EIF4H RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-93	BG293LV06-94
idx	0	0
TRCN#_or_BGC#	TRCN0000275601	TRCN0000275601
shRNA_or_gRNA_sequence	CCGGGAGTGCATGTCAGCTGTTAACCTCGAGGTTAACAGCTGACATGCACTCTTTTTG	CCGGGAGTGCATGTCAGCTGTTAACCTCGAGGTTAACAGCTGACATGCACTCTTTTTG
PAM
Name	EIF4H	EIF4H
Sample_ID	BG293LV06-93	BG293LV06-94
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	EIF4H	EIF4H
qPCR_result	90.9	83.7
Ave_qPCR	87.3
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	12228	12229

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-93	BG293LV06-94
Sample_ID	BG293LV06-93	BG293LV06-94
Sample Name
Sample Name	EIF4H-BG293LV06-93B	EIF4H-BG293LV06-94B
RBP	EIF4H	EIF4H
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13530	13531

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-93	BG293LV06-94
Sample #	93	94
Sample Name	EIF4H-BG293LV06-93B	EIF4H-BG293LV06-94B
Sample_Name_Alias
Index Well Position	E05	F05
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	273	277
Peak_Molarity	76.30	87.70
libSampleQC_DNA_Well	DNA_Library_set72/set1/E5.png	DNA_Library_set72/set1/F5.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set72/set1/E5.png	RNA_Library_set72/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-93	BG293LV06-94
RBP	EIF4H	EIF4H
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4518	4519

Sequencing Information

	BG293LV06-93	BG293LV06-94
Sample_ID	BG293LV06-93	BG293LV06-94
Sample Name	EIF4H-BG293LV06-93B	EIF4H-BG293LV06-94B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	18,508,773	26,701,083
total_aligned_reads	16,253,206	23,015,108
unique_aligned_reads	15,190,850	21,587,135
percent_uniqueAligned	0.82074	0.80847
correlation_replicates	0.991686	0.991686
spikein_reads	54,802	83,752
percent_spikeins	0.00296	0.00314
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3087	3088

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-BG293LV06-93B_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3087	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29776
EIF4H-BG293LV06-93B_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3087	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29848
EIF4H-BG293LV06-93B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3087					GRCh38	V40	EIF4H-BG293LV06-93B_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BG293LV06-93B_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29920
EIF4H-BG293LV06-93B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3087					GRCh38	V40	EIF4H-BG293LV06-93B_Aligned.sortedByCoord.out.bam		ENCORE2	29992
EIF4H-BG293LV06-93B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3087					GRCh38	V40	EIF4H-BG293LV06-93B_Aligned.sortedByCoord.out.bam		ENCORE2	30064
EIF4H-BG293LV06-93B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3087					GRCh38	V40	EIF4H-BG293LV06-93B_Aligned.sortedByCoord.out.bam		ENCORE2	30136
EIF4H-BG293LV06-93B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3087					GRCh38	V40	EIF4H-BG293LV06-93B_Aligned.sortedByCoord.out.bam		ENCORE2	30208
EIF4H-BG293LV06-93B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3087					GRCh38	V40	EIF4H-BG293LV06-93B_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BG293LV06-93B_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30280
EIF4H-BG293LV06-94B_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3088	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29777
EIF4H-BG293LV06-94B_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3088	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29849
EIF4H-BG293LV06-94B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3088					GRCh38	V40	EIF4H-BG293LV06-94B_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BG293LV06-94B_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29921
EIF4H-BG293LV06-94B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3088					GRCh38	V40	EIF4H-BG293LV06-94B_Aligned.sortedByCoord.out.bam		ENCORE2	29993
EIF4H-BG293LV06-94B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3088					GRCh38	V40	EIF4H-BG293LV06-94B_Aligned.sortedByCoord.out.bam		ENCORE2	30065
EIF4H-BG293LV06-94B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3088					GRCh38	V40	EIF4H-BG293LV06-94B_Aligned.sortedByCoord.out.bam		ENCORE2	30137
EIF4H-BG293LV06-94B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3088					GRCh38	V40	EIF4H-BG293LV06-94B_Aligned.sortedByCoord.out.bam		ENCORE2	30209
EIF4H-BG293LV06-94B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3088					GRCh38	V40	EIF4H-BG293LV06-94B_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4H-BG293LV06-94B_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30281