ZNF354A RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV08-25	BGRSLV08-26
idx	0	0
TRCN#_or_BGC#	TRCN0000329892	TRCN0000329892
shRNA_or_gRNA_sequence	CCGGTCTCAGTACATCCCTTTATAACTCGAGTTATAAAGGGATGTACTGAGATTTTTG	CCGGTTAGCCCTCATTAGGTATTTACTCGAGTAAATACCTAATGAGGGCTAATTTTTG
PAM
Name	ZNF354A	ZNF354A
Sample_ID	BGRSLV08-25	BGRSLV08-26
transduction_Date	4/22/23	4/22/23
days	D4	D4
RBP_name	ZNF354A	ZNF354A
qPCR_result	64.0	63.2
Ave_qPCR	63.6
RT-qPCR_primer-F	gtggagaaagacggttctgg
RT-qPCR_primer-R	tgtttgcgttgactttgtgg
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	8674	8675

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV08-25	BGRSLV08-26
Sample_ID	BGRSLV08-25	BGRSLV08-26
Sample Name
Sample Name	ZNF354A-BGRSLV08-25	ZNF354A-BGRSLV08-26
RBP	ZNF354A	ZNF354A
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	11786	11787

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV08-25	BGRSLV08-26
Sample #	51	52
Sample Name	ZNF354A-BGRSLV08-25	ZNF354A-BGRSLV08-26
Sample_Name_Alias
Index Well Position	C07	D07
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	295	300
Peak_Molarity	82.30	80.10
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/C7.png	DNA_Library_set60-62/set4/D7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/C7.png	RNA_Library_set60-62/set2/D7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV08-25	BGRSLV08-26
RBP	ZNF354A	ZNF354A
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	3734	3735

Sequencing Information

	BGRSLV08-25	BGRSLV08-26
Sample_ID	BGRSLV08-25	BGRSLV08-26
Sample Name	ZNF354A-BGRSLV08-25	ZNF354A-BGRSLV08-26
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	28,729,255	27,812,603
total_aligned_reads	24,756,282	24,228,727
unique_aligned_reads	23,197,119	22,720,655
percent_uniqueAligned	0.80744	0.81692
correlation_replicates	0.997370	0.997370
spikein_reads	33,466	18,682
percent_spikeins	0.00116	0.00067
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2605	2606

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
ZNF354A-BGRSLV08-25_S51_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2605	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	7908
ZNF354A-BGRSLV08-25_S51_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2605	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	7952
ZNF354A-BGRSLV08-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2605					GRCh38	V40	ZNF354A-BGRSLV08-25_S51_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF354A-BGRSLV08-25_S51_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10213
ZNF354A-BGRSLV08-25_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	2605					GRCh38	V40	ZNF354A-BGRSLV08-25/Aligned.sortedByCoord.out.bam		ENCORE2	10257
ZNF354A-BGRSLV08-25_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	2605					GRCh38	V40	ZNF354A-BGRSLV08-25/Aligned.sortedByCoord.out.bam		ENCORE2	10301
ZNF354A-BGRSLV08-25_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	2605					GRCh38	V40	ZNF354A-BGRSLV08-25/Aligned.sortedByCoord.out.bam		ENCORE2	10345
ZNF354A-BGRSLV08-25_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	2605					GRCh38	V40	ZNF354A-BGRSLV08-25/Aligned.sortedByCoord.out.bam		ENCORE2	10389
ZNF354A-BGRSLV08-25_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2605					GRCh38	V40	ZNF354A-BGRSLV08-25_S51_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF354A-BGRSLV08-25_S51_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10433
ZNF354A-BGRSLV08-26_S52_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2606	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	7909
ZNF354A-BGRSLV08-26_S52_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2606	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	7953
ZNF354A-BGRSLV08-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2606					GRCh38	V40	ZNF354A-BGRSLV08-26_S52_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF354A-BGRSLV08-26_S52_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10214
ZNF354A-BGRSLV08-26_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	2606					GRCh38	V40	ZNF354A-BGRSLV08-26/Aligned.sortedByCoord.out.bam		ENCORE2	10258
ZNF354A-BGRSLV08-26_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	2606					GRCh38	V40	ZNF354A-BGRSLV08-26/Aligned.sortedByCoord.out.bam		ENCORE2	10302
ZNF354A-BGRSLV08-26_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	2606					GRCh38	V40	ZNF354A-BGRSLV08-26/Aligned.sortedByCoord.out.bam		ENCORE2	10346
ZNF354A-BGRSLV08-26_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	2606					GRCh38	V40	ZNF354A-BGRSLV08-26/Aligned.sortedByCoord.out.bam		ENCORE2	10390
ZNF354A-BGRSLV08-26_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2606					GRCh38	V40	ZNF354A-BGRSLV08-26_S52_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF354A-BGRSLV08-26_S52_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10434