STAU2 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-57	BG293LV05-58
idx	0	0
TRCN#_or_BGC#	TRCN0000157149	TRCN0000157149
shRNA_or_gRNA_sequence	CCGGGCCAGGGAACTCCTTATGAATCTCGAGATTCATAAGGAGTTCCCTGGCTTTTTTG	CCGGGCCAGGGAACTCCTTATGAATCTCGAGATTCATAAGGAGTTCCCTGGCTTTTTTG
PAM
Name	STAU2	STAU2
Sample_ID	BG293LV05-57	BG293LV05-58
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	STAU2	STAU2
qPCR_result	95	91.2
Ave_qPCR	93.1
RT-qPCR_primer-F	ATCCAATCGATGGAGCAATG
RT-qPCR_primer-R	CCTGGTTATTGTCCGCTTTC
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	10029	10030

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-57	BG293LV05-58
Sample_ID	BG293LV05-57	BG293LV05-58
Sample Name
Sample Name	STAU2-BG293LV05-57	STAU2-BG293LV05-58
RBP	STAU2	STAU2
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12862	12863

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-57	BG293LV05-58
Sample #	29	30
Sample Name	STAU2-BG293LV05-57	STAU2-BG293LV05-58
Sample_Name_Alias
Index Well Position	E10	F10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	272	269
Peak_Molarity	85.00	55.20
libSampleQC_DNA_Well	DNA_Library_set69/set1/E4.png	DNA_Library_set69/set1/F4.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set69/set1/F9.png	RNA_Library_set69/set1/G9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-57	BG293LV05-58
RBP	STAU2	STAU2
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4210	4211

Sequencing Information

	BG293LV05-57	BG293LV05-58
Sample_ID	BG293LV05-57	BG293LV05-58
Sample Name	STAU2-BG293LV05-57	STAU2-BG293LV05-58
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	20,336,341	17,788,968
total_aligned_reads	17,380,696	12,647,903
unique_aligned_reads	16,136,263	11,705,971
percent_uniqueAligned	0.79347	0.65805
correlation_replicates	0.985198	0.985198
spikein_reads	3,422	8,762
percent_spikeins	0.00017	0.00049
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2929	2930

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
STAU2-BG293LV05-57_S161_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2929	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28525
STAU2-BG293LV05-57_S161_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2929	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28569
STAU2-BG293LV05-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2929					GRCh38	V40	STAU2-BG293LV05-57_S161_L002_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BG293LV05-57_S161_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28613
STAU2-BG293LV05-57_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2929					GRCh38	V40	STAU2-BG293LV05-57/Aligned.sortedByCoord.out.bam		ENCORE2	28657
STAU2-BG293LV05-57_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2929					GRCh38	V40	STAU2-BG293LV05-57/Aligned.sortedByCoord.out.bam		ENCORE2	28701
STAU2-BG293LV05-57_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2929					GRCh38	V40	STAU2-BG293LV05-57/Aligned.sortedByCoord.out.bam		ENCORE2	28745
STAU2-BG293LV05-57_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2929					GRCh38	V40	STAU2-BG293LV05-57/Aligned.sortedByCoord.out.bam		ENCORE2	28789
STAU2-BG293LV05-57_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2929					GRCh38	V40	STAU2-BG293LV05-57_S161_L002_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BG293LV05-57_S161_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28833
STAU2-BG293LV05-58_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2930	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28526
STAU2-BG293LV05-58_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2930	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28570
STAU2-BG293LV05-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2930					GRCh38	V40	STAU2-BG293LV05-58_merged_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BG293LV05-58_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28614
STAU2-BG293LV05-58_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2930					GRCh38	V40	STAU2-BG293LV05-58/Aligned.sortedByCoord.out.bam		ENCORE2	28658
STAU2-BG293LV05-58_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2930					GRCh38	V40	STAU2-BG293LV05-58/Aligned.sortedByCoord.out.bam		ENCORE2	28702
STAU2-BG293LV05-58_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2930					GRCh38	V40	STAU2-BG293LV05-58/Aligned.sortedByCoord.out.bam		ENCORE2	28746
STAU2-BG293LV05-58_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2930					GRCh38	V40	STAU2-BG293LV05-58/Aligned.sortedByCoord.out.bam		ENCORE2	28790
STAU2-BG293LV05-58_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2930					GRCh38	V40	STAU2-BG293LV05-58_merged_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BG293LV05-58_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28834