C1QBP RNA-Seq in K562

General Information


RBP	C1QBP
Cell_Line	K562
Method	CRISPR
Exp_Name	C1QBP-BGKcLV35-K562
ENCODE_series_ID
Batch_ID	BGKcLV35
Pool ID	Pool-220720
Local_Set_Name	set54
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	C1QBP-BGKcLV35-5
Rep2	C1QBP-BGKcLV35-6
CN1	NT-BGKcLV35-1
CN2	NT-BGKcLV35-2
Rep1_qPCR	20.5
Rep2_qPCR	31.3
Rep1_WB	56.7
Rep2_WB	52.1
Antibody Cat#	A302-861A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB868FMO
Status	Submitted
Project	ENCORE2
ID	952

Experiment Information (Status: Submitting)

	BGKcLV35-5	BGKcLV35-6
idx	1282	1283
TRCN#_or_BGC#	BGC#0000655	BGC#0000655
shRNA_or_gRNA_sequence	CTTCCATTCAGACTCGCCAG	CTTCCATTCAGACTCGCCAG
PAM	TGG	TGG
Name	C1QBP_89	C1QBP_89
Sample_ID	BGKcLV35-5	BGKcLV35-6
transduction_Date	4/28/22	4/28/22
days	D6	D6
RBP_name	C1QBP	C1QBP
qPCR_result	20.5	31.3
Ave_qPCR	25.9
RT-qPCR_primer-F	cccaatttcgtggttgaagt
RT-qPCR_primer-R	gcctcgtcttcttgtccaac
protein_conc	3380	3105
WB_result	56.7	52.1
Ave_WB	54.4
WB_DONE_date	5/12/22
MW	31kDa
IP	Rabbit / I
antibody_Cat#	A302-861A	LOT# 1
Antibody DCC ID	ENCAB868FMO
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	06/17/22	06/17/22
repeat_library
Note
ID	5426	5427

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

Experiment Status

	BGKcLV35-5	BGKcLV35-6
Sample_ID	BGKcLV35-5	BGKcLV35-6
Sample Name
Sample Name	C1QBP-BGKcLV35-5	C1QBP-BGKcLV35-6
RBP	C1QBP	C1QBP
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2023-04-14	2023-04-14
Project	ENCORE2	ENCORE2
Note
ID	10861	10862

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV35-5	BGKcLV35-6
Sample #	27	28
Sample Name	C1QBP-BGKcLV35-5	C1QBP-BGKcLV35-6
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-06-17	2022-06-17
Lib_ID	Lib-220617	Lib-220617
Tecan_Location
Tecan
Tecan_date
Size_bp	289	287
Peak_Molarity	9.94	30.70
libSampleQC_DNA_Well	DNA_Library_set54-56/set3/C8.png	DNA_Library_set54-56/set3/D8.png
RIN	9.7	10.0
libSample_RNA_Well	RNA_Library_set54-56/set2/C4.png	RNA_Library_set54-56/set2/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-06-20	2022-06-20
Sample_ID	BGKcLV35-5	BGKcLV35-6
RBP	C1QBP	C1QBP
Batch_ID	BGKcLV35	BGKcLV35
WB_result	56.700	52.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3344	3345

Sequencing Information

	BGKcLV35-5	BGKcLV35-6
Sample_ID	BGKcLV35-5	BGKcLV35-6
Sample Name	C1QBP-BGKcLV35-5	C1QBP-BGKcLV35-6
Pool ID	Pool-220720	Pool-220720
LocalServer_folder	set54	set54
total_reads	63,064,364	64,182,478
total_aligned_reads	54,459,396	60,172,314
unique_aligned_reads	49,982,172	55,039,260
percent_uniqueAligned	0.79256	0.85754
correlation_replicates	0.983730	0.983730
spikein_reads	2,524	3,408
percent_spikeins	0.00004	0.00005
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2223	2224

Data Submission Information DCC submission information was not avaliable

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-BGKcLV35-5_S29_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2223	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8480
C1QBP-BGKcLV35-5_S29_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2223	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8530
C1QBP-BGKcLV35-5_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2223					GRCh38	V40	C1QBP-BGKcLV35-5/Aligned.sortedByCoord.out.bam		ENCORE2	17726
C1QBP-BGKcLV35-5_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2223					GRCh38	V40	C1QBP-BGKcLV35-5/Aligned.sortedByCoord.out.bam		ENCORE2	17776
C1QBP-BGKcLV35-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2223					GRCh38	V40	C1QBP-BGKcLV35-5/Aligned.sortedByCoord.out.bam		ENCORE2	17826
C1QBP-BGKcLV35-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2223					GRCh38	V40	C1QBP-BGKcLV35-5/Aligned.sortedByCoord.out.bam		ENCORE2	17876
C1QBP-BGKcLV35-5_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2223					GRCh38	V40	C1QBP-BGKcLV35-5_S29_R1_001.filtered.trimmed.paired.fastq.gz,C1QBP-BGKcLV35-5_S29_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17926
C1QBP-BGKcLV35-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2223					GRCh38	V40	C1QBP-BGKcLV35-5_S29_R1_001.filtered.trimmed.paired.fastq.gz,C1QBP-BGKcLV35-5_S29_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29267
C1QBP-BGKcLV35-6_S30_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2224	NovaSeq6000	100	paired-ended	1				NT-BGKcLV35-1_S25_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8481
C1QBP-BGKcLV35-6_S30_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set54/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2224	NovaSeq6000	100	paired-ended	2				NT-BGKcLV35-1_S25_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV35-2_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8531
C1QBP-BGKcLV35-6_Signal.Unique.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2224					GRCh38	V40	C1QBP-BGKcLV35-6/Aligned.sortedByCoord.out.bam		ENCORE2	17727
C1QBP-BGKcLV35-6_Signal.Unique.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2224					GRCh38	V40	C1QBP-BGKcLV35-6/Aligned.sortedByCoord.out.bam		ENCORE2	17777
C1QBP-BGKcLV35-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2224					GRCh38	V40	C1QBP-BGKcLV35-6/Aligned.sortedByCoord.out.bam		ENCORE2	17827
C1QBP-BGKcLV35-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2224					GRCh38	V40	C1QBP-BGKcLV35-6/Aligned.sortedByCoord.out.bam		ENCORE2	17877
C1QBP-BGKcLV35-6_quant.sf	ENCODE_DATA/set54/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2224					GRCh38	V40	C1QBP-BGKcLV35-6_S30_R1_001.filtered.trimmed.paired.fastq.gz,C1QBP-BGKcLV35-6_S30_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	17927
C1QBP-BGKcLV35-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set54/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2224					GRCh38	V40	C1QBP-BGKcLV35-6_S30_R1_001.filtered.trimmed.paired.fastq.gz,C1QBP-BGKcLV35-6_S30_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29268