UBE2I RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV03-27	BG293LV03-28
idx	0	0
TRCN#_or_BGC#	TRCN0000320448	TRCN0000320448
shRNA_or_gRNA_sequence	CCGGAGCAGAGGCCTACACGATTTACTCGAGTAAATCGTGTAGGCCTCTGCTTTTTTG	CCGGAGCAGAGGCCTACACGATTTACTCGAGTAAATCGTGTAGGCCTCTGCTTTTTTG
PAM
Name	UBE2I	UBE2I
Sample_ID	BG293LV03-27	BG293LV03-28
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	UBE2I	UBE2I
qPCR_result	85.1	78.9
Ave_qPCR	82.0
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	9877	9878

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV03-27	BG293LV03-28
Sample_ID	BG293LV03-27	BG293LV03-28
Sample Name
Sample Name	UBE2I-BG293LV03-27	UBE2I-BG293LV03-28
RBP	UBE2I	UBE2I
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11748	11749

Library-Prep
Sequencing

Library-Prep Information

	BG293LV03-27	BG293LV03-28
Sample #	13	14
Sample Name	UBE2I-BG293LV03-27	UBE2I-BG293LV03-28
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	306	304
Peak_Molarity	74.00	90.50
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/E2.png	DNA_Library_set60-62/set4/F2.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set60-62/set2/E2.png	RNA_Library_set60-62/set2/F2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BG293LV03-27	BG293LV03-28
RBP	UBE2I	UBE2I
Batch_ID	BG293LV03	BG293LV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3696	3697

Sequencing Information

	BG293LV03-27	BG293LV03-28
Sample_ID	BG293LV03-27	BG293LV03-28
Sample Name	UBE2I-BG293LV03-27	UBE2I-BG293LV03-28
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_W	set62_W
total_reads	38,129,708	27,640,911
total_aligned_reads	32,229,621	22,773,176
unique_aligned_reads	30,127,623	21,346,470
percent_uniqueAligned	0.79014	0.77228
correlation_replicates	0.992639	0.992639
spikein_reads	51,496	35,690
percent_spikeins	0.00135	0.00129
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2567	2568

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-BG293LV03-27_S13_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2567	NovaSeq6000	100	paired-ended	1				NT-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7854
UBE2I-BG293LV03-27_S13_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2567	NovaSeq6000	100	paired-ended	2				NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7870
UBE2I-BG293LV03-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2567					GRCh38	V40	UBE2I-BG293LV03-27_S13_L003_R1_001.filtered.trimmed.paired.fastq.gz,UBE2I-BG293LV03-27_S13_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10095
UBE2I-BG293LV03-27_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2567					GRCh38	V40	UBE2I-BG293LV03-27/Aligned.sortedByCoord.out.bam		ENCORE2	10111
UBE2I-BG293LV03-27_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2567					GRCh38	V40	UBE2I-BG293LV03-27/Aligned.sortedByCoord.out.bam		ENCORE2	10127
UBE2I-BG293LV03-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2567					GRCh38	V40	UBE2I-BG293LV03-27/Aligned.sortedByCoord.out.bam		ENCORE2	10143
UBE2I-BG293LV03-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2567					GRCh38	V40	UBE2I-BG293LV03-27/Aligned.sortedByCoord.out.bam		ENCORE2	10159
UBE2I-BG293LV03-27_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2567					GRCh38	V40	UBE2I-BG293LV03-27_S13_L003_R1_001.filtered.trimmed.paired.fastq.gz,UBE2I-BG293LV03-27_S13_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10175
UBE2I-BG293LV03-28_S14_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2568	NovaSeq6000	100	paired-ended	1				NT-BG293LV03-1_S1_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7855
UBE2I-BG293LV03-28_S14_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2568	NovaSeq6000	100	paired-ended	2				NT-BG293LV03-1_S1_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV03-2_S2_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7871
UBE2I-BG293LV03-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2568					GRCh38	V40	UBE2I-BG293LV03-28_S14_L003_R1_001.filtered.trimmed.paired.fastq.gz,UBE2I-BG293LV03-28_S14_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10096
UBE2I-BG293LV03-28_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2568					GRCh38	V40	UBE2I-BG293LV03-28/Aligned.sortedByCoord.out.bam		ENCORE2	10112
UBE2I-BG293LV03-28_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2568					GRCh38	V40	UBE2I-BG293LV03-28/Aligned.sortedByCoord.out.bam		ENCORE2	10128
UBE2I-BG293LV03-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2568					GRCh38	V40	UBE2I-BG293LV03-28/Aligned.sortedByCoord.out.bam		ENCORE2	10144
UBE2I-BG293LV03-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2568					GRCh38	V40	UBE2I-BG293LV03-28/Aligned.sortedByCoord.out.bam		ENCORE2	10160
UBE2I-BG293LV03-28_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2568					GRCh38	V40	UBE2I-BG293LV03-28_S14_L003_R1_001.filtered.trimmed.paired.fastq.gz,UBE2I-BG293LV03-28_S14_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10176