CDK9 RNA-Seq in K562

General Information


RBP	CDK9
Cell_Line	K562
Method	CRISPR
Exp_Name	CDK9-BGKcLV28-K562
ENCODE_series_ID	ENCSR661PBE
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR049YEZ
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	CDK9-BGKcLV28-13
Rep2	CDK9-BGKcLV28-14
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	28.4
Rep2_qPCR	30.0
Rep1_WB	57.5
Rep2_WB	61.3
Antibody Cat#	A303-493A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB348XND
Status	Released
Project	ENCODE4
ID	823

Experiment Information (Status: Released)

	BGKcLV28-13	BGKcLV28-14
idx	947	948
TRCN#_or_BGC#	BGC#0000689	BGC#0000689
shRNA_or_gRNA_sequence	GGCAAAGCAGTACGACTCGG	GGCAAAGCAGTACGACTCGG
PAM	TGG	TGG
Name	CDK9_97	CDK9_97
Sample_ID	BGKcLV28-13	BGKcLV28-14
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	CDK9	CDK9
qPCR_result	28.4	30.0
Ave_qPCR	29.2
RT-qPCR_primer-F	gggctgttgagcaatgtttt
RT-qPCR_primer-R	cccatcacgagtgataagca
protein_conc	1651	1971
WB_result	57.5	61.3
Ave_WB	59.4
WB_DONE_date	6/22/21	JESS
MW	43kd
IP
antibody_Cat#	A303-493A	LOT #1
Antibody DCC ID	ENCAB348XND	1/19/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/23/21	09/23/21
repeat_library
Note
ID	5081	5082

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

Experiment Status

	BGKcLV28-13	BGKcLV28-14
Sample_ID	BGKcLV28-13	BGKcLV28-14
Sample Name
Sample Name	CDK9-BGKcLV28-13	CDK9-BGKcLV28-14
RBP	CDK9	CDK9
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9905	9906

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-13	BGKcLV28-14
Sample #	13	14
Sample Name	CDK9-BGKcLV28-13	CDK9-BGKcLV28-14
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	377	329
Peak_Molarity	103.00	124.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/E2.png	DNA_Library_set48-49/set3/F2.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set48-49/set2/E2.png	RNA_Library_set48-49/set2/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-13	BGKcLV28-14
RBP	CDK9	CDK9
Batch_ID	BGKcLV28	BGKcLV28
WB_result	57.500	61.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2074	2075

Sequencing Information

	BGKcLV28-13	BGKcLV28-14
Sample_ID	BGKcLV28-13	BGKcLV28-14
Sample Name	CDK9-BGKcLV28-13	CDK9-BGKcLV28-14
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	111,041,196	93,960,734
total_aligned_reads	106,452,776	87,579,112
unique_aligned_reads	97,955,060	80,378,036
percent_uniqueAligned	0.88215	0.85544
correlation_replicates	0.997701	0.997701
spikein_reads	26,878	27,042
percent_spikeins	0.00024	0.00029
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1825	1826

Data Submission Information

	BGKcLV28-13	BGKcLV28-13	BGKcLV28-13	BGKcLV28-13	BGKcLV28-13	BGKcLV28-13	BGKcLV28-14	BGKcLV28-14	BGKcLV28-14	BGKcLV28-14
ENCODE_alias	brenton-graveley:CDK9-BGKcLV28	brenton-graveley:CDK9-BGKcLV28-13	brenton-graveley:L-CDK9-BGKcLV28-13	brenton-graveley:CDK9-BGKcLV28-13_S95_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDK9-BGKcLV28-13_S95_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDK9-BGKcLV28-K562	brenton-graveley:CDK9-BGKcLV28-14	brenton-graveley:L-CDK9-BGKcLV28-14	brenton-graveley:CDK9-BGKcLV28-14_S96_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CDK9-BGKcLV28-14_S96_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR049YEZ	ENCBS426GBU	ENCLB815AWZ	ENCFF282GWG	ENCFF805ZWC	ENCSR661PBE	ENCBS853HUJ	ENCLB744MWI	ENCFF555BVX	ENCFF637JJQ
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	BGKcLV28-13	BGKcLV28-13	BGKcLV28-13	BGKcLV28-13	BGKcLV28-13	BGKcLV28-13	BGKcLV28-14	BGKcLV28-14	BGKcLV28-14	BGKcLV28-14
Sample Name	CDK9-BGKcLV28-13	CDK9-BGKcLV28-13	CDK9-BGKcLV28-13	CDK9-BGKcLV28-13	CDK9-BGKcLV28-13	CDK9-BGKcLV28-13	CDK9-BGKcLV28-14	CDK9-BGKcLV28-14	CDK9-BGKcLV28-14	CDK9-BGKcLV28-14
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV49_biosample_protocol	LV49_library_protocol				LV49_biosample_protocol	LV49_library_protocol
protocol_URL		CDK9-BGKcLV28-13.pdf	L-CDK9-BGKcLV28-13.pdf				CDK9-BGKcLV28-14.pdf	L-CDK9-BGKcLV28-14.pdf
ID	3477	3588	3722	3856	3990	7130	3589	3723	3857	3991

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-BGKcLV28-13_S95_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1825	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3942
CDK9-BGKcLV28-13_S95_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1825	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4000
CDK9-BGKcLV28-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1825					GRCh38	V40	CDK9-BGKcLV28-13_S95_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDK9-BGKcLV28-13_S95_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19224
CDK9-BGKcLV28-13_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1825					GRCh38	V40	CDK9-BGKcLV28-13/Aligned.sortedByCoord.out.bam		ENCORE2	19282
CDK9-BGKcLV28-13_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1825					GRCh38	V40	CDK9-BGKcLV28-13/Aligned.sortedByCoord.out.bam		ENCORE2	19340
CDK9-BGKcLV28-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1825					GRCh38	V40	CDK9-BGKcLV28-13/Aligned.sortedByCoord.out.bam		ENCORE2	19398
CDK9-BGKcLV28-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1825					GRCh38	V40	CDK9-BGKcLV28-13/Aligned.sortedByCoord.out.bam		ENCORE2	19456
CDK9-BGKcLV28-13_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1825					GRCh38	V40	CDK9-BGKcLV28-13_S95_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDK9-BGKcLV28-13_S95_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19514
CDK9-BGKcLV28-14_S96_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1826	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3943
CDK9-BGKcLV28-14_S96_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1826	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4001
CDK9-BGKcLV28-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1826					GRCh38	V40	CDK9-BGKcLV28-14_S96_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDK9-BGKcLV28-14_S96_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19225
CDK9-BGKcLV28-14_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1826					GRCh38	V40	CDK9-BGKcLV28-14/Aligned.sortedByCoord.out.bam		ENCORE2	19283
CDK9-BGKcLV28-14_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1826					GRCh38	V40	CDK9-BGKcLV28-14/Aligned.sortedByCoord.out.bam		ENCORE2	19341
CDK9-BGKcLV28-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1826					GRCh38	V40	CDK9-BGKcLV28-14/Aligned.sortedByCoord.out.bam		ENCORE2	19399
CDK9-BGKcLV28-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1826					GRCh38	V40	CDK9-BGKcLV28-14/Aligned.sortedByCoord.out.bam		ENCORE2	19457
CDK9-BGKcLV28-14_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1826					GRCh38	V40	CDK9-BGKcLV28-14_S96_L004_R1_001.filtered.trimmed.paired.fastq.gz,CDK9-BGKcLV28-14_S96_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19515