ZNF706 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSLV03-67	BGRSLV03-68
idx	0	0
TRCN#_or_BGC#	TRCN0000219803	TRCN0000219803
shRNA_or_gRNA_sequence	CCGGTTCAGGCATAAGGTTGTTTACCTCGAGGTAAACAACCTTATGCCTGAATTTTTG	CCGGTTCAGGCATAAGGTTGTTTACCTCGAGGTAAACAACCTTATGCCTGAATTTTTG
PAM
Name	ZNF706	ZNF706
Sample_ID	BGRSLV03-67	BGRSLV03-68
transduction_Date	1/30/23	1/30/23
days	D4	D4
RBP_name	ZNF706	ZNF706
qPCR_result	78.2	76.2
Ave_qPCR	77.2
RT-qPCR_primer-F	gacatgaccaaaaggctgct
RT-qPCR_primer-R	tgcttgctctcaaagtgctg
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	8377	8378

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSLV03-67	BGRSLV03-68
Sample_ID	BGRSLV03-67	BGRSLV03-68
Sample Name
Sample Name	ZNF706-BGRSLV03-67	ZNF706-BGRSLV03-68
RBP	ZNF706	ZNF706
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	11410	11411

Library-Prep
Sequencing

Library-Prep Information

	BGRSLV03-67	BGRSLV03-68
Sample #	41	42
Sample Name	ZNF706-BGRSLV03-67	ZNF706-BGRSLV03-68
Sample_Name_Alias
Index Well Position	A12	B12
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	286	288
Peak_Molarity	52.40	63.00
libSampleQC_DNA_Well	DNA_Library_set58/set1/A12.png	DNA_Library_set58/set1/B12.png
RIN	9.7	9.9
libSample_RNA_Well	RNA_Library_set58/set1/A6.png	RNA_Library_set58/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-02-17	2023-02-17
Sample_ID	BGRSLV03-67	BGRSLV03-68
RBP	ZNF706	ZNF706
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	3548	3549

Sequencing Information

	BGRSLV03-67	BGRSLV03-68
Sample_ID	BGRSLV03-67	BGRSLV03-68
Sample Name	ZNF706-BGRSLV03-67	ZNF706-BGRSLV03-68
Pool ID	Pool-230217	Pool-230217
LocalServer_folder	set58	set58
total_reads	39,072,017	39,281,135
total_aligned_reads	32,233,476	30,905,831
unique_aligned_reads	30,146,990	28,790,817
percent_uniqueAligned	0.77157	0.73294
correlation_replicates	0.993084	0.993084
spikein_reads	253,194	161,988
percent_spikeins	0.00648	0.00412
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2419	2420

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
ZNF706-BGRSLV03-67_S175_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2419	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	8166
ZNF706-BGRSLV03-67_S175_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2419	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	8208
ZNF706-BGRSLV03-67_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2419					GRCh38	V40	ZNF706-BGRSLV03-67_S175_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF706-BGRSLV03-67_S175_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11287
ZNF706-BGRSLV03-67_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	2419					GRCh38	V40	ZNF706-BGRSLV03-67/Aligned.sortedByCoord.out.bam		ENCORE2	11329
ZNF706-BGRSLV03-67_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	2419					GRCh38	V40	ZNF706-BGRSLV03-67/Aligned.sortedByCoord.out.bam		ENCORE2	11371
ZNF706-BGRSLV03-67_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	2419					GRCh38	V40	ZNF706-BGRSLV03-67/Aligned.sortedByCoord.out.bam		ENCORE2	11413
ZNF706-BGRSLV03-67_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	2419					GRCh38	V40	ZNF706-BGRSLV03-67/Aligned.sortedByCoord.out.bam		ENCORE2	11455
ZNF706-BGRSLV03-67_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2419					GRCh38	V40	ZNF706-BGRSLV03-67_S175_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF706-BGRSLV03-67_S175_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11497
ZNF706-BGRSLV03-68_S176_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2420	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	8167
ZNF706-BGRSLV03-68_S176_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set58/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2420	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	8209
ZNF706-BGRSLV03-68_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set58/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2420					GRCh38	V40	ZNF706-BGRSLV03-68_S176_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF706-BGRSLV03-68_S176_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11288
ZNF706-BGRSLV03-68_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	2420					GRCh38	V40	ZNF706-BGRSLV03-68/Aligned.sortedByCoord.out.bam		ENCORE2	11330
ZNF706-BGRSLV03-68_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	2420					GRCh38	V40	ZNF706-BGRSLV03-68/Aligned.sortedByCoord.out.bam		ENCORE2	11372
ZNF706-BGRSLV03-68_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	2420					GRCh38	V40	ZNF706-BGRSLV03-68/Aligned.sortedByCoord.out.bam		ENCORE2	11414
ZNF706-BGRSLV03-68_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	2420					GRCh38	V40	ZNF706-BGRSLV03-68/Aligned.sortedByCoord.out.bam		ENCORE2	11456
ZNF706-BGRSLV03-68_quant.sf	ENCODE_DATA/set58/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2420					GRCh38	V40	ZNF706-BGRSLV03-68_S176_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF706-BGRSLV03-68_S176_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	11498