599VKY
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	BGHcLV27-31	BGHcLV27-31	BGHcLV27-31	BGHcLV27-31	BGHcLV27-31	BGHcLV27-31	BGHcLV27-32	BGHcLV27-32	BGHcLV27-32	BGHcLV27-32
Sample Name	C1QBP-BGHcLV27-31	C1QBP-BGHcLV27-31	C1QBP-BGHcLV27-31	C1QBP-BGHcLV27-31	C1QBP-BGHcLV27-31	C1QBP-BGHcLV27-31	C1QBP-BGHcLV27-32	C1QBP-BGHcLV27-32	C1QBP-BGHcLV27-32	C1QBP-BGHcLV27-32
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48H_biosample_protocol	LV48H_library_protocol				LV48H_biosample_protocol	LV48H_library_protocol
protocol_URL		C1QBP-BGHcLV27-31.pdf	L-C1QBP-BGHcLV27-31.pdf				C1QBP-BGHcLV27-32.pdf	L-C1QBP-BGHcLV27-32.pdf
ID	3440	3514	3648	3782	3916	7107	3515	3649	3783	3917

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
C1QBP-BGHcLV27-31_S71_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1801	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3792
C1QBP-BGHcLV27-31_S71_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1801	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3818
C1QBP-BGHcLV27-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1801					GRCh38	V40	C1QBP-BGHcLV27-31_S71_L003_R1_001.filtered.trimmed.paired.fastq.gz,C1QBP-BGHcLV27-31_S71_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25479
C1QBP-BGHcLV27-31_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1801					GRCh38	V40	C1QBP-BGHcLV27-31_S71_L003_R1_001.filtered.trimmed.paired.fastq.gz,C1QBP-BGHcLV27-31_S71_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25505
C1QBP-BGHcLV27-31_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1801					GRCh38	V40	C1QBP-BGHcLV27-31/Aligned.sortedByCoord.out.bam		ENCORE2	26443
C1QBP-BGHcLV27-31_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1801					GRCh38	V40	C1QBP-BGHcLV27-31/Aligned.sortedByCoord.out.bam		ENCORE2	26469
C1QBP-BGHcLV27-31_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1801					GRCh38	V40	C1QBP-BGHcLV27-31/Aligned.sortedByCoord.out.bam		ENCORE2	26495
C1QBP-BGHcLV27-31_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1801					GRCh38	V40	C1QBP-BGHcLV27-31/Aligned.sortedByCoord.out.bam		ENCORE2	26521
C1QBP-BGHcLV27-32_S72_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1802	NovaSeq6000	100	paired-ended	1				NT-BGHcLV27-1_S57_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3793
C1QBP-BGHcLV27-32_S72_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1802	NovaSeq6000	100	paired-ended	2				NT-BGHcLV27-1_S57_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV27-2_S58_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3819
C1QBP-BGHcLV27-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1802					GRCh38	V40	C1QBP-BGHcLV27-32_S72_L003_R1_001.filtered.trimmed.paired.fastq.gz,C1QBP-BGHcLV27-32_S72_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25480
C1QBP-BGHcLV27-32_quant.sf	ENCODE_DATA/set48_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1802					GRCh38	V40	C1QBP-BGHcLV27-32_S72_L003_R1_001.filtered.trimmed.paired.fastq.gz,C1QBP-BGHcLV27-32_S72_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25506
C1QBP-BGHcLV27-32_Signal.Unique.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1802					GRCh38	V40	C1QBP-BGHcLV27-32/Aligned.sortedByCoord.out.bam		ENCORE2	26444
C1QBP-BGHcLV27-32_Signal.Unique.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1802					GRCh38	V40	C1QBP-BGHcLV27-32/Aligned.sortedByCoord.out.bam		ENCORE2	26470
C1QBP-BGHcLV27-32_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1802					GRCh38	V40	C1QBP-BGHcLV27-32/Aligned.sortedByCoord.out.bam		ENCORE2	26496
C1QBP-BGHcLV27-32_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1802					GRCh38	V40	C1QBP-BGHcLV27-32/Aligned.sortedByCoord.out.bam		ENCORE2	26522