METTL3 RNA-Seq in K562

General Information


RBP	METTL3
Cell_Line	K562
Method	CRISPR
Exp_Name	METTL3-BGKcLV23-K562
ENCODE_series_ID	ENCSR156YXM
Batch_ID	BGKcLV23
Pool ID	Pool-201204
Local_Set_Name	set46_K
ENCODE_KD_Exp_ID	ENCSR335KFN
ENCODE_CN_Exp_ID	ENCSR877JEM
Rep1	METTL3-BGKcLV23-53
Rep2	METTL3-BGKcLV23-54
CN1	NT-BGKcLV23-1
CN2	NT-BGKcLV23-2
Rep1_qPCR	21.0
Rep2_qPCR	10.0
Rep1_WB	61.3
Rep2_WB	66.3
Antibody Cat#	A301-568A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB373NTV
Status	Released
Project	ENCODE4
ID	33

Experiment Information (Status: Released)

	BGKcLV23-53	BGKcLV23-53	BGKcLV23-54	BGKcLV23-54
idx	839	839	840	840
TRCN#_or_BGC#	BGC#0000523	BGC#0000523	BGC#0000523	BGC#0000523
shRNA_or_gRNA_sequence	TCTGAACCAACAGTCCACTA	TCTGAACCAACAGTCCACTA	TCTGAACCAACAGTCCACTA	TCTGAACCAACAGTCCACTA
PAM	AGG	AGG	AGG	AGG
Name	METTL3_86	METTL3_86	METTL3_86	METTL3_86
Sample_ID	BGKcLV23-53	BGKcLV23-53	BGKcLV23-54	BGKcLV23-54
transduction_Date	9/17/20	9/17/20	9/17/20	9/17/20
days	Day 6	Day 6	Day 6	Day 6
RBP_name	METTL3	METTL3	METTL3	METTL3
qPCR_result	21.0	21.0	10.0	10.0
Ave_qPCR	15.5	15.5
RT-qPCR_primer-F	TTGATCTGGAGATAGAGAGCCTTC	TTGATCTGGAGATAGAGAGCCTTC
RT-qPCR_primer-R	TGGATTGTTCCTTGGCTGTT	TGGATTGTTCCTTGGCTGTT
protein_conc	2406	2406	2541	2541
WB_result	61.3	65.1	66.3	53.2213
Ave_WB	63.8	59.2
WB_DONE_date	9/24/29	4/5/24	JESS
MW	64.5KD	64.5KD
IP	Rabbit / I
antibody_Cat#	A301-568A	86132S	LOT# 1	LOT# 1
Antibody DCC ID	ENCAB373NTV
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	11/24/20		11/24/20
repeat_library
Note
ID	4969	4971	4970	4972

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
METTL3	Product_ID: A301-568A Lot_ID: 1 Source: Bethyl Labs Target Name: METTL3-human
METTL3	Product_ID: 86132S Lot_ID: 1 Source: Cell Signaling Technology Target Name: METTL3-human

Experiment Status

	BGKcLV23-53	BGKcLV23-54
Sample_ID	BGKcLV23-53	BGKcLV23-54
Sample Name
Sample Name	METTL3-BGKcLV23-53	METTL3-BGKcLV23-54
RBP	METTL3	METTL3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7455	7456

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV23-53	BGKcLV23-54
Sample #	57	58
Sample Name	METTL3-BGKcLV23-53	METTL3-BGKcLV23-54
Sample_Name_Alias
Index Well Position	A08	B08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	293	300
Peak_Molarity	103.00	105.00
libSampleQC_DNA_Well	DNA_Library_set46/set1/A8.png	DNA_Library_set46/set1/B8.png
RIN	9.2	9.2
libSample_RNA_Well	RNA_Library_set46/set2/A12.png	RNA_Library_set46/set2/B12.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGKcLV23-53	BGKcLV23-54
RBP	METTL3	METTL3
Batch_ID	BGKcLV23	BGKcLV23
WB_result	61.300	66.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1432	1433

Sequencing Information

	BGKcLV23-53	BGKcLV23-54
Sample_ID	BGKcLV23-53	BGKcLV23-54
Sample Name	METTL3-BGKcLV23-53	METTL3-BGKcLV23-54
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_K	set46_K
total_reads	266,619,640	126,277,928
total_aligned_reads	232,623,344	110,718,910
unique_aligned_reads	211,520,664	100,671,952
percent_uniqueAligned	0.79334	0.79723
correlation_replicates	0.998513	0.998513
spikein_reads	188,454	57,926
percent_spikeins	0.00071	0.00046
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	538	539

Data Submission Information

	BGKcLV23-53	BGKcLV23-53	BGKcLV23-53	BGKcLV23-53	BGKcLV23-53	BGKcLV23-53	BGKcLV23-54	BGKcLV23-54	BGKcLV23-54	BGKcLV23-54
ENCODE_alias	brenton-graveley:METTL3-BGKcLV23	brenton-graveley:METTL3-BGKcLV23-53	brenton-graveley:L-METTL3-BGKcLV23-53	brenton-graveley:METTL3-BGKcLV23-53_TGCGGCGT+TACCGAGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:METTL3-BGKcLV23-53_TGCGGCGT+TACCGAGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:METTL3-BGKcLV23-K562	brenton-graveley:METTL3-BGKcLV23-54	brenton-graveley:L-METTL3-BGKcLV23-54	brenton-graveley:METTL3-BGKcLV23-54_CATAATAC+CGTTAGAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:METTL3-BGKcLV23-54_CATAATAC+CGTTAGAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR335KFN	ENCBS082RXU	ENCLB422GFB	ENCFF170IXA	ENCFF140KLQ	ENCSR156YXM	ENCBS960LGF	ENCLB913WIF	ENCFF332DGA	ENCFF831XZB
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV23-53	BGKcLV23-53	BGKcLV23-53	BGKcLV23-53	BGKcLV23-53	BGKcLV23-53	BGKcLV23-54	BGKcLV23-54	BGKcLV23-54	BGKcLV23-54
Sample Name	METTL3-BGKcLV23-53	METTL3-BGKcLV23-53	METTL3-BGKcLV23-53	METTL3-BGKcLV23-53	METTL3-BGKcLV23-53	METTL3-BGKcLV23-53	METTL3-BGKcLV23-54	METTL3-BGKcLV23-54	METTL3-BGKcLV23-54	METTL3-BGKcLV23-54
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46K_biosample_protocol	LV46K_library_protocol				LV46K_biosample_protocol	LV46K_library_protocol
protocol_URL		METTL3-BGKcLV23-53.pdf	L-METTL3-BGKcLV23-53.pdf				METTL3-BGKcLV23-54.pdf	L-METTL3-BGKcLV23-54.pdf
ID	2423	2483	2547	2641	2675	7258	2484	2548	2642	2676

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
METTL3-BGKcLV23-53_TGCGGCGT+TACCGAGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	538	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1402
METTL3-BGKcLV23-53_TGCGGCGT+TACCGAGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	538	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1466
METTL3-BGKcLV23-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	538					GRCh38	V40	METTL3-BGKcLV23-53_TGCGGCGT+TACCGAGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,METTL3-BGKcLV23-53_TGCGGCGT+TACCGAGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25305
METTL3-BGKcLV23-53_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	538					GRCh38	V40	METTL3-BGKcLV23-53_TGCGGCGT+TACCGAGG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,METTL3-BGKcLV23-53_TGCGGCGT+TACCGAGG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25339
METTL3-BGKcLV23-53_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	538					GRCh38	V40	METTL3-BGKcLV23-53/Aligned.sortedByCoord.out.bam		ENCORE2	26143
METTL3-BGKcLV23-53_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	538					GRCh38	V40	METTL3-BGKcLV23-53/Aligned.sortedByCoord.out.bam		ENCORE2	26177
METTL3-BGKcLV23-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	538					GRCh38	V40	METTL3-BGKcLV23-53/Aligned.sortedByCoord.out.bam		ENCORE2	26211
METTL3-BGKcLV23-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	538					GRCh38	V40	METTL3-BGKcLV23-53/Aligned.sortedByCoord.out.bam		ENCORE2	26245
METTL3-BGKcLV23-54_CATAATAC+CGTTAGAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	539	NovaSeq6000	100	paired-ended	1				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1403
METTL3-BGKcLV23-54_CATAATAC+CGTTAGAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	539	NovaSeq6000	100	paired-ended	2				NT-BGKcLV23-1_GGCATTCT+CAAGCTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV23-2_AATGCCTC+TGGATCGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1467
METTL3-BGKcLV23-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	539					GRCh38	V40	METTL3-BGKcLV23-54_CATAATAC+CGTTAGAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,METTL3-BGKcLV23-54_CATAATAC+CGTTAGAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25306
METTL3-BGKcLV23-54_quant.sf	ENCODE_DATA/set46_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	539					GRCh38	V40	METTL3-BGKcLV23-54_CATAATAC+CGTTAGAA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,METTL3-BGKcLV23-54_CATAATAC+CGTTAGAA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25340
METTL3-BGKcLV23-54_Signal.Unique.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	539					GRCh38	V40	METTL3-BGKcLV23-54/Aligned.sortedByCoord.out.bam		ENCORE2	26144
METTL3-BGKcLV23-54_Signal.Unique.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	539					GRCh38	V40	METTL3-BGKcLV23-54/Aligned.sortedByCoord.out.bam		ENCORE2	26178
METTL3-BGKcLV23-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	539					GRCh38	V40	METTL3-BGKcLV23-54/Aligned.sortedByCoord.out.bam		ENCORE2	26212
METTL3-BGKcLV23-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	539					GRCh38	V40	METTL3-BGKcLV23-54/Aligned.sortedByCoord.out.bam		ENCORE2	26246