none RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV03-35	BG293LV03-36
idx	0	0
TRCN#_or_BGC#
shRNA_or_gRNA_sequence
PAM
Name	baseline	baseline
Sample_ID	BG293LV03-35	BG293LV03-36
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	none	none
qPCR_result
Ave_qPCR
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	9885	9886

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV03-35	BG293LV03-36
Sample_ID	BG293LV03-35	BG293LV03-36
Sample Name
Sample Name	BL-BG293LV03-35	BL-BG293LV03-36
RBP	none	none
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2023-09-20	2023-09-20
Project	ENCORE2	ENCORE2
Note
ID	11752	11753

Library-Prep
Sequencing

Library-Prep Information

	BG293LV03-35	BG293LV03-36
Sample #	3	4
Sample Name	BL-BG293LV03-35	BL-BG293LV03-36
Sample_Name_Alias
Index Well Position	C01	D01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-05-02	2023-05-02
Lib_ID	Lib-230502	Lib-230502
Tecan_Location
Tecan
Tecan_date
Size_bp	294	297
Peak_Molarity	27.30	55.10
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/C1.png	DNA_Library_set60-62/set4/D1.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/C1.png	RNA_Library_set60-62/set2/D1.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BG293LV03-35	BG293LV03-36
RBP	BL	BL
Batch_ID	BG293LV03	BG293LV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3686	3687

Sequencing Information

	BG293LV03-35	BG293LV03-36
Sample_ID	BG293LV03-35	BG293LV03-36
Sample Name	BL-BG293LV03-35	BL-BG293LV03-36
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_W	set62_W
total_reads	28,966,721	32,419,873
total_aligned_reads	22,242,454	25,149,866
unique_aligned_reads	20,831,458	23,508,011
percent_uniqueAligned	0.71915	0.72511
correlation_replicates	0.992402	0.992402
spikein_reads	113,688	70,888
percent_spikeins	0.00392	0.00219
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2557	2558

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	Project	FILE_ID
BL-BG293LV03-35_S3_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2557	NovaSeq6000	100	paired-ended	1				ENCORE2	7842
BL-BG293LV03-35_S3_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2557	NovaSeq6000	100	paired-ended	2				ENCORE2	7858
BL-BG293LV03-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2557					GRCh38	V40	BL-BG293LV03-35_S3_L003_R1_001.filtered.trimmed.paired.fastq.gz,BL-BG293LV03-35_S3_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10083
BL-BG293LV03-35_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2557					GRCh38	V40	BL-BG293LV03-35/Aligned.sortedByCoord.out.bam	ENCORE2	10099
BL-BG293LV03-35_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2557					GRCh38	V40	BL-BG293LV03-35/Aligned.sortedByCoord.out.bam	ENCORE2	10115
BL-BG293LV03-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2557					GRCh38	V40	BL-BG293LV03-35/Aligned.sortedByCoord.out.bam	ENCORE2	10131
BL-BG293LV03-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2557					GRCh38	V40	BL-BG293LV03-35/Aligned.sortedByCoord.out.bam	ENCORE2	10147
BL-BG293LV03-35_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2557					GRCh38	V40	BL-BG293LV03-35_S3_L003_R1_001.filtered.trimmed.paired.fastq.gz,BL-BG293LV03-35_S3_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10163
BL-BG293LV03-36_S4_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2558	NovaSeq6000	100	paired-ended	1				ENCORE2	7843
BL-BG293LV03-36_S4_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_W/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2558	NovaSeq6000	100	paired-ended	2				ENCORE2	7859
BL-BG293LV03-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2558					GRCh38	V40	BL-BG293LV03-36_S4_L003_R1_001.filtered.trimmed.paired.fastq.gz,BL-BG293LV03-36_S4_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10084
BL-BG293LV03-36_Signal.Unique.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2558					GRCh38	V40	BL-BG293LV03-36/Aligned.sortedByCoord.out.bam	ENCORE2	10100
BL-BG293LV03-36_Signal.Unique.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2558					GRCh38	V40	BL-BG293LV03-36/Aligned.sortedByCoord.out.bam	ENCORE2	10116
BL-BG293LV03-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2558					GRCh38	V40	BL-BG293LV03-36/Aligned.sortedByCoord.out.bam	ENCORE2	10132
BL-BG293LV03-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_W/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2558					GRCh38	V40	BL-BG293LV03-36/Aligned.sortedByCoord.out.bam	ENCORE2	10148
BL-BG293LV03-36_quant.sf	ENCODE_DATA/set62_W/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2558					GRCh38	V40	BL-BG293LV03-36_S4_L003_R1_001.filtered.trimmed.paired.fastq.gz,BL-BG293LV03-36_S4_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	10164