PHF7 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-35	BGRSLV04-36
idx	0	0
TRCN#_or_BGC#	TRCN0000016795	TRCN0000016795
shRNA_or_gRNA_sequence	CCGGCCGCAAGTGCATACAGAAATACTCGAGTATTTCTGTATGCACTTGCGGTTTTT	CCGGCCGCAAGTGCATACAGAAATACTCGAGTATTTCTGTATGCACTTGCGGTTTTT
PAM
Name	PHF7	PHF7
Sample_ID	BGRSLV04-35	BGRSLV04-36
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	PHF7	PHF7
qPCR_result	79.8	84.9
Ave_qPCR	82.3
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	8415	8416

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-35	BGRSLV04-36
Sample_ID	BGRSLV04-35	BGRSLV04-36
Sample Name
Sample Name	PHF7-BGRSLV04-35	PHF7-BGRSLV04-36
RBP	PHF7	PHF7
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	11454	11455

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-35	BGRSLV04-36
Sample #	19	20
Sample Name	PHF7-BGRSLV04-35	PHF7-BGRSLV04-36
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-03-02	2023-03-02
Lib_ID	Lib-230302	Lib-230302
Tecan_Location
Tecan
Tecan_date
Size_bp	291	290
Peak_Molarity	80.60	68.10
libSampleQC_DNA_Well	DNA_Library_set59/set1/C9.png	DNA_Library_set59/set1/D9.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set59/set1/C4.png	RNA_Library_set59/set1/D4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-35	BGRSLV04-36
RBP	PHF7	PHF7
Batch_ID	BGRSLV04	BGRSLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3568	3569

Sequencing Information

	BGRSLV04-35	BGRSLV04-36
Sample_ID	BGRSLV04-35	BGRSLV04-36
Sample Name	PHF7-BGRSLV04-35	PHF7-BGRSLV04-36
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	61,350,479	51,075,083
total_aligned_reads	52,091,853	43,514,257
unique_aligned_reads	47,861,341	40,272,166
percent_uniqueAligned	0.78013	0.78849
correlation_replicates	0.996839	0.996839
spikein_reads	264,638	194,940
percent_spikeins	0.00431	0.00382
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2439	2440

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-BGRSLV04-35_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2439	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8068
PHF7-BGRSLV04-35_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2439	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8106
PHF7-BGRSLV04-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2439					GRCh38	V40	PHF7-BGRSLV04-35_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSLV04-35_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11037
PHF7-BGRSLV04-35_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2439					GRCh38	V40	PHF7-BGRSLV04-35/Aligned.sortedByCoord.out.bam		ENCORE2	11075
PHF7-BGRSLV04-35_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2439					GRCh38	V40	PHF7-BGRSLV04-35/Aligned.sortedByCoord.out.bam		ENCORE2	11113
PHF7-BGRSLV04-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2439					GRCh38	V40	PHF7-BGRSLV04-35/Aligned.sortedByCoord.out.bam		ENCORE2	11151
PHF7-BGRSLV04-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2439					GRCh38	V40	PHF7-BGRSLV04-35/Aligned.sortedByCoord.out.bam		ENCORE2	11189
PHF7-BGRSLV04-35_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2439					GRCh38	V40	PHF7-BGRSLV04-35_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSLV04-35_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11227
PHF7-BGRSLV04-36_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2440	NovaSeq6000	100	paired-ended	1				NT-BGRSLV04-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8069
PHF7-BGRSLV04-36_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2440	NovaSeq6000	100	paired-ended	2				NT-BGRSLV04-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV04-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8107
PHF7-BGRSLV04-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2440					GRCh38	V40	PHF7-BGRSLV04-36_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSLV04-36_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11038
PHF7-BGRSLV04-36_Signal.Unique.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2440					GRCh38	V40	PHF7-BGRSLV04-36/Aligned.sortedByCoord.out.bam		ENCORE2	11076
PHF7-BGRSLV04-36_Signal.Unique.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2440					GRCh38	V40	PHF7-BGRSLV04-36/Aligned.sortedByCoord.out.bam		ENCORE2	11114
PHF7-BGRSLV04-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2440					GRCh38	V40	PHF7-BGRSLV04-36/Aligned.sortedByCoord.out.bam		ENCORE2	11152
PHF7-BGRSLV04-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2440					GRCh38	V40	PHF7-BGRSLV04-36/Aligned.sortedByCoord.out.bam		ENCORE2	11190
PHF7-BGRSLV04-36_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2440					GRCh38	V40	PHF7-BGRSLV04-36_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,PHF7-BGRSLV04-36_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11228