CDK11B RNA-Seq in HepG2

General Information


RBP	CDK11B
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CDK11B-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	CDK11B-BGHcLV45-11
Rep2	CDK11B-BGHcLV45-12
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	67.8
Rep2_WB	60.8
Antibody Cat#	5524S
Antibody Lot#	lot # 3
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1619

Experiment Information (Status: Submitting)

	BGHcLV45-11	BGHcLV45-12
idx	1444	1445
TRCN#_or_BGC#	BGC#0001119	BGC#0001119
shRNA_or_gRNA_sequence	CTTGAGCTCGATGGGCGACA	CTTGAGCTCGATGGGCGACA
PAM	GGG	GGG
Name	CDK11B_68	CDK11B_68
Sample_ID	BGHcLV45-11	BGHcLV45-12
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	CDK11B	CDK11B
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ctatgtggagcacgacctca
RT-qPCR_primer-R	cagttgtcgtgcaggtgttt
protein_conc	3849	3153
WB_result	67.8	60.8
Ave_WB
WB_DONE_date	10/9/24,11/1/24
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	9699	9700

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV45-11	BGHcLV45-12
Sample_ID	BGHcLV45-11	BGHcLV45-12
Sample Name
Sample Name	CDK11B-BGHcLV45-11	CDK11B-BGHcLV45-12
RBP	CDK11B	CDK11B
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13696	13697

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-11	BGHcLV45-12
Sample #	11	12
Sample Name	CDK11B-BGHcLV45-11	CDK11B-BGHcLV45-12
Sample_Name_Alias
Index Well Position	C08	D08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	293	293
Peak_Molarity	89.00	77.80
libSampleQC_DNA_Well	DNA_Library_set76/set1/C8.png	DNA_Library_set76/set1/D8.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set76/set1/C2.png	RNA_Library_set76/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-11	BGHcLV45-12
RBP	CDK11B	CDK11B
Batch_ID	BGHcLV45	BGHcLV45
WB_result	67.800	60.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4620	4621

Sequencing Information

	BGHcLV45-11	BGHcLV45-12
Sample_ID	BGHcLV45-11	BGHcLV45-12
Sample Name	CDK11B-BGHcLV45-11	CDK11B-BGHcLV45-12
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	37,229,731	40,617,794
total_aligned_reads	33,574,448	36,609,466
unique_aligned_reads	31,623,831	34,466,820
percent_uniqueAligned	0.84942	0.84856
correlation_replicates	0.994687	0.994687
spikein_reads	29,370	30,192
percent_spikeins	0.00079	0.00074
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3331	3332

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-BGHcLV45-11_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3331	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31820
CDK11B-BGHcLV45-11_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3331	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31862
CDK11B-BGHcLV45-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3331					GRCh38	V40	CDK11B-BGHcLV45-11_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK11B-BGHcLV45-11_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31904
CDK11B-BGHcLV45-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3331					GRCh38	V40	CDK11B-BGHcLV45-11_Aligned.sortedByCoord.out.bam		ENCORE2	31946
CDK11B-BGHcLV45-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3331					GRCh38	V40	CDK11B-BGHcLV45-11_Aligned.sortedByCoord.out.bam		ENCORE2	31988
CDK11B-BGHcLV45-11_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3331					GRCh38	V40	CDK11B-BGHcLV45-11_Aligned.sortedByCoord.out.bam		ENCORE2	32030
CDK11B-BGHcLV45-11_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3331					GRCh38	V40	CDK11B-BGHcLV45-11_Aligned.sortedByCoord.out.bam		ENCORE2	32072
CDK11B-BGHcLV45-11_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3331					GRCh38	V40	CDK11B-BGHcLV45-11_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK11B-BGHcLV45-11_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32114
CDK11B-BGHcLV45-12_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3332	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31821
CDK11B-BGHcLV45-12_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3332	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31863
CDK11B-BGHcLV45-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3332					GRCh38	V40	CDK11B-BGHcLV45-12_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK11B-BGHcLV45-12_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31905
CDK11B-BGHcLV45-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3332					GRCh38	V40	CDK11B-BGHcLV45-12_Aligned.sortedByCoord.out.bam		ENCORE2	31947
CDK11B-BGHcLV45-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3332					GRCh38	V40	CDK11B-BGHcLV45-12_Aligned.sortedByCoord.out.bam		ENCORE2	31989
CDK11B-BGHcLV45-12_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3332					GRCh38	V40	CDK11B-BGHcLV45-12_Aligned.sortedByCoord.out.bam		ENCORE2	32031
CDK11B-BGHcLV45-12_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3332					GRCh38	V40	CDK11B-BGHcLV45-12_Aligned.sortedByCoord.out.bam		ENCORE2	32073
CDK11B-BGHcLV45-12_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3332					GRCh38	V40	CDK11B-BGHcLV45-12_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK11B-BGHcLV45-12_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32115