CSTF2T RNA-Seq in 293T

Experiment Information (Status: Released)

	BG293LV06-97	BG293LV06-98
idx	0	0
TRCN#_or_BGC#	TRCN0000145349	TRCN0000145349
shRNA_or_gRNA_sequence	GCGTCTGTTCACTTTAAGTTACTCGAGTAACTTAAAGTGAACAGACGC	GCGTCTGTTCACTTTAAGTTACTCGAGTAACTTAAAGTGAACAGACGC
PAM
Name	CSTF2T	CSTF2T
Sample_ID	BG293LV06-97	BG293LV06-98
transduction_Date	9/5/24	9/5/24
days	D4	D4
RBP_name	CSTF2T	CSTF2T
qPCR_result	53.4	58.9
Ave_qPCR	56.2
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	12232	12233

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV06-97	BG293LV06-98
Sample_ID	BG293LV06-97	BG293LV06-98
Sample Name
Sample Name	CSTF2T-BG293LV06-97B	CSTF2T-BG293LV06-98B
RBP	CSTF2T	CSTF2T
Cell_Line	293T	293T
Exp UID
Status	Released	Released
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13534	13535

Library-Prep
Sequencing

Library-Prep Information

	BG293LV06-97	BG293LV06-98
Sample #	97	98
Sample Name	CSTF2T-BG293LV06-97B	CSTF2T-BG293LV06-98B
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-10-02	2024-10-02
Lib_ID	Lib-241002	Lib-241002
Tecan_Location
Tecan
Tecan_date
Size_bp	301	285
Peak_Molarity	99.40	85.10
libSampleQC_DNA_Well	DNA_Library_set72/set1/A6.png	DNA_Library_set72/set1/B6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set72/set1/A6.png	RNA_Library_set72/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-10-04	2024-10-04
Sample_ID	BG293LV06-97	BG293LV06-98
RBP	CSTF2T	CSTF2T
Batch_ID	BG293LV06	BG293LV06
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4522	4523

Sequencing Information

	BG293LV06-97	BG293LV06-98
Sample_ID	BG293LV06-97	BG293LV06-98
Sample Name	CSTF2T-BG293LV06-97B	CSTF2T-BG293LV06-98B
Pool ID	Pool-241004	Pool-241004
LocalServer_folder	set72	set72
total_reads	22,746,326	24,159,084
total_aligned_reads	21,105,378	22,470,968
unique_aligned_reads	19,732,168	21,060,478
percent_uniqueAligned	0.86749	0.87174
correlation_replicates	0.984214	0.984214
spikein_reads	94,042	108,718
percent_spikeins	0.00413	0.00450
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	3091	3092

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
CSTF2T-BG293LV06-97B_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3091	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29770
CSTF2T-BG293LV06-97B_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3091	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29842
CSTF2T-BG293LV06-97B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3091					GRCh38	V40	CSTF2T-BG293LV06-97B_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF2T-BG293LV06-97B_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29914
CSTF2T-BG293LV06-97B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3091					GRCh38	V40	CSTF2T-BG293LV06-97B_Aligned.sortedByCoord.out.bam		ENCORE2	29986
CSTF2T-BG293LV06-97B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3091					GRCh38	V40	CSTF2T-BG293LV06-97B_Aligned.sortedByCoord.out.bam		ENCORE2	30058
CSTF2T-BG293LV06-97B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3091					GRCh38	V40	CSTF2T-BG293LV06-97B_Aligned.sortedByCoord.out.bam		ENCORE2	30130
CSTF2T-BG293LV06-97B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3091					GRCh38	V40	CSTF2T-BG293LV06-97B_Aligned.sortedByCoord.out.bam		ENCORE2	30202
CSTF2T-BG293LV06-97B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3091					GRCh38	V40	CSTF2T-BG293LV06-97B_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF2T-BG293LV06-97B_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30274
CSTF2T-BG293LV06-98B_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3092	NovaSeq6000	100	paired-ended	1				NT-BG293LV06-1Bmerged_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29771
CSTF2T-BG293LV06-98B_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set72/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3092	NovaSeq6000	100	paired-ended	2				NT-BG293LV06-1Bmerged_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV06-2Bmerged_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	29843
CSTF2T-BG293LV06-98B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3092					GRCh38	V40	CSTF2T-BG293LV06-98B_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF2T-BG293LV06-98B_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	29915
CSTF2T-BG293LV06-98B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3092					GRCh38	V40	CSTF2T-BG293LV06-98B_Aligned.sortedByCoord.out.bam		ENCORE2	29987
CSTF2T-BG293LV06-98B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3092					GRCh38	V40	CSTF2T-BG293LV06-98B_Aligned.sortedByCoord.out.bam		ENCORE2	30059
CSTF2T-BG293LV06-98B_Signal.Unique.strand-.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3092					GRCh38	V40	CSTF2T-BG293LV06-98B_Aligned.sortedByCoord.out.bam		ENCORE2	30131
CSTF2T-BG293LV06-98B_Signal.Unique.strand+.bw	ENCODE_DATA/set72/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3092					GRCh38	V40	CSTF2T-BG293LV06-98B_Aligned.sortedByCoord.out.bam		ENCORE2	30203
CSTF2T-BG293LV06-98B_quant.sf	ENCODE_DATA/set72/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3092					GRCh38	V40	CSTF2T-BG293LV06-98B_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF2T-BG293LV06-98B_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	30275