TOB2 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-117	BG293LV06-118
idx	0	0
TRCN#_or_BGC#	TRCN0000004165	TRCN0000004165
shRNA_or_gRNA_sequence	CCGGGAGCTGAGTGTCTGGATTGATCTCGAGATCAATCCAGACACTCAGCTCTTTTT	CCGGGAGCTGAGTGTCTGGATTGATCTCGAGATCAATCCAGACACTCAGCTCTTTTT
PAM
Name	TOB2	TOB2
Sample_ID	BG293LV06-117	BG293LV06-118
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	TOB2	TOB2
qPCR_result	71.5	76.1
Ave_qPCR	73.8
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	12252	12253

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-117	BG293LV06-118
Sample_ID	BG293LV06-117	BG293LV06-118
Sample Name
Sample Name	TOB2-BG293LV06-117B	TOB2-BG293LV06-118B
RBP	TOB2	TOB2
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13554	13555

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-117	BG293LV06-118
Sample #	117	118
Sample Name	TOB2-BG293LV06-117B	TOB2-BG293LV06-118B
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	285	300
Peak_Molarity	82.00	96.10
libSampleQC_DNA_Well	DNA_Library_set72/set1/E8.png	DNA_Library_set72/set1/F8.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set72/set1/E8.png	RNA_Library_set72/set1/F8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-117	BG293LV06-118
RBP	TOB2	TOB2
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4542	4543

Sequencing Information

	BG293LV06-117	BG293LV06-118
Sample_ID	BG293LV06-117	BG293LV06-118
Sample Name	TOB2-BG293LV06-117B	TOB2-BG293LV06-118B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	37,565,439	34,614,760
total_aligned_reads	35,068,774	32,923,907
unique_aligned_reads	32,906,617	30,967,675
percent_uniqueAligned	0.87598	0.89464
correlation_replicates	0.996244	0.996244
spikein_reads	116,714	110,146
percent_spikeins	0.00311	0.00318
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3111	3112

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-BG293LV06-117B_S69_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3111	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29820
TOB2-BG293LV06-117B_S69_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3111	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29892
TOB2-BG293LV06-117B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3111					GRCh38	V40	TOB2-BG293LV06-117B_S69_L001_R1_001.filtered.trimmed.paired.fastq.gz,TOB2-BG293LV06-117B_S69_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29964
TOB2-BG293LV06-117B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3111					GRCh38	V40	TOB2-BG293LV06-117B_Aligned.sortedByCoord.out.bam		ENCORE2	30036
TOB2-BG293LV06-117B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3111					GRCh38	V40	TOB2-BG293LV06-117B_Aligned.sortedByCoord.out.bam		ENCORE2	30108
TOB2-BG293LV06-117B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3111					GRCh38	V40	TOB2-BG293LV06-117B_Aligned.sortedByCoord.out.bam		ENCORE2	30180
TOB2-BG293LV06-117B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3111					GRCh38	V40	TOB2-BG293LV06-117B_Aligned.sortedByCoord.out.bam		ENCORE2	30252
TOB2-BG293LV06-117B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3111					GRCh38	V40	TOB2-BG293LV06-117B_S69_L001_R1_001.filtered.trimmed.paired.fastq.gz,TOB2-BG293LV06-117B_S69_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30324
TOB2-BG293LV06-118B_S70_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3112	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29821
TOB2-BG293LV06-118B_S70_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3112	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29893
TOB2-BG293LV06-118B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3112					GRCh38	V40	TOB2-BG293LV06-118B_S70_L001_R1_001.filtered.trimmed.paired.fastq.gz,TOB2-BG293LV06-118B_S70_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29965
TOB2-BG293LV06-118B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3112					GRCh38	V40	TOB2-BG293LV06-118B_Aligned.sortedByCoord.out.bam		ENCORE2	30037
TOB2-BG293LV06-118B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3112					GRCh38	V40	TOB2-BG293LV06-118B_Aligned.sortedByCoord.out.bam		ENCORE2	30109
TOB2-BG293LV06-118B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3112					GRCh38	V40	TOB2-BG293LV06-118B_Aligned.sortedByCoord.out.bam		ENCORE2	30181
TOB2-BG293LV06-118B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3112					GRCh38	V40	TOB2-BG293LV06-118B_Aligned.sortedByCoord.out.bam		ENCORE2	30253
TOB2-BG293LV06-118B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3112					GRCh38	V40	TOB2-BG293LV06-118B_S70_L001_R1_001.filtered.trimmed.paired.fastq.gz,TOB2-BG293LV06-118B_S70_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30325