EIF4H RNA-Seq in HepG2

General Information


RBP	EIF4H
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF4H-BGHcLV43-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV43
Pool ID	Pool-240723
Local_Set_Name	set74
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	EIF4H-BGHcLV43-21
Rep2	EIF4H-BGHcLV43-22
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	10.6
Rep2_qPCR	15.7
Rep1_WB	94.8
Rep2_WB	92.4
Antibody Cat#	3469S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1576

Experiment Information (Status: Submitting)

	BGHcLV43-21	BGHcLV43-22
idx	1389	1390
TRCN#_or_BGC#	BGC#0001139	BGC#0001139
shRNA_or_gRNA_sequence	AATCCATGTTGGATCCACGG	AATCCATGTTGGATCCACGG
PAM	AGG	AGG
Name	EIF4H_74	EIF4H_74
Sample_ID	BGHcLV43-21	BGHcLV43-22
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	EIF4H	EIF4H
qPCR_result	10.6	15.7
Ave_qPCR	13.1
RT-qPCR_primer-F	atacggttcagggcgacata
RT-qPCR_primer-R	gggaatccacttcatcgaat
protein_conc	3321	3973
WB_result	94.8	92.4
Ave_WB	93.6
WB_DONE_date	6/13/24
MW	25,27kd
IP
antibody_Cat#	3469S	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	9642	9643

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF4H	Product_ID: 3469S Lot_ID: 1 Source: Cell Signaling Technology Target Name: EIF4H-human

Experiment Status

	BGHcLV43-21	BGHcLV43-22
Sample_ID	BGHcLV43-21	BGHcLV43-22
Sample Name
Sample Name	EIF4H-BGHcLV43-21	EIF4H-BGHcLV43-22
RBP	EIF4H	EIF4H
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13242	13243

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-21	BGHcLV43-22
Sample #	15	16
Sample Name	EIF4H-BGHcLV43-21	EIF4H-BGHcLV43-22
Sample_Name_Alias
Index Well Position	G07	H07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-07-22	2024-07-22
Lib_ID	Lib-240722	Lib-240722
Tecan_Location
Tecan
Tecan_date
Size_bp	301	287
Peak_Molarity	79.10	45.40
libSampleQC_DNA_Well	DNA_Library_set74/set1/G2.png	DNA_Library_set74/set1/H2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/C8.png	RNA_Library_set74/set1/D8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-21	BGHcLV43-22
RBP	EIF4H	EIF4H
Batch_ID	BGHcLV43	BGHcLV43
WB_result	94.800	92.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4374	4375

Sequencing Information

	BGHcLV43-21	BGHcLV43-22
Sample_ID	BGHcLV43-21	BGHcLV43-22
Sample Name	EIF4H-BGHcLV43-21	EIF4H-BGHcLV43-22
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	34,084,786	27,461,507
total_aligned_reads	30,997,435	25,156,604
unique_aligned_reads	29,150,108	23,629,998
percent_uniqueAligned	0.85522	0.86048
correlation_replicates	0.997348	0.997348
spikein_reads	19,382	14,676
percent_spikeins	0.00057	0.00053
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3241	3242

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
EIF4H-BGHcLV43-21_S105_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3241	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30532
EIF4H-BGHcLV43-21_S105_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3241	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30584
EIF4H-BGHcLV43-21_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3241					GRCh38	V40	EIF4H-BGHcLV43-21_S105_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BGHcLV43-21_S105_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30636
EIF4H-BGHcLV43-21_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3241					GRCh38	V40	EIF4H-BGHcLV43-21_Aligned.sortedByCoord.out.bam		ENCORE2	30688
EIF4H-BGHcLV43-21_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3241					GRCh38	V40	EIF4H-BGHcLV43-21_Aligned.sortedByCoord.out.bam		ENCORE2	30740
EIF4H-BGHcLV43-21_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3241					GRCh38	V40	EIF4H-BGHcLV43-21_Aligned.sortedByCoord.out.bam		ENCORE2	30792
EIF4H-BGHcLV43-21_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3241					GRCh38	V40	EIF4H-BGHcLV43-21_Aligned.sortedByCoord.out.bam		ENCORE2	30844
EIF4H-BGHcLV43-21_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3241					GRCh38	V40	EIF4H-BGHcLV43-21_S105_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BGHcLV43-21_S105_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30896
EIF4H-BGHcLV43-22_S106_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3242	NovaSeq6000	100	paired-ended	1				NT-BGHcLV43-1_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30533
EIF4H-BGHcLV43-22_S106_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3242	NovaSeq6000	100	paired-ended	2				NT-BGHcLV43-1_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV43-2_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	30585
EIF4H-BGHcLV43-22_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3242					GRCh38	V40	EIF4H-BGHcLV43-22_S106_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BGHcLV43-22_S106_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30637
EIF4H-BGHcLV43-22_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3242					GRCh38	V40	EIF4H-BGHcLV43-22_Aligned.sortedByCoord.out.bam		ENCORE2	30689
EIF4H-BGHcLV43-22_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3242					GRCh38	V40	EIF4H-BGHcLV43-22_Aligned.sortedByCoord.out.bam		ENCORE2	30741
EIF4H-BGHcLV43-22_Signal.Unique.strand-.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3242					GRCh38	V40	EIF4H-BGHcLV43-22_Aligned.sortedByCoord.out.bam		ENCORE2	30793
EIF4H-BGHcLV43-22_Signal.Unique.strand+.bw	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3242					GRCh38	V40	EIF4H-BGHcLV43-22_Aligned.sortedByCoord.out.bam		ENCORE2	30845
EIF4H-BGHcLV43-22_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3242					GRCh38	V40	EIF4H-BGHcLV43-22_S106_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BGHcLV43-22_S106_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30897