GTSF1 RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-19	BG293LV02-20
idx	0	0
TRCN#_or_BGC#	TRCN0000130086	TRCN0000130086
shRNA_or_gRNA_sequence	CCGGCATAAGAATAACCTGGCTTCACTCGAGTGAAGCCAGGTTATTCTTATGTTTTTTG	CCGGCATAAGAATAACCTGGCTTCACTCGAGTGAAGCCAGGTTATTCTTATGTTTTTTG
PAM
Name	GTSF1	GTSF1
Sample_ID	BG293LV02-19	BG293LV02-20
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	GTSF1	GTSF1
qPCR_result	64.2	64.0
Ave_qPCR	64.1
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	11862	11863

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-19	BG293LV02-20
Sample_ID	BG293LV02-19	BG293LV02-20
Sample Name
Sample Name	GTSF1-BG293LV02-19	GTSF1-BG293LV02-20
RBP	GTSF1	GTSF1
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11574	11575

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-19	BG293LV02-20
Sample #	17	18
Sample Name	GTSF1-BG293LV02-19	GTSF1-BG293LV02-20
Sample_Name_Alias
Index Well Position	A03	B03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-04-12	2023-04-12
Lib_ID	Lib-230412	Lib-230412
Tecan_Location
Tecan
Tecan_date
Size_bp	291	294
Peak_Molarity	79.90	76.00
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/A3.png	DNA_Library_set60-62/set2/B3.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set60-62/set1/A3.png	RNA_Library_set60-62/set1/B3.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-19	BG293LV02-20
RBP	GTSF1	GTSF1
Batch_ID	BG293LV02	BG293LV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3604	3605

Sequencing Information

	BG293LV02-19	BG293LV02-20
Sample_ID	BG293LV02-19	BG293LV02-20
Sample Name	GTSF1-BG293LV02-19	GTSF1-BG293LV02-20
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	40,503,420	49,054,571
total_aligned_reads	33,059,719	43,879,798
unique_aligned_reads	30,685,781	40,985,185
percent_uniqueAligned	0.75761	0.83550
correlation_replicates	0.967586	0.967586
spikein_reads	143,100	135,858
percent_spikeins	0.00353	0.00277
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2475	2476

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-BG293LV02-19_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2475	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7976
GTSF1-BG293LV02-19_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2475	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8020
GTSF1-BG293LV02-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2475					GRCh38	V40	GTSF1-BG293LV02-19_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,GTSF1-BG293LV02-19_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10769
GTSF1-BG293LV02-19_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2475					GRCh38	V40	GTSF1-BG293LV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	10813
GTSF1-BG293LV02-19_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2475					GRCh38	V40	GTSF1-BG293LV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	10857
GTSF1-BG293LV02-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2475					GRCh38	V40	GTSF1-BG293LV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	10901
GTSF1-BG293LV02-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2475					GRCh38	V40	GTSF1-BG293LV02-19/Aligned.sortedByCoord.out.bam		ENCORE2	10945
GTSF1-BG293LV02-19_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2475					GRCh38	V40	GTSF1-BG293LV02-19_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,GTSF1-BG293LV02-19_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10989
GTSF1-BG293LV02-20_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2476	NovaSeq6000	100	paired-ended	1				NT-BG293LV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7977
GTSF1-BG293LV02-20_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2476	NovaSeq6000	100	paired-ended	2				NT-BG293LV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8021
GTSF1-BG293LV02-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2476					GRCh38	V40	GTSF1-BG293LV02-20_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,GTSF1-BG293LV02-20_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10770
GTSF1-BG293LV02-20_Signal.Unique.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2476					GRCh38	V40	GTSF1-BG293LV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	10814
GTSF1-BG293LV02-20_Signal.Unique.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2476					GRCh38	V40	GTSF1-BG293LV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	10858
GTSF1-BG293LV02-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2476					GRCh38	V40	GTSF1-BG293LV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	10902
GTSF1-BG293LV02-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2476					GRCh38	V40	GTSF1-BG293LV02-20/Aligned.sortedByCoord.out.bam		ENCORE2	10946
GTSF1-BG293LV02-20_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2476					GRCh38	V40	GTSF1-BG293LV02-20_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,GTSF1-BG293LV02-20_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10990