PHF7 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV02-49	BGRSDLV02-50
idx	0	0
TRCN#_or_BGC#	TRCN0000016795	TRCN0000016795
shRNA_or_gRNA_sequence	CCGGCCGCAAGTGCATACAGAAATACTCGAGTATTTCTGTATGCACTTGCGGTTTTT	CCGGCCGCAAGTGCATACAGAAATACTCGAGTATTTCTGTATGCACTTGCGGTTTTT
PAM
Name	PHF7	PHF7
Sample_ID	BGRSDLV02-49	BGRSDLV02-50
transduction_Date	9/15/23	9/15/23
days	4 days	4 days
RBP_name	PHF7	PHF7
qPCR_result	84.3	92.1
Ave_qPCR	88.2
RT-qPCR_primer-F	cagagcccgtgttgtagtca
RT-qPCR_primer-R	tgctgatgtgtgggcatatt
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	9260	9261

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV02-49	BGRSDLV02-50
Sample_ID	BGRSDLV02-49	BGRSDLV02-50
Sample Name
Sample Name	PHF7-BGRSDLV02-49	PHF7-BGRSDLV02-50
RBP	PHF7	PHF7
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12364	12365

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV02-49	BGRSDLV02-50
Sample #	45	46
Sample Name	PHF7-BGRSDLV02-49	PHF7-BGRSDLV02-50
Sample_Name_Alias
Index Well Position	E06	F06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-09-26	2023-09-26
Lib_ID	Lib-230926	Lib-230926
Tecan_Location
Tecan
Tecan_date
Size_bp	289	288
Peak_Molarity	86.40	84.50
libSampleQC_DNA_Well	DNA_Library_set65/set1/E6.png	DNA_Library_set65/set1/F6.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set65/set1/E6.png	RNA_Library_set65/set1/F6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-09-27	2023-09-27
Sample_ID	BGRSDLV02-49	BGRSDLV02-50
RBP	PHF7	PHF7
Batch_ID	BGRSDLV02	BGRSDLV02
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3966	3967

Sequencing Information

	BGRSDLV02-49	BGRSDLV02-50
Sample_ID	BGRSDLV02-49	BGRSDLV02-50
Sample Name	PHF7-BGRSDLV02-49	PHF7-BGRSDLV02-50
Pool ID	Pool-231003	Pool-231003
LocalServer_folder	set65	set65
total_reads	25,187,316	19,417,322
total_aligned_reads	23,419,636	18,261,752
unique_aligned_reads	21,891,587	17,048,843
percent_uniqueAligned	0.86915	0.87802
correlation_replicates	0.993865	0.993865
spikein_reads	3,372	4,672
percent_spikeins	0.00013	0.00024
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	2713	2714

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
PHF7-BGRSDLV02-49_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2713	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8786
PHF7-BGRSDLV02-49_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2713	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8862
PHF7-BGRSDLV02-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2713					GRCh38	V40	PHF7-BGRSDLV02-49_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSDLV02-49_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9351
PHF7-BGRSDLV02-49_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2713					GRCh38	V40	PHF7-BGRSDLV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	9427
PHF7-BGRSDLV02-49_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2713					GRCh38	V40	PHF7-BGRSDLV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	9503
PHF7-BGRSDLV02-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2713					GRCh38	V40	PHF7-BGRSDLV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	9579
PHF7-BGRSDLV02-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2713					GRCh38	V40	PHF7-BGRSDLV02-49/Aligned.sortedByCoord.out.bam		ENCORE2	9655
PHF7-BGRSDLV02-49_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2713					GRCh38	V40	PHF7-BGRSDLV02-49_S45_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSDLV02-49_S45_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9731
PHF7-BGRSDLV02-50_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2714	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV02-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8787
PHF7-BGRSDLV02-50_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set65/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2714	NovaSeq6000	100	paired-ended	2				NT-BGRSDLV02-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV02-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8863
PHF7-BGRSDLV02-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2714					GRCh38	V40	PHF7-BGRSDLV02-50_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSDLV02-50_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9352
PHF7-BGRSDLV02-50_Signal.Unique.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2714					GRCh38	V40	PHF7-BGRSDLV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	9428
PHF7-BGRSDLV02-50_Signal.Unique.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2714					GRCh38	V40	PHF7-BGRSDLV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	9504
PHF7-BGRSDLV02-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2714					GRCh38	V40	PHF7-BGRSDLV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	9580
PHF7-BGRSDLV02-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set65/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2714					GRCh38	V40	PHF7-BGRSDLV02-50/Aligned.sortedByCoord.out.bam		ENCORE2	9656
PHF7-BGRSDLV02-50_quant.sf	ENCODE_DATA/set65/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2714					GRCh38	V40	PHF7-BGRSDLV02-50_S46_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSDLV02-50_S46_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	9732