YTHDF1 RNA-Seq in 293T

Experiment Information (Status: Submitting)

	BG293LV05-25	BG293LV05-26
idx	0	0
TRCN#_or_BGC#	TRCN0000062770	TRCN0000062770
shRNA_or_gRNA_sequence	CCGGCCCGAAAGAGTTTGAGTGGAACTCGAGTTCCACTCAAACTCTTTCGGGTTTTTG	CCGGCCCGAAAGAGTTTGAGTGGAACTCGAGTTCCACTCAAACTCTTTCGGGTTTTTG
PAM
Name	YTHDF1	YTHDF1
Sample_ID	BG293LV05-25	BG293LV05-26
transduction_Date	12/18/23	12/18/23
days	D4	D4
RBP_name	YTHDF1	YTHDF1
qPCR_result	62.1	67.4
Ave_qPCR	64.75
RT-qPCR_primer-F	tgagccctaccttactggaca
RT-qPCR_primer-R	gtagaccacggagcctcatt
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	9997	9998

Western Blot Western Blot info was not avaliable

Experiment Status

	BG293LV05-25	BG293LV05-26
Sample_ID	BG293LV05-25	BG293LV05-26
Sample Name
Sample Name	YTHDF1-BG293LV05-25	YTHDF1-BG293LV05-26
RBP	YTHDF1	YTHDF1
Cell_Line	293T	293T
Exp UID
Status	Submitting	Submitting
Status_date	2024-05-07	2024-05-07
Project	ENCORE2	ENCORE2
Note
ID	12846	12847

Library-Prep
Sequencing

Library-Prep Information

	BG293LV05-25	BG293LV05-26
Sample #	13	14
Sample Name	YTHDF1-BG293LV05-25	YTHDF1-BG293LV05-26
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2024-01-16	2024-01-16
Lib_ID	Lib-240116	Lib-240116
Tecan_Location
Tecan
Tecan_date
Size_bp	280	279
Peak_Molarity	81.30	86.40
libSampleQC_DNA_Well	DNA_Library_set69/set1/E2.png	DNA_Library_set69/set1/F2.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set69/set1/E7.png	RNA_Library_set69/set1/F7.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-01-19	2024-01-19
Sample_ID	BG293LV05-25	BG293LV05-26
RBP	YTHDF1	YTHDF1
Batch_ID	BG293LV05	BG293LV05
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4194	4195

Sequencing Information

	BG293LV05-25	BG293LV05-26
Sample_ID	BG293LV05-25	BG293LV05-26
Sample Name	YTHDF1-BG293LV05-25	YTHDF1-BG293LV05-26
Pool ID	Pool-240119	Pool-240119
LocalServer_folder	set69	set69
total_reads	19,902,195	21,565,227
total_aligned_reads	17,064,562	17,832,860
unique_aligned_reads	15,807,389	16,556,383
percent_uniqueAligned	0.79425	0.76774
correlation_replicates	0.988889	0.988889
spikein_reads	3,664	7,460
percent_spikeins	0.00018	0.00035
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	2913	2914

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
YTHDF1-BG293LV05-25_S145_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2913	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28531
YTHDF1-BG293LV05-25_S145_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2913	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28575
YTHDF1-BG293LV05-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2913					GRCh38	V40	YTHDF1-BG293LV05-25_S145_L002_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF1-BG293LV05-25_S145_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28619
YTHDF1-BG293LV05-25_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2913					GRCh38	V40	YTHDF1-BG293LV05-25/Aligned.sortedByCoord.out.bam		ENCORE2	28663
YTHDF1-BG293LV05-25_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2913					GRCh38	V40	YTHDF1-BG293LV05-25/Aligned.sortedByCoord.out.bam		ENCORE2	28707
YTHDF1-BG293LV05-25_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2913					GRCh38	V40	YTHDF1-BG293LV05-25/Aligned.sortedByCoord.out.bam		ENCORE2	28751
YTHDF1-BG293LV05-25_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2913					GRCh38	V40	YTHDF1-BG293LV05-25/Aligned.sortedByCoord.out.bam		ENCORE2	28795
YTHDF1-BG293LV05-25_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2913					GRCh38	V40	YTHDF1-BG293LV05-25_S145_L002_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF1-BG293LV05-25_S145_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28839
YTHDF1-BG293LV05-26_S146_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2914	NovaSeq6000	100	paired-ended	1				NT-BG293LV05-1_merged_R1_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28532
YTHDF1-BG293LV05-26_S146_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set69/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2914	NovaSeq6000	100	paired-ended	2				NT-BG293LV05-1_merged_R2_001.filtered.trimmed.paired.fastq.gz,NT-BG293LV05-2_S134_L002_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	28576
YTHDF1-BG293LV05-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2914					GRCh38	V40	YTHDF1-BG293LV05-26_S146_L002_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF1-BG293LV05-26_S146_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28620
YTHDF1-BG293LV05-26_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2914					GRCh38	V40	YTHDF1-BG293LV05-26/Aligned.sortedByCoord.out.bam		ENCORE2	28664
YTHDF1-BG293LV05-26_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2914					GRCh38	V40	YTHDF1-BG293LV05-26/Aligned.sortedByCoord.out.bam		ENCORE2	28708
YTHDF1-BG293LV05-26_Signal.Unique.strand-.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2914					GRCh38	V40	YTHDF1-BG293LV05-26/Aligned.sortedByCoord.out.bam		ENCORE2	28752
YTHDF1-BG293LV05-26_Signal.Unique.strand+.bw	ENCODE_DATA/set69/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2914					GRCh38	V40	YTHDF1-BG293LV05-26/Aligned.sortedByCoord.out.bam		ENCORE2	28796
YTHDF1-BG293LV05-26_quant.sf	ENCODE_DATA/set69/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2914					GRCh38	V40	YTHDF1-BG293LV05-26_S146_L002_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF1-BG293LV05-26_S146_L002_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	28840