E4F1 RNA-Seq in K562

General Information


RBP	E4F1
Cell_Line	K562
Method	CRISPR
Exp_Name	E4F1-BGKcLV17-K562
ENCODE_series_ID	ENCSR623NZK
Batch_ID	BGKcLV17
Pool ID	Pool-200103
Local_Set_Name	set44_K
ENCODE_KD_Exp_ID	ENCSR916PCG
ENCODE_CN_Exp_ID	ENCSR516TLX
Rep1	E4F1-BGKcLV17-15
Rep2	E4F1-BGKcLV17-16
CN1	NT-BGKcLV17-1
CN2	NT-BGKcLV17-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	65.9
Rep2_WB	74.7
Antibody Cat#	PA5-67167
Antibody Lot#	lot# UC2739267A
Antibody DCC ID	ENCAB559HVW
Status	Released
Project	ENCODE4
ID	83

Experiment Information (Status: Released)

	BGKcLV17-15	BGKcLV17-16
idx	622	623
TRCN#_or_BGC#	BGC#0000433	BGC#0000433
shRNA_or_gRNA_sequence	TTGCGACATGGAGGGCGCGA	TTGCGACATGGAGGGCGCGA
PAM	TGG	TGG
Name	E4F1_96	E4F1_96
Sample_ID	BGKcLV17-15	BGKcLV17-16
transduction_Date	7/2/19	7/2/19
days	Day 6	Day 6
RBP_name	E4F1	E4F1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GACGTGGTTGTCAGCAAAGA
RT-qPCR_primer-R	CTATAGGCTCGCCTGTCACC
protein_conc	5511	5446
WB_result	65.9	74.7
Ave_WB	70.3
WB_DONE_date	8/30/19	WES
MW	83KD
IP	Rabbit / I
antibody_Cat#	PA5-67167	lot# UC2739267A
Antibody DCC ID	ENCAB559HVW
submitted_to_DCC_date
Rep1_TPM	16.9	0
Rep2_TPM	3.8	0
Action	Ready	Ready
Library_start_date	12/05/19	12/05/19
repeat_library
Note
ID	4738	4739

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
E4F1	Product_ID: PA5-67167 Lot_ID: UC2739267A Source: Thermo Fisher Target Name: E4F1-human

Experiment Status

	BGKcLV17-15	BGKcLV17-16
Sample_ID	BGKcLV17-15	BGKcLV17-16
Sample Name
Sample Name	E4F1-BGKcLV17-15	E4F1-BGKcLV17-16
RBP	E4F1	E4F1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5499	5500

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV17-15	BGKcLV17-16
Sample #	89	90
Sample Name	E4F1-BGKcLV17-15	E4F1-BGKcLV17-16
Sample_Name_Alias
Index Well Position	G11	H11
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	1-E1	1-F1
Tecan	33.83	31.43
Tecan_date	2019-12-16	2019-12-16
Size_bp	274	276
Peak_Molarity	23.90	18.30
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/G7.png	DNA_Library_set43-44/set1/H7.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/G2.png	RNA_Library_set43-44/set4/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV17-15	BGKcLV17-16
RBP	E4F1	E4F1
Batch_ID	BGKcLV17	BGKcLV17
WB_result	65.900	74.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	665	666

Sequencing Information

	BGKcLV17-15	BGKcLV17-16
Sample_ID	BGKcLV17-15	BGKcLV17-16
Sample Name	E4F1-BGKcLV17-15	E4F1-BGKcLV17-16
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_K	set44_K
total_reads	127,764,524	219,108,388
total_aligned_reads	121,859,152	202,118,536
unique_aligned_reads	110,961,546	183,685,668
percent_uniqueAligned	0.86848	0.83833
correlation_replicates	0.998081	0.998081
spikein_reads	24,532	72,960
percent_spikeins	0.00019	0.00033
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	171	172

Data Submission Information

	BGKcLV17-15	BGKcLV17-15	BGKcLV17-15	BGKcLV17-15	BGKcLV17-15	BGKcLV17-15	BGKcLV17-16	BGKcLV17-16	BGKcLV17-16	BGKcLV17-16
ENCODE_alias	brenton-graveley:E4F1-BGKcLV17	brenton-graveley:E4F1-BGKcLV17-15	brenton-graveley:L-E4F1-BGKcLV17-15	brenton-graveley:E4F1-BGKcLV17-15_S1_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:E4F1-BGKcLV17-15_S1_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:E4F1-BGKcLV17-K562	brenton-graveley:E4F1-BGKcLV17-16	brenton-graveley:L-E4F1-BGKcLV17-16	brenton-graveley:E4F1-BGKcLV17-16_S2_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:E4F1-BGKcLV17-16_S2_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR916PCG	ENCBS605NDI	ENCLB260ZWH	ENCFF731MFE	ENCFF884OET	ENCSR623NZK	ENCBS805LKE	ENCLB128JEB	ENCFF788UWZ	ENCFF392YGE
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	BGKcLV17-15	BGKcLV17-15	BGKcLV17-15	BGKcLV17-15	BGKcLV17-15	BGKcLV17-15	BGKcLV17-16	BGKcLV17-16	BGKcLV17-16	BGKcLV17-16
Sample Name	E4F1-BGKcLV17-15	E4F1-BGKcLV17-15	E4F1-BGKcLV17-15	E4F1-BGKcLV17-15	E4F1-BGKcLV17-15	E4F1-BGKcLV17-15	E4F1-BGKcLV17-16	E4F1-BGKcLV17-16	E4F1-BGKcLV17-16	E4F1-BGKcLV17-16
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2020-12-01	2022-02-04	2020-12-01	2020-12-01	2020-12-01	2022-03-02	2022-02-04	2020-12-01	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV44K_biosample_protocol	LV44K_library_protocol				LV44K_biosample_protocol	LV44K_library_protocol
protocol_URL		E4F1-BGKcLV17-15.pdf	L-E4F1-BGKcLV17-15.pdf				E4F1-BGKcLV17-16.pdf	L-E4F1-BGKcLV17-16.pdf
ID	69	218	384	686	716	7195	219	385	687	717

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
E4F1-BGKcLV17-15_S1_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	171	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	273
E4F1-BGKcLV17-15_S1_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	171	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	303
E4F1-BGKcLV17-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	171					GRCh38	V40	E4F1-BGKcLV17-15_S1_R1_001.filtered.trimmed.paired.fastq.gz,E4F1-BGKcLV17-15_S1_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24669
E4F1-BGKcLV17-15_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	171					GRCh38	V40	E4F1-BGKcLV17-15/Aligned.sortedByCoord.out.bam		ENCORE2	24699
E4F1-BGKcLV17-15_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	171					GRCh38	V40	E4F1-BGKcLV17-15/Aligned.sortedByCoord.out.bam		ENCORE2	24729
E4F1-BGKcLV17-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	171					GRCh38	V40	E4F1-BGKcLV17-15/Aligned.sortedByCoord.out.bam		ENCORE2	24759
E4F1-BGKcLV17-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	171					GRCh38	V40	E4F1-BGKcLV17-15/Aligned.sortedByCoord.out.bam		ENCORE2	24789
E4F1-BGKcLV17-15_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	171					GRCh38	V40	E4F1-BGKcLV17-15_S1_R1_001.filtered.trimmed.paired.fastq.gz,E4F1-BGKcLV17-15_S1_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24819
E4F1-BGKcLV17-16_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	172	NovaSeq6000	100	paired-ended	1				NT-BGKcLV17-1_S71_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	274
E4F1-BGKcLV17-16_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	172	NovaSeq6000	100	paired-ended	2				NT-BGKcLV17-1_S71_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV17-2_S72_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	304
E4F1-BGKcLV17-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	172					GRCh38	V40	E4F1-BGKcLV17-16_S2_R1_001.filtered.trimmed.paired.fastq.gz,E4F1-BGKcLV17-16_S2_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24670
E4F1-BGKcLV17-16_Signal.Unique.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	172					GRCh38	V40	E4F1-BGKcLV17-16/Aligned.sortedByCoord.out.bam		ENCORE2	24700
E4F1-BGKcLV17-16_Signal.Unique.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	172					GRCh38	V40	E4F1-BGKcLV17-16/Aligned.sortedByCoord.out.bam		ENCORE2	24730
E4F1-BGKcLV17-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	172					GRCh38	V40	E4F1-BGKcLV17-16/Aligned.sortedByCoord.out.bam		ENCORE2	24760
E4F1-BGKcLV17-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	172					GRCh38	V40	E4F1-BGKcLV17-16/Aligned.sortedByCoord.out.bam		ENCORE2	24790
E4F1-BGKcLV17-16_quant.sf	ENCODE_DATA/set44_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	172					GRCh38	V40	E4F1-BGKcLV17-16_S2_R1_001.filtered.trimmed.paired.fastq.gz,E4F1-BGKcLV17-16_S2_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24820