CDK9 RNA-Seq in HepG2

General Information


RBP	CDK9
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CDK9-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR361EKV
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR470SBK
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	CDK9-BGHcLV29-13
Rep2	CDK9-BGHcLV29-14
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	6.1
Rep2_qPCR	0
Rep1_WB	70.4
Rep2_WB	83.8
Antibody Cat#	A303-493A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB348XND
Status	Submitted
Project	ENCODE4
ID	848

Experiment Information (Status: Released)

	BGHcLV29-13	BGHcLV29-13	BGHcLV29-14	BGHcLV29-14
idx	844	844	845	845
TRCN#_or_BGC#	BGC#0000689	BGC#0000689	BGC#0000689	BGC#0000689
shRNA_or_gRNA_sequence	GGCAAAGCAGTACGACTCGG	GGCAAAGCAGTACGACTCGG	GGCAAAGCAGTACGACTCGG	GGCAAAGCAGTACGACTCGG
PAM	TGG	TGG	TGG	TGG
Name	CDK9_97	CDK9_97	CDK9_97	CDK9_97
Sample_ID	BGHcLV29-13	BGHcLV29-13	BGHcLV29-14	BGHcLV29-14
transduction_Date	7/20	7/20	7/20	7/20
days	D6	D6	D6	D6
RBP_name	CDK9	CDK9	CDK9	CDK9
qPCR_result	6.1	6.1	0	0
Ave_qPCR	3.05	3.05
RT-qPCR_primer-F	gggctgttgagcaatgtttt	gggctgttgagcaatgtttt
RT-qPCR_primer-R	cccatcacgagtgataagca	cccatcacgagtgataagca
protein_conc	0	0	4708	4708
WB_result	70.4	54.6	83.8	53.8
Ave_WB	77.1	54.2
WB_DONE_date		4/9/24
MW	43kd	43kd
IP	Rabbit / I
antibody_Cat#	A303-493A	2316S	LOT #1	LOT3 9
Antibody DCC ID	ENCAB348XND
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	11/5/21		11/5/21
repeat_library
Note
ID	7019	7021	7020	7022

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CDK9	Product_ID: A303-493A Lot_ID: 1 Source: Bethyl Labs Target Name: CDK9-human
CDK9	Product_ID: 2316S Lot_ID: 9 Source: Cell Signaling Technology Target Name: CDK9-human

Experiment Status

	BGHcLV29-13	BGHcLV29-14
Sample_ID	BGHcLV29-13	BGHcLV29-14
Sample Name
Sample Name	CDK9-BGHcLV29-13	CDK9-BGHcLV29-14
RBP	CDK9	CDK9
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	9981	9982

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-13	BGHcLV29-14
Sample #	9	10
Sample Name	CDK9-BGHcLV29-13	CDK9-BGHcLV29-14
Sample_Name_Alias
Index Well Position	A02	B02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	298	296
Peak_Molarity	51.40	35.40
libSampleQC_DNA_Well	DNA_Library_set50/set1/A2.png	DNA_Library_set50/set1/B2.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set50/set1/A8.png	RNA_Library_set50/set1/B8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-13	BGHcLV29-14
RBP	CDK9	CDK9
Batch_ID	BGHcLV29	BGHcLV29
WB_result	70.400	83.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3096	3097

Sequencing Information

	BGHcLV29-13	BGHcLV29-14
Sample_ID	BGHcLV29-13	BGHcLV29-14
Sample Name	CDK9-BGHcLV29-13	CDK9-BGHcLV29-14
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	57,176,520	67,772,752
total_aligned_reads	53,268,854	63,070,056
unique_aligned_reads	50,380,352	59,561,070
percent_uniqueAligned	0.88114	0.87884
correlation_replicates	0.993162	0.993162
spikein_reads	19,322	22,556
percent_spikeins	0.00034	0.00033
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1877	1878

Data Submission Information

	BGHcLV29-13	BGHcLV29-13	BGHcLV29-13	BGHcLV29-13	BGHcLV29-13	BGHcLV29-13	BGHcLV29-14	BGHcLV29-14	BGHcLV29-14	BGHcLV29-14
ENCODE_alias	brenton-graveley:CDK9-BGHcLV29	brenton-graveley:CDK9-BGHcLV29-13	brenton-graveley:L-CDK9-BGHcLV29-13	brenton-graveley:CDK9-BGHcLV29-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDK9-BGHcLV29-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDK9-BGHcLV29-HepG2	brenton-graveley:CDK9-BGHcLV29-14	brenton-graveley:L-CDK9-BGHcLV29-14	brenton-graveley:CDK9-BGHcLV29-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDK9-BGHcLV29-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR470SBK	ENCBS784CQN	ENCLB152HHN	ENCFF002HWI	ENCFF478DHP	ENCSR361EKV	ENCBS409RMM	ENCLB700SMY	ENCFF855KOE	ENCFF518WNH
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV29-13	BGHcLV29-13	BGHcLV29-13	BGHcLV29-13	BGHcLV29-13	BGHcLV29-13	BGHcLV29-14	BGHcLV29-14	BGHcLV29-14	BGHcLV29-14
Sample Name	CDK9-BGHcLV29-13	CDK9-BGHcLV29-13	CDK9-BGHcLV29-13	CDK9-BGHcLV29-13	CDK9-BGHcLV29-13	CDK9-BGHcLV29-13	CDK9-BGHcLV29-14	CDK9-BGHcLV29-14	CDK9-BGHcLV29-14	CDK9-BGHcLV29-14
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50H_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		CDK9-BGHcLV29-13.pdf	L-CDK9-BGHcLV29-13.pdf				CDK9-BGHcLV29-14.pdf	L-CDK9-BGHcLV29-14.pdf
ID	5846	5885	5957	6029	6101	6169	5886	5958	6030	6102

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
CDK9-BGHcLV29-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1877	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5765
CDK9-BGHcLV29-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1877	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5807
CDK9-BGHcLV29-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1877					GRCh38	V40	CDK9-BGHcLV29-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK9-BGHcLV29-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18932
CDK9-BGHcLV29-13_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1877					GRCh38	V40	CDK9-BGHcLV29-13/Aligned.sortedByCoord.out.bam		ENCORE2	18990
CDK9-BGHcLV29-13_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1877					GRCh38	V40	CDK9-BGHcLV29-13/Aligned.sortedByCoord.out.bam		ENCORE2	19036
CDK9-BGHcLV29-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1877					GRCh38	V40	CDK9-BGHcLV29-13/Aligned.sortedByCoord.out.bam		ENCORE2	19082
CDK9-BGHcLV29-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1877					GRCh38	V40	CDK9-BGHcLV29-13/Aligned.sortedByCoord.out.bam		ENCORE2	19128
CDK9-BGHcLV29-13_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1877					GRCh38	V40	CDK9-BGHcLV29-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK9-BGHcLV29-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19174
CDK9-BGHcLV29-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1878	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5766
CDK9-BGHcLV29-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1878	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5808
CDK9-BGHcLV29-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1878					GRCh38	V40	CDK9-BGHcLV29-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK9-BGHcLV29-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18933
CDK9-BGHcLV29-14_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1878					GRCh38	V40	CDK9-BGHcLV29-14/Aligned.sortedByCoord.out.bam		ENCORE2	18991
CDK9-BGHcLV29-14_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1878					GRCh38	V40	CDK9-BGHcLV29-14/Aligned.sortedByCoord.out.bam		ENCORE2	19037
CDK9-BGHcLV29-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1878					GRCh38	V40	CDK9-BGHcLV29-14/Aligned.sortedByCoord.out.bam		ENCORE2	19083
CDK9-BGHcLV29-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1878					GRCh38	V40	CDK9-BGHcLV29-14/Aligned.sortedByCoord.out.bam		ENCORE2	19129
CDK9-BGHcLV29-14_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1878					GRCh38	V40	CDK9-BGHcLV29-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,CDK9-BGHcLV29-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19175