EIF3L RNA-Seq in HepG2

General Information


RBP	EIF3L
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF3L-BGHcLV39-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV39
Pool ID	Pool-230830
Local_Set_Name	set63
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF3L-BGHcLV39-61
Rep2	EIF3L-BGHcLV39-62
CN1	NT-BGHcLV39-1
CN2	NT-BGHcLV39-2
Rep1_qPCR	63.8
Rep2_qPCR	55.2
Rep1_WB	80.2
Rep2_WB	76.1
Antibody Cat#	A304-754A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1252

Experiment Information (Status: Submitting)

	BGHcLV39-61	BGHcLV39-62
idx	1263	1264
TRCN#_or_BGC#	BGC#0000975	BGC#0000975
shRNA_or_gRNA_sequence	GCAGGCGGAGAAGCCCGACC	GCAGGCGGAGAAGCCCGACC
PAM	AGG	AGG
Name	EIF3L_83	EIF3L_83
Sample_ID	BGHcLV39-61	BGHcLV39-62
transduction_Date	6/10/23	6/10/23
days	D6	D6
RBP_name	EIF3L	EIF3L
qPCR_result	63.8	55.2
Ave_qPCR	59.5
RT-qPCR_primer-F	gctacaggccagtcgtgtct
RT-qPCR_primer-R	gggccaaggtgtattcttga
protein_conc	1435	2149
WB_result	80.2	76.1
Ave_WB	78.1
WB_DONE_date	7/5/23
MW	67KD
IP
antibody_Cat#	A304-754A	lot # 1
Antibody DCC ID
submitted_to_DCC_date	9/6/23
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	7454	7455

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF3L	Product_ID: A304-754A Lot_ID: 1 Source: Bethyl Labs Target Name: EIF3L-human

Experiment Status

	BGHcLV39-61	BGHcLV39-62
Sample_ID	BGHcLV39-61	BGHcLV39-62
Sample Name
Sample Name	EIF3L-BGHcLV39-61	EIF3L-BGHcLV39-62
RBP	EIF3L	EIF3L
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	11996	11997

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV39-61	BGHcLV39-62
Sample #	23	24
Sample Name	EIF3L-BGHcLV39-61	EIF3L-BGHcLV39-62
Sample_Name_Alias
Index Well Position	G03	H03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-08-28	2023-08-28
Lib_ID	Lib-230828	Lib-230828
Tecan_Location
Tecan
Tecan_date
Size_bp	277	278
Peak_Molarity	19.50	48.90
libSampleQC_DNA_Well	DNA_Library_set63/set1/G11.png	DNA_Library_set63/set1/H11.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set63/set1/G11.png	RNA_Library_set63/set1/H11.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-08-30	2023-08-30
Sample_ID	BGHcLV39-61	BGHcLV39-62
RBP	EIF3L	EIF3L
Batch_ID	BGHcLV39	BGHcLV39
WB_result	80.200	76.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3766	3767

Sequencing Information

	BGHcLV39-61	BGHcLV39-62
Sample_ID	BGHcLV39-61	BGHcLV39-62
Sample Name	EIF3L-BGHcLV39-61	EIF3L-BGHcLV39-62
Pool ID	Pool-230830	Pool-230830
LocalServer_folder	set63	set63
total_reads	46,029,314	53,127,453
total_aligned_reads	28,955,941	40,742,204
unique_aligned_reads	27,312,614	38,450,669
percent_uniqueAligned	0.59337	0.72374
correlation_replicates	0.999233	0.999233
spikein_reads	19,702	18,778
percent_spikeins	0.00043	0.00035
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2665	2666

Data Submission Information DCC submission information was not avaliable

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
EIF3L-BGHcLV39-61_S17_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2665	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8650
EIF3L-BGHcLV39-61_S17_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2665	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8676
EIF3L-BGHcLV39-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2665					GRCh38	V40	EIF3L-BGHcLV39-61_S17_R1_001.filtered.trimmed.paired.fastq.gz,EIF3L-BGHcLV39-61_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9947
EIF3L-BGHcLV39-61_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2665					GRCh38	V40	EIF3L-BGHcLV39-61/Aligned.sortedByCoord.out.bam		ENCORE2	9973
EIF3L-BGHcLV39-61_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2665					GRCh38	V40	EIF3L-BGHcLV39-61/Aligned.sortedByCoord.out.bam		ENCORE2	9999
EIF3L-BGHcLV39-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2665					GRCh38	V40	EIF3L-BGHcLV39-61/Aligned.sortedByCoord.out.bam		ENCORE2	10025
EIF3L-BGHcLV39-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2665					GRCh38	V40	EIF3L-BGHcLV39-61/Aligned.sortedByCoord.out.bam		ENCORE2	10051
EIF3L-BGHcLV39-61_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2665					GRCh38	V40	EIF3L-BGHcLV39-61_S17_R1_001.filtered.trimmed.paired.fastq.gz,EIF3L-BGHcLV39-61_S17_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10077
EIF3L-BGHcLV39-62_S18_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2666	NovaSeq6000	100	paired-ended	1				NT-BGHcLV39-1_S476_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8651
EIF3L-BGHcLV39-62_S18_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set63/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2666	NovaSeq6000	100	paired-ended	2				NT-BGHcLV39-1_S476_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV39-2_S477_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8677
EIF3L-BGHcLV39-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2666					GRCh38	V40	EIF3L-BGHcLV39-62_S18_R1_001.filtered.trimmed.paired.fastq.gz,EIF3L-BGHcLV39-62_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9948
EIF3L-BGHcLV39-62_Signal.Unique.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2666					GRCh38	V40	EIF3L-BGHcLV39-62/Aligned.sortedByCoord.out.bam		ENCORE2	9974
EIF3L-BGHcLV39-62_Signal.Unique.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2666					GRCh38	V40	EIF3L-BGHcLV39-62/Aligned.sortedByCoord.out.bam		ENCORE2	10000
EIF3L-BGHcLV39-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2666					GRCh38	V40	EIF3L-BGHcLV39-62/Aligned.sortedByCoord.out.bam		ENCORE2	10026
EIF3L-BGHcLV39-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set63/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2666					GRCh38	V40	EIF3L-BGHcLV39-62/Aligned.sortedByCoord.out.bam		ENCORE2	10052
EIF3L-BGHcLV39-62_quant.sf	ENCODE_DATA/set63/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2666					GRCh38	V40	EIF3L-BGHcLV39-62_S18_R1_001.filtered.trimmed.paired.fastq.gz,EIF3L-BGHcLV39-62_S18_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10078