GTF3C4 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-35dox	BGRSDLV02-36dox
idx	0	0
TRCN#_or_BGC#	TRCN0000013400	TRCN0000013400
shRNA_or_gRNA_sequence	CCGGCCATCTCTTCATGCAACACAACTCGAGTTGTGTTGCATGAAGAGATGGTTTTT	CCGGCCATCTCTTCATGCAACACAACTCGAGTTGTGTTGCATGAAGAGATGGTTTTT
PAM
Name	GTF3C4	GTF3C4
Sample_ID	BGRSDLV02-35dox	BGRSDLV02-36dox
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	GTF3C4	GTF3C4
qPCR_result	90.9	85.4
Ave_qPCR	88.1
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	9246	9247

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-35dox	BGRSDLV02-36dox
Sample_ID	BGRSDLV02-35dox	BGRSDLV02-36dox
Sample Name
Sample Name	GTF3C4-BGRSDLV02-35dox	GTF3C4-BGRSDLV02-36dox
RBP	GTF3C4	GTF3C4
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12350	12351

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-35dox	BGRSDLV02-36dox
Sample #	31	32
Sample Name	GTF3C4-BGRSDLV02-35dox	GTF3C4-BGRSDLV02-36dox
Sample_Name_Alias
Index Well Position	G04	H04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	289	290
Peak_Molarity	84.00	82.10
libSampleQC_DNA_Well	DNA_Library_set65/set1/G4.png	DNA_Library_set65/set1/H4.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_set65/set1/G4.png	RNA_Library_set65/set1/H4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-35dox	BGRSDLV02-36dox
RBP	GTF3C4	GTF3C4
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3952	3953

Sequencing Information

	BGRSDLV02-35dox	BGRSDLV02-36dox
Sample_ID	BGRSDLV02-35dox	BGRSDLV02-36dox
Sample Name	GTF3C4-BGRSDLV02-35dox	GTF3C4-BGRSDLV02-36dox
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	26,340,783	28,815,619
total_aligned_reads	24,749,114	26,159,249
unique_aligned_reads	23,062,190	24,355,608
percent_uniqueAligned	0.87553	0.84522
correlation_replicates	0.994565	0.994565
spikein_reads	1,148	6,512
percent_spikeins	0.00004	0.00023
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2699	2700

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
GTF3C4-BGRSDLV02-35dox_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2699	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8768
GTF3C4-BGRSDLV02-35dox_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2699	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8844
GTF3C4-BGRSDLV02-35dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2699					GRCh38	V40	GTF3C4-BGRSDLV02-35dox_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,GTF3C4-BGRSDLV02-35dox_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9333
GTF3C4-BGRSDLV02-35dox_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2699					GRCh38	V40	GTF3C4-BGRSDLV02-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	9409
GTF3C4-BGRSDLV02-35dox_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2699					GRCh38	V40	GTF3C4-BGRSDLV02-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	9485
GTF3C4-BGRSDLV02-35dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2699					GRCh38	V40	GTF3C4-BGRSDLV02-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	9561
GTF3C4-BGRSDLV02-35dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2699					GRCh38	V40	GTF3C4-BGRSDLV02-35dox/Aligned.sortedByCoord.out.bam		ENCORE2	9637
GTF3C4-BGRSDLV02-35dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2699					GRCh38	V40	GTF3C4-BGRSDLV02-35dox_S31_L001_R1_001.filtered.trimmed.paired.fastq.gz,GTF3C4-BGRSDLV02-35dox_S31_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9713
GTF3C4-BGRSDLV02-36dox_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2700	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-3dox_S3_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8769
GTF3C4-BGRSDLV02-36dox_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2700	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-3dox_S3_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-4dox_S4_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8845
GTF3C4-BGRSDLV02-36dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2700					GRCh38	V40	GTF3C4-BGRSDLV02-36dox_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,GTF3C4-BGRSDLV02-36dox_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9334
GTF3C4-BGRSDLV02-36dox_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2700					GRCh38	V40	GTF3C4-BGRSDLV02-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	9410
GTF3C4-BGRSDLV02-36dox_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2700					GRCh38	V40	GTF3C4-BGRSDLV02-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	9486
GTF3C4-BGRSDLV02-36dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2700					GRCh38	V40	GTF3C4-BGRSDLV02-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	9562
GTF3C4-BGRSDLV02-36dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2700					GRCh38	V40	GTF3C4-BGRSDLV02-36dox/Aligned.sortedByCoord.out.bam		ENCORE2	9638
GTF3C4-BGRSDLV02-36dox_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2700					GRCh38	V40	GTF3C4-BGRSDLV02-36dox_S32_L001_R1_001.filtered.trimmed.paired.fastq.gz,GTF3C4-BGRSDLV02-36dox_S32_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9714