SRP68 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV04-77	BG293LV04-78
idx	0	0
TRCN#_or_BGC#	TRCN0000075078	TRCN0000075078
shRNA_or_gRNA_sequence	CCGGCCCAGCAAGTTCCATGATATTCTCGAGAATATCATGGAACTTGCTGGGTTTTTG	CCGGCCCAGCAAGTTCCATGATATTCTCGAGAATATCATGGAACTTGCTGGGTTTTTG
PAM
Name	SRP68	SRP68
Sample_ID	BG293LV04-77	BG293LV04-78
transduction_Date	9/7/23	9/7/23
days	D4	D4
RBP_name	SRP68	SRP68
qPCR_result	84.1	87.5
Ave_qPCR	85.8
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	9964	9965

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV04-77	BG293LV04-78
Sample_ID	BG293LV04-77	BG293LV04-78
Sample Name
Sample Name	SRP68-BG293LV04-77	SRP68-BG293LV04-78
RBP	SRP68	SRP68
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-12-30	2023-12-30
Project	ENCORE2	ENCORE2
Note
ID	12540	12541

Library-Prep
Sequencing

Library-Prep Information

	BG293LV04-77	BG293LV04-78
Sample #	27	28
Sample Name	SRP68-BG293LV04-77	SRP68-BG293LV04-78
Sample_Name_Alias
Index Well Position	C04	D04
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	270	265
Peak_Molarity	55.10	73.50
libSampleQC_DNA_Well	DNA_Library_set64/set1/C12.png	DNA_Library_set64/set1/D12.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set64/set1/C8.png	RNA_Library_set64/set1/D8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-10-12	2023-10-12
Sample_ID	BG293LV04-77	BG293LV04-78
RBP	SRP68	SRP68
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	4032	4033

Sequencing Information

	BG293LV04-77	BG293LV04-78
Sample_ID	BG293LV04-77	BG293LV04-78
Sample Name	SRP68-BG293LV04-77	SRP68-BG293LV04-78
Pool ID	Pool-231012	Pool-231012
LocalServer_folder	set64	set64
total_reads	24,480,541	25,457,224
total_aligned_reads	21,295,359	22,939,692
unique_aligned_reads	19,819,668	21,467,299
percent_uniqueAligned	0.80961	0.84327
correlation_replicates	0.987178	0.987178
spikein_reads	9,314	3,494
percent_spikeins	0.00038	0.00014
original_ReadLength	100	100
QC_Status	Submitting	Submitting
ID	2641	2642

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
SRP68-BG293LV04-77_S27_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2641	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	8708
SRP68-BG293LV04-77_S27_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2641	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	8736
SRP68-BG293LV04-77_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2641					GRCh38	V40	SRP68-BG293LV04-77_S27_R1_001.filtered.trimmed.paired.fastq.gz,SRP68-BG293LV04-77_S27_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9785
SRP68-BG293LV04-77_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	2641					GRCh38	V40	SRP68-BG293LV04-77/Aligned.sortedByCoord.out.bam		ENCORE2	9813
SRP68-BG293LV04-77_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	2641					GRCh38	V40	SRP68-BG293LV04-77/Aligned.sortedByCoord.out.bam		ENCORE2	9841
SRP68-BG293LV04-77_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	2641					GRCh38	V40	SRP68-BG293LV04-77/Aligned.sortedByCoord.out.bam		ENCORE2	9869
SRP68-BG293LV04-77_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	2641					GRCh38	V40	SRP68-BG293LV04-77/Aligned.sortedByCoord.out.bam		ENCORE2	9897
SRP68-BG293LV04-77_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2641					GRCh38	V40	SRP68-BG293LV04-77_S27_R1_001.filtered.trimmed.paired.fastq.gz,SRP68-BG293LV04-77_S27_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9925
SRP68-BG293LV04-78_S28_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2642	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	8709
SRP68-BG293LV04-78_S28_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set64/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2642	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	8737
SRP68-BG293LV04-78_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set64/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2642					GRCh38	V40	SRP68-BG293LV04-78_S28_R1_001.filtered.trimmed.paired.fastq.gz,SRP68-BG293LV04-78_S28_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9786
SRP68-BG293LV04-78_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	2642					GRCh38	V40	SRP68-BG293LV04-78/Aligned.sortedByCoord.out.bam		ENCORE2	9814
SRP68-BG293LV04-78_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	2642					GRCh38	V40	SRP68-BG293LV04-78/Aligned.sortedByCoord.out.bam		ENCORE2	9842
SRP68-BG293LV04-78_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	2642					GRCh38	V40	SRP68-BG293LV04-78/Aligned.sortedByCoord.out.bam		ENCORE2	9870
SRP68-BG293LV04-78_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	2642					GRCh38	V40	SRP68-BG293LV04-78/Aligned.sortedByCoord.out.bam		ENCORE2	9898
SRP68-BG293LV04-78_quant.sf	ENCODE_DATA/set64/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2642					GRCh38	V40	SRP68-BG293LV04-78_S28_R1_001.filtered.trimmed.paired.fastq.gz,SRP68-BG293LV04-78_S28_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9926