CRKL RNA-Seq in K562

General Information


RBP	CRKL
Cell_Line	K562
Method	CRISPR
Exp_Name	CRKL-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	CRKL-BGKcLV42-19
Rep2	CRKL-BGKcLV42-20
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	42.2
Rep2_qPCR	44.4
Rep1_WB	87.2
Rep2_WB	84.8
Antibody Cat#	38710S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1533

Experiment Information (Status: Submitting)

	BGKcLV42-19	BGKcLV42-20
idx	0	0
TRCN#_or_BGC#	BGC#0001121	BGC#0001121
shRNA_or_gRNA_sequence	GTCCGAGGAGTCGAACCTGG	GTCCGAGGAGTCGAACCTGG
PAM	CGG	CGG
Name	CRKL_91	CRKL_91
Sample_ID	BGKcLV42-19	BGKcLV42-20
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	CRKL	CRKL
qPCR_result	42.2	44.4
Ave_qPCR	43.3
RT-qPCR_primer-F	taagatcggggaccaggaat
RT-qPCR_primer-R	ggttgggtgctgagacagat
protein_conc	2076	2373
WB_result	87.2	84.8
Ave_WB	86.0
WB_DONE_date	5/6/24
MW	39KD	TUBULIN
IP
antibody_Cat#	38710S	lot # 1
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	5779	5780

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CRKL	Product_ID: 38710S Lot_ID: 1 Source: Cell Signaling Technology Target Name: CRKL-human

Experiment Status

	BGKcLV42-19	BGKcLV42-20
Sample_ID	BGKcLV42-19	BGKcLV42-20
Sample Name
Sample Name	CRKL-BGKcLV42-19	CRKL-BGKcLV42-20
RBP	CRKL	CRKL
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13060	13061

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-19	BGKcLV42-20
Sample #	17	18
Sample Name	CRKL-BGKcLV42-19	CRKL-BGKcLV42-20
Sample_Name_Alias
Index Well Position	A03	B03
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	297	292
Peak_Molarity	83.10	99.30
libSampleQC_DNA_Well	DNA_Library_set73/set1/A3.png	DNA_Library_set73/set1/B3.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/A3.png	RNA_Library_set73/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-19	BGKcLV42-20
RBP	CRKL	CRKL
Batch_ID	BGKcLV42	BGKcLV42
WB_result	87.200	84.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4286	4287

Sequencing Information

	BGKcLV42-19	BGKcLV42-20
Sample_ID	BGKcLV42-19	BGKcLV42-20
Sample Name	CRKL-BGKcLV42-19	CRKL-BGKcLV42-20
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	95,563,636	30,845,781
total_aligned_reads	81,623,059	26,578,344
unique_aligned_reads	74,719,285	24,418,449
percent_uniqueAligned	0.78188	0.79163
correlation_replicates	0.995604	0.995604
spikein_reads	12,028	962
percent_spikeins	0.00013	0.00003
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3153	3154

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
CRKL-BGKcLV42-19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3153	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	30354
CRKL-BGKcLV42-19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3153	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	30444
CRKL-BGKcLV42-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3153					GRCh38	V40	CRKL-BGKcLV42-19_L001_R1_001.filtered.trimmed.paired.fastq.gz,CRKL-BGKcLV42-19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31286
CRKL-BGKcLV42-19_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	3153					GRCh38	V40	CRKL-BGKcLV42-19_Aligned.sortedByCoord.out.bam		ENCORE2	31376
CRKL-BGKcLV42-19_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	3153					GRCh38	V40	CRKL-BGKcLV42-19_Aligned.sortedByCoord.out.bam		ENCORE2	31466
CRKL-BGKcLV42-19_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	3153					GRCh38	V40	CRKL-BGKcLV42-19_Aligned.sortedByCoord.out.bam		ENCORE2	31556
CRKL-BGKcLV42-19_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	3153					GRCh38	V40	CRKL-BGKcLV42-19_Aligned.sortedByCoord.out.bam		ENCORE2	31646
CRKL-BGKcLV42-19_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3153					GRCh38	V40	CRKL-BGKcLV42-19_L001_R1_001.filtered.trimmed.paired.fastq.gz,CRKL-BGKcLV42-19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31736
CRKL-BGKcLV42-20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3154	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	30355
CRKL-BGKcLV42-20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3154	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	30445
CRKL-BGKcLV42-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3154					GRCh38	V40	CRKL-BGKcLV42-20_L001_R1_001.filtered.trimmed.paired.fastq.gz,CRKL-BGKcLV42-20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31287
CRKL-BGKcLV42-20_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	3154					GRCh38	V40	CRKL-BGKcLV42-20_Aligned.sortedByCoord.out.bam		ENCORE2	31377
CRKL-BGKcLV42-20_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	3154					GRCh38	V40	CRKL-BGKcLV42-20_Aligned.sortedByCoord.out.bam		ENCORE2	31467
CRKL-BGKcLV42-20_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	3154					GRCh38	V40	CRKL-BGKcLV42-20_Aligned.sortedByCoord.out.bam		ENCORE2	31557
CRKL-BGKcLV42-20_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	3154					GRCh38	V40	CRKL-BGKcLV42-20_Aligned.sortedByCoord.out.bam		ENCORE2	31647
CRKL-BGKcLV42-20_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3154					GRCh38	V40	CRKL-BGKcLV42-20_L001_R1_001.filtered.trimmed.paired.fastq.gz,CRKL-BGKcLV42-20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31737