CSTF2T RNA-Seq in 293T

Experiment Information (Status: Revoked)

	BG293LV02-11	BG293LV02-12
idx	0	0
TRCN#_or_BGC#	TRCN0000145349	TRCN0000145349
shRNA_or_gRNA_sequence	GCGTCTGTTCACTTTAAGTTACTCGAGTAACTTAAAGTGAACAGACGC	GCGTCTGTTCACTTTAAGTTACTCGAGTAACTTAAAGTGAACAGACGC
PAM
Name	CSTF2T	CSTF2T
Sample_ID	BG293LV02-11	BG293LV02-12
transduction_Date	3/20/23	3/20/23
days	D4	D4
RBP_name	CSTF2T	CSTF2T
qPCR_result	70.2	67.9
Ave_qPCR	69.1
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	9806	9807

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV02-11	BG293LV02-12
Sample_ID	BG293LV02-11	BG293LV02-12
Sample Name
Sample Name	CSTF2T-BG293LV02-11	CSTF2T-BG293LV02-12
RBP	CSTF2T	CSTF2T
Cell_Line	293T	293T
Exp UID
Status	Revoked	Revoked
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11566	11567

Library-Prep
Sequencing

Library-Prep Information

	BG293LV02-11	BG293LV02-12
Sample #	9	10
Sample Name	CSTF2T-BG293LV02-11	CSTF2T-BG293LV02-12
Sample_Name_Alias
Index Well Position	A02	B02
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	292	296
Peak_Molarity	65.70	85.90
libSampleQC_DNA_Well	DNA_Library_set60-62/set2/A2.png	DNA_Library_set60-62/set2/B2.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set60-62/set1/A2.png	RNA_Library_set60-62/set1/B2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-04-17	2023-04-17
Sample_ID	BG293LV02-11	BG293LV02-12
RBP	CSTF2T	CSTF2T
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	3596	3597

Sequencing Information

	BG293LV02-11	BG293LV02-12
Sample_ID	BG293LV02-11	BG293LV02-12
Sample Name	CSTF2T-BG293LV02-11	CSTF2T-BG293LV02-12
Pool ID	Pool-230417	Pool-230417
LocalServer_folder	set60	set60
total_reads	41,995,369	39,112,363
total_aligned_reads	34,143,747	31,855,712
unique_aligned_reads	31,876,028	29,687,168
percent_uniqueAligned	0.75904	0.75902
correlation_replicates	0.994894	0.994894
spikein_reads	144,722	124,512
percent_spikeins	0.00345	0.00318
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2467	2468

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-BG293LV02-11_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2467	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	7968
CSTF2T-BG293LV02-11_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2467	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	8012
CSTF2T-BG293LV02-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2467					GRCh38	V40	CSTF2T-BG293LV02-11_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF2T-BG293LV02-11_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10761
CSTF2T-BG293LV02-11_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	2467					GRCh38	V40	CSTF2T-BG293LV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	10805
CSTF2T-BG293LV02-11_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	2467					GRCh38	V40	CSTF2T-BG293LV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	10849
CSTF2T-BG293LV02-11_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	2467					GRCh38	V40	CSTF2T-BG293LV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	10893
CSTF2T-BG293LV02-11_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	2467					GRCh38	V40	CSTF2T-BG293LV02-11/Aligned.sortedByCoord.out.bam		ENCORE2	10937
CSTF2T-BG293LV02-11_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2467					GRCh38	V40	CSTF2T-BG293LV02-11_S9_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF2T-BG293LV02-11_S9_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10981
CSTF2T-BG293LV02-12_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2468	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	7969
CSTF2T-BG293LV02-12_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set60/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2468	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	8013
CSTF2T-BG293LV02-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set60/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2468					GRCh38	V40	CSTF2T-BG293LV02-12_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF2T-BG293LV02-12_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10762
CSTF2T-BG293LV02-12_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	2468					GRCh38	V40	CSTF2T-BG293LV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	10806
CSTF2T-BG293LV02-12_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	2468					GRCh38	V40	CSTF2T-BG293LV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	10850
CSTF2T-BG293LV02-12_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	2468					GRCh38	V40	CSTF2T-BG293LV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	10894
CSTF2T-BG293LV02-12_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	2468					GRCh38	V40	CSTF2T-BG293LV02-12/Aligned.sortedByCoord.out.bam		ENCORE2	10938
CSTF2T-BG293LV02-12_quant.sf	ENCODE_DATA/set60/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2468					GRCh38	V40	CSTF2T-BG293LV02-12_S10_L001_R1_001.filtered.trimmed.paired.fastq.gz,CSTF2T-BG293LV02-12_S10_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10982