EIF4B RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-13	BG293LV02-14
idx	0	0
TRCN#_or_BGC#	TRCN0000062598	TRCN0000062598
shRNA_or_gRNA_sequence	GCGGAGAAACACCTTGATCTTCTCGAGAAGATCAAGGTGTTTCTCCGC	GCGGAGAAACACCTTGATCTTCTCGAGAAGATCAAGGTGTTTCTCCGC
PAM
Name	EIF4B	EIF4B
Sample_ID	BG293LV02-13	BG293LV02-14
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	EIF4B	EIF4B
qPCR_result	57.0	60.3
Ave_qPCR	58.6
RT-qPCR_primer-F	x
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	9808	9809

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-13	BG293LV02-14
Sample_ID	BG293LV02-13	BG293LV02-14
Sample Name
Sample Name	EIF4B-BG293LV02-13	EIF4B-BG293LV02-14
RBP	EIF4B	EIF4B
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11568	11569

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-13	BG293LV02-14
Sample #	11	12
Sample Name	EIF4B-BG293LV02-13	EIF4B-BG293LV02-14
Sample_Name_Alias
Index Well Position	C02	D02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412	Lib-230412
Tecan_Location
Tecan
Tecan_date
Size_bp	295	289
Peak_Molarity	87.90	98.40
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/C2.png	DNA_Library_set60-62/set2/D2.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set60-62/set1/C2.png	RNA_Library_set60-62/set1/D2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-13	BG293LV02-14
RBP	EIF4B	EIF4B
Batch_ID	BG293LV02	BG293LV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3598	3599

Sequencing Information

	BG293LV02-13	BG293LV02-14
Sample_ID	BG293LV02-13	BG293LV02-14
Sample Name	EIF4B-BG293LV02-13	EIF4B-BG293LV02-14
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	48,392,966	44,833,497
total_aligned_reads	41,139,609	37,800,422
unique_aligned_reads	38,131,239	35,017,754
percent_uniqueAligned	0.78795	0.78106
correlation_replicates	0.995778	0.995778
spikein_reads	173,414	106,078
percent_spikeins	0.00358	0.00237
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2469	2470

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-BG293LV02-13_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2469	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7970
EIF4B-BG293LV02-13_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2469	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8014
EIF4B-BG293LV02-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2469					GRCh38	V40	EIF4B-BG293LV02-13_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BG293LV02-13_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10763
EIF4B-BG293LV02-13_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2469					GRCh38	V40	EIF4B-BG293LV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	10807
EIF4B-BG293LV02-13_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2469					GRCh38	V40	EIF4B-BG293LV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	10851
EIF4B-BG293LV02-13_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2469					GRCh38	V40	EIF4B-BG293LV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	10895
EIF4B-BG293LV02-13_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2469					GRCh38	V40	EIF4B-BG293LV02-13/Aligned.sortedByCoord.out.bam		ENCORE2	10939
EIF4B-BG293LV02-13_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2469					GRCh38	V40	EIF4B-BG293LV02-13_S11_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BG293LV02-13_S11_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10983
EIF4B-BG293LV02-14_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2470	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7971
EIF4B-BG293LV02-14_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2470	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8015
EIF4B-BG293LV02-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2470					GRCh38	V40	EIF4B-BG293LV02-14_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BG293LV02-14_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10764
EIF4B-BG293LV02-14_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2470					GRCh38	V40	EIF4B-BG293LV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	10808
EIF4B-BG293LV02-14_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2470					GRCh38	V40	EIF4B-BG293LV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	10852
EIF4B-BG293LV02-14_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2470					GRCh38	V40	EIF4B-BG293LV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	10896
EIF4B-BG293LV02-14_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2470					GRCh38	V40	EIF4B-BG293LV02-14/Aligned.sortedByCoord.out.bam		ENCORE2	10940
EIF4B-BG293LV02-14_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2470					GRCh38	V40	EIF4B-BG293LV02-14_S12_L001_R1_001.filtered.trimmed.paired.fastq.gz,EIF4B-BG293LV02-14_S12_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10984