EIF4E RNA-Seq in HepG2

General Information


RBP	EIF4E
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF4E-BGHcLV16-HepG2
ENCODE_series_ID	ENCSR879ASO
Batch_ID	BGHcLV16
Pool ID	Pool-200102
Local_Set_Name	set43_H
ENCODE_KD_Exp_ID	ENCSR294DOR
ENCODE_CN_Exp_ID	ENCSR964HKT
Rep1	EIF4E-BGHcLV16-29
Rep2	EIF4E-BGHcLV16-30
CN1	NT-BGHcLV16-1
CN2	NT-BGHcLV16-2
Rep1_qPCR	79.7
Rep2_qPCR	81.7
Rep1_WB	90.3
Rep2_WB	92.8
Antibody Cat#	MA1-089
Antibody Lot#	LOT# TD257774
Antibody DCC ID	ENCAB864VOP
Status	Released
Project	ENCODE4
ID	150

Experiment Information (Status: Released)

	BGHcLV16-29	BGHcLV16-29	BGHcLV16-30	BGHcLV16-30
idx	457	459	458	460
TRCN#_or_BGC#	BGC#0000390	BGC#0000390	BGC#0000390	BGC#0000390
shRNA_or_gRNA_sequence	AAAGCTTACCTGTTCTGTAG	AAAGCTTACCTGTTCTGTAG	AAAGCTTACCTGTTCTGTAG	AAAGCTTACCTGTTCTGTAG
PAM	GGG	GGG	GGG	GGG
Name	EIF4E_80	EIF4E_80	EIF4E_80	EIF4E_80
Sample_ID	BGHcLV16-29	BGHcLV16-29	BGHcLV16-30	BGHcLV16-30
transduction_Date	4/16/19	4/16/19	4/16/19	4/16/19
days	D6	D6	D6	D6
RBP_name	EIF4E	EIF4E	EIF4E	EIF4E
qPCR_result	79.7		81.7
Ave_qPCR	80.7
RT-qPCR_primer-F	AGAAAAACAAACGGGGAGGA
RT-qPCR_primer-R	TCAAAAGATTCTCCAATAAGGCA
protein_conc	4991	4991	4257	4257
WB_result	90.3	77.4	92.8	75.7
Ave_WB	91.5	76.5
WB_DONE_date	4/29/19	5/7/19
MW	25KD	25KD
IP	Mouse / Ig	Rabbit / I		EIF4E pSer
antibody_Cat#	MA1-089	44-528G	LOT# TD257774	LOT# SG256167
Antibody DCC ID	ENCAB864VOP
submitted_to_DCC_date	4/17/19
Rep1_TPM	107	107	0	0
Rep2_TPM	111	111	0	0
Action	Ready		Ready
Library_start_date	12/03/19		12/03/19
repeat_library
Note
ID	6606	6608	6607	6609

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4E	Product_ID: MA1-089 Lot_ID: TD257774 Source: Thermo Fisher Target Name: EIF4E-human
EIF4E	Product_ID: 44-528G Lot_ID: SG256167 Source: Thermo Fisher Target Name: EIF4EphosphoS209-human Phosphate: pSer209

Experiment Status

	BGHcLV16-29	BGHcLV16-30
Sample_ID	BGHcLV16-29	BGHcLV16-30
Sample Name
Sample Name	EIF4E-BGHcLV16-29	EIF4E-BGHcLV16-30
RBP	EIF4E	EIF4E
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5419	5420

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV16-29	BGHcLV16-30
Sample #	53	54
Sample Name	EIF4E-BGHcLV16-29	EIF4E-BGHcLV16-30
Sample_Name_Alias
Index Well Position	A07	B07
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-C2	1-D2
Tecan	39.98	38.36
Tecan_date	2019-12-10	2019-12-10
Size_bp	328	283
Peak_Molarity	13.60	34.10
libSampleQC_DNA_Well	DNA_Library_set43-44/set2/C2.png	DNA_Library_set43-44/set2/D2.png
RIN	9.7	9.6
libSample_RNA_Well	RNA_Library_set43-44/set1/C7.png	RNA_Library_set43-44/set1/D7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-13	2019-12-13
Sample_ID	BGHcLV16-29	BGHcLV16-30
RBP	EIF4E	EIF4E
Batch_ID	BGHcLV16	BGHcLV16
WB_result	90.300	92.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	629	630

Sequencing Information

	BGHcLV16-29	BGHcLV16-30
Sample_ID	BGHcLV16-29	BGHcLV16-30
Sample Name	EIF4E-BGHcLV16-29	EIF4E-BGHcLV16-30
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_H	set43_H
total_reads	182,063,002	117,818,160
total_aligned_reads	170,016,916	109,817,870
unique_aligned_reads	159,060,038	102,740,232
percent_uniqueAligned	0.87365	0.87202
correlation_replicates	0.999590	0.999590
spikein_reads	259,762	150,238
percent_spikeins	0.00143	0.00128
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	131	132

Data Submission Information

	BGHcLV16-29	BGHcLV16-29	BGHcLV16-29	BGHcLV16-29	BGHcLV16-29	BGHcLV16-29	BGHcLV16-30	BGHcLV16-30	BGHcLV16-30	BGHcLV16-30
ENCODE_alias	brenton-graveley:EIF4E-BGHcLV16	brenton-graveley:EIF4E-BGHcLV16-29	brenton-graveley:L-EIF4E-BGHcLV16-29	brenton-graveley:EIF4E-BGHcLV16-29_S49_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4E-BGHcLV16-29_S49_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4E-BGHcLV16-HepG2	brenton-graveley:EIF4E-BGHcLV16-30	brenton-graveley:L-EIF4E-BGHcLV16-30	brenton-graveley:EIF4E-BGHcLV16-30_S50_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:EIF4E-BGHcLV16-30_S50_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR294DOR	ENCBS732KMO	ENCLB382RMY	ENCFF723EHK	ENCFF631HOG	ENCSR879ASO	ENCBS865GQD	ENCLB184OXM	ENCFF248EWK	ENCFF491CVX
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	BGHcLV16-29	BGHcLV16-29	BGHcLV16-29	BGHcLV16-29	BGHcLV16-29	BGHcLV16-29	BGHcLV16-30	BGHcLV16-30	BGHcLV16-30	BGHcLV16-30
Sample Name	EIF4E-BGHcLV16-29	EIF4E-BGHcLV16-29	EIF4E-BGHcLV16-29	EIF4E-BGHcLV16-29	EIF4E-BGHcLV16-29	EIF4E-BGHcLV16-29	EIF4E-BGHcLV16-30	EIF4E-BGHcLV16-30	EIF4E-BGHcLV16-30	EIF4E-BGHcLV16-30
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		EIF4E-BGHcLV16-29.pdf	L-EIF4E-BGHcLV16-29.pdf				EIF4E-BGHcLV16-30.pdf	L-EIF4E-BGHcLV16-30.pdf
ID	6	94	258	424	456	7203	95	259	425	457

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
EIF4E-BGHcLV16-29_S49_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	131	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	9
EIF4E-BGHcLV16-29_S49_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	131	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	41
EIF4E-BGHcLV16-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	131					GRCh38	V40	EIF4E-BGHcLV16-29_S49_R1_001.filtered.trimmed.paired.fastq.gz,EIF4E-BGHcLV16-29_S49_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24172
EIF4E-BGHcLV16-29_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	131					GRCh38	V40	EIF4E-BGHcLV16-29/Aligned.sortedByCoord.out.bam		ENCORE2	24204
EIF4E-BGHcLV16-29_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	131					GRCh38	V40	EIF4E-BGHcLV16-29/Aligned.sortedByCoord.out.bam		ENCORE2	24236
EIF4E-BGHcLV16-29_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	131					GRCh38	V40	EIF4E-BGHcLV16-29/Aligned.sortedByCoord.out.bam		ENCORE2	24268
EIF4E-BGHcLV16-29_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	131					GRCh38	V40	EIF4E-BGHcLV16-29/Aligned.sortedByCoord.out.bam		ENCORE2	24300
EIF4E-BGHcLV16-29_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	131					GRCh38	V40	EIF4E-BGHcLV16-29_S49_R1_001.filtered.trimmed.paired.fastq.gz,EIF4E-BGHcLV16-29_S49_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24332
EIF4E-BGHcLV16-30_S50_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	132	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	10
EIF4E-BGHcLV16-30_S50_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	132	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	42
EIF4E-BGHcLV16-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	132					GRCh38	V40	EIF4E-BGHcLV16-30_S50_R1_001.filtered.trimmed.paired.fastq.gz,EIF4E-BGHcLV16-30_S50_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24173
EIF4E-BGHcLV16-30_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	132					GRCh38	V40	EIF4E-BGHcLV16-30/Aligned.sortedByCoord.out.bam		ENCORE2	24205
EIF4E-BGHcLV16-30_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	132					GRCh38	V40	EIF4E-BGHcLV16-30/Aligned.sortedByCoord.out.bam		ENCORE2	24237
EIF4E-BGHcLV16-30_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	132					GRCh38	V40	EIF4E-BGHcLV16-30/Aligned.sortedByCoord.out.bam		ENCORE2	24269
EIF4E-BGHcLV16-30_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	132					GRCh38	V40	EIF4E-BGHcLV16-30/Aligned.sortedByCoord.out.bam		ENCORE2	24301
EIF4E-BGHcLV16-30_quant.sf	ENCODE_DATA/set43_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	132					GRCh38	V40	EIF4E-BGHcLV16-30_S50_R1_001.filtered.trimmed.paired.fastq.gz,EIF4E-BGHcLV16-30_S50_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24333