EZH2 RNA-Seq in K562

General Information


RBP	EZH2
Cell_Line	K562
Method	CRISPR
Exp_Name	EZH2-BGKcLV40-K562
ENCODE_series_ID
Batch_ID	BGKcLV40
Pool ID	Pool-231226
Local_Set_Name	set67
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EZH2-BGKcLV40-41
Rep2	EZH2-BGKcLV40-42
CN1	NT-BGKcLV40-1
CN2	NT-BGKcLV40-2
Rep1_qPCR	0.0
Rep2_qPCR	12.0
Rep1_WB	86.5
Rep2_WB	90.7
Antibody Cat#	A304-197A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1368

Experiment Information (Status: Submitting)

	BGKcLV40-41	BGKcLV40-41	BGKcLV40-42	BGKcLV40-42
idx	0	0	0	0
TRCN#_or_BGC#	BGC#0001007	BGC#0001007	BGC#0001007	BGC#0001007
shRNA_or_gRNA_sequence	TGCGACTGAGACAGCTCAAG	TGCGACTGAGACAGCTCAAG	TGCGACTGAGACAGCTCAAG	TGCGACTGAGACAGCTCAAG
PAM	AGG	AGG	AGG	AGG
Name	EZH2_82	EZH2_82	EZH2_82	EZH2_82
Sample_ID	BGKcLV40-41	BGKcLV40-41	BGKcLV40-42	BGKcLV40-42
transduction_Date	10/31/23	10/31/23	10/31/23	10/31/23
days	D6	D6	D6	D6
RBP_name	EZH2	EZH2	EZH2	EZH2
qPCR_result	0.0	0.0	12.0	12.0
Ave_qPCR	6.0	6.0
RT-qPCR_primer-F	tagggaagcagggactgaaa	tagggaagcagggactgaaa
RT-qPCR_primer-R	ttggtgtttgacaccgagaa	ttggtgtttgacaccgagaa
protein_conc	4116	4116	3996	3996
WB_result	86.5	61.3	90.7	62.3
Ave_WB	88.6
WB_DONE_date	11/17/23	2/6/24
MW	85kd	85kd
IP
antibody_Cat#	A304-197A	5246S	lot # 1	lot # 10
Antibody DCC ID
submitted_to_DCC_date	1/4/24
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date
repeat_library
Note
ID	5718	5720	5719	5721

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EZH2	Product_ID: A304-197A Lot_ID: 1 Source: Bethyl Labs Target Name: EZH2-human
EZH2	Product_ID: 5246S Lot_ID: 10 Source: Cell Signaling Technology Target Name: EZH2-human

Experiment Status

	BGKcLV40-41	BGKcLV40-42
Sample_ID	BGKcLV40-41	BGKcLV40-42
Sample Name
Sample Name	EZH2-BGKcLV40-41	EZH2-BGKcLV40-42
RBP	EZH2	EZH2
Cell_Line	K562	K562
Exp UID
Status	Submitting	Submitting
Status_date	2024-02-16	2024-02-16
Project	ENCORE2	ENCORE2
Note
ID	12780	12781

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV40-41	BGKcLV40-42
Sample #	27	28
Sample Name	EZH2-BGKcLV40-41	EZH2-BGKcLV40-42
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-12-19	2023-12-19
Lib_ID	Lib-231219	Lib-231219
Tecan_Location
Tecan
Tecan_date
Size_bp	283	288
Peak_Molarity	83.90	68.70
libSampleQC_DNA_Well	DNA_Library_set67/set1/C10.png	DNA_Library_set67/set1/D10.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set67/set1/C4.png	RNA_Library_set67/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-12-26	2023-12-26
Sample_ID	BGKcLV40-41	BGKcLV40-42
RBP	EZH2	EZH2
Batch_ID	BGKcLV40	BGKcLV40
WB_result	86.500	90.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4164	4165

Sequencing Information

	BGKcLV40-41	BGKcLV40-42
Sample_ID	BGKcLV40-41	BGKcLV40-42
Sample Name	EZH2-BGKcLV40-41	EZH2-BGKcLV40-42
Pool ID	Pool-231226	Pool-231226
LocalServer_folder	set67	set67
total_reads	69,416,561	36,247,778
total_aligned_reads	59,890,725	30,664,943
unique_aligned_reads	55,106,512	28,139,630
percent_uniqueAligned	0.79385	0.77631
correlation_replicates	0.998063	0.998063
spikein_reads	11,078	706
percent_spikeins	0.00016	0.00002
original_ReadLength	151	151
QC_Status	Submitting	Submitting
ID	2819	2820

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
EZH2-BGKcLV40-41_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2819	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28165
EZH2-BGKcLV40-41_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2819	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28209
EZH2-BGKcLV40-41_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2819					GRCh38	V40	EZH2-BGKcLV40-41_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,EZH2-BGKcLV40-41_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28253
EZH2-BGKcLV40-41_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2819					GRCh38	V40	EZH2-BGKcLV40-41/Aligned.sortedByCoord.out.bam		ENCORE2	28297
EZH2-BGKcLV40-41_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2819					GRCh38	V40	EZH2-BGKcLV40-41/Aligned.sortedByCoord.out.bam		ENCORE2	28341
EZH2-BGKcLV40-41_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2819					GRCh38	V40	EZH2-BGKcLV40-41/Aligned.sortedByCoord.out.bam		ENCORE2	28385
EZH2-BGKcLV40-41_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2819					GRCh38	V40	EZH2-BGKcLV40-41/Aligned.sortedByCoord.out.bam		ENCORE2	28429
EZH2-BGKcLV40-41_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2819					GRCh38	V40	EZH2-BGKcLV40-41_S27_L001_R1_001.filtered.trimmed.paired.fastq.gz,EZH2-BGKcLV40-41_S27_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28473
EZH2-BGKcLV40-42_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2820	NovaSeq6000	100	paired-ended	1				NT-BGKcLV40-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28166
EZH2-BGKcLV40-42_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set67/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2820	NovaSeq6000	100	paired-ended	2				NT-BGKcLV40-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV40-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28210
EZH2-BGKcLV40-42_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2820					GRCh38	V40	EZH2-BGKcLV40-42_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,EZH2-BGKcLV40-42_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28254
EZH2-BGKcLV40-42_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2820					GRCh38	V40	EZH2-BGKcLV40-42/Aligned.sortedByCoord.out.bam		ENCORE2	28298
EZH2-BGKcLV40-42_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2820					GRCh38	V40	EZH2-BGKcLV40-42/Aligned.sortedByCoord.out.bam		ENCORE2	28342
EZH2-BGKcLV40-42_Signal.Unique.strand-.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2820					GRCh38	V40	EZH2-BGKcLV40-42/Aligned.sortedByCoord.out.bam		ENCORE2	28386
EZH2-BGKcLV40-42_Signal.Unique.strand+.bw	ENCODE_DATA/set67/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2820					GRCh38	V40	EZH2-BGKcLV40-42/Aligned.sortedByCoord.out.bam		ENCORE2	28430
EZH2-BGKcLV40-42_quant.sf	ENCODE_DATA/set67/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2820					GRCh38	V40	EZH2-BGKcLV40-42_S28_L001_R1_001.filtered.trimmed.paired.fastq.gz,EZH2-BGKcLV40-42_S28_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28474