CXXC1 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-19	BGRSLV03-20
idx	0	0
TRCN#_or_BGC#	TRCN0000155700	TRCN0000155700
shRNA_or_gRNA_sequence	CCGGCGTTCCTCCACTCATCTGTTTCTCGAGAAACAGATGAGTGGAGGAACGTTTTTTG	CCGGCGTTCCTCCACTCATCTGTTTCTCGAGAAACAGATGAGTGGAGGAACGTTTTTTG
PAM
Name	CXXC1	CXXC1
Sample_ID	BGRSLV03-19	BGRSLV03-20
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	CXXC1	CXXC1
qPCR_result	78.6	80.3
Ave_qPCR	79.5
RT-qPCR_primer-F	AACAAGATCCGGCAGAAGTG
RT-qPCR_primer-R	cactggtgagagcgaggaa
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	8329	8330

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-19	BGRSLV03-20
Sample_ID	BGRSLV03-19	BGRSLV03-20
Sample Name
Sample Name	CXXC1-BGRSLV03-19	CXXC1-BGRSLV03-20
RBP	CXXC1	CXXC1
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	11384	11385

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-19	BGRSLV03-20
Sample #	15	16
Sample Name	CXXC1-BGRSLV03-19	CXXC1-BGRSLV03-20
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-02-15	2023-02-15
Lib_ID	Lib-230215	Lib-230215
Tecan_Location
Tecan
Tecan_date
Size_bp	301	307
Peak_Molarity	82.90	39.70
libSampleQC_DNA_Well	DNA_Library_set58/set1/G8.png	DNA_Library_set58/set1/H8.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set58/set1/G2.png	RNA_Library_set58/set1/H2.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-19	BGRSLV03-20
RBP	CXXC1	CXXC1
Batch_ID	BGRSLV03	BGRSLV03
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3522	3523

Sequencing Information

	BGRSLV03-19	BGRSLV03-20
Sample_ID	BGRSLV03-19	BGRSLV03-20
Sample Name	CXXC1-BGRSLV03-19	CXXC1-BGRSLV03-20
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	53,670,514	66,969,837
total_aligned_reads	47,795,685	58,293,645
unique_aligned_reads	44,570,626	54,396,393
percent_uniqueAligned	0.83045	0.81225
correlation_replicates	0.978558	0.978558
spikein_reads	320,152	316,180
percent_spikeins	0.00597	0.00472
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2393	2394

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
CXXC1-BGRSLV03-19_S149_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2393	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8138
CXXC1-BGRSLV03-19_S149_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2393	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8180
CXXC1-BGRSLV03-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2393					GRCh38	V40	CXXC1-BGRSLV03-19_S149_L004_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGRSLV03-19_S149_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11259
CXXC1-BGRSLV03-19_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2393					GRCh38	V40	CXXC1-BGRSLV03-19/Aligned.sortedByCoord.out.bam		ENCORE2	11301
CXXC1-BGRSLV03-19_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2393					GRCh38	V40	CXXC1-BGRSLV03-19/Aligned.sortedByCoord.out.bam		ENCORE2	11343
CXXC1-BGRSLV03-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2393					GRCh38	V40	CXXC1-BGRSLV03-19/Aligned.sortedByCoord.out.bam		ENCORE2	11385
CXXC1-BGRSLV03-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2393					GRCh38	V40	CXXC1-BGRSLV03-19/Aligned.sortedByCoord.out.bam		ENCORE2	11427
CXXC1-BGRSLV03-19_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2393					GRCh38	V40	CXXC1-BGRSLV03-19_S149_L004_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGRSLV03-19_S149_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11469
CXXC1-BGRSLV03-20_S150_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2394	NovaSeq6000	100	paired-ended	1				NT-BGRSLV03-1_S135_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8139
CXXC1-BGRSLV03-20_S150_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2394	NovaSeq6000	100	paired-ended	2				NT-BGRSLV03-1_S135_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV03-2_S136_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	8181
CXXC1-BGRSLV03-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2394					GRCh38	V40	CXXC1-BGRSLV03-20_S150_L004_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGRSLV03-20_S150_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11260
CXXC1-BGRSLV03-20_Signal.Unique.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2394					GRCh38	V40	CXXC1-BGRSLV03-20/Aligned.sortedByCoord.out.bam		ENCORE2	11302
CXXC1-BGRSLV03-20_Signal.Unique.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2394					GRCh38	V40	CXXC1-BGRSLV03-20/Aligned.sortedByCoord.out.bam		ENCORE2	11344
CXXC1-BGRSLV03-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2394					GRCh38	V40	CXXC1-BGRSLV03-20/Aligned.sortedByCoord.out.bam		ENCORE2	11386
CXXC1-BGRSLV03-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2394					GRCh38	V40	CXXC1-BGRSLV03-20/Aligned.sortedByCoord.out.bam		ENCORE2	11428
CXXC1-BGRSLV03-20_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2394					GRCh38	V40	CXXC1-BGRSLV03-20_S150_L004_R1_001.filtered.trimmed.paired.fastq.gz,CXXC1-BGRSLV03-20_S150_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11470