GTSF1 RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-23	BG293LV06-24
idx	0	0
TRCN#_or_BGC#	TRCN0000130086	TRCN0000130086
shRNA_or_gRNA_sequence	CCGGCATAAGAATAACCTGGCTTCACTCGAGTGAAGCCAGGTTATTCTTATGTTTTTTG	CCGGCATAAGAATAACCTGGCTTCACTCGAGTGAAGCCAGGTTATTCTTATGTTTTTTG
PAM
Name	GTSF1	GTSF1
Sample_ID	BG293LV06-23	BG293LV06-24
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	GTSF1	GTSF1
qPCR_result	27.1	32.0
Ave_qPCR	29.6
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	12158	12159

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-23	BG293LV06-24
Sample_ID	BG293LV06-23	BG293LV06-24
Sample Name
Sample Name	GTSF1-BG293LV06-23	GTSF1-BG293LV06-24
RBP	GTSF1	GTSF1
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13460	13461

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-23	BG293LV06-24
Sample #	27	28
Sample Name	GTSF1-BG293LV06-23	GTSF1-BG293LV06-24
Sample_Name_Alias
Index Well Position	C04	D04
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-09-25	2024-09-25
Lib_ID	Lib-240925B	Lib-240925B
Tecan_Location
Tecan
Tecan_date
Size_bp	289	285
Peak_Molarity	99.90	101.00
libSampleQC_DNA_Well	DNA_Library_set71/set1/C4.png	DNA_Library_set71/set1/D4.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set71/set1/C4.png	RNA_Library_set71/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-09-30	2024-09-30
Sample_ID	BG293LV06-23	BG293LV06-24
RBP	GTSF1	GTSF1
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4452	4453

Sequencing Information

	BG293LV06-23	BG293LV06-24
Sample_ID	BG293LV06-23	BG293LV06-24
Sample Name	GTSF1-BG293LV06-23	GTSF1-BG293LV06-24
Pool ID	Pool-240930	Pool-240930
LocalServer_folder	set71	set71
total_reads	40,498,914	33,725,433
total_aligned_reads	37,059,547	30,586,973
unique_aligned_reads	34,714,175	28,636,478
percent_uniqueAligned	0.85716	0.84911
correlation_replicates	0.996832	0.996832
spikein_reads	96,516	76,204
percent_spikeins	0.00238	0.00226
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3021	3022

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
GTSF1-BG293LV06-23_S27_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3021	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29325
GTSF1-BG293LV06-23_S27_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3021	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29389
GTSF1-BG293LV06-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3021					GRCh38	V40	GTSF1-BG293LV06-23_S27_L002_R1_001.filtered.trimmed.paired.fastq.gz,GTSF1-BG293LV06-23_S27_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29454
GTSF1-BG293LV06-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3021					GRCh38	V40	GTSF1-BG293LV06-23_Aligned.sortedByCoord.out.bam		ENCORE2	29518
GTSF1-BG293LV06-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3021					GRCh38	V40	GTSF1-BG293LV06-23_Aligned.sortedByCoord.out.bam		ENCORE2	29582
GTSF1-BG293LV06-23_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3021					GRCh38	V40	GTSF1-BG293LV06-23_Aligned.sortedByCoord.out.bam		ENCORE2	29646
GTSF1-BG293LV06-23_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3021					GRCh38	V40	GTSF1-BG293LV06-23_S27_L002_R1_001.filtered.trimmed.paired.fastq.gz,GTSF1-BG293LV06-23_S27_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29710
GTSF1-BG293LV06-24_S28_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3022	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1merged_S1_L002_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29326
GTSF1-BG293LV06-24_S28_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set71/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3022	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1merged_S1_L002_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2merged_S2_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29390
GTSF1-BG293LV06-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3022					GRCh38	V40	GTSF1-BG293LV06-24_S28_L002_R1_001.filtered.trimmed.paired.fastq.gz,GTSF1-BG293LV06-24_S28_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29455
GTSF1-BG293LV06-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3022					GRCh38	V40	GTSF1-BG293LV06-24_Aligned.sortedByCoord.out.bam		ENCORE2	29519
GTSF1-BG293LV06-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3022					GRCh38	V40	GTSF1-BG293LV06-24_Aligned.sortedByCoord.out.bam		ENCORE2	29583
GTSF1-BG293LV06-24_Signal.Unique.strand-.bw	ENCODE_DATA/set71/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3022					GRCh38	V40	GTSF1-BG293LV06-24_Aligned.sortedByCoord.out.bam		ENCORE2	29647
GTSF1-BG293LV06-24_quant.sf	ENCODE_DATA/set71/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3022					GRCh38	V40	GTSF1-BG293LV06-24_S28_L002_R1_001.filtered.trimmed.paired.fastq.gz,GTSF1-BG293LV06-24_S28_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29711