BRD4 RNA-Seq in HepG2

General Information


RBP	BRD4
Cell_Line	HepG2
Method	CRISPR
Exp_Name	BRD4-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	BRD4-BGHcLV43-7
Rep2	BRD4-BGHcLV43-8
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	60.2
Rep2_qPCR	55.7
Rep1_WB	89.7
Rep2_WB	86.2
Antibody Cat#	83375S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1570

Experiment Information (Status: Submitting)

	BGHcLV43-7	BGHcLV43-7	BGHcLV43-8	BGHcLV43-8
idx	1375	1375	1376	1376
TRCN#_or_BGC#	BGC#0001115	BGC#0001115	BGC#0001115	BGC#0001115
shRNA_or_gRNA_sequence	GGGAACAATAAAGAAGCGCT	GGGAACAATAAAGAAGCGCT	GGGAACAATAAAGAAGCGCT	GGGAACAATAAAGAAGCGCT
PAM	TGG	TGG	TGG	TGG
Name	BRD4_85	BRD4_85	BRD4_85	BRD4_85
Sample_ID	BGHcLV43-7	BGHcLV43-7	BGHcLV43-8	BGHcLV43-8
transduction_Date	6/6/24	6/6/24	6/6/24	6/6/24
days	D6	D6	D6	D6
RBP_name	BRD4	BRD4	BRD4	BRD4
qPCR_result	60.2	60.2	55.7	55.7
Ave_qPCR	57.9
RT-qPCR_primer-F	acccacagaagaaaccgaga	acccacagaagaaaccgaga
RT-qPCR_primer-R	tgtgtttggtaccgtggaaa	tgtgtttggtaccgtggaaa
protein_conc	2761	2761	3382	3382
WB_result	89.7	88.1	86.2	87.2
Ave_WB	88.0	87.7
WB_DONE_date	6/13/24	6/13/24
MW	200,110kd	200,110kd	200KD	110KD
IP
antibody_Cat#	83375S	83375S	lot # 1	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	9620	9622	9621	9623

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV43-7	BGHcLV43-7	BGHcLV43-8	BGHcLV43-8
Sample_ID	BGHcLV43-7	BGHcLV43-7	BGHcLV43-8	BGHcLV43-8
Sample Name
Sample Name	BRD4-BGHcLV43-7		BRD4-BGHcLV43-8
RBP	BRD4	BRD4	BRD4	BRD4
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	Submitting	NotSatisfied	Submitting	NotSatisfied
Status_date	2025-02-11	2024-07-16	2025-02-11	2024-07-16
Project	ENCORE2	ENCORE2	ENCORE2	ENCORE2
Note
ID	13230	13284	13231	13285

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-7	BGHcLV43-8
Sample #	3	4
Sample Name	BRD4-BGHcLV43-7	BRD4-BGHcLV43-8
Sample_Name_Alias
Index Well Position	C06	D06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	302	301
Peak_Molarity	118.00	91.60
libSampleQC_DNA_Well	DNA_Library_set74/set1/C1.png	DNA_Library_set74/set1/D1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/G6.png	RNA_Library_set74/set1/H6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-7	BGHcLV43-8
RBP	BRD4	BRD4
Batch_ID	BGHcLV43	BGHcLV43
WB_result	89.700	86.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4362	4363

Sequencing Information

	BGHcLV43-7	BGHcLV43-8
Sample_ID	BGHcLV43-7	BGHcLV43-8
Sample Name	BRD4-BGHcLV43-7	BRD4-BGHcLV43-8
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	34,422,258	31,438,588
total_aligned_reads	31,964,495	29,157,974
unique_aligned_reads	30,105,036	27,449,051
percent_uniqueAligned	0.87458	0.87310
correlation_replicates	0.999143	0.999143
spikein_reads	34,672	8,616
percent_spikeins	0.00101	0.00027
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3229	3230

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-BGHcLV43-7_S93_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3229	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30520
BRD4-BGHcLV43-7_S93_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3229	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30572
BRD4-BGHcLV43-7_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3229					GRCh38	V40	BRD4-BGHcLV43-7_S93_L003_R1_001.filtered.trimmed.paired.fastq.gz,BRD4-BGHcLV43-7_S93_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30624
BRD4-BGHcLV43-7_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3229					GRCh38	V40	BRD4-BGHcLV43-7_Aligned.sortedByCoord.out.bam		ENCORE2	30676
BRD4-BGHcLV43-7_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3229					GRCh38	V40	BRD4-BGHcLV43-7_Aligned.sortedByCoord.out.bam		ENCORE2	30728
BRD4-BGHcLV43-7_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3229					GRCh38	V40	BRD4-BGHcLV43-7_Aligned.sortedByCoord.out.bam		ENCORE2	30780
BRD4-BGHcLV43-7_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3229					GRCh38	V40	BRD4-BGHcLV43-7_Aligned.sortedByCoord.out.bam		ENCORE2	30832
BRD4-BGHcLV43-7_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3229					GRCh38	V40	BRD4-BGHcLV43-7_S93_L003_R1_001.filtered.trimmed.paired.fastq.gz,BRD4-BGHcLV43-7_S93_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30884
BRD4-BGHcLV43-8_S94_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3230	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30521
BRD4-BGHcLV43-8_S94_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3230	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30573
BRD4-BGHcLV43-8_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3230					GRCh38	V40	BRD4-BGHcLV43-8_S94_L003_R1_001.filtered.trimmed.paired.fastq.gz,BRD4-BGHcLV43-8_S94_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30625
BRD4-BGHcLV43-8_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3230					GRCh38	V40	BRD4-BGHcLV43-8_Aligned.sortedByCoord.out.bam		ENCORE2	30677
BRD4-BGHcLV43-8_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3230					GRCh38	V40	BRD4-BGHcLV43-8_Aligned.sortedByCoord.out.bam		ENCORE2	30729
BRD4-BGHcLV43-8_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3230					GRCh38	V40	BRD4-BGHcLV43-8_Aligned.sortedByCoord.out.bam		ENCORE2	30781
BRD4-BGHcLV43-8_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3230					GRCh38	V40	BRD4-BGHcLV43-8_Aligned.sortedByCoord.out.bam		ENCORE2	30833
BRD4-BGHcLV43-8_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3230					GRCh38	V40	BRD4-BGHcLV43-8_S94_L003_R1_001.filtered.trimmed.paired.fastq.gz,BRD4-BGHcLV43-8_S94_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30885