EIF5B RNA-Seq in HepG2

General Information


RBP	EIF5B
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF5B-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF5B-BGHcLV45-29
Rep2	EIF5B-BGHcLV45-30
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	73.1
Rep2_WB	77.8
Antibody Cat#	A301-745A
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1623

Experiment Information (Status: Submitting)

	BGHcLV45-29	BGHcLV45-30
idx	1217	1217
TRCN#_or_BGC#	BGC#0000985	BGC#0000985
shRNA_or_gRNA_sequence	AGCGCCATTGACAAGCAATG	AGCGCCATTGACAAGCAATG
PAM	GGG	GGG
Name	EIF5B_81	EIF5B_81
Sample_ID	BGHcLV45-29	BGHcLV45-30
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	EIF5B	EIF5B
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	agagagaagccagagccaga
RT-qPCR_primer-R	tttgatggcacttcaacacc
protein_conc	2448	3280
WB_result	73.1	77.8
Ave_WB
WB_DONE_date	10/15/24
MW	139kd
IP
antibody_Cat#	A301-745A	lot # 1
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date
repeat_library
Note
ID	9719	9720

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHcLV45-29	BGHcLV45-30
Sample_ID	BGHcLV45-29	BGHcLV45-30
Sample Name
Sample Name	EIF5B-BGHcLV45-29	EIF5B-BGHcLV45-30
RBP	EIF5B	EIF5B
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13704	13705

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-29	BGHcLV45-30
Sample #	19	20
Sample Name	EIF5B-BGHcLV45-29	EIF5B-BGHcLV45-30
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	288	291
Peak_Molarity	83.40	76.50
libSampleQC_DNA_Well	DNA_Library_set76/set1/C9.png	DNA_Library_set76/set1/D9.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set76/set1/C3.png	RNA_Library_set76/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-29	BGHcLV45-30
RBP	EIF5B	EIF5B
Batch_ID	BGHcLV45	BGHcLV45
WB_result	73.100	77.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4628	4629

Sequencing Information

	BGHcLV45-29	BGHcLV45-30
Sample_ID	BGHcLV45-29	BGHcLV45-30
Sample Name	EIF5B-BGHcLV45-29	EIF5B-BGHcLV45-30
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	42,293,417	35,671,368
total_aligned_reads	38,150,673	32,263,580
unique_aligned_reads	35,917,467	30,378,277
percent_uniqueAligned	0.84924	0.85162
correlation_replicates	0.999146	0.999146
spikein_reads	42,904	19,442
percent_spikeins	0.00101	0.00055
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3339	3340

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
EIF5B-BGHcLV45-29_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3339	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31828
EIF5B-BGHcLV45-29_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3339	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31870
EIF5B-BGHcLV45-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3339					GRCh38	V40	EIF5B-BGHcLV45-29_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF5B-BGHcLV45-29_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31912
EIF5B-BGHcLV45-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3339					GRCh38	V40	EIF5B-BGHcLV45-29_Aligned.sortedByCoord.out.bam		ENCORE2	31954
EIF5B-BGHcLV45-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3339					GRCh38	V40	EIF5B-BGHcLV45-29_Aligned.sortedByCoord.out.bam		ENCORE2	31996
EIF5B-BGHcLV45-29_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3339					GRCh38	V40	EIF5B-BGHcLV45-29_Aligned.sortedByCoord.out.bam		ENCORE2	32038
EIF5B-BGHcLV45-29_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3339					GRCh38	V40	EIF5B-BGHcLV45-29_Aligned.sortedByCoord.out.bam		ENCORE2	32080
EIF5B-BGHcLV45-29_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3339					GRCh38	V40	EIF5B-BGHcLV45-29_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF5B-BGHcLV45-29_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32122
EIF5B-BGHcLV45-30_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3340	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31829
EIF5B-BGHcLV45-30_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3340	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31871
EIF5B-BGHcLV45-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3340					GRCh38	V40	EIF5B-BGHcLV45-30_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF5B-BGHcLV45-30_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31913
EIF5B-BGHcLV45-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3340					GRCh38	V40	EIF5B-BGHcLV45-30_Aligned.sortedByCoord.out.bam		ENCORE2	31955
EIF5B-BGHcLV45-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3340					GRCh38	V40	EIF5B-BGHcLV45-30_Aligned.sortedByCoord.out.bam		ENCORE2	31997
EIF5B-BGHcLV45-30_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3340					GRCh38	V40	EIF5B-BGHcLV45-30_Aligned.sortedByCoord.out.bam		ENCORE2	32039
EIF5B-BGHcLV45-30_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3340					GRCh38	V40	EIF5B-BGHcLV45-30_Aligned.sortedByCoord.out.bam		ENCORE2	32081
EIF5B-BGHcLV45-30_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3340					GRCh38	V40	EIF5B-BGHcLV45-30_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF5B-BGHcLV45-30_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32123