BRD4 RNA-Seq in K562

General Information


RBP	BRD4
Cell_Line	K562
Method	CRISPR
Exp_Name	BRD4-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	BRD4-BGKcLV42-11
Rep2	BRD4-BGKcLV42-12
CN1	NT-BGKcLV42-1
CN2	NT-BGKcLV42-2
Rep1_qPCR	78.1
Rep2_qPCR	81.6
Rep1_WB	86.8
Rep2_WB	72.0
Antibody Cat#	83375S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1529

Experiment Information (Status: Submitting)

	BGKcLV42-11	BGKcLV42-11	BGKcLV42-11	BGKcLV42-11	BGKcLV42-12	BGKcLV42-12	BGKcLV42-12	BGKcLV42-12
idx	0	0	0	0	0	0	0	0
TRCN#_or_BGC#	BGC#0001115	BGC#0001115	BGC#0001115	BGC#0001115	BGC#0001115	BGC#0001115	BGC#0001115	BGC#0001115
shRNA_or_gRNA_sequence	GGGAACAATAAAGAAGCGCT	GGGAACAATAAAGAAGCGCT	GGGAACAATAAAGAAGCGCT	GGGAACAATAAAGAAGCGCT	GGGAACAATAAAGAAGCGCT	GGGAACAATAAAGAAGCGCT	GGGAACAATAAAGAAGCGCT	GGGAACAATAAAGAAGCGCT
PAM	TGG	TGG	TGG	TGG	TGG	TGG	TGG	TGG
Name	BRD4_85	BRD4_85	BRD4_85	BRD4_85	BRD4_85	BRD4_85	BRD4_85	BRD4_85
Sample_ID	BGKcLV42-11	BGKcLV42-11	BGKcLV42-11	BGKcLV42-11	BGKcLV42-12	BGKcLV42-12	BGKcLV42-12	BGKcLV42-12
transduction_Date	4/23/24	4/23/24	4/23/24	4/23/24	4/23/24	4/23/24	4/23/24	4/23/24
days	D6	D6	D6	D6	D6	D6	D6	D6
RBP_name	BRD4	BRD4	BRD4	BRD4	BRD4	BRD4	BRD4	BRD4
qPCR_result	78.1			78.1	81.6			81.6
Ave_qPCR	79.9			79.9
RT-qPCR_primer-F	acccacagaagaaaccgaga			acccacagaagaaaccgaga
RT-qPCR_primer-R	tgtgtttggtaccgtggaaa			tgtgtttggtaccgtggaaa
protein_conc	2293	2293	2293	2293	1942	1942	1942	1942
WB_result	86.8	86.7	79.2	64.9	72.0	82.9	72.8672	75.0
Ave_WB	79.4	84.8	76.0	69.9
WB_DONE_date	5/2/24,5/8/24	5/2/24,5/8/24	5/2/24,5/8/24	6/24/24	isoA	isoB	isoC
MW	200,110kd	200,110kd		200kd
IP
antibody_Cat#	83375S	83375S	83375S	13440S	lot # 1	lot # 1	lot # 1	lot # 9
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0	0	0	0	0
Rep2_TPM	0	0	0	0	0	0	0	0
Action	Ready				Ready
Library_start_date
repeat_library
Note
ID	5765	5767	5769	5771	5766	5768	5770	5772

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BRD4	Product_ID: 13440S Lot_ID: 9 Source: Cell Signaling Technology Target Name: BRD4-human

Experiment Status

	BGKcLV42-11	BGKcLV42-11	BGKcLV42-11	BGKcLV42-12	BGKcLV42-12	BGKcLV42-12
Sample_ID	BGKcLV42-11	BGKcLV42-11	BGKcLV42-11	BGKcLV42-12	BGKcLV42-12	BGKcLV42-12
Sample Name
Sample Name	BRD4-BGKcLV42-11			BRD4-BGKcLV42-12
RBP	BRD4	BRD4	BRD4	BRD4	BRD4	BRD4
Cell_Line	K562	K562	K562	K562	K562	K562
Exp UID
Status	Submitting	NotSatisfied	NotSatisfied	Submitting	NotSatisfied	NotSatisfied
Status_date	2025-02-13	2024-06-21	2024-06-21	2025-02-13	2024-06-21	2024-06-21
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	13052	13136	13138	13053	13137	13139

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV42-11	BGKcLV42-12
Sample #	9	10
Sample Name	BRD4-BGKcLV42-11	BRD4-BGKcLV42-12
Sample_Name_Alias
Index Well Position	A02	B02
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	300	310
Peak_Molarity	89.20	75.30
libSampleQC_DNA_Well	DNA_Library_set73/set1/A2.png	DNA_Library_set73/set1/B2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set73/set1/A2.png	RNA_Library_set73/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-15	2024-07-15
Sample_ID	BGKcLV42-11	BGKcLV42-12
RBP	BRD4	BRD4
Batch_ID	BGKcLV42	BGKcLV42
WB_result	86.800	72.008
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4278	4279

Sequencing Information

	BGKcLV42-11	BGKcLV42-12
Sample_ID	BGKcLV42-11	BGKcLV42-12
Sample Name	BRD4-BGKcLV42-11	BRD4-BGKcLV42-12
Pool ID	Pool-240715	Pool-240715
LocalServer_folder	set73	set73
total_reads	55,750,652	43,242,654
total_aligned_reads	50,816,212	38,320,561
unique_aligned_reads	46,757,873	35,364,863
percent_uniqueAligned	0.83870	0.81782
correlation_replicates	0.980765	0.980765
spikein_reads	8,502	1,148
percent_spikeins	0.00015	0.00003
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3145	3146

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
BRD4-BGKcLV42-11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3145	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	30346
BRD4-BGKcLV42-11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3145	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	30436
BRD4-BGKcLV42-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3145					GRCh38	V40	BRD4-BGKcLV42-11_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRD4-BGKcLV42-11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31278
BRD4-BGKcLV42-11_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	3145					GRCh38	V40	BRD4-BGKcLV42-11_Aligned.sortedByCoord.out.bam		ENCORE2	31368
BRD4-BGKcLV42-11_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	3145					GRCh38	V40	BRD4-BGKcLV42-11_Aligned.sortedByCoord.out.bam		ENCORE2	31458
BRD4-BGKcLV42-11_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	3145					GRCh38	V40	BRD4-BGKcLV42-11_Aligned.sortedByCoord.out.bam		ENCORE2	31548
BRD4-BGKcLV42-11_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	3145					GRCh38	V40	BRD4-BGKcLV42-11_Aligned.sortedByCoord.out.bam		ENCORE2	31638
BRD4-BGKcLV42-11_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3145					GRCh38	V40	BRD4-BGKcLV42-11_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRD4-BGKcLV42-11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31728
BRD4-BGKcLV42-12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3146	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	30347
BRD4-BGKcLV42-12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set73/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3146	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	30437
BRD4-BGKcLV42-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set73/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3146					GRCh38	V40	BRD4-BGKcLV42-12_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRD4-BGKcLV42-12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31279
BRD4-BGKcLV42-12_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	3146					GRCh38	V40	BRD4-BGKcLV42-12_Aligned.sortedByCoord.out.bam		ENCORE2	31369
BRD4-BGKcLV42-12_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	3146					GRCh38	V40	BRD4-BGKcLV42-12_Aligned.sortedByCoord.out.bam		ENCORE2	31459
BRD4-BGKcLV42-12_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	3146					GRCh38	V40	BRD4-BGKcLV42-12_Aligned.sortedByCoord.out.bam		ENCORE2	31549
BRD4-BGKcLV42-12_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	3146					GRCh38	V40	BRD4-BGKcLV42-12_Aligned.sortedByCoord.out.bam		ENCORE2	31639
BRD4-BGKcLV42-12_quant.sf	ENCODE_DATA/set73/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3146					GRCh38	V40	BRD4-BGKcLV42-12_L001_R1_001.filtered.trimmed.paired.fastq.gz,BRD4-BGKcLV42-12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31729