CAB39 RNA-Seq in K562

General Information


RBP	CAB39
Cell_Line	K562
Method	CRISPR
Exp_Name	CAB39-BGKcLV42-K562
ENCODE_series_ID
Batch_ID	BGKcLV42
Pool ID	Pool-240715
Local_Set_Name	set73
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CAB39-BGKcLV42-13
Rep2	CAB39-BGKcLV42-14
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	13.4
Rep2_qPCR	21.6
Rep1_WB	57.3
Rep2_WB	66.1
Antibody Cat#	2716S
Antibody Lot#	lot # 2
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1530

Experiment Information (Status: Submitting)

	BGKcLV42-13	BGKcLV42-14
idx	0	0
TRCN#_or_BGC#	BGC#0001116	BGC#0001116
shRNA_or_gRNA_sequence	TGAGACTTCCCAAACGGGAA	TGAGACTTCCCAAACGGGAA
PAM	CGG	CGG
Name	CAB39_87	CAB39_87
Sample_ID	BGKcLV42-13	BGKcLV42-14
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	CAB39	CAB39
qPCR_result	13.4	21.6
Ave_qPCR	17.5
RT-qPCR_primer-F	aggagagcatggctgttctg
RT-qPCR_primer-R	atggcaaccagatttttgga
protein_conc	4076	3294
WB_result	57.3	66.1
Ave_WB	61.7
WB_DONE_date	5/2/24
MW	39kd
IP
antibody_Cat#	2716S	lot # 2
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	5773	5774

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CAB39	Product_ID: 2716S Lot_ID: 2 Source: Cell Signaling Technology Target Name: CAB39-human

Experiment Status

	BGKcLV42-13	BGKcLV42-14
Sample_ID	BGKcLV42-13	BGKcLV42-14
Sample Name
Sample Name	CAB39-BGKcLV42-13	CAB39-BGKcLV42-14
RBP	CAB39	CAB39
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13054	13055

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-13	BGKcLV42-14
Sample #	11	12
Sample Name	CAB39-BGKcLV42-13	CAB39-BGKcLV42-14
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-06-21	2024-06-21
Lib_ID	Lib-240621	Lib-240621
Tecan_Location
Tecan
Tecan_date
Size_bp	304	310
Peak_Molarity	80.50	74.80
libSampleQC_DNA_Well	DNA_Library_set73/set1/C2.png	DNA_Library_set73/set1/D2.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set73/set1/C2.png	RNA_Library_set73/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-13	BGKcLV42-14
RBP	CAB39	CAB39
Batch_ID	BGKcLV42	BGKcLV42
WB_result	57.300	66.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4280	4281

Sequencing Information

	BGKcLV42-13	BGKcLV42-14
Sample_ID	BGKcLV42-13	BGKcLV42-14
Sample Name	CAB39-BGKcLV42-13	CAB39-BGKcLV42-14
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	30,716,944	36,619,296
total_aligned_reads	26,819,275	31,961,716
unique_aligned_reads	24,775,991	29,507,844
percent_uniqueAligned	0.80659	0.80580
correlation_replicates	0.992807	0.992807
spikein_reads	3,218	1,110
percent_spikeins	0.00010	0.00003
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3147	3148

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
CAB39-BGKcLV42-13_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3147	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30348
CAB39-BGKcLV42-13_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3147	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30438
CAB39-BGKcLV42-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3147					GRCh38	V40	CAB39-BGKcLV42-13_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAB39-BGKcLV42-13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31280
CAB39-BGKcLV42-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3147					GRCh38	V40	CAB39-BGKcLV42-13_Aligned.sortedByCoord.out.bam		ENCORE2	31370
CAB39-BGKcLV42-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3147					GRCh38	V40	CAB39-BGKcLV42-13_Aligned.sortedByCoord.out.bam		ENCORE2	31460
CAB39-BGKcLV42-13_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3147					GRCh38	V40	CAB39-BGKcLV42-13_Aligned.sortedByCoord.out.bam		ENCORE2	31550
CAB39-BGKcLV42-13_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3147					GRCh38	V40	CAB39-BGKcLV42-13_Aligned.sortedByCoord.out.bam		ENCORE2	31640
CAB39-BGKcLV42-13_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3147					GRCh38	V40	CAB39-BGKcLV42-13_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAB39-BGKcLV42-13_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31730
CAB39-BGKcLV42-14_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3148	NovaSeq6000	100	paired-ended	1				NT-BGKcLV42-1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30349
CAB39-BGKcLV42-14_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3148	NovaSeq6000	100	paired-ended	2				NT-BGKcLV42-1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV42-2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30439
CAB39-BGKcLV42-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3148					GRCh38	V40	CAB39-BGKcLV42-14_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAB39-BGKcLV42-14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31281
CAB39-BGKcLV42-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3148					GRCh38	V40	CAB39-BGKcLV42-14_Aligned.sortedByCoord.out.bam		ENCORE2	31371
CAB39-BGKcLV42-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3148					GRCh38	V40	CAB39-BGKcLV42-14_Aligned.sortedByCoord.out.bam		ENCORE2	31461
CAB39-BGKcLV42-14_Signal.Unique.strand-.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3148					GRCh38	V40	CAB39-BGKcLV42-14_Aligned.sortedByCoord.out.bam		ENCORE2	31551
CAB39-BGKcLV42-14_Signal.Unique.strand+.bw	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3148					GRCh38	V40	CAB39-BGKcLV42-14_Aligned.sortedByCoord.out.bam		ENCORE2	31641
CAB39-BGKcLV42-14_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3148					GRCh38	V40	CAB39-BGKcLV42-14_L001_R1_001.filtered.trimmed.paired.fastq.gz,CAB39-BGKcLV42-14_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31731