ZNF214 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV07-59	BGRSLV07-60
idx	0	0
TRCN#_or_BGC#	TRCN0000013048	TRCN0000013048
shRNA_or_gRNA_sequence	CCGGCCTGCTGTTAAGGAAATCTTACTCGAGTAAGATTTCCTTAACAGCAGGTTTTT	CCGGCCTGCTGTTAAGGAAATCTTACTCGAGTAAGATTTCCTTAACAGCAGGTTTTT
PAM
Name	ZNF214	ZNF214
Sample_ID	BGRSLV07-59	BGRSLV07-60
transduction_Date	4/10/23	4/10/23
days	D4	D4
RBP_name	ZNF214	ZNF214
qPCR_result	53.9	57.3
Ave_qPCR	55.6
RT-qPCR_primer-F	GACTCTACAGGGAGGTCATGTG
RT-qPCR_primer-R	CATTCCACCAGCCTTGCCAGTA
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	8641	8642

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV07-59	BGRSLV07-60
Sample_ID	BGRSLV07-59	BGRSLV07-60
Sample Name
Sample Name	ZNF214-BGRSLV07-59	ZNF214-BGRSLV07-60
RBP	ZNF214	ZNF214
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	11854	11855

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV07-59	BGRSLV07-60
Sample #	35	36
Sample Name	ZNF214-BGRSLV07-59	ZNF214-BGRSLV07-60
Sample_Name_Alias
Index Well Position	C05	D05
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	290	297
Peak_Molarity	81.60	78.70
libSampleQC_DNA_Well	DNA_Library_set60-62/set4/C5.png	DNA_Library_set60-62/set4/D5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set60-62/set2/C5.png	RNA_Library_set60-62/set2/D5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-05-04	2023-05-04
Sample_ID	BGRSLV07-59	BGRSLV07-60
RBP	ZNF214	ZNF214
Batch_ID	BGRSLV07	BGRSLV07
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	3718	3719

Sequencing Information

	BGRSLV07-59	BGRSLV07-60
Sample_ID	BGRSLV07-59	BGRSLV07-60
Sample Name	ZNF214-BGRSLV07-59	ZNF214-BGRSLV07-60
Pool ID	Pool-230504	Pool-230504
LocalServer_folder	set62_R	set62_R
total_reads	47,772,341	29,004,188
total_aligned_reads	35,949,541	25,376,593
unique_aligned_reads	33,630,667	23,709,914
percent_uniqueAligned	0.70398	0.81747
correlation_replicates	0.996515	0.996515
spikein_reads	65,874	24,814
percent_spikeins	0.00138	0.00086
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2589	2590

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
ZNF214-BGRSLV07-59_S35_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2589	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7904
ZNF214-BGRSLV07-59_S35_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2589	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7948
ZNF214-BGRSLV07-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2589					GRCh38	V40	ZNF214-BGRSLV07-59_S35_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF214-BGRSLV07-59_S35_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10209
ZNF214-BGRSLV07-59_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	2589					GRCh38	V40	ZNF214-BGRSLV07-59/Aligned.sortedByCoord.out.bam		ENCORE2	10253
ZNF214-BGRSLV07-59_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	2589					GRCh38	V40	ZNF214-BGRSLV07-59/Aligned.sortedByCoord.out.bam		ENCORE2	10297
ZNF214-BGRSLV07-59_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	2589					GRCh38	V40	ZNF214-BGRSLV07-59/Aligned.sortedByCoord.out.bam		ENCORE2	10341
ZNF214-BGRSLV07-59_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	2589					GRCh38	V40	ZNF214-BGRSLV07-59/Aligned.sortedByCoord.out.bam		ENCORE2	10385
ZNF214-BGRSLV07-59_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2589					GRCh38	V40	ZNF214-BGRSLV07-59_S35_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF214-BGRSLV07-59_S35_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10429
ZNF214-BGRSLV07-60_S36_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2590	NovaSeq6000	100	paired-ended	1				NT-BGRSLV07-1_S17_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7905
ZNF214-BGRSLV07-60_S36_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set62_R/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2590	NovaSeq6000	100	paired-ended	2				NT-BGRSLV07-1_S17_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSLV07-2_S18_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	7949
ZNF214-BGRSLV07-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set62_R/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2590					GRCh38	V40	ZNF214-BGRSLV07-60_S36_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF214-BGRSLV07-60_S36_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10210
ZNF214-BGRSLV07-60_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	2590					GRCh38	V40	ZNF214-BGRSLV07-60/Aligned.sortedByCoord.out.bam		ENCORE2	10254
ZNF214-BGRSLV07-60_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	2590					GRCh38	V40	ZNF214-BGRSLV07-60/Aligned.sortedByCoord.out.bam		ENCORE2	10298
ZNF214-BGRSLV07-60_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	2590					GRCh38	V40	ZNF214-BGRSLV07-60/Aligned.sortedByCoord.out.bam		ENCORE2	10342
ZNF214-BGRSLV07-60_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	2590					GRCh38	V40	ZNF214-BGRSLV07-60/Aligned.sortedByCoord.out.bam		ENCORE2	10386
ZNF214-BGRSLV07-60_quant.sf	ENCODE_DATA/set62_R/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2590					GRCh38	V40	ZNF214-BGRSLV07-60_S36_L003_R1_001.filtered.trimmed.paired.fastq.gz,ZNF214-BGRSLV07-60_S36_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	10430