CD3EAP RNA-Seq in HepG2

General Information


RBP	CD3EAP
Cell_Line	HepG2
Method	CRISPR
Exp_Name	CD3EAP-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR164NKE
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR400XYB
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	CD3EAP-BGHcLV16-11
Rep2	CD3EAP-BGHcLV16-12
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	52.9
Rep2_WB	52.4
Antibody Cat#	PA5-27632
Antibody Lot#	TL2692990
Antibody DCC ID	ENCAB088EWX
Status	Released
Project	ENCODE4
ID	146

Experiment Information (Status: Released)

	BGHcLV16-11	BGHcLV16-12
idx	439	440
TRCN#_or_BGC#	BGC#0000339	BGC#0000339
shRNA_or_gRNA_sequence	GGCTTCGCGGTAAAGTTGGG	GGCTTCGCGGTAAAGTTGGG
PAM	ggg	ggg
Name	CD3EAP-90	CD3EAP-90
Sample_ID	BGHcLV16-11	BGHcLV16-12
transduction_Date	4/16/19	4/16/19
days	D6	D6
RBP_name	CD3EAP	CD3EAP
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	CAGATACGGAGCTGTGGCTT
RT-qPCR_primer-R	CAATTTGCCCTTGACGATCT
protein_conc	4803	4960
WB_result	52.9	52.4
Ave_WB	52.7
WB_DONE_date	4/26/19,5/7/19	WES,Licor
MW	55D	~80KD
IP	Rabbit
antibody_Cat#	PA5-27632	TL2692990
Antibody DCC ID	ENCAB088EWX	11/24/20
submitted_to_DCC_date
Rep1_TPM	25	0
Rep2_TPM	21	0
Action	Ready	Ready
Library_start_date	12/03/19	12/03/19
repeat_library
Note
ID	6584	6585

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

	BGHcLV16-11	BGHcLV16-12
Sample_ID	BGHcLV16-11	BGHcLV16-12
Sample Name	CD3EAP-BGHcLV16-11	CD3EAP-BGHcLV16-12
Sample Name	CD3EAP-BGHcLV16-11	CD3EAP-BGHcLV16-12
RBP	CD3EAP	CD3EAP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5411	5412

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-11	BGHcLV16-12
Sample #	45	46
Sample Name	CD3EAP-BGHcLV16-11	CD3EAP-BGHcLV16-12
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-31	2020-08-31
Lib_ID	Lib-200831	Lib-200831
Tecan_Location	1-C1	1-D1
Tecan	38.18	33.49
Tecan_date	2019-12-10	2019-12-10
Size_bp	273	277
Peak_Molarity	45.10	36.20
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/C1.png	DNA_Library_set43-44/set2/D1.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set43-44/set1/C6.png	RNA_Library_set43-44/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-11	BGHcLV16-12
RBP	CD3EAP	CD3EAP
Batch_ID	BGHcLV16	BGHcLV16
WB_result	77.200	75.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	621	622

Sequencing Information

	BGHcLV16-11	BGHcLV16-12
Sample_ID	BGHcLV16-11	BGHcLV16-12
Sample Name	CD3EAP-BGHcLV16-11	CD3EAP-BGHcLV16-12
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	123,203,008	118,450,718
total_aligned_reads	112,473,498	110,340,322
unique_aligned_reads	105,358,146	103,318,732
percent_uniqueAligned	0.85516	0.87225
correlation_replicates	0.999404	0.999404
spikein_reads	143,860	167,752
percent_spikeins	0.00117	0.00142
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	123	124

Data Submission Information

	BGHcLV16-11	BGHcLV16-11	BGHcLV16-11	BGHcLV16-11	BGHcLV16-11	BGHcLV16-11	BGHcLV16-12	BGHcLV16-12	BGHcLV16-12	BGHcLV16-12
ENCODE_alias	brenton-graveley:CD3EAP-BGHcLV16	brenton-graveley:CD3EAP-BGHcLV16-11	brenton-graveley:L-CD3EAP-BGHcLV16-11	brenton-graveley:CD3EAP-BGHcLV16-11_S41_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD3EAP-BGHcLV16-11_S41_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD3EAP-BGHcLV16-HepG2	brenton-graveley:CD3EAP-BGHcLV16-12	brenton-graveley:L-CD3EAP-BGHcLV16-12	brenton-graveley:CD3EAP-BGHcLV16-12_S42_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CD3EAP-BGHcLV16-12_S42_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR400XYB	ENCBS539IKE	ENCLB643EOU	ENCFF112QUX	ENCFF459ILB	ENCSR164NKE	ENCBS888MPT	ENCLB947RPT	ENCFF515GRY	ENCFF346QAG
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	BGHcLV16-11	BGHcLV16-11	BGHcLV16-11	BGHcLV16-11	BGHcLV16-11	BGHcLV16-11	BGHcLV16-12	BGHcLV16-12	BGHcLV16-12	BGHcLV16-12
Sample Name	CD3EAP-BGHcLV16-11	CD3EAP-BGHcLV16-11	CD3EAP-BGHcLV16-11	CD3EAP-BGHcLV16-11	CD3EAP-BGHcLV16-11	CD3EAP-BGHcLV16-11	CD3EAP-BGHcLV16-12	CD3EAP-BGHcLV16-12	CD3EAP-BGHcLV16-12	CD3EAP-BGHcLV16-12
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2020-12-01	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43H_biosample_protocol	LV43H_library_protocol				LV43H_biosample_protocol	LV43H_library_protocol
protocol_URL		CD3EAP-BGHcLV16-11.pdf	L-CD3EAP-BGHcLV16-11.pdf				CD3EAP-BGHcLV16-12.pdf	L-CD3EAP-BGHcLV16-12.pdf
ID	2	86	250	416	448	7125	87	251	417	449

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-BGHcLV16-11_S41_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	123	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1
CD3EAP-BGHcLV16-11_S41_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	123	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	33
CD3EAP-BGHcLV16-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	123					GRCh38	V40	CD3EAP-BGHcLV16-11_S41_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGHcLV16-11_S41_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24164
CD3EAP-BGHcLV16-11_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	123					GRCh38	V40	CD3EAP-BGHcLV16-11/Aligned.sortedByCoord.out.bam		ENCORE2	24196
CD3EAP-BGHcLV16-11_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	123					GRCh38	V40	CD3EAP-BGHcLV16-11/Aligned.sortedByCoord.out.bam		ENCORE2	24228
CD3EAP-BGHcLV16-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	123					GRCh38	V40	CD3EAP-BGHcLV16-11/Aligned.sortedByCoord.out.bam		ENCORE2	24260
CD3EAP-BGHcLV16-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	123					GRCh38	V40	CD3EAP-BGHcLV16-11/Aligned.sortedByCoord.out.bam		ENCORE2	24292
CD3EAP-BGHcLV16-11_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	123					GRCh38	V40	CD3EAP-BGHcLV16-11_S41_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGHcLV16-11_S41_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24324
CD3EAP-BGHcLV16-12_S42_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	124	NovaSeq6000	100	paired-ended	1				NT-BGHcLV16-1_S39_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	2
CD3EAP-BGHcLV16-12_S42_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	124	NovaSeq6000	100	paired-ended	2				NT-BGHcLV16-1_S39_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV16-2_S40_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	34
CD3EAP-BGHcLV16-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	124					GRCh38	V40	CD3EAP-BGHcLV16-12_S42_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGHcLV16-12_S42_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24165
CD3EAP-BGHcLV16-12_Signal.Unique.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	124					GRCh38	V40	CD3EAP-BGHcLV16-12/Aligned.sortedByCoord.out.bam		ENCORE2	24197
CD3EAP-BGHcLV16-12_Signal.Unique.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	124					GRCh38	V40	CD3EAP-BGHcLV16-12/Aligned.sortedByCoord.out.bam		ENCORE2	24229
CD3EAP-BGHcLV16-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	124					GRCh38	V40	CD3EAP-BGHcLV16-12/Aligned.sortedByCoord.out.bam		ENCORE2	24261
CD3EAP-BGHcLV16-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	124					GRCh38	V40	CD3EAP-BGHcLV16-12/Aligned.sortedByCoord.out.bam		ENCORE2	24293
CD3EAP-BGHcLV16-12_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	124					GRCh38	V40	CD3EAP-BGHcLV16-12_S42_R1_001.filtered.trimmed.paired.fastq.gz,CD3EAP-BGHcLV16-12_S42_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24325