EIF4B RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-15	BG293LV06-16
idx	0	0
TRCN#_or_BGC#	TRCN0000062598	TRCN0000062598
shRNA_or_gRNA_sequence	GCGGAGAAACACCTTGATCTTCTCGAGAAGATCAAGGTGTTTCTCCGC	GCGGAGAAACACCTTGATCTTCTCGAGAAGATCAAGGTGTTTCTCCGC
PAM
Name	EIF4B	EIF4B
Sample_ID	BG293LV06-15	BG293LV06-16
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	EIF4B	EIF4B
qPCR_result	69.5	70.1
Ave_qPCR	69.8
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	12150	12151

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-15	BG293LV06-16
Sample_ID	BG293LV06-15	BG293LV06-16
Sample Name
Sample Name	EIF4B-BG293LV06-15	EIF4B-BG293LV06-16
RBP	EIF4B	EIF4B
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13452	13453

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-15	BG293LV06-16
Sample #	19	20
Sample Name	EIF4B-BG293LV06-15	EIF4B-BG293LV06-16
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-09-25
Lib_ID	Lib-240925B	Lib-240925B
Tecan_Location
Tecan
Tecan_date
Size_bp	272	279
Peak_Molarity	115.00	87.90
libSampleQC_DNA_Well	DNA_Library_set71/set1/C3.png	DNA_Library_set71/set1/D3.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set71/set1/C3.png	RNA_Library_set71/set1/D3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-15	BG293LV06-16
RBP	EIF4B	EIF4B
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4444	4445

Sequencing Information

	BG293LV06-15	BG293LV06-16
Sample_ID	BG293LV06-15	BG293LV06-16
Sample Name	EIF4B-BG293LV06-15	EIF4B-BG293LV06-16
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	37,512,035	28,800,798
total_aligned_reads	33,215,527	26,220,017
unique_aligned_reads	31,101,819	24,478,746
percent_uniqueAligned	0.82912	0.84993
correlation_replicates	0.978257	0.978257
spikein_reads	96,088	78,920
percent_spikeins	0.00256	0.00274
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3013	3014

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
EIF4B-BG293LV06-15_S19_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3013	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29321
EIF4B-BG293LV06-15_S19_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3013	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29385
EIF4B-BG293LV06-15_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3013					GRCh38	V40	EIF4B-BG293LV06-15_S19_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BG293LV06-15_S19_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29450
EIF4B-BG293LV06-15_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3013					GRCh38	V40	EIF4B-BG293LV06-15_Aligned.sortedByCoord.out.bam		ENCORE2	29514
EIF4B-BG293LV06-15_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3013					GRCh38	V40	EIF4B-BG293LV06-15_Aligned.sortedByCoord.out.bam		ENCORE2	29578
EIF4B-BG293LV06-15_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3013					GRCh38	V40	EIF4B-BG293LV06-15_Aligned.sortedByCoord.out.bam		ENCORE2	29642
EIF4B-BG293LV06-15_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3013					GRCh38	V40	EIF4B-BG293LV06-15_S19_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BG293LV06-15_S19_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29706
EIF4B-BG293LV06-16_S20_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3014	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29322
EIF4B-BG293LV06-16_S20_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3014	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29386
EIF4B-BG293LV06-16_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3014					GRCh38	V40	EIF4B-BG293LV06-16_S20_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BG293LV06-16_S20_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29451
EIF4B-BG293LV06-16_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3014					GRCh38	V40	EIF4B-BG293LV06-16_Aligned.sortedByCoord.out.bam		ENCORE2	29515
EIF4B-BG293LV06-16_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3014					GRCh38	V40	EIF4B-BG293LV06-16_Aligned.sortedByCoord.out.bam		ENCORE2	29579
EIF4B-BG293LV06-16_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3014					GRCh38	V40	EIF4B-BG293LV06-16_Aligned.sortedByCoord.out.bam		ENCORE2	29643
EIF4B-BG293LV06-16_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3014					GRCh38	V40	EIF4B-BG293LV06-16_S20_L002_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BG293LV06-16_S20_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29707