YWHAG RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-47	BG293LV05-48
idx	0	0
TRCN#_or_BGC#	TRCN0000078159	TRCN0000078159
shRNA_or_gRNA_sequence	CCGGCCTGCTGGATAACTACCTGATCTCGAGATCAGGTAGTTATCCAGCAGGTTTTTG	CCGGCCTGCTGGATAACTACCTGATCTCGAGATCAGGTAGTTATCCAGCAGGTTTTTG
PAM
Name	YWHAG	YWHAG
Sample_ID	BG293LV05-47	BG293LV05-48
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	YWHAG	YWHAG
qPCR_result	76.8	76.2
Ave_qPCR	76.5
RT-qPCR_primer-F	gccatgaagaacgtgacaga
RT-qPCR_primer-R	tgtaggccacagacagaagg
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	10019	10020

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-47	BG293LV05-48
Sample_ID	BG293LV05-47	BG293LV05-48
Sample Name
Sample Name	YWHAG-BG293LV05-47	YWHAG-BG293LV05-48
RBP	YWHAG	YWHAG
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12856	12857

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-47	BG293LV05-48
Sample #	23	24
Sample Name	YWHAG-BG293LV05-47	YWHAG-BG293LV05-48
Sample_Name_Alias
Index Well Position	G09	H09
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	274	273
Peak_Molarity	80.50	81.80
libSampleQC_DNA_Well	DNA_Library_set69/set1/G3.png	DNA_Library_set69/set1/H3.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set69/set1/H8.png	RNA_Library_set69/set1/A9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-47	BG293LV05-48
RBP	YWHAG	YWHAG
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	4204	4205

Sequencing Information

	BG293LV05-47	BG293LV05-48
Sample_ID	BG293LV05-47	BG293LV05-48
Sample Name	YWHAG-BG293LV05-47	YWHAG-BG293LV05-48
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	24,398,996	17,623,790
total_aligned_reads	21,675,291	14,047,853
unique_aligned_reads	20,073,165	12,987,036
percent_uniqueAligned	0.82270	0.73690
correlation_replicates	0.982960	0.982960
spikein_reads	7,462	7,296
percent_spikeins	0.00031	0.00041
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2923	2924

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
YWHAG-BG293LV05-47_S155_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2923	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	28533
YWHAG-BG293LV05-47_S155_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2923	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	28577
YWHAG-BG293LV05-47_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2923					GRCh38	V40	YWHAG-BG293LV05-47_S155_L002_R1_001.filtered.trimmed.paired.fastq.gz,YWHAG-BG293LV05-47_S155_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28621
YWHAG-BG293LV05-47_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	2923					GRCh38	V40	YWHAG-BG293LV05-47/Aligned.sortedByCoord.out.bam		ENCORE2	28665
YWHAG-BG293LV05-47_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	2923					GRCh38	V40	YWHAG-BG293LV05-47/Aligned.sortedByCoord.out.bam		ENCORE2	28709
YWHAG-BG293LV05-47_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	2923					GRCh38	V40	YWHAG-BG293LV05-47/Aligned.sortedByCoord.out.bam		ENCORE2	28753
YWHAG-BG293LV05-47_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	2923					GRCh38	V40	YWHAG-BG293LV05-47/Aligned.sortedByCoord.out.bam		ENCORE2	28797
YWHAG-BG293LV05-47_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2923					GRCh38	V40	YWHAG-BG293LV05-47_S155_L002_R1_001.filtered.trimmed.paired.fastq.gz,YWHAG-BG293LV05-47_S155_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28841
YWHAG-BG293LV05-48_S156_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2924	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	28534
YWHAG-BG293LV05-48_S156_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2924	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	28578
YWHAG-BG293LV05-48_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2924					GRCh38	V40	YWHAG-BG293LV05-48_S156_L002_R1_001.filtered.trimmed.paired.fastq.gz,YWHAG-BG293LV05-48_S156_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28622
YWHAG-BG293LV05-48_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	2924					GRCh38	V40	YWHAG-BG293LV05-48/Aligned.sortedByCoord.out.bam		ENCORE2	28666
YWHAG-BG293LV05-48_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	2924					GRCh38	V40	YWHAG-BG293LV05-48/Aligned.sortedByCoord.out.bam		ENCORE2	28710
YWHAG-BG293LV05-48_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	2924					GRCh38	V40	YWHAG-BG293LV05-48/Aligned.sortedByCoord.out.bam		ENCORE2	28754
YWHAG-BG293LV05-48_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	2924					GRCh38	V40	YWHAG-BG293LV05-48/Aligned.sortedByCoord.out.bam		ENCORE2	28798
YWHAG-BG293LV05-48_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2924					GRCh38	V40	YWHAG-BG293LV05-48_S156_L002_R1_001.filtered.trimmed.paired.fastq.gz,YWHAG-BG293LV05-48_S156_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28842