CRKL RNA-Seq in HepG2

General Information


RBP	CRKL
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CRKL-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CRKL-BGHcLV43-11
Rep2	CRKL-BGHcLV43-12
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	16.7
Rep2_qPCR	36.7
Rep1_WB	87.5
Rep2_WB	89.4
Antibody Cat#	38710S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1572

Experiment Information (Status: Submitting)

	BGHcLV43-11	BGHcLV43-12
idx	1379	1380
TRCN#_or_BGC#	BGC#0001123	BGC#0001123
shRNA_or_gRNA_sequence	GTCCGAGGAGTCGAACCTGG	GTCCGAGGAGTCGAACCTGG
PAM	CGG	CGG
Name	CRKL_91	CRKL_91
Sample_ID	BGHcLV43-11	BGHcLV43-12
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	CRKL	CRKL
qPCR_result	16.7	36.7
Ave_qPCR	26.7
RT-qPCR_primer-F	taagatcggggaccaggaat
RT-qPCR_primer-R	ggttgggtgctgagacagat
protein_conc	3099	3339
WB_result	87.5	89.4
Ave_WB	88.5
WB_DONE_date	6/13/24
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	9630	9631

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

	BGHcLV43-11	BGHcLV43-12
Sample_ID	BGHcLV43-11	BGHcLV43-12
Sample Name
Sample Name	CRKL-BGHcLV43-11	CRKL-BGHcLV43-12
RBP	CRKL	CRKL
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13234	13235

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-11	BGHcLV43-12
Sample #	7	8
Sample Name	CRKL-BGHcLV43-11	CRKL-BGHcLV43-12
Sample_Name_Alias
Index Well Position	G06	H06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	288	293
Peak_Molarity	72.30	68.60
libSampleQC_DNA_Well	DNA_Library_set74/set1/G1.png	DNA_Library_set74/set1/H1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/C7.png	RNA_Library_set74/set1/D7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-11	BGHcLV43-12
RBP	CRKL	CRKL
Batch_ID	BGHcLV43	BGHcLV43
WB_result	87.500	89.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4366	4367

Sequencing Information

	BGHcLV43-11	BGHcLV43-12
Sample_ID	BGHcLV43-11	BGHcLV43-12
Sample Name	CRKL-BGHcLV43-11	CRKL-BGHcLV43-12
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	43,322,711	40,952,934
total_aligned_reads	38,769,983	37,841,262
unique_aligned_reads	36,419,237	35,499,916
percent_uniqueAligned	0.84065	0.86685
correlation_replicates	0.996196	0.996196
spikein_reads	26,608	13,592
percent_spikeins	0.00061	0.00033
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3233	3234

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-BGHcLV43-11_S97_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3233	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30524
CRKL-BGHcLV43-11_S97_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3233	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30576
CRKL-BGHcLV43-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3233					GRCh38	V40	CRKL-BGHcLV43-11_S97_L003_R1_001.filtered.trimmed.paired.fastq.gz,CRKL-BGHcLV43-11_S97_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30628
CRKL-BGHcLV43-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3233					GRCh38	V40	CRKL-BGHcLV43-11_Aligned.sortedByCoord.out.bam		ENCORE2	30680
CRKL-BGHcLV43-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3233					GRCh38	V40	CRKL-BGHcLV43-11_Aligned.sortedByCoord.out.bam		ENCORE2	30732
CRKL-BGHcLV43-11_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3233					GRCh38	V40	CRKL-BGHcLV43-11_Aligned.sortedByCoord.out.bam		ENCORE2	30784
CRKL-BGHcLV43-11_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3233					GRCh38	V40	CRKL-BGHcLV43-11_Aligned.sortedByCoord.out.bam		ENCORE2	30836
CRKL-BGHcLV43-11_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3233					GRCh38	V40	CRKL-BGHcLV43-11_S97_L003_R1_001.filtered.trimmed.paired.fastq.gz,CRKL-BGHcLV43-11_S97_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30888
CRKL-BGHcLV43-12_S98_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3234	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30525
CRKL-BGHcLV43-12_S98_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3234	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30577
CRKL-BGHcLV43-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3234					GRCh38	V40	CRKL-BGHcLV43-12_S98_L003_R1_001.filtered.trimmed.paired.fastq.gz,CRKL-BGHcLV43-12_S98_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30629
CRKL-BGHcLV43-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3234					GRCh38	V40	CRKL-BGHcLV43-12_Aligned.sortedByCoord.out.bam		ENCORE2	30681
CRKL-BGHcLV43-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3234					GRCh38	V40	CRKL-BGHcLV43-12_Aligned.sortedByCoord.out.bam		ENCORE2	30733
CRKL-BGHcLV43-12_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3234					GRCh38	V40	CRKL-BGHcLV43-12_Aligned.sortedByCoord.out.bam		ENCORE2	30785
CRKL-BGHcLV43-12_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3234					GRCh38	V40	CRKL-BGHcLV43-12_Aligned.sortedByCoord.out.bam		ENCORE2	30837
CRKL-BGHcLV43-12_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3234					GRCh38	V40	CRKL-BGHcLV43-12_S98_L003_R1_001.filtered.trimmed.paired.fastq.gz,CRKL-BGHcLV43-12_S98_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30889