YAF2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV08-5	BGRSLV08-6
idx	0	0
TRCN#_or_BGC#	TRCN0000108026	TRCN0000108026
shRNA_or_gRNA_sequence	CCGGCCTCCTACACAGTCAAAGAAACTCGAGTTTCTTTGACTGTGTAGGAGGTTTTTG	CCGGCCTCCTACACAGTCAAAGAAACTCGAGTTTCTTTGACTGTGTAGGAGGTTTTTG
PAM
Name	YAF2	YAF2
Sample_ID	BGRSLV08-5	BGRSLV08-6
transduction_Date	4/22/23	4/22/23
days	D4	D4
RBP_name	YAF2	YAF2
qPCR_result	92.5	93.6
Ave_qPCR	93.0
RT-qPCR_primer-F	tcctcggatgagggttactg
RT-qPCR_primer-R	caaccaactgggagacaggt
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	8654	8655

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV08-5	BGRSLV08-6
Sample_ID	BGRSLV08-5	BGRSLV08-6
Sample Name
Sample Name	YAF2-BGRSLV08-5	YAF2-BGRSLV08-6
RBP	YAF2	YAF2
Cell_Line	Ribo-STAMP-293T	Ribo-STAMP-293T
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	11778	11779

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV08-5	BGRSLV08-6
Sample #	43	44
Sample Name	YAF2-BGRSLV08-5	YAF2-BGRSLV08-6
Sample_Name_Alias
Index Well Position	C06	D06
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	285	295
Peak_Molarity	88.70	90.40
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/C6.png	DNA_Library_set60-62/set4/D6.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_set60-62/set2/C6.png	RNA_Library_set60-62/set2/D6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV08-5	BGRSLV08-6
RBP	YAF2	YAF2
Batch_ID	BGRSLV08	BGRSLV08
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3726	3727

Sequencing Information

	BGRSLV08-5	BGRSLV08-6
Sample_ID	BGRSLV08-5	BGRSLV08-6
Sample Name	YAF2-BGRSLV08-5	YAF2-BGRSLV08-6
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	22,451,810	27,273,551
total_aligned_reads	17,481,875	23,375,168
unique_aligned_reads	16,449,324	22,038,631
percent_uniqueAligned	0.73265	0.80806
correlation_replicates	0.990664	0.990664
spikein_reads	25,064	20,368
percent_spikeins	0.00112	0.00075
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2597	2598

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
YAF2-BGRSLV08-5_S43_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2597	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7894
YAF2-BGRSLV08-5_S43_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2597	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7938
YAF2-BGRSLV08-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2597					GRCh38	V40	YAF2-BGRSLV08-5_S43_L003_R1_001.filtered.trimmed.paired.fastq.gz,YAF2-BGRSLV08-5_S43_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10199
YAF2-BGRSLV08-5_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2597					GRCh38	V40	YAF2-BGRSLV08-5/Aligned.sortedByCoord.out.bam		ENCORE2	10243
YAF2-BGRSLV08-5_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2597					GRCh38	V40	YAF2-BGRSLV08-5/Aligned.sortedByCoord.out.bam		ENCORE2	10287
YAF2-BGRSLV08-5_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2597					GRCh38	V40	YAF2-BGRSLV08-5/Aligned.sortedByCoord.out.bam		ENCORE2	10331
YAF2-BGRSLV08-5_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2597					GRCh38	V40	YAF2-BGRSLV08-5/Aligned.sortedByCoord.out.bam		ENCORE2	10375
YAF2-BGRSLV08-5_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2597					GRCh38	V40	YAF2-BGRSLV08-5_S43_L003_R1_001.filtered.trimmed.paired.fastq.gz,YAF2-BGRSLV08-5_S43_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10419
YAF2-BGRSLV08-6_S44_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2598	NovaSeq6000	100	paired-ended	1				NT-BGRSLV08-1_S39_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7895
YAF2-BGRSLV08-6_S44_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2598	NovaSeq6000	100	paired-ended	2				NT-BGRSLV08-1_S39_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV08-2_S40_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7939
YAF2-BGRSLV08-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2598					GRCh38	V40	YAF2-BGRSLV08-6_S44_L003_R1_001.filtered.trimmed.paired.fastq.gz,YAF2-BGRSLV08-6_S44_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10200
YAF2-BGRSLV08-6_Signal.Unique.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2598					GRCh38	V40	YAF2-BGRSLV08-6/Aligned.sortedByCoord.out.bam		ENCORE2	10244
YAF2-BGRSLV08-6_Signal.Unique.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2598					GRCh38	V40	YAF2-BGRSLV08-6/Aligned.sortedByCoord.out.bam		ENCORE2	10288
YAF2-BGRSLV08-6_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2598					GRCh38	V40	YAF2-BGRSLV08-6/Aligned.sortedByCoord.out.bam		ENCORE2	10332
YAF2-BGRSLV08-6_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2598					GRCh38	V40	YAF2-BGRSLV08-6/Aligned.sortedByCoord.out.bam		ENCORE2	10376
YAF2-BGRSLV08-6_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2598					GRCh38	V40	YAF2-BGRSLV08-6_S44_L003_R1_001.filtered.trimmed.paired.fastq.gz,YAF2-BGRSLV08-6_S44_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10420