UBE2I RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-33	BG293LV06-34
idx	0	0
TRCN#_or_BGC#	TRCN0000320448	TRCN0000320448
shRNA_or_gRNA_sequence	CCGGAGCAGAGGCCTACACGATTTACTCGAGTAAATCGTGTAGGCCTCTGCTTTTTTG	CCGGAGCAGAGGCCTACACGATTTACTCGAGTAAATCGTGTAGGCCTCTGCTTTTTTG
PAM
Name	UBE2I	UBE2I
Sample_ID	BG293LV06-33	BG293LV06-34
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	UBE2I	UBE2I
qPCR_result	85.7	84.7
Ave_qPCR	85.2
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	12168	12169

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-33	BG293LV06-34
Sample_ID	BG293LV06-33	BG293LV06-34
Sample Name
Sample Name	UBE2I-BG293LV06-33	UBE2I-BG293LV06-34
RBP	UBE2I	UBE2I
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13470	13471

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-33	BG293LV06-34
Sample #	37	38
Sample Name	UBE2I-BG293LV06-33	UBE2I-BG293LV06-34
Sample_Name_Alias
Index Well Position	E05	F05
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	280	276
Peak_Molarity	92.60	90.80
libSampleQC_DNA_Well	DNA_Library_set71/set1/E5.png	DNA_Library_set71/set1/F5.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set71/set1/E5.png	RNA_Library_set71/set1/F5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-33	BG293LV06-34
RBP	UBE2I	UBE2I
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	4462	4463

Sequencing Information

	BG293LV06-33	BG293LV06-34
Sample_ID	BG293LV06-33	BG293LV06-34
Sample Name	UBE2I-BG293LV06-33	UBE2I-BG293LV06-34
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	39,086,368	33,615,326
total_aligned_reads	36,017,347	29,582,291
unique_aligned_reads	33,737,197	27,728,675
percent_uniqueAligned	0.86314	0.82488
correlation_replicates	0.998540	0.998540
spikein_reads	72,100	63,524
percent_spikeins	0.00184	0.00189
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3031	3032

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
UBE2I-BG293LV06-33_S37_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3031	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	29375
UBE2I-BG293LV06-33_S37_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3031	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	29439
UBE2I-BG293LV06-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3031					GRCh38	V40	UBE2I-BG293LV06-33_S37_L002_R1_001.filtered.trimmed.paired.fastq.gz,UBE2I-BG293LV06-33_S37_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29504
UBE2I-BG293LV06-33_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	3031					GRCh38	V40	UBE2I-BG293LV06-33_Aligned.sortedByCoord.out.bam		ENCORE2	29568
UBE2I-BG293LV06-33_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	3031					GRCh38	V40	UBE2I-BG293LV06-33_Aligned.sortedByCoord.out.bam		ENCORE2	29632
UBE2I-BG293LV06-33_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	3031					GRCh38	V40	UBE2I-BG293LV06-33_Aligned.sortedByCoord.out.bam		ENCORE2	29696
UBE2I-BG293LV06-33_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3031					GRCh38	V40	UBE2I-BG293LV06-33_S37_L002_R1_001.filtered.trimmed.paired.fastq.gz,UBE2I-BG293LV06-33_S37_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29760
UBE2I-BG293LV06-34_S38_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3032	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	29376
UBE2I-BG293LV06-34_S38_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3032	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	29440
UBE2I-BG293LV06-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3032					GRCh38	V40	UBE2I-BG293LV06-34_S38_L002_R1_001.filtered.trimmed.paired.fastq.gz,UBE2I-BG293LV06-34_S38_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29505
UBE2I-BG293LV06-34_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	3032					GRCh38	V40	UBE2I-BG293LV06-34_Aligned.sortedByCoord.out.bam		ENCORE2	29569
UBE2I-BG293LV06-34_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	3032					GRCh38	V40	UBE2I-BG293LV06-34_Aligned.sortedByCoord.out.bam		ENCORE2	29633
UBE2I-BG293LV06-34_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	3032					GRCh38	V40	UBE2I-BG293LV06-34_Aligned.sortedByCoord.out.bam		ENCORE2	29697
UBE2I-BG293LV06-34_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3032					GRCh38	V40	UBE2I-BG293LV06-34_S38_L002_R1_001.filtered.trimmed.paired.fastq.gz,UBE2I-BG293LV06-34_S38_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29761