BRD2 RNA-Seq in K562

General Information


RBP	BRD2
Cell_Line	K562
Method	CRISPR
Exp_Name	BRD2-BGKcLV26-K562
ENCODE_series_ID	ENCSR919QXA
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR046XQE
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	BRD2-BGKcLV26-41
Rep2	BRD2-BGKcLV26-42
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	73.4
Rep2_WB	72.1
Antibody Cat#	A302-582A
Antibody Lot#	LOT# 2
Antibody DCC ID	ENCAB518SCS
Status	Released
Project	ENCODE4
ID	796

Experiment Information (Status: Released)

	BGKcLV26-41	BGKcLV26-42
idx	902	903
TRCN#_or_BGC#	BGC#0000650	BGC#0000650
shRNA_or_gRNA_sequence	CCCCCTATGCGTAGAGAGAG	CCCCCTATGCGTAGAGAGAG
PAM	TGG	TGG
Name	BRD2_83	BRD2_83
Sample_ID	BGKcLV26-41	BGKcLV26-42
transduction_Date	3/30/21	3/30/21
days	Day 6	Day 6
RBP_name	BRD2	BRD2
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	5129	4992
WB_result	73.4	72.1
Ave_WB	72.8
WB_DONE_date	5/26/21	JESS
MW	88kDa
IP	Rabbit / I
antibody_Cat#	A302-582A	LOT# 2
Antibody DCC ID	ENCAB518SCS	6/25/24
submitted_to_DCC_date
Rep1_TPM	156.4	0
Rep2_TPM	169.1	0
Action	Ready	Ready
Library_start_date	09/01/21	09/01/21
repeat_library
Note
ID	5034	5035

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BRD2	Product_ID: A302-582A Lot_ID: 2 Source: Bethyl Labs Target Name: BRD2-human

Experiment Status

	BGKcLV26-41	BGKcLV26-42
Sample_ID	BGKcLV26-41	BGKcLV26-42
Sample Name
Sample Name	BRD2-BGKcLV26-41	BRD2-BGKcLV26-42
RBP	BRD2	BRD2
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9773	9774

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-41	BGKcLV26-42
Sample #	31	32
Sample Name	BRD2-BGKcLV26-41	BRD2-BGKcLV26-42
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	289	283
Peak_Molarity	131.00	121.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/G4.png	DNA_Library_set48-49/set1/H4.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set48-49/set1/G4.png	RNA_Library_set48-49/set1/H4.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-41	BGKcLV26-42
RBP	BRD2	BRD2
Batch_ID	BGKcLV26	BGKcLV26
WB_result	73.400	72.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1590	1591

Sequencing Information

	BGKcLV26-41	BGKcLV26-42
Sample_ID	BGKcLV26-41	BGKcLV26-42
Sample Name	BRD2-BGKcLV26-41	BRD2-BGKcLV26-42
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	55,647,850	61,816,204
total_aligned_reads	49,366,252	53,887,986
unique_aligned_reads	45,162,752	49,334,590
percent_uniqueAligned	0.81158	0.79809
correlation_replicates	0.995035	0.995035
spikein_reads	19,000	12,486
percent_spikeins	0.00034	0.00020
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1767	1768

Data Submission Information

	BGKcLV26-41	BGKcLV26-41	BGKcLV26-41	BGKcLV26-41	BGKcLV26-41	BGKcLV26-41	BGKcLV26-42	BGKcLV26-42	BGKcLV26-42	BGKcLV26-42
ENCODE_alias	brenton-graveley:BRD2-BGKcLV26	brenton-graveley:BRD2-BGKcLV26-41	brenton-graveley:L-BRD2-BGKcLV26-41	brenton-graveley:BRD2-BGKcLV26-41_S37_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BRD2-BGKcLV26-41_S37_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BRD2-BGKcLV26-K562	brenton-graveley:BRD2-BGKcLV26-42	brenton-graveley:L-BRD2-BGKcLV26-42	brenton-graveley:BRD2-BGKcLV26-42_S38_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:BRD2-BGKcLV26-42_S38_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR046XQE	ENCBS706ZAQ	ENCLB368KUX	ENCFF122GPA	ENCFF472TJM	ENCSR919QXA	ENCBS816PZZ	ENCLB160MQI	ENCFF411LVC	ENCFF544NPJ
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	BGKcLV26-41	BGKcLV26-41	BGKcLV26-41	BGKcLV26-41	BGKcLV26-41	BGKcLV26-41	BGKcLV26-42	BGKcLV26-42	BGKcLV26-42	BGKcLV26-42
Sample Name	BRD2-BGKcLV26-41	BRD2-BGKcLV26-41	BRD2-BGKcLV26-41	BRD2-BGKcLV26-41	BRD2-BGKcLV26-41	BRD2-BGKcLV26-41	BRD2-BGKcLV26-42	BRD2-BGKcLV26-42	BRD2-BGKcLV26-42	BRD2-BGKcLV26-42
Selected	Yes	No	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2021-11-19	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
			LV48K_library_protocol					LV48K_library_protocol
protocol_URL			L-BRD2-BGKcLV26-41.pdf					L-BRD2-BGKcLV26-42.pdf
ID	3461	3556	3690	3824	3958	7101	3557	3691	3825	3959

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
BRD2-BGKcLV26-41_S37_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1767	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3860
BRD2-BGKcLV26-41_S37_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1767	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3910
BRD2-BGKcLV26-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1767					GRCh38	V40	BRD2-BGKcLV26-41_S37_L003_R1_001.filtered.trimmed.paired.fastq.gz,BRD2-BGKcLV26-41_S37_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25547
BRD2-BGKcLV26-41_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1767					GRCh38	V40	BRD2-BGKcLV26-41_S37_L003_R1_001.filtered.trimmed.paired.fastq.gz,BRD2-BGKcLV26-41_S37_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25597
BRD2-BGKcLV26-41_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1767					GRCh38	V40	BRD2-BGKcLV26-41/Aligned.sortedByCoord.out.bam		ENCORE2	26563
BRD2-BGKcLV26-41_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1767					GRCh38	V40	BRD2-BGKcLV26-41/Aligned.sortedByCoord.out.bam		ENCORE2	26613
BRD2-BGKcLV26-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1767					GRCh38	V40	BRD2-BGKcLV26-41/Aligned.sortedByCoord.out.bam		ENCORE2	26663
BRD2-BGKcLV26-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1767					GRCh38	V40	BRD2-BGKcLV26-41/Aligned.sortedByCoord.out.bam		ENCORE2	26713
BRD2-BGKcLV26-42_S38_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1768	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3861
BRD2-BGKcLV26-42_S38_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1768	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3911
BRD2-BGKcLV26-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1768					GRCh38	V40	BRD2-BGKcLV26-42_S38_L003_R1_001.filtered.trimmed.paired.fastq.gz,BRD2-BGKcLV26-42_S38_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25548
BRD2-BGKcLV26-42_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1768					GRCh38	V40	BRD2-BGKcLV26-42_S38_L003_R1_001.filtered.trimmed.paired.fastq.gz,BRD2-BGKcLV26-42_S38_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25598
BRD2-BGKcLV26-42_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1768					GRCh38	V40	BRD2-BGKcLV26-42/Aligned.sortedByCoord.out.bam		ENCORE2	26564
BRD2-BGKcLV26-42_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1768					GRCh38	V40	BRD2-BGKcLV26-42/Aligned.sortedByCoord.out.bam		ENCORE2	26614
BRD2-BGKcLV26-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1768					GRCh38	V40	BRD2-BGKcLV26-42/Aligned.sortedByCoord.out.bam		ENCORE2	26664
BRD2-BGKcLV26-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1768					GRCh38	V40	BRD2-BGKcLV26-42/Aligned.sortedByCoord.out.bam		ENCORE2	26714