CDK11B RNA-Seq in K562

General Information


RBP	CDK11B
Cell_Line	K562
Method	CRISPR
Exp_Name	CDK11B-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	CDK11B-BGKcLV42-15
Rep2	CDK11B-BGKcLV42-16
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	no good prmers
Rep2_qPCR
Rep1_WB	50.3
Rep2_WB	52.4
Antibody Cat#	5524S
Antibody Lot#	lot # 3
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1531

Experiment Information (Status: Submitting)

	BGKcLV42-15	BGKcLV42-16
idx	0	0
TRCN#_or_BGC#	BGC#0001118	BGC#0001118
shRNA_or_gRNA_sequence	ACGGTTCGACCGAGATTCCG	ACGGTTCGACCGAGATTCCG
PAM	GGG	GGG
Name	CDK11B_50	CDK11B_50
Sample_ID	BGKcLV42-15	BGKcLV42-16
transduction_Date	4/23/24	4/23/24
days	D6	D6
RBP_name	CDK11B	CDK11B
qPCR_result	no good prmers
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	2581	2537
WB_result	50.3	52.4
Ave_WB	51.4
WB_DONE_date	5/2/24,5/7/24
MW	110kd
IP
antibody_Cat#	5524S	lot # 3
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	5775	5776

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKcLV42-15	BGKcLV42-16
Sample_ID	BGKcLV42-15	BGKcLV42-16
Sample Name
Sample Name	CDK11B-BGKcLV42-15	CDK11B-BGKcLV42-16
RBP	CDK11B	CDK11B
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-13	2025-02-13
Project	ENCORE2	ENCORE2
Note
ID	13056	13057

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-15	BGKcLV42-16
Sample #	13	14
Sample Name	CDK11B-BGKcLV42-15	CDK11B-BGKcLV42-16
Sample_Name_Alias
Index Well Position	E02	F02
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	310	303
Peak_Molarity	95.50	73.30
libSampleQC_DNA_Well	DNA_Library_set73/set1/E2.png	DNA_Library_set73/set1/F2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/E2.png	RNA_Library_set73/set1/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-15	BGKcLV42-16
RBP	CDK11B	CDK11B
Batch_ID	BGKcLV42	BGKcLV42
WB_result	50.300	52.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4282	4283

Sequencing Information

	BGKcLV42-15	BGKcLV42-16
Sample_ID	BGKcLV42-15	BGKcLV42-16
Sample Name	CDK11B-BGKcLV42-15	CDK11B-BGKcLV42-16
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	42,343,971	36,775,135
total_aligned_reads	38,049,601	32,859,759
unique_aligned_reads	35,231,567	30,381,658
percent_uniqueAligned	0.83203	0.82615
correlation_replicates	0.998739	0.998739
spikein_reads	2,932	4,430
percent_spikeins	0.00007	0.00012
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3149	3150

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
CDK11B-BGKcLV42-15_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3149	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	30350
CDK11B-BGKcLV42-15_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3149	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	30440
CDK11B-BGKcLV42-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3149					GRCh38	V40	CDK11B-BGKcLV42-15_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK11B-BGKcLV42-15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31282
CDK11B-BGKcLV42-15_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	3149					GRCh38	V40	CDK11B-BGKcLV42-15_Aligned.sortedByCoord.out.bam		ENCORE2	31372
CDK11B-BGKcLV42-15_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	3149					GRCh38	V40	CDK11B-BGKcLV42-15_Aligned.sortedByCoord.out.bam		ENCORE2	31462
CDK11B-BGKcLV42-15_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	3149					GRCh38	V40	CDK11B-BGKcLV42-15_Aligned.sortedByCoord.out.bam		ENCORE2	31552
CDK11B-BGKcLV42-15_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	3149					GRCh38	V40	CDK11B-BGKcLV42-15_Aligned.sortedByCoord.out.bam		ENCORE2	31642
CDK11B-BGKcLV42-15_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3149					GRCh38	V40	CDK11B-BGKcLV42-15_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK11B-BGKcLV42-15_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31732
CDK11B-BGKcLV42-16_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3150	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	30351
CDK11B-BGKcLV42-16_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3150	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	30441
CDK11B-BGKcLV42-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3150					GRCh38	V40	CDK11B-BGKcLV42-16_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK11B-BGKcLV42-16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31283
CDK11B-BGKcLV42-16_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	3150					GRCh38	V40	CDK11B-BGKcLV42-16_Aligned.sortedByCoord.out.bam		ENCORE2	31373
CDK11B-BGKcLV42-16_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	3150					GRCh38	V40	CDK11B-BGKcLV42-16_Aligned.sortedByCoord.out.bam		ENCORE2	31463
CDK11B-BGKcLV42-16_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	3150					GRCh38	V40	CDK11B-BGKcLV42-16_Aligned.sortedByCoord.out.bam		ENCORE2	31553
CDK11B-BGKcLV42-16_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	3150					GRCh38	V40	CDK11B-BGKcLV42-16_Aligned.sortedByCoord.out.bam		ENCORE2	31643
CDK11B-BGKcLV42-16_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3150					GRCh38	V40	CDK11B-BGKcLV42-16_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK11B-BGKcLV42-16_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31733