SCAF8 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV04-71	BG293LV04-72
idx	0	0
TRCN#_or_BGC#	TRCN0000156141	TRCN0000156141
shRNA_or_gRNA_sequence	CCGGCGACATCAGTTTGGTCAAGAACTCGAGTTCTTGACCAAACTGATGTCGTTTTTTG	CCGGCGACATCAGTTTGGTCAAGAACTCGAGTTCTTGACCAAACTGATGTCGTTTTTTG
PAM
Name	SCAF8	SCAF8
Sample_ID	BG293LV04-71	BG293LV04-72
transduction_Date	9/7/23	9/7/23
days	D4	D4
RBP_name	SCAF8	SCAF8
qPCR_result	52.7	45.7
Ave_qPCR	49.2
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	9958	9959

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV04-71	BG293LV04-72
Sample_ID	BG293LV04-71	BG293LV04-72
Sample Name
Sample Name	SCAF8-BG293LV04-71	SCAF8-BG293LV04-72
RBP	SCAF8	SCAF8
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	12538	12539

Library-Prep
Sequencing

Library-Prep Information

	BG293LV04-71	BG293LV04-72
Sample #	25	26
Sample Name	SCAF8-BG293LV04-71	SCAF8-BG293LV04-72
Sample_Name_Alias
Index Well Position	A04	B04
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-10-10	2023-10-10
Lib_ID	Lib-231010	Lib-231010
Tecan_Location
Tecan
Tecan_date
Size_bp	273	272
Peak_Molarity	48.20	29.90
libSampleQC_DNA_Well	DNA_Library_set64/set1/A12.png	DNA_Library_set64/set1/B12.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set64/set1/A8.png	RNA_Library_set64/set1/B8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-12	2023-10-12
Sample_ID	BG293LV04-71	BG293LV04-72
RBP	SCAF8	SCAF8
Batch_ID	BG293LV04	BG293LV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4030	4031

Sequencing Information

	BG293LV04-71	BG293LV04-72
Sample_ID	BG293LV04-71	BG293LV04-72
Sample Name	SCAF8-BG293LV04-71	SCAF8-BG293LV04-72
Pool ID	Pool-231012	Pool-231012
LocalServer_folder	set64	set64
total_reads	32,316,972	27,137,639
total_aligned_reads	28,375,415	22,067,290
unique_aligned_reads	26,394,239	20,567,240
percent_uniqueAligned	0.81673	0.75789
correlation_replicates	0.988466	0.988466
spikein_reads	3,914	19,942
percent_spikeins	0.00012	0.00073
original_ReadLength	100	100
QC_Status	Submitting	Submitting
ID	2639	2640

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
SCAF8-BG293LV04-71_S25_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2639	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8706
SCAF8-BG293LV04-71_S25_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2639	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8734
SCAF8-BG293LV04-71_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2639					GRCh38	V40	SCAF8-BG293LV04-71_S25_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BG293LV04-71_S25_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9783
SCAF8-BG293LV04-71_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2639					GRCh38	V40	SCAF8-BG293LV04-71/Aligned.sortedByCoord.out.bam		ENCORE2	9811
SCAF8-BG293LV04-71_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2639					GRCh38	V40	SCAF8-BG293LV04-71/Aligned.sortedByCoord.out.bam		ENCORE2	9839
SCAF8-BG293LV04-71_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2639					GRCh38	V40	SCAF8-BG293LV04-71/Aligned.sortedByCoord.out.bam		ENCORE2	9867
SCAF8-BG293LV04-71_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2639					GRCh38	V40	SCAF8-BG293LV04-71/Aligned.sortedByCoord.out.bam		ENCORE2	9895
SCAF8-BG293LV04-71_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2639					GRCh38	V40	SCAF8-BG293LV04-71_S25_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BG293LV04-71_S25_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9923
SCAF8-BG293LV04-72_S26_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2640	NextSeq2000	100	paired-ended	1				NT-BG293LV04-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8707
SCAF8-BG293LV04-72_S26_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2640	NextSeq2000	100	paired-ended	2				NT-BG293LV04-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV04-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8735
SCAF8-BG293LV04-72_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2640					GRCh38	V40	SCAF8-BG293LV04-72_S26_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BG293LV04-72_S26_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9784
SCAF8-BG293LV04-72_Signal.Unique.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2640					GRCh38	V40	SCAF8-BG293LV04-72/Aligned.sortedByCoord.out.bam		ENCORE2	9812
SCAF8-BG293LV04-72_Signal.Unique.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2640					GRCh38	V40	SCAF8-BG293LV04-72/Aligned.sortedByCoord.out.bam		ENCORE2	9840
SCAF8-BG293LV04-72_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2640					GRCh38	V40	SCAF8-BG293LV04-72/Aligned.sortedByCoord.out.bam		ENCORE2	9868
SCAF8-BG293LV04-72_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2640					GRCh38	V40	SCAF8-BG293LV04-72/Aligned.sortedByCoord.out.bam		ENCORE2	9896
SCAF8-BG293LV04-72_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2640					GRCh38	V40	SCAF8-BG293LV04-72_S26_R1_001.filtered.trimmed.paired.fastq.gz,SCAF8-BG293LV04-72_S26_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9924