TOB2 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV03-19	BG293LV03-20
idx	0	0
TRCN#_or_BGC#	TRCN0000004165	TRCN0000004164
shRNA_or_gRNA_sequence	CCGGGAGCTGAGTGTCTGGATTGATCTCGAGATCAATCCAGACACTCAGCTCTTTTT	CCGGCTGGCTTCCGCTGTGTTCACACTCGAGTGTGAACACAGCGGAAGCCAGTTTTT
PAM
Name	TOB2	TOB2
Sample_ID	BG293LV03-19	BG293LV03-20
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	TOB2	TOB2
qPCR_result	63	54
Ave_qPCR	58.5
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	9869	9870

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV03-19	BG293LV03-20
Sample_ID	BG293LV03-19	BG293LV03-20
Sample Name
Sample Name	TOB2-BG293LV03-19	TOB2-BG293LV03-20
RBP	TOB2	TOB2
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11744	11745

Library-Prep
Sequencing

Library-Prep Information

	BG293LV03-19	BG293LV03-20
Sample #	9	10
Sample Name	TOB2-BG293LV03-19	TOB2-BG293LV03-20
Sample_Name_Alias
Index Well Position	A02	B02
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	290	298
Peak_Molarity	53.90	65.60
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/A2.png	DNA_Library_set60-62/set4/B2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/A2.png	RNA_Library_set60-62/set2/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BG293LV03-19	BG293LV03-20
RBP	TOB2	TOB2
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	3692	3693

Sequencing Information

	BG293LV03-19	BG293LV03-20
Sample_ID	BG293LV03-19	BG293LV03-20
Sample Name	TOB2-BG293LV03-19	TOB2-BG293LV03-20
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_W	set62_W
total_reads	36,533,875	30,143,616
total_aligned_reads	30,626,496	25,082,812
unique_aligned_reads	28,531,488	23,393,299
percent_uniqueAligned	0.78096	0.77606
correlation_replicates	0.995857	0.995857
spikein_reads	155,712	83,098
percent_spikeins	0.00426	0.00276
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2563	2564

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
TOB2-BG293LV03-19_S9_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2563	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	7850
TOB2-BG293LV03-19_S9_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2563	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	7866
TOB2-BG293LV03-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2563					GRCh38	V40	TOB2-BG293LV03-19_S9_L003_R1_001.filtered.trimmed.paired.fastq.gz,TOB2-BG293LV03-19_S9_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10091
TOB2-BG293LV03-19_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	2563					GRCh38	V40	TOB2-BG293LV03-19/Aligned.sortedByCoord.out.bam		ENCORE2	10107
TOB2-BG293LV03-19_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	2563					GRCh38	V40	TOB2-BG293LV03-19/Aligned.sortedByCoord.out.bam		ENCORE2	10123
TOB2-BG293LV03-19_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	2563					GRCh38	V40	TOB2-BG293LV03-19/Aligned.sortedByCoord.out.bam		ENCORE2	10139
TOB2-BG293LV03-19_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	2563					GRCh38	V40	TOB2-BG293LV03-19/Aligned.sortedByCoord.out.bam		ENCORE2	10155
TOB2-BG293LV03-19_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2563					GRCh38	V40	TOB2-BG293LV03-19_S9_L003_R1_001.filtered.trimmed.paired.fastq.gz,TOB2-BG293LV03-19_S9_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10171
TOB2-BG293LV03-20_S10_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2564	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	7851
TOB2-BG293LV03-20_S10_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2564	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	7867
TOB2-BG293LV03-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2564					GRCh38	V40	TOB2-BG293LV03-20_S10_L003_R1_001.filtered.trimmed.paired.fastq.gz,TOB2-BG293LV03-20_S10_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10092
TOB2-BG293LV03-20_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	2564					GRCh38	V40	TOB2-BG293LV03-20/Aligned.sortedByCoord.out.bam		ENCORE2	10108
TOB2-BG293LV03-20_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	2564					GRCh38	V40	TOB2-BG293LV03-20/Aligned.sortedByCoord.out.bam		ENCORE2	10124
TOB2-BG293LV03-20_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	2564					GRCh38	V40	TOB2-BG293LV03-20/Aligned.sortedByCoord.out.bam		ENCORE2	10140
TOB2-BG293LV03-20_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	2564					GRCh38	V40	TOB2-BG293LV03-20/Aligned.sortedByCoord.out.bam		ENCORE2	10156
TOB2-BG293LV03-20_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2564					GRCh38	V40	TOB2-BG293LV03-20_S10_L003_R1_001.filtered.trimmed.paired.fastq.gz,TOB2-BG293LV03-20_S10_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10172