CD3EAP RNA-Seq in K562

General Information


RBP	CD3EAP
Cell_Line	K562
Method	CRISPR
Exp_Name	CD3EAP-BGKcLV15-K562
ENCODE_series_ID	ENCSR884ELU
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR443BEF
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	CD3EAP-BGKcLV15-9
Rep2	CD3EAP-BGKcLV15-10
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	70.4
Rep2_qPCR	64.9
Rep1_WB	51.4
Rep2_WB	66.4
Antibody Cat#	PA5-27632
Antibody Lot#	LOT# TL2692990
Antibody DCC ID	ENCAB088EWX
Status	Released
Project	ENCODE4
ID	122

Experiment Information (Status: Released)

	BGKcLV15-9	BGKcLV15-10
idx	537	538
TRCN#_or_BGC#	BGC#0000339	BGC#0000339
shRNA_or_gRNA_sequence	GGCTTCGCGGTAAAGTTGGG	GGCTTCGCGGTAAAGTTGGG
PAM	ggg	ggg
Name	CD3EAP-90	CD3EAP-90
Sample_ID	BGKcLV15-9	BGKcLV15-10
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	CD3EAP	CD3EAP
qPCR_result	70.4	64.9
Ave_qPCR	67.7
RT-qPCR_primer-F	CAGATACGGAGCTGTGGCTT
RT-qPCR_primer-R	CAATTTGCCCTTGACGATCT
protein_conc	4829	5075
WB_result	51.4	66.4
Ave_WB	58.9
WB_DONE_date	4/9/19	WES
MW	55D	~80KD
IP	Rabbit
antibody_Cat#	PA5-27632	LOT# TL2692990
Antibody DCC ID	ENCAB088EWX
submitted_to_DCC_date	4/17/19
Rep1_TPM	23.8	0
Rep2_TPM	25.4	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4647	4648

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CD3EAP	Product_ID: PA5-27632 Lot_ID: TL2692990 Source: Thermo Fisher Target Name: CD3EAP-human

Experiment Status

	BGKcLV15-9	BGKcLV15-10
Sample_ID	BGKcLV15-9	BGKcLV15-10
Sample Name
Sample Name	CD3EAP-BGKcLV15-9	CD3EAP-BGKcLV15-10
RBP	CD3EAP	CD3EAP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5333	5334

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-9	BGKcLV15-10
Sample #	3	4
Sample Name	CD3EAP-BGKcLV15-9	CD3EAP-BGKcLV15-10
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	1-C1	1-D1
Tecan	32.22	33.49
Tecan_date	2019-12-10	2019-12-10
Size_bp	266	264
Peak_Molarity	28.40	27.70
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/C1.png	DNA_Library_set43-44/set1/D1.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set43-44/set1/C1.png	RNA_Library_set43-44/set1/D1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-9	BGKcLV15-10
RBP	CD3EAP	CD3EAP
Batch_ID	BGKcLV15	BGKcLV15
WB_result	51.400	66.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	579	580

Sequencing Information

	BGKcLV15-9	BGKcLV15-10
Sample_ID	BGKcLV15-9	BGKcLV15-10
Sample Name	CD3EAP-BGKcLV15-9	CD3EAP-BGKcLV15-10
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	71,840,684	89,018,400
total_aligned_reads	65,953,304	82,940,312
unique_aligned_reads	60,177,368	75,562,776
percent_uniqueAligned	0.83765	0.84884
correlation_replicates	0.999056	0.999056
spikein_reads	42,380	71,862
percent_spikeins	0.00059	0.00081
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	85	86

Data Submission Information

	BGKcLV15-9	BGKcLV15-9	BGKcLV15-9	BGKcLV15-9	BGKcLV15-9	BGKcLV15-9	BGKcLV15-10	BGKcLV15-10	BGKcLV15-10	BGKcLV15-10
ENCODE_alias	brenton-graveley:CD3EAP-BGKcLV15	brenton-graveley:CD3EAP-BGKcLV15-9	brenton-graveley:L-CD3EAP-BGKcLV15-9	brenton-graveley:CD3EAP-BGKcLV15-9_S3_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD3EAP-BGKcLV15-9_S3_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD3EAP-BGKcLV15-K562	brenton-graveley:CD3EAP-BGKcLV15-10	brenton-graveley:L-CD3EAP-BGKcLV15-10	brenton-graveley:CD3EAP-BGKcLV15-10_S4_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD3EAP-BGKcLV15-10_S4_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR443BEF	ENCBS291VMZ	ENCLB963ZFF	ENCFF625CED	ENCFF465VVH	ENCSR884ELU	ENCBS227RMN	ENCLB409WOH	ENCFF973YEI	ENCFF436PEC
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	BGKcLV15-9	BGKcLV15-9	BGKcLV15-9	BGKcLV15-9	BGKcLV15-9	BGKcLV15-9	BGKcLV15-10	BGKcLV15-10	BGKcLV15-10	BGKcLV15-10
Sample Name	CD3EAP-BGKcLV15-9	CD3EAP-BGKcLV15-9	CD3EAP-BGKcLV15-9	CD3EAP-BGKcLV15-9	CD3EAP-BGKcLV15-9	CD3EAP-BGKcLV15-9	CD3EAP-BGKcLV15-10	CD3EAP-BGKcLV15-10	CD3EAP-BGKcLV15-10	CD3EAP-BGKcLV15-10
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		CD3EAP-BGKcLV15-9.pdf	L-CD3EAP-BGKcLV15-10.pdf				CD3EAP-BGKcLV15-10.pdf	L-CD3EAP-BGKcLV15-9.pdf
ID	18	118	282	480	532	7126	119	283	481	533

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
CD3EAP-BGKcLV15-9_S3_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	85	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	68
CD3EAP-BGKcLV15-9_S3_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	85	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	120
CD3EAP-BGKcLV15-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	85					GRCh38	V40	CD3EAP-BGKcLV15-9_S3_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGKcLV15-9_S3_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24359
CD3EAP-BGKcLV15-9_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	85					GRCh38	V40	CD3EAP-BGKcLV15-9/Aligned.sortedByCoord.out.bam		ENCORE2	24411
CD3EAP-BGKcLV15-9_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	85					GRCh38	V40	CD3EAP-BGKcLV15-9/Aligned.sortedByCoord.out.bam		ENCORE2	24463
CD3EAP-BGKcLV15-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	85					GRCh38	V40	CD3EAP-BGKcLV15-9/Aligned.sortedByCoord.out.bam		ENCORE2	24515
CD3EAP-BGKcLV15-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	85					GRCh38	V40	CD3EAP-BGKcLV15-9/Aligned.sortedByCoord.out.bam		ENCORE2	24567
CD3EAP-BGKcLV15-9_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	85					GRCh38	V40	CD3EAP-BGKcLV15-9_S3_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGKcLV15-9_S3_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24619
CD3EAP-BGKcLV15-10_S4_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	86	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	67
CD3EAP-BGKcLV15-10_S4_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	86	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	119
CD3EAP-BGKcLV15-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	86					GRCh38	V40	CD3EAP-BGKcLV15-10_S4_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGKcLV15-10_S4_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24358
CD3EAP-BGKcLV15-10_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	86					GRCh38	V40	CD3EAP-BGKcLV15-10/Aligned.sortedByCoord.out.bam		ENCORE2	24410
CD3EAP-BGKcLV15-10_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	86					GRCh38	V40	CD3EAP-BGKcLV15-10/Aligned.sortedByCoord.out.bam		ENCORE2	24462
CD3EAP-BGKcLV15-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	86					GRCh38	V40	CD3EAP-BGKcLV15-10/Aligned.sortedByCoord.out.bam		ENCORE2	24514
CD3EAP-BGKcLV15-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	86					GRCh38	V40	CD3EAP-BGKcLV15-10/Aligned.sortedByCoord.out.bam		ENCORE2	24566
CD3EAP-BGKcLV15-10_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	86					GRCh38	V40	CD3EAP-BGKcLV15-10_S4_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGKcLV15-10_S4_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24618