TEX13A RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-93	BGRSDLV04-94
idx	0	0
TRCN#_or_BGC#	TRCN0000133962	TRCN0000133962
shRNA_or_gRNA_sequence	CCGGCCACATCTTATTTCTCTGGAACTCGAGTTCCAGAGAAATAAGATGTGGTTTTTTG	CCGGCCACATCTTATTTCTCTGGAACTCGAGTTCCAGAGAAATAAGATGTGGTTTTTTG
PAM
Name	TEX13A	TEX13A
Sample_ID	BGRSDLV04-93	BGRSDLV04-94
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	TEX13A	TEX13A
qPCR_result
Ave_qPCR
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	9457	9458

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-93	BGRSDLV04-94
Sample_ID	BGRSDLV04-93	BGRSDLV04-94
Sample Name
Sample Name	TEX13A-BGRSDLV04-93	TEX13A-BGRSDLV04-94
RBP	TEX13A	TEX13A
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12694	12695

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-93	BGRSDLV04-94
Sample #	49	50
Sample Name	TEX13A-BGRSDLV04-93	TEX13A-BGRSDLV04-94
Sample_Name_Alias
Index Well Position	A07	B07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	291	292
Peak_Molarity	76.10	62.10
libSampleQC_DNA_Well	DNA_Library_set68/set1/A7.png	DNA_Library_set68/set1/B7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set68/set1/A7.png	RNA_Library_set68/set1/B7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-93	BGRSDLV04-94
RBP	TEX13A	TEX13A
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4122	4123

Sequencing Information

	BGRSDLV04-93	BGRSDLV04-94
Sample_ID	BGRSDLV04-93	BGRSDLV04-94
Sample Name	TEX13A-BGRSDLV04-93	TEX13A-BGRSDLV04-94
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	50,914,983	57,761,557
total_aligned_reads	44,927,260	51,249,223
unique_aligned_reads	42,221,175	48,196,310
percent_uniqueAligned	0.82925	0.83440
correlation_replicates	0.983690	0.983690
spikein_reads	14,722	11,594
percent_spikeins	0.00029	0.00020
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2885	2886

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
TEX13A-BGRSDLV04-93_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2885	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27657
TEX13A-BGRSDLV04-93_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2885	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27721
TEX13A-BGRSDLV04-93_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2885					GRCh38	V40	TEX13A-BGRSDLV04-93_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,TEX13A-BGRSDLV04-93_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27785
TEX13A-BGRSDLV04-93_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2885					GRCh38	V40	TEX13A-BGRSDLV04-93/Aligned.sortedByCoord.out.bam		ENCORE2	27849
TEX13A-BGRSDLV04-93_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2885					GRCh38	V40	TEX13A-BGRSDLV04-93/Aligned.sortedByCoord.out.bam		ENCORE2	27913
TEX13A-BGRSDLV04-93_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2885					GRCh38	V40	TEX13A-BGRSDLV04-93/Aligned.sortedByCoord.out.bam		ENCORE2	27977
TEX13A-BGRSDLV04-93_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2885					GRCh38	V40	TEX13A-BGRSDLV04-93/Aligned.sortedByCoord.out.bam		ENCORE2	28041
TEX13A-BGRSDLV04-93_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2885					GRCh38	V40	TEX13A-BGRSDLV04-93_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,TEX13A-BGRSDLV04-93_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28105
TEX13A-BGRSDLV04-94_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2886	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27658
TEX13A-BGRSDLV04-94_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2886	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-1_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-2_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27722
TEX13A-BGRSDLV04-94_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2886					GRCh38	V40	TEX13A-BGRSDLV04-94_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz,TEX13A-BGRSDLV04-94_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27786
TEX13A-BGRSDLV04-94_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2886					GRCh38	V40	TEX13A-BGRSDLV04-94/Aligned.sortedByCoord.out.bam		ENCORE2	27850
TEX13A-BGRSDLV04-94_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2886					GRCh38	V40	TEX13A-BGRSDLV04-94/Aligned.sortedByCoord.out.bam		ENCORE2	27914
TEX13A-BGRSDLV04-94_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2886					GRCh38	V40	TEX13A-BGRSDLV04-94/Aligned.sortedByCoord.out.bam		ENCORE2	27978
TEX13A-BGRSDLV04-94_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2886					GRCh38	V40	TEX13A-BGRSDLV04-94/Aligned.sortedByCoord.out.bam		ENCORE2	28042
TEX13A-BGRSDLV04-94_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2886					GRCh38	V40	TEX13A-BGRSDLV04-94_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz,TEX13A-BGRSDLV04-94_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28106