PCGF1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV04-31	BGRSLV04-32
idx	0	0
TRCN#_or_BGC#	TRCN0000073129	TRCN0000073129
shRNA_or_gRNA_sequence	CCGGCCACTCTAAAGCCCACTACTACTCGAGTAGTAGTGGGCTTTAGAGTGGTTTTTG	CCGGCCACTCTAAAGCCCACTACTACTCGAGTAGTAGTGGGCTTTAGAGTGGTTTTTG
PAM
Name	PCGF1	PCGF1
Sample_ID	BGRSLV04-31	BGRSLV04-32
transduction_Date	2/14/23	2/14/23
days	D4	D4
RBP_name	PCGF1	PCGF1
qPCR_result	72.7	70.4
Ave_qPCR	71.5
RT-qPCR_primer-F	gagacacagccactgctcaa
RT-qPCR_primer-R	attcccgaatccgtttctct
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	8411	8412

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV04-31	BGRSLV04-32
Sample_ID	BGRSLV04-31	BGRSLV04-32
Sample Name
Sample Name	PCGF1-BGRSLV04-31	PCGF1-BGRSLV04-32
RBP	PCGF1	PCGF1
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	11452	11453

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV04-31	BGRSLV04-32
Sample #	17	18
Sample Name	PCGF1-BGRSLV04-31	PCGF1-BGRSLV04-32
Sample_Name_Alias
Index Well Position	A03	B03
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	290	291
Peak_Molarity	44.70	47.70
libSampleQC_DNA_Well	DNA_Library_set59/set1/A9.png	DNA_Library_set59/set1/B9.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set59/set1/A4.png	RNA_Library_set59/set1/B4.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-03-06	2023-03-06
Sample_ID	BGRSLV04-31	BGRSLV04-32
RBP	PCGF1	PCGF1
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	3566	3567

Sequencing Information

	BGRSLV04-31	BGRSLV04-32
Sample_ID	BGRSLV04-31	BGRSLV04-32
Sample Name	PCGF1-BGRSLV04-31	PCGF1-BGRSLV04-32
Pool ID	Pool-230306	Pool-230306
LocalServer_folder	set59	set59
total_reads	58,377,970	57,735,218
total_aligned_reads	47,127,316	50,010,644
unique_aligned_reads	43,614,445	46,193,297
percent_uniqueAligned	0.74710	0.80009
correlation_replicates	0.996068	0.996068
spikein_reads	283,502	291,212
percent_spikeins	0.00486	0.00504
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2437	2438

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
PCGF1-BGRSLV04-31_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2437	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	8066
PCGF1-BGRSLV04-31_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2437	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	8104
PCGF1-BGRSLV04-31_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2437					GRCh38	V40	PCGF1-BGRSLV04-31_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCGF1-BGRSLV04-31_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11035
PCGF1-BGRSLV04-31_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	2437					GRCh38	V40	PCGF1-BGRSLV04-31/Aligned.sortedByCoord.out.bam		ENCORE2	11073
PCGF1-BGRSLV04-31_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	2437					GRCh38	V40	PCGF1-BGRSLV04-31/Aligned.sortedByCoord.out.bam		ENCORE2	11111
PCGF1-BGRSLV04-31_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	2437					GRCh38	V40	PCGF1-BGRSLV04-31/Aligned.sortedByCoord.out.bam		ENCORE2	11149
PCGF1-BGRSLV04-31_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	2437					GRCh38	V40	PCGF1-BGRSLV04-31/Aligned.sortedByCoord.out.bam		ENCORE2	11187
PCGF1-BGRSLV04-31_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2437					GRCh38	V40	PCGF1-BGRSLV04-31_S17_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCGF1-BGRSLV04-31_S17_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11225
PCGF1-BGRSLV04-32_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2438	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	8067
PCGF1-BGRSLV04-32_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set59/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2438	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	8105
PCGF1-BGRSLV04-32_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set59/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2438					GRCh38	V40	PCGF1-BGRSLV04-32_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCGF1-BGRSLV04-32_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11036
PCGF1-BGRSLV04-32_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	2438					GRCh38	V40	PCGF1-BGRSLV04-32/Aligned.sortedByCoord.out.bam		ENCORE2	11074
PCGF1-BGRSLV04-32_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	2438					GRCh38	V40	PCGF1-BGRSLV04-32/Aligned.sortedByCoord.out.bam		ENCORE2	11112
PCGF1-BGRSLV04-32_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	2438					GRCh38	V40	PCGF1-BGRSLV04-32/Aligned.sortedByCoord.out.bam		ENCORE2	11150
PCGF1-BGRSLV04-32_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	2438					GRCh38	V40	PCGF1-BGRSLV04-32/Aligned.sortedByCoord.out.bam		ENCORE2	11188
PCGF1-BGRSLV04-32_quant.sf	ENCODE_DATA/set59/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2438					GRCh38	V40	PCGF1-BGRSLV04-32_S18_L001_R1_001.filtered.trimmed.paired.fastq.gz,PCGF1-BGRSLV04-32_S18_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11226