TAF15 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV02-9	BGRSLV02-10
idx	0	0
TRCN#_or_BGC#	TRCN0000020143	TRCN0000020143
shRNA_or_gRNA_sequence	GCTCGAAGGAATTCCTGCAATCTCGAGATTGCAGGAATTCCTTCNA	GCTCGAAGGAATTCCTGCAATCTCGAGATTGCAGGAATTCCTTCNA
PAM
Name	TAF15	TAF15
Sample_ID	BGRSLV02-9	BGRSLV02-10
transduction_Date	12/5/22	12/5/22
days	D4	D4
RBP_name	TAF15	TAF15
qPCR_result	66.1	53.6
Ave_qPCR	59.8
RT-qPCR_primer-F	GGGAGGCAACAGTGTCATTT
RT-qPCR_primer-R	ACCTCCACTTCCACCTCCTC
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	8246	8247

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV02-9	BGRSLV02-10
Sample_ID	BGRSLV02-9	BGRSLV02-10
Sample Name
Sample Name	TAF15-BGRSLV02-9	TAF15-BGRSLV02-10
RBP	TAF15	TAF15
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11300	11301

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV02-9	BGRSLV02-10
Sample #	3	4
Sample Name	TAF15-BGRSLV02-9	TAF15-BGRSLV02-10
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-07	2023-02-07
Lib_ID	Lib-230207	Lib-230207
Tecan_Location
Tecan
Tecan_date
Size_bp	274	283
Peak_Molarity	60.20	62.20
libSampleQC_DNA_Well	DNA_Library_set57/set1/C7.png	DNA_Library_set57/set1/D7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set57/set1/C1.png	RNA_Library_set57/set1/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-07	2023-02-07
Sample_ID	BGRSLV02-9	BGRSLV02-10
RBP	TAF15	TAF15
Batch_ID	BGRSLV02	BGRSLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3464	3465

Sequencing Information

	BGRSLV02-9	BGRSLV02-10
Sample_ID	BGRSLV02-9	BGRSLV02-10
Sample Name	TAF15-BGRSLV02-9	TAF15-BGRSLV02-10
Pool ID	Pool-230207	Pool-230207
LocalServer_folder	set57	set57
total_reads	29,716,548	43,159,077
total_aligned_reads	24,483,217	38,925,848
unique_aligned_reads	22,577,843	36,044,224
percent_uniqueAligned	0.75977	0.83515
correlation_replicates	0.983032	0.983032
spikein_reads	14,004	23,834
percent_spikeins	0.00047	0.00055
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2335	2336

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
TAF15-BGRSLV02-9_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2335	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8231
TAF15-BGRSLV02-9_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2335	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8277
TAF15-BGRSLV02-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2335					GRCh38	V40	TAF15-BGRSLV02-9_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,TAF15-BGRSLV02-9_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11520
TAF15-BGRSLV02-9_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2335					GRCh38	V40	TAF15-BGRSLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	11566
TAF15-BGRSLV02-9_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2335					GRCh38	V40	TAF15-BGRSLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	11612
TAF15-BGRSLV02-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2335					GRCh38	V40	TAF15-BGRSLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	11658
TAF15-BGRSLV02-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2335					GRCh38	V40	TAF15-BGRSLV02-9/Aligned.sortedByCoord.out.bam		ENCORE2	11704
TAF15-BGRSLV02-9_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2335					GRCh38	V40	TAF15-BGRSLV02-9_S91_L003_R1_001.filtered.trimmed.paired.fastq.gz,TAF15-BGRSLV02-9_S91_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11750
TAF15-BGRSLV02-10_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2336	NovaSeq6000	100	paired-ended	1				NT-BGRSLV02-1_S89_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8230
TAF15-BGRSLV02-10_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set57/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2336	NovaSeq6000	100	paired-ended	2				NT-BGRSLV02-1_S89_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV02-2_S90_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8276
TAF15-BGRSLV02-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2336					GRCh38	V40	TAF15-BGRSLV02-10_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz,TAF15-BGRSLV02-10_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11519
TAF15-BGRSLV02-10_Signal.Unique.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2336					GRCh38	V40	TAF15-BGRSLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	11565
TAF15-BGRSLV02-10_Signal.Unique.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2336					GRCh38	V40	TAF15-BGRSLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	11611
TAF15-BGRSLV02-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2336					GRCh38	V40	TAF15-BGRSLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	11657
TAF15-BGRSLV02-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set57/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2336					GRCh38	V40	TAF15-BGRSLV02-10/Aligned.sortedByCoord.out.bam		ENCORE2	11703
TAF15-BGRSLV02-10_quant.sf	ENCODE_DATA/set57/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2336					GRCh38	V40	TAF15-BGRSLV02-10_S92_L003_R1_001.filtered.trimmed.paired.fastq.gz,TAF15-BGRSLV02-10_S92_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11749