ZNF2 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-57	BGRSLV03-58
idx	0	0
TRCN#_or_BGC#	TRCN0000016209	TRCN0000016209
shRNA_or_gRNA_sequence	CCGGCGTCTCTGAATAGACATCAGACTCGAGTCTGATGTCTATTCAGAGACGTTTTT	CCGGCGTCTCTGAATAGACATCAGACTCGAGTCTGATGTCTATTCAGAGACGTTTTT
PAM
Name	ZNF2	ZNF2
Sample_ID	BGRSLV03-57	BGRSLV03-58
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	ZNF2	ZNF2
qPCR_result	69.3	88.2
Ave_qPCR	78.7
RT-qPCR_primer-F	GGACAAGCCGTGGATGGTAGAT
RT-qPCR_primer-R	AGCATCGTGAATCTCAGGCTTAG
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	8367	8368

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-57	BGRSLV03-58
Sample_ID	BGRSLV03-57	BGRSLV03-58
Sample Name
Sample Name	ZNF2-BGRSLV03-57	ZNF2-BGRSLV03-58
RBP	ZNF2	ZNF2
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	11404	11405

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-57	BGRSLV03-58
Sample #	35	36
Sample Name	ZNF2-BGRSLV03-57	ZNF2-BGRSLV03-58
Sample_Name_Alias
Index Well Position	C11	D11
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	287	285
Peak_Molarity	142.00	135.00
libSampleQC_DNA_Well	DNA_Library_set58/set1/C11.png	DNA_Library_set58/set1/D11.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_set58/set1/C5.png	RNA_Library_set58/set1/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-57	BGRSLV03-58
RBP	ZNF2	ZNF2
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	3542	3543

Sequencing Information

	BGRSLV03-57	BGRSLV03-58
Sample_ID	BGRSLV03-57	BGRSLV03-58
Sample Name	ZNF2-BGRSLV03-57	ZNF2-BGRSLV03-58
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	65,937,449	45,391,907
total_aligned_reads	58,526,328	40,246,188
unique_aligned_reads	54,589,022	37,577,842
percent_uniqueAligned	0.82789	0.82785
correlation_replicates	0.992468	0.992468
spikein_reads	521,446	314,924
percent_spikeins	0.00791	0.00694
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2413	2414

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
ZNF2-BGRSLV03-57_S169_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2413	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	8162
ZNF2-BGRSLV03-57_S169_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2413	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	8204
ZNF2-BGRSLV03-57_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2413					GRCh38	V40	ZNF2-BGRSLV03-57_S169_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF2-BGRSLV03-57_S169_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11283
ZNF2-BGRSLV03-57_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	2413					GRCh38	V40	ZNF2-BGRSLV03-57/Aligned.sortedByCoord.out.bam		ENCORE2	11325
ZNF2-BGRSLV03-57_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	2413					GRCh38	V40	ZNF2-BGRSLV03-57/Aligned.sortedByCoord.out.bam		ENCORE2	11367
ZNF2-BGRSLV03-57_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	2413					GRCh38	V40	ZNF2-BGRSLV03-57/Aligned.sortedByCoord.out.bam		ENCORE2	11409
ZNF2-BGRSLV03-57_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	2413					GRCh38	V40	ZNF2-BGRSLV03-57/Aligned.sortedByCoord.out.bam		ENCORE2	11451
ZNF2-BGRSLV03-57_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2413					GRCh38	V40	ZNF2-BGRSLV03-57_S169_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF2-BGRSLV03-57_S169_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11493
ZNF2-BGRSLV03-58_S170_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2414	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	8163
ZNF2-BGRSLV03-58_S170_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2414	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	8205
ZNF2-BGRSLV03-58_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2414					GRCh38	V40	ZNF2-BGRSLV03-58_S170_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF2-BGRSLV03-58_S170_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11284
ZNF2-BGRSLV03-58_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	2414					GRCh38	V40	ZNF2-BGRSLV03-58/Aligned.sortedByCoord.out.bam		ENCORE2	11326
ZNF2-BGRSLV03-58_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	2414					GRCh38	V40	ZNF2-BGRSLV03-58/Aligned.sortedByCoord.out.bam		ENCORE2	11368
ZNF2-BGRSLV03-58_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	2414					GRCh38	V40	ZNF2-BGRSLV03-58/Aligned.sortedByCoord.out.bam		ENCORE2	11410
ZNF2-BGRSLV03-58_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	2414					GRCh38	V40	ZNF2-BGRSLV03-58/Aligned.sortedByCoord.out.bam		ENCORE2	11452
ZNF2-BGRSLV03-58_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2414					GRCh38	V40	ZNF2-BGRSLV03-58_S170_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF2-BGRSLV03-58_S170_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11494