ZNF706 RNA-Seq in Ribo-STAMP-293T

Experiment Information (Status: Submitted)

	BGRSDLV04-79dox	BGRSDLV04-80dox
idx	0	0
TRCN#_or_BGC#	TRCN0000219803	TRCN0000219803
shRNA_or_gRNA_sequence	CCGGTTCAGGCATAAGGTTGTTTACCTCGAGGTAAACAACCTTATGCCTGAATTTTTG	CCGGTTCAGGCATAAGGTTGTTTACCTCGAGGTAAACAACCTTATGCCTGAATTTTTG
PAM
Name	ZNF706	ZNF706
Sample_ID	BGRSDLV04-79dox	BGRSDLV04-80dox
transduction_Date	10/16/23	10/16/23
days	4 days	4 days
RBP_name	ZNF706	ZNF706
qPCR_result	83.95088	76.81886
Ave_qPCR	80.38487
RT-qPCR_primer-F
RT-qPCR_primer-R
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	9443	9444

Western Blot Western Blot info was not avaliable

Experiment Status

	BGRSDLV04-79dox	BGRSDLV04-80dox
Sample_ID	BGRSDLV04-79dox	BGRSDLV04-80dox
Sample Name
Sample Name	ZNF706-BGRSDLV04-79dox	ZNF706-BGRSDLV04-80dox
RBP	ZNF706	ZNF706
Cell_Line	DOX-RS293	DOX-RS293
Exp UID
Status	Submitted	Submitted
Status_date	2024-12-03	2024-12-03
Project	ENCORE2	ENCORE2
Note
ID	12684	12685

Library-Prep
Sequencing

Library-Prep Information

	BGRSDLV04-79dox	BGRSDLV04-80dox
Sample #	39	40
Sample Name	ZNF706-BGRSDLV04-79dox	ZNF706-BGRSDLV04-80dox
Sample_Name_Alias
Index Well Position	G05	H05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2023-11-14	2023-11-14
Lib_ID	Lib-231114	Lib-231114
Tecan_Location
Tecan
Tecan_date
Size_bp	289	288
Peak_Molarity	35.10	65.80
libSampleQC_DNA_Well	DNA_Library_set68/set1/G5.png	DNA_Library_set68/set1/H5.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_set68/set1/G5.png	RNA_Library_set68/set1/H5.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2023-11-16	2023-11-16
Sample_ID	BGRSDLV04-79dox	BGRSDLV04-80dox
RBP	ZNF706	ZNF706
Batch_ID	BGRSDLV04	BGRSDLV04
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4112	4113

Sequencing Information

	BGRSDLV04-79dox	BGRSDLV04-80dox
Sample_ID	BGRSDLV04-79dox	BGRSDLV04-80dox
Sample Name	ZNF706-BGRSDLV04-79dox	ZNF706-BGRSDLV04-80dox
Pool ID	Pool-231116	Pool-231116
LocalServer_folder	set68	set68
total_reads	38,528,670	33,279,532
total_aligned_reads	32,748,035	28,759,882
unique_aligned_reads	30,679,126	26,875,063
percent_uniqueAligned	0.79627	0.80756
correlation_replicates	0.998274	0.998274
spikein_reads	4,460	7,712
percent_spikeins	0.00012	0.00023
original_ReadLength	151	151
QC_Status	Submitted	Submitted
ID	2875	2876

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-BGRSDLV04-79dox_S39_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2875	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27687
ZNF706-BGRSDLV04-79dox_S39_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2875	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27751
ZNF706-BGRSDLV04-79dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2875					GRCh38	V40	ZNF706-BGRSDLV04-79dox_S39_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF706-BGRSDLV04-79dox_S39_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27815
ZNF706-BGRSDLV04-79dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2875					GRCh38	V40	ZNF706-BGRSDLV04-79dox/Aligned.sortedByCoord.out.bam		ENCORE2	27879
ZNF706-BGRSDLV04-79dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2875					GRCh38	V40	ZNF706-BGRSDLV04-79dox/Aligned.sortedByCoord.out.bam		ENCORE2	27943
ZNF706-BGRSDLV04-79dox_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2875					GRCh38	V40	ZNF706-BGRSDLV04-79dox/Aligned.sortedByCoord.out.bam		ENCORE2	28007
ZNF706-BGRSDLV04-79dox_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2875					GRCh38	V40	ZNF706-BGRSDLV04-79dox/Aligned.sortedByCoord.out.bam		ENCORE2	28071
ZNF706-BGRSDLV04-79dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2875					GRCh38	V40	ZNF706-BGRSDLV04-79dox_S39_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF706-BGRSDLV04-79dox_S39_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28135
ZNF706-BGRSDLV04-80dox_S40_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2876	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27688
ZNF706-BGRSDLV04-80dox_S40_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set68/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2876	NovaSeq6000	100	paired-ended	1				NT-BGRSDLV04-3dox_S3_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGRSDLV04-4dox_S4_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	27752
ZNF706-BGRSDLV04-80dox_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2876					GRCh38	V40	ZNF706-BGRSDLV04-80dox_S40_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF706-BGRSDLV04-80dox_S40_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27816
ZNF706-BGRSDLV04-80dox_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2876					GRCh38	V40	ZNF706-BGRSDLV04-80dox/Aligned.sortedByCoord.out.bam		ENCORE2	27880
ZNF706-BGRSDLV04-80dox_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2876					GRCh38	V40	ZNF706-BGRSDLV04-80dox/Aligned.sortedByCoord.out.bam		ENCORE2	27944
ZNF706-BGRSDLV04-80dox_Signal.Unique.strand-.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2876					GRCh38	V40	ZNF706-BGRSDLV04-80dox/Aligned.sortedByCoord.out.bam		ENCORE2	28008
ZNF706-BGRSDLV04-80dox_Signal.Unique.strand+.bw	ENCODE_DATA/set68/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2876					GRCh38	V40	ZNF706-BGRSDLV04-80dox/Aligned.sortedByCoord.out.bam		ENCORE2	28072
ZNF706-BGRSDLV04-80dox_quant.sf	ENCODE_DATA/set68/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2876					GRCh38	V40	ZNF706-BGRSDLV04-80dox_S40_L004_R1_001.filtered.trimmed.paired.fastq.gz,ZNF706-BGRSDLV04-80dox_S40_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28136