AHNAK RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-49	BG293LV05-50
idx	0	0
TRCN#_or_BGC#	TRCN0000123212	TRCN0000123212
shRNA_or_gRNA_sequence	CCGGGCAGCTCTGAAGTGGTTCTGACTCGAGTCAGAACCACTTCAGAGCTGCTTTTTG	CCGGGCAGCTCTGAAGTGGTTCTGACTCGAGTCAGAACCACTTCAGAGCTGCTTTTTG
PAM
Name	AHNAK	AHNAK
Sample_ID	BG293LV05-49	BG293LV05-50
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	AHNAK	AHNAK
qPCR_result	88	89
Ave_qPCR	88.5
RT-qPCR_primer-F	tcttcagctcctgcagctct
RT-qPCR_primer-R	ctccatcttccgacttcagc
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	10021	10022

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-49	BG293LV05-50
Sample_ID	BG293LV05-49	BG293LV05-50
Sample Name
Sample Name	AHNAK-BG293LV05-49	AHNAK-BG293LV05-50
RBP	AHNAK	AHNAK
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12858	12859

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-49	BG293LV05-50
Sample #	25	26
Sample Name	AHNAK-BG293LV05-49	AHNAK-BG293LV05-50
Sample_Name_Alias
Index Well Position	A10	B10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	273	269
Peak_Molarity	60.30	80.00
libSampleQC_DNA_Well	DNA_Library_set69/set1/A4.png	DNA_Library_set69/set1/B4.png
RIN	9.6	9.4
libSample_RNA_Well	RNA_Library_set69/set1/B9.png	RNA_Library_set69/set1/C9.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-49	BG293LV05-50
RBP	AHNAK	AHNAK
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4206	4207

Sequencing Information

	BG293LV05-49	BG293LV05-50
Sample_ID	BG293LV05-49	BG293LV05-50
Sample Name	AHNAK-BG293LV05-49	AHNAK-BG293LV05-50
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	16,770,507	17,857,802
total_aligned_reads	12,363,868	15,241,233
unique_aligned_reads	11,462,867	14,136,726
percent_uniqueAligned	0.68351	0.79163
correlation_replicates	0.983694	0.983694
spikein_reads	5,516	1,484
percent_spikeins	0.00033	0.00008
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2925	2926

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
AHNAK-BG293LV05-49_merged_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2925	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28493
AHNAK-BG293LV05-49_merged_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2925	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28537
AHNAK-BG293LV05-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2925					GRCh38	V40	AHNAK-BG293LV05-49_merged_R1_001.filtered.trimmed.paired.fastq.gz,AHNAK-BG293LV05-49_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28581
AHNAK-BG293LV05-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2925					GRCh38	V40	AHNAK-BG293LV05-49/Aligned.sortedByCoord.out.bam		ENCORE2	28625
AHNAK-BG293LV05-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2925					GRCh38	V40	AHNAK-BG293LV05-49/Aligned.sortedByCoord.out.bam		ENCORE2	28669
AHNAK-BG293LV05-49_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2925					GRCh38	V40	AHNAK-BG293LV05-49/Aligned.sortedByCoord.out.bam		ENCORE2	28713
AHNAK-BG293LV05-49_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2925					GRCh38	V40	AHNAK-BG293LV05-49/Aligned.sortedByCoord.out.bam		ENCORE2	28757
AHNAK-BG293LV05-49_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2925					GRCh38	V40	AHNAK-BG293LV05-49_merged_R1_001.filtered.trimmed.paired.fastq.gz,AHNAK-BG293LV05-49_merged_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28801
AHNAK-BG293LV05-50_S158_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2926	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28494
AHNAK-BG293LV05-50_S158_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2926	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28538
AHNAK-BG293LV05-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2926					GRCh38	V40	AHNAK-BG293LV05-50_S158_L002_R1_001.filtered.trimmed.paired.fastq.gz,AHNAK-BG293LV05-50_S158_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28582
AHNAK-BG293LV05-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2926					GRCh38	V40	AHNAK-BG293LV05-50/Aligned.sortedByCoord.out.bam		ENCORE2	28626
AHNAK-BG293LV05-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2926					GRCh38	V40	AHNAK-BG293LV05-50/Aligned.sortedByCoord.out.bam		ENCORE2	28670
AHNAK-BG293LV05-50_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2926					GRCh38	V40	AHNAK-BG293LV05-50/Aligned.sortedByCoord.out.bam		ENCORE2	28714
AHNAK-BG293LV05-50_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2926					GRCh38	V40	AHNAK-BG293LV05-50/Aligned.sortedByCoord.out.bam		ENCORE2	28758
AHNAK-BG293LV05-50_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2926					GRCh38	V40	AHNAK-BG293LV05-50_S158_L002_R1_001.filtered.trimmed.paired.fastq.gz,AHNAK-BG293LV05-50_S158_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28802