EIF4H RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-111	BG293LV05-112
idx	0	0
TRCN#_or_BGC#	TRCN0000275601	TRCN0000275601
shRNA_or_gRNA_sequence	CCGGGAGTGCATGTCAGCTGTTAACCTCGAGGTTAACAGCTGACATGCACTCTTTTTG	CCGGGAGTGCATGTCAGCTGTTAACCTCGAGGTTAACAGCTGACATGCACTCTTTTTG
PAM
Name	EIF4H	EIF4H
Sample_ID	BG293LV05-111	BG293LV05-112
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	EIF4H	EIF4H
qPCR_result	86.6	85.6
Ave_qPCR	86.1
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	0	0
WB_result
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#
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	10083	10084

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-111	BG293LV05-112
Sample_ID	BG293LV05-111	BG293LV05-112
Sample Name
Sample Name	EIF4H-BG293LV05-111	EIF4H-BG293LV05-112
RBP	EIF4H	EIF4H
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12876	12877

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-111	BG293LV05-112
Sample #	43	44
Sample Name	EIF4H-BG293LV05-111	EIF4H-BG293LV05-112
Sample_Name_Alias
Index Well Position	C12	D12
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	270	264
Peak_Molarity	75.40	88.30
libSampleQC_DNA_Well	DNA_Library_set69/set1/C6.png	DNA_Library_set69/set1/D6.png
RIN	9.9	9.6
libSample_RNA_Well	RNA_Library_set69/set2/C8.png	RNA_Library_set69/set2/D8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-111	BG293LV05-112
RBP	EIF4H	EIF4H
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4224	4225

Sequencing Information

	BG293LV05-111	BG293LV05-112
Sample_ID	BG293LV05-111	BG293LV05-112
Sample Name	EIF4H-BG293LV05-111	EIF4H-BG293LV05-112
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	15,457,778	14,690,752
total_aligned_reads	12,775,434	11,538,544
unique_aligned_reads	11,912,493	10,749,820
percent_uniqueAligned	0.77065	0.73174
correlation_replicates	0.983586	0.983586
spikein_reads	3,412	1,782
percent_spikeins	0.00022	0.00012
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2943	2944

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-BG293LV05-111_S175_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2943	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28499
EIF4H-BG293LV05-111_S175_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2943	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28543
EIF4H-BG293LV05-111_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2943					GRCh38	V40	EIF4H-BG293LV05-111_S175_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BG293LV05-111_S175_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28587
EIF4H-BG293LV05-111_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2943					GRCh38	V40	EIF4H-BG293LV05-111/Aligned.sortedByCoord.out.bam		ENCORE2	28631
EIF4H-BG293LV05-111_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2943					GRCh38	V40	EIF4H-BG293LV05-111/Aligned.sortedByCoord.out.bam		ENCORE2	28675
EIF4H-BG293LV05-111_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2943					GRCh38	V40	EIF4H-BG293LV05-111/Aligned.sortedByCoord.out.bam		ENCORE2	28719
EIF4H-BG293LV05-111_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2943					GRCh38	V40	EIF4H-BG293LV05-111/Aligned.sortedByCoord.out.bam		ENCORE2	28763
EIF4H-BG293LV05-111_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2943					GRCh38	V40	EIF4H-BG293LV05-111_S175_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BG293LV05-111_S175_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28807
EIF4H-BG293LV05-112_S176_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2944	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28500
EIF4H-BG293LV05-112_S176_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2944	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28544
EIF4H-BG293LV05-112_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2944					GRCh38	V40	EIF4H-BG293LV05-112_S176_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BG293LV05-112_S176_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28588
EIF4H-BG293LV05-112_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2944					GRCh38	V40	EIF4H-BG293LV05-112/Aligned.sortedByCoord.out.bam		ENCORE2	28632
EIF4H-BG293LV05-112_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2944					GRCh38	V40	EIF4H-BG293LV05-112/Aligned.sortedByCoord.out.bam		ENCORE2	28676
EIF4H-BG293LV05-112_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2944					GRCh38	V40	EIF4H-BG293LV05-112/Aligned.sortedByCoord.out.bam		ENCORE2	28720
EIF4H-BG293LV05-112_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2944					GRCh38	V40	EIF4H-BG293LV05-112/Aligned.sortedByCoord.out.bam		ENCORE2	28764
EIF4H-BG293LV05-112_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2944					GRCh38	V40	EIF4H-BG293LV05-112_S176_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BG293LV05-112_S176_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28808