YTHDF2 RNA-Seq in HepG2

General Information


RBP	YTHDF2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	YTHDF2-BGHcLV45-HepG2
ENCODE_series_ID
Batch_ID	BGHcLV45
Pool ID	Pool-241205
Local_Set_Name	set76
ENCODE_KD_Exp_ID
ENCODE_CN_Exp_ID
Rep1	YTHDF2-BGHcLV45-87
Rep2	YTHDF2-BGHcLV45-88
CN1	NT-BGHcLV45-1
CN2	NT-BGHcLV45-2
Rep1_qPCR	23.0
Rep2_qPCR	0.0
Rep1_WB	70.7
Rep2_WB	75.3
Antibody Cat#	71283S
Antibody Lot#	lot # 1
Antibody DCC ID
Status	Submitted
Project	ENCORE2
ID	1634

Experiment Information (Status: Submitting)

	BGHcLV45-87	BGHcLV45-88
idx	0	0
TRCN#_or_BGC#	BGC#0001213	BGC#0001213
shRNA_or_gRNA_sequence	TGAACCTTACTTGAGTCCAC	TGAACCTTACTTGAGTCCAC
PAM	AGG	AGG
Name	YTHDF2_84	YTHDF2_84
Sample_ID	BGHcLV45-87	BGHcLV45-88
transduction_Date	10/1/24	10/1/24
days	D6	D6
RBP_name	YTHDF2	YTHDF2
qPCR_result	23.0	0.0
Ave_qPCR	11.5
RT-qPCR_primer-F	gagaaacgccaagaggaaga
RT-qPCR_primer-R	ctgccttttatttcccacga
protein_conc	4247	4019
WB_result	70.7	75.3
Ave_WB
WB_DONE_date	11/1/24
MW	65kd
IP
antibody_Cat#	71283S	lot # 1
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	9783	9784

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
YTHDF2	Product_ID: 71283S Lot_ID: 1 Source: Cell Signaling Technology Target Name: YTHDF2-human

Experiment Status

	BGHcLV45-87	BGHcLV45-88
Sample_ID	BGHcLV45-87	BGHcLV45-88
Sample Name
Sample Name	YTHDF2-BGHcLV45-87	YTHDF2-BGHcLV45-88
RBP	YTHDF2	YTHDF2
Cell_Line	HepG2	HepG2
Exp UID
Status	Submitting	Submitting
Status_date	2025-04-21	2025-04-21
Project	ENCORE2	ENCORE2
Note
ID	13726	13727

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV45-87	BGHcLV45-88
Sample #	41	42
Sample Name	YTHDF2-BGHcLV45-87	YTHDF2-BGHcLV45-88
Sample_Name_Alias
Index Well Position	A12	B12
Index_table	IDT_UniqueDualIndex_96_V2	IDT_UniqueDualIndex_96_V2
LibPrep_date	2024-12-02	2024-12-02
Lib_ID	Lib-241202	Lib-241202
Tecan_Location
Tecan
Tecan_date
Size_bp	286	283
Peak_Molarity	80.00	81.20
libSampleQC_DNA_Well	DNA_Library_set76/set1/A12.png	DNA_Library_set76/set1/B12.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set76/set1/A6.png	RNA_Library_set76/set1/B6.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2024-12-05	2024-12-05
Sample_ID	BGHcLV45-87	BGHcLV45-88
RBP	YTHDF2	YTHDF2
Batch_ID	BGHcLV45	BGHcLV45
WB_result	70.700	75.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCORE2	ENCORE2
ID	4650	4651

Sequencing Information

	BGHcLV45-87	BGHcLV45-88
Sample_ID	BGHcLV45-87	BGHcLV45-88
Sample Name	YTHDF2-BGHcLV45-87	YTHDF2-BGHcLV45-88
Pool ID	Pool-241205	Pool-241205
LocalServer_folder	set76	set76
total_reads	38,718,833	38,741,320
total_aligned_reads	35,550,994	35,826,218
unique_aligned_reads	33,494,704	33,766,567
percent_uniqueAligned	0.86508	0.87159
correlation_replicates	0.991942	0.991942
spikein_reads	59,230	18,894
percent_spikeins	0.00153	0.00049
original_ReadLength	101	101
QC_Status	Submitting	Submitting
ID	3361	3362

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
YTHDF2-BGHcLV45-87_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3361	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31852
YTHDF2-BGHcLV45-87_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3361	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31894
YTHDF2-BGHcLV45-87_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3361					GRCh38	V40	YTHDF2-BGHcLV45-87_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF2-BGHcLV45-87_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31936
YTHDF2-BGHcLV45-87_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3361					GRCh38	V40	YTHDF2-BGHcLV45-87_Aligned.sortedByCoord.out.bam		ENCORE2	31978
YTHDF2-BGHcLV45-87_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3361					GRCh38	V40	YTHDF2-BGHcLV45-87_Aligned.sortedByCoord.out.bam		ENCORE2	32020
YTHDF2-BGHcLV45-87_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3361					GRCh38	V40	YTHDF2-BGHcLV45-87_Aligned.sortedByCoord.out.bam		ENCORE2	32062
YTHDF2-BGHcLV45-87_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3361					GRCh38	V40	YTHDF2-BGHcLV45-87_Aligned.sortedByCoord.out.bam		ENCORE2	32104
YTHDF2-BGHcLV45-87_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3361					GRCh38	V40	YTHDF2-BGHcLV45-87_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF2-BGHcLV45-87_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32146
YTHDF2-BGHcLV45-88_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3362	NovaSeq6000	100	paired-ended	1				NT-BGHcLV45-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31853
YTHDF2-BGHcLV45-88_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set76/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3362	NovaSeq6000	100	paired-ended	2				NT-BGHcLV45-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV45-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCORE2	31895
YTHDF2-BGHcLV45-88_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3362					GRCh38	V40	YTHDF2-BGHcLV45-88_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF2-BGHcLV45-88_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	31937
YTHDF2-BGHcLV45-88_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3362					GRCh38	V40	YTHDF2-BGHcLV45-88_Aligned.sortedByCoord.out.bam		ENCORE2	31979
YTHDF2-BGHcLV45-88_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3362					GRCh38	V40	YTHDF2-BGHcLV45-88_Aligned.sortedByCoord.out.bam		ENCORE2	32021
YTHDF2-BGHcLV45-88_Signal.Unique.strand-.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3362					GRCh38	V40	YTHDF2-BGHcLV45-88_Aligned.sortedByCoord.out.bam		ENCORE2	32063
YTHDF2-BGHcLV45-88_Signal.Unique.strand+.bw	ENCODE_DATA/set76/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3362					GRCh38	V40	YTHDF2-BGHcLV45-88_Aligned.sortedByCoord.out.bam		ENCORE2	32105
YTHDF2-BGHcLV45-88_quant.sf	ENCODE_DATA/set76/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3362					GRCh38	V40	YTHDF2-BGHcLV45-88_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,YTHDF2-BGHcLV45-88_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	32147