E4F1 RNA-Seq in HepG2

General Information


RBP	E4F1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	E4F1-BGHcLV18-HepG2
ENCODE_series_ID	ENCSR237FWP
Batch_ID	BGHcLV18
Pool ID	Pool-200103
Local_Set_Name	set44_H
ENCODE_KD_Exp_ID	ENCSR308EYT
ENCODE_CN_Exp_ID	ENCSR670KAS
Rep1	E4F1-BGHcLV18-15
Rep2	E4F1-BGHcLV18-16
CN1	NT-BGHcLV18-1
CN2	NT-BGHcLV18-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	97.4
Rep2_WB	97.9
Antibody Cat#	PA5-67167
Antibody Lot#	lot# UC2739267A
Antibody DCC ID	ENCAB559HVW
Status	Released
Project	ENCODE4
ID	105

Experiment Information (Status: Released)

	BGHcLV18-15	BGHcLV18-16
idx	508	509
TRCN#_or_BGC#	BGC#0000434	BGC#0000434
shRNA_or_gRNA_sequence	CTGGGCTTCTGCCGTATGAG	CTGGGCTTCTGCCGTATGAG
PAM	CGG	CGG
Name	E4F1_92	E4F1_92
Sample_ID	BGHcLV18-15	BGHcLV18-16
transduction_Date	8/13/19	8/13/19
days	D6	D6
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	4260	4197
WB_result	97.4	97.9
Ave_WB	97.7
WB_DONE_date	8/26/19	WES
MW	83KD
IP	Rabbit / I
antibody_Cat#	PA5-67167	lot# UC2739267A
Antibody DCC ID	ENCAB559HVW
submitted_to_DCC_date
Rep1_TPM	19	0
Rep2_TPM	2	0
Action	Ready	Ready
Library_start_date	12/11/19	12/11/19
repeat_library
Note
ID	6661	6662

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

	BGHcLV18-15	BGHcLV18-16
Sample_ID	BGHcLV18-15	BGHcLV18-16
Sample Name
Sample Name	E4F1-BGHcLV18-15	E4F1-BGHcLV18-16
RBP	E4F1	E4F1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5627	5628

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV18-15	BGHcLV18-16
Sample #	133	134
Sample Name	E4F1-BGHcLV18-15	E4F1-BGHcLV18-16
Sample_Name_Alias
Index Well Position	G05	H05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-01-02	2020-01-02
Lib_ID	Lib-200102	Lib-200102
Tecan_Location	4-A1	4-B1
Tecan	41.22	37.79
Tecan_date	2019-12-16	2019-12-16
Size_bp	302	266
Peak_Molarity	22.20	20.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/G6.png	DNA_Library_set43-44/set2/H6.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set43-44/set4/C8.png	RNA_Library_set43-44/set4/D8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV18-15	BGHcLV18-16
RBP	E4F1	E4F1
Batch_ID	BGHcLV18	BGHcLV18
WB_result	97.400	97.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	709	710

Sequencing Information

	BGHcLV18-15	BGHcLV18-16
Sample_ID	BGHcLV18-15	BGHcLV18-16
Sample Name	E4F1-BGHcLV18-15	E4F1-BGHcLV18-16
Pool ID	Pool-200103	Pool-200103
LocalServer_folder	set44_H	set44_H
total_reads	224,004,854	217,488,570
total_aligned_reads	213,330,344	212,470,410
unique_aligned_reads	199,516,702	198,540,624
percent_uniqueAligned	0.89068	0.91288
correlation_replicates	0.999064	0.999064
spikein_reads	368,832	376,470
percent_spikeins	0.00165	0.00173
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	215	216

Data Submission Information

	BGHcLV18-15	BGHcLV18-15	BGHcLV18-15	BGHcLV18-15	BGHcLV18-15	BGHcLV18-15	BGHcLV18-16	BGHcLV18-16	BGHcLV18-16	BGHcLV18-16
ENCODE_alias	brenton-graveley:E4F1-BGHcLV18	brenton-graveley:E4F1-BGHcLV18-15	brenton-graveley:L-E4F1-BGHcLV18-15	brenton-graveley:E4F1-BGHcLV18-15_S49_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:E4F1-BGHcLV18-15_S49_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:E4F1-BGHcLV18-HepG2	brenton-graveley:E4F1-BGHcLV18-16	brenton-graveley:L-E4F1-BGHcLV18-16	brenton-graveley:E4F1-BGHcLV18-16_S50_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:E4F1-BGHcLV18-16_S50_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR308EYT	ENCBS074IQT	ENCLB518TBS	ENCFF377IEQ	ENCFF060WBA	ENCSR237FWP	ENCBS641IRB	ENCLB066KIU	ENCFF208OYF	ENCFF826MOB
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	BGHcLV18-15	BGHcLV18-15	BGHcLV18-15	BGHcLV18-15	BGHcLV18-15	BGHcLV18-15	BGHcLV18-16	BGHcLV18-16	BGHcLV18-16	BGHcLV18-16
Sample Name	E4F1-BGHcLV18-15	E4F1-BGHcLV18-15	E4F1-BGHcLV18-15	E4F1-BGHcLV18-15	E4F1-BGHcLV18-15	E4F1-BGHcLV18-15	E4F1-BGHcLV18-16	E4F1-BGHcLV18-16	E4F1-BGHcLV18-16	E4F1-BGHcLV18-16
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
		LV44H_biosample_protocol	LV44H_library_protocol				LV44H_biosample_protocol	LV44H_library_protocol
protocol_URL		E4F1-BGHcLV18-15.pdf	L-E4F1-BGHcLV18-15.pdf				E4F1-BGHcLV18-16.pdf	L-E4F1-BGHcLV18-16.pdf
ID	52	184	350	600	652	7194	185	351	601	653

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-BGHcLV18-15_S49_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	215	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	181
E4F1-BGHcLV18-15_S49_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	215	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	233
E4F1-BGHcLV18-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	215					GRCh38	V40	E4F1-BGHcLV18-15_S49_R1_001.filtered.trimmed.paired.fastq.gz,E4F1-BGHcLV18-15_S49_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24901
E4F1-BGHcLV18-15_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	215					GRCh38	V40	E4F1-BGHcLV18-15/Aligned.sortedByCoord.out.bam		ENCORE2	24953
E4F1-BGHcLV18-15_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	215					GRCh38	V40	E4F1-BGHcLV18-15/Aligned.sortedByCoord.out.bam		ENCORE2	25005
E4F1-BGHcLV18-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	215					GRCh38	V40	E4F1-BGHcLV18-15/Aligned.sortedByCoord.out.bam		ENCORE2	25057
E4F1-BGHcLV18-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	215					GRCh38	V40	E4F1-BGHcLV18-15/Aligned.sortedByCoord.out.bam		ENCORE2	25109
E4F1-BGHcLV18-15_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	215					GRCh38	V40	E4F1-BGHcLV18-15_S49_R1_001.filtered.trimmed.paired.fastq.gz,E4F1-BGHcLV18-15_S49_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25161
E4F1-BGHcLV18-16_S50_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	216	NovaSeq6000	100	paired-ended	1				NT-BGHcLV18-1_S35_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	182
E4F1-BGHcLV18-16_S50_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set44_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	216	NovaSeq6000	100	paired-ended	2				NT-BGHcLV18-1_S35_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV18-2_S36_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	234
E4F1-BGHcLV18-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	216					GRCh38	V40	E4F1-BGHcLV18-16_S50_R1_001.filtered.trimmed.paired.fastq.gz,E4F1-BGHcLV18-16_S50_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24902
E4F1-BGHcLV18-16_Signal.Unique.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	216					GRCh38	V40	E4F1-BGHcLV18-16/Aligned.sortedByCoord.out.bam		ENCORE2	24954
E4F1-BGHcLV18-16_Signal.Unique.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	216					GRCh38	V40	E4F1-BGHcLV18-16/Aligned.sortedByCoord.out.bam		ENCORE2	25006
E4F1-BGHcLV18-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	216					GRCh38	V40	E4F1-BGHcLV18-16/Aligned.sortedByCoord.out.bam		ENCORE2	25058
E4F1-BGHcLV18-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set44_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	216					GRCh38	V40	E4F1-BGHcLV18-16/Aligned.sortedByCoord.out.bam		ENCORE2	25110
E4F1-BGHcLV18-16_quant.sf	ENCODE_DATA/set44_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	216					GRCh38	V40	E4F1-BGHcLV18-16_S50_R1_001.filtered.trimmed.paired.fastq.gz,E4F1-BGHcLV18-16_S50_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25162