EIF1 RNA-Seq in HepG2

General Information


RBP	EIF1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	EIF1-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	EIF1-BGHcLV43-17
Rep2	EIF1-BGHcLV43-18
CN1	NT-BGHcLV43-1
CN2	NT-BGHcLV43-2
Rep1_qPCR	45.9
Rep2_qPCR	40.1
Rep1_WB	60.5
Rep2_WB	75.6716
Antibody Cat#	12496S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1575

Experiment Information (Status: Submitting)

	BGHcLV43-17	BGHcLV43-18
idx	1385	1386
TRCN#_or_BGC#	BGC#0001134	BGC#0001134
shRNA_or_gRNA_sequence	CCACTCTTTCGGTAAGCTAT	CCACTCTTTCGGTAAGCTAT
PAM	GGG	GGG
Name	EIF1_94	EIF1_94
Sample_ID	BGHcLV43-17	BGHcLV43-18
transduction_Date	6/6/24	6/6/24
days	D6	D6
RBP_name	EIF1	EIF1
qPCR_result	45.9	40.1
Ave_qPCR	43.0
RT-qPCR_primer-F	cagagaaacggcaggaagac
RT-qPCR_primer-R	tctccatattccggatgctc
protein_conc	2915	3113
WB_result	60.5	75.6716
Ave_WB	68.1
WB_DONE_date	6/13/24,6/21/24
MW	13kd
IP
antibody_Cat#	12496S	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	9638	9639

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
EIF1	Product_ID: 12496S Lot_ID: 1 Source: Cell Signaling Technology Target Name: EIF1-human

Experiment Status

	BGHcLV43-17	BGHcLV43-18
Sample_ID	BGHcLV43-17	BGHcLV43-18
Sample Name
Sample Name	EIF1-BGHcLV43-17	EIF1-BGHcLV43-18
RBP	EIF1	EIF1
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-02-11	2025-02-11
Project	ENCORE2	ENCORE2
Note
ID	13240	13241

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV43-17	BGHcLV43-18
Sample #	13	14
Sample Name	EIF1-BGHcLV43-17	EIF1-BGHcLV43-18
Sample_Name_Alias
Index Well Position	E07	F07
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	300
Peak_Molarity	89.60	86.80
libSampleQC_DNA_Well	DNA_Library_set74/set1/E2.png	DNA_Library_set74/set1/F2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set74/set1/A8.png	RNA_Library_set74/set1/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-07-23	2024-07-23
Sample_ID	BGHcLV43-17	BGHcLV43-18
RBP	EIF1	EIF1
Batch_ID	BGHcLV43	BGHcLV43
WB_result	60.500	75.672
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4372	4373

Sequencing Information

	BGHcLV43-17	BGHcLV43-18
Sample_ID	BGHcLV43-17	BGHcLV43-18
Sample Name	EIF1-BGHcLV43-17	EIF1-BGHcLV43-18
Pool ID	Pool-240723	Pool-240723
LocalServer_folder	set74	set74
total_reads	41,881,700	33,289,508
total_aligned_reads	38,464,264	31,129,192
unique_aligned_reads	36,176,265	29,278,489
percent_uniqueAligned	0.86377	0.87951
correlation_replicates	0.999819	0.999819
spikein_reads	21,914	14,600
percent_spikeins	0.00052	0.00044
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3239	3240

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
EIF1-BGHcLV43-17_S103_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3239	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	30528
EIF1-BGHcLV43-17_S103_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3239	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	30580
EIF1-BGHcLV43-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3239					GRCh38	V40	EIF1-BGHcLV43-17_S103_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGHcLV43-17_S103_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30632
EIF1-BGHcLV43-17_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	3239					GRCh38	V40	EIF1-BGHcLV43-17_Aligned.sortedByCoord.out.bam		ENCORE2	30684
EIF1-BGHcLV43-17_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	3239					GRCh38	V40	EIF1-BGHcLV43-17_Aligned.sortedByCoord.out.bam		ENCORE2	30736
EIF1-BGHcLV43-17_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	3239					GRCh38	V40	EIF1-BGHcLV43-17_Aligned.sortedByCoord.out.bam		ENCORE2	30788
EIF1-BGHcLV43-17_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	3239					GRCh38	V40	EIF1-BGHcLV43-17_Aligned.sortedByCoord.out.bam		ENCORE2	30840
EIF1-BGHcLV43-17_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3239					GRCh38	V40	EIF1-BGHcLV43-17_S103_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGHcLV43-17_S103_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30892
EIF1-BGHcLV43-18_S104_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3240	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	30529
EIF1-BGHcLV43-18_S104_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set74/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3240	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	30581
EIF1-BGHcLV43-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set74/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3240					GRCh38	V40	EIF1-BGHcLV43-18_S104_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGHcLV43-18_S104_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30633
EIF1-BGHcLV43-18_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	3240					GRCh38	V40	EIF1-BGHcLV43-18_Aligned.sortedByCoord.out.bam		ENCORE2	30685
EIF1-BGHcLV43-18_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	3240					GRCh38	V40	EIF1-BGHcLV43-18_Aligned.sortedByCoord.out.bam		ENCORE2	30737
EIF1-BGHcLV43-18_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	3240					GRCh38	V40	EIF1-BGHcLV43-18_Aligned.sortedByCoord.out.bam		ENCORE2	30789
EIF1-BGHcLV43-18_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	3240					GRCh38	V40	EIF1-BGHcLV43-18_Aligned.sortedByCoord.out.bam		ENCORE2	30841
EIF1-BGHcLV43-18_quant.sf	ENCODE_DATA/set74/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3240					GRCh38	V40	EIF1-BGHcLV43-18_S104_L003_R1_001.filtered.trimmed.paired.fastq.gz,EIF1-BGHcLV43-18_S104_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30893