DNMT1 RNA-Seq in K562

General Information


RBP	DNMT1
Cell_Line	K562
Method	CRISPR
Exp_Name	DNMT1-BGKcLV13-K562
ENCODE_series_ID	ENCSR464FRN
Batch_ID	BGKcLV13
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR600OWF
ENCODE_CN_Exp_ID	ENCSR712CQC
Rep1	DNMT1-BGKcLV13-19
Rep2	DNMT1-BGKcLV13-20
CN1	NT-BGKcLV13-1
CN2	NT-BGKcLV13-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	85.6
Rep2_WB	78.0
Antibody Cat#	PA1-880
Antibody Lot#	LOT # SH257771
Antibody DCC ID	ENCAB197TCQ
Status	Released
Project	ENCODE4
ID	168

Experiment Information (Status: Released)

	BGKcLV13-19	BGKcLV13-20
idx	464	465
TRCN#_or_BGC#	BGC#0000312	BGC#0000312
shRNA_or_gRNA_sequence	GAGGAGCAAGTCCGATGGAG	GAGGAGCAAGTCCGATGGAG
PAM	agg	agg
Name	DNMT1_81	DNMT1_81
Sample_ID	BGKcLV13-19	BGKcLV13-20
transduction_Date	11/28/18	11/28/18
days	Day 6	Day 6
RBP_name	DNMT1	DNMT1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ctcaggcgctggagaaatac
RT-qPCR_primer-R	atgccaggtgggattgtact
protein_conc	4557	4181
WB_result	85.6	78.0
Ave_WB	81.8
WB_DONE_date	12/6/18	wes
MW	183kd
IP	Rabbit
antibody_Cat#	PA1-880	LOT # SH257771
Antibody DCC ID	ENCAB197TCQ
submitted_to_DCC_date	3/11/19
Rep1_TPM	117.2	0
Rep2_TPM	119.3	0
Action	Ready	Ready
Library_start_date	03/18/19	03/18/19
repeat_library
Note
ID	4568	4569

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DNMT1	Product_ID: PA1-880 Lot_ID: SH257771 Source: Thermo Fisher Target Name: DNMT1-human

Experiment Status

	BGKcLV13-19	BGKcLV13-20
Sample_ID	BGKcLV13-19	BGKcLV13-20
Sample Name	DNMT1-BGKcLV13-19	DNMT1-BGKcLV13-20
Sample Name	DNMT1-BGKcLV13-19	DNMT1-BGKcLV13-20
RBP	DNMT1	DNMT1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2899	2900

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV13-19	BGKcLV13-20
Sample #	53	54
Sample Name	DNMT1-BGKcLV13-19	DNMT1-BGKcLV13-20
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-18	2019-03-18
Lib_ID	Lib-190318	Lib-190318
Tecan_Location	1-E1	1-F1
Tecan	47.89	69.83
Tecan_date	2019-03-18	2019-03-18
Size_bp	282	286
Peak_Molarity	33.50	44.40
libSampleQC_DNA_Well	DNA_Library_set42/set1/E7.png	DNA_Library_set42/set1/F7.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set42/set1/E7.png	RNA_Library_set42/set1/F7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-18	2019-03-18
Sample_ID	BGKcLV13-19	BGKcLV13-20
RBP	DNMT1	DNMT1
Batch_ID	BGKcLV13	BGKcLV13
WB_result	85.600	78.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	53	54

Sequencing Information

	BGKcLV13-19	BGKcLV13-20
Sample_ID	BGKcLV13-19	BGKcLV13-20
Sample Name	DNMT1-BGKcLV13-19	DNMT1-BGKcLV13-20
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	61,135,582	54,328,440
total_aligned_reads	58,563,826	51,978,126
unique_aligned_reads	53,424,170	47,436,712
percent_uniqueAligned	0.87386	0.87315
correlation_replicates	0.998011	0.998011
spikein_reads	42,910	57,594
percent_spikeins	0.00070	0.00106
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	15	16

Data Submission Information

	BGKcLV13-19	BGKcLV13-19	BGKcLV13-19	BGKcLV13-19	BGKcLV13-19	BGKcLV13-19	BGKcLV13-20	BGKcLV13-20	BGKcLV13-20	BGKcLV13-20
ENCODE_alias	brenton-graveley:DNMT1-BGKcLV13	brenton-graveley:DNMT1-BGKcLV13-19	brenton-graveley:L-DNMT1-BGKcLV13-19	brenton-graveley:DNMT1-BGKcLV13-19_CAACAATG+CTTCACGG_HK3H2DSXX_S53_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DNMT1-BGKcLV13-19_CAACAATG+CTTCACGG_HK3H2DSXX_S53_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DNMT1-BGKcLV13-K562	brenton-graveley:DNMT1-BGKcLV13-20	brenton-graveley:L-DNMT1-BGKcLV13-20	brenton-graveley:DNMT1-BGKcLV13-20_TGGTGGCA+TCCTGTAA_HK3H2DSXX_S54_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DNMT1-BGKcLV13-20_TGGTGGCA+TCCTGTAA_HK3H2DSXX_S54_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR600OWF	ENCBS404MEW	ENCLB578HXA	ENCFF955MNM	ENCFF110TKK	ENCSR464FRN	ENCBS476ZSX	ENCLB504ZUM	ENCFF287TBO	ENCFF777LCP
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	BGKcLV13-19	BGKcLV13-19	BGKcLV13-19	BGKcLV13-19	BGKcLV13-19	BGKcLV13-19	BGKcLV13-20	BGKcLV13-20	BGKcLV13-20	BGKcLV13-20
Sample Name	DNMT1-BGKcLV13-19	DNMT1-BGKcLV13-19	DNMT1-BGKcLV13-19	DNMT1-BGKcLV13-19	DNMT1-BGKcLV13-19	DNMT1-BGKcLV13-19	DNMT1-BGKcLV13-20	DNMT1-BGKcLV13-20	DNMT1-BGKcLV13-20	DNMT1-BGKcLV13-20
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		DNMT1-BGKcLV13-19.pdf	L-DNMT1-BGKcLV13-19.pdf				DNMT1-BGKcLV13-20.pdf	L-DNMT1-BGKcLV13-20.pdf
ID	777	849	931	965	1047	7190	850	932	966	1048

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
DNMT1-BGKcLV13-19_CAACAATG+CTTCACGG_HK3H2DSXX_S53_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	15	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	347
DNMT1-BGKcLV13-19_CAACAATG+CTTCACGG_HK3H2DSXX_S53_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	15	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	429
DNMT1-BGKcLV13-19_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	15					GRCh38	V40	DNMT1-BGKcLV13-19_CAACAATG+CTTCACGG_HK3H2DSXX_S53_L004_R1_001.filtered.trimmed.paired.fastq.gz,DNMT1-BGKcLV13-19_CAACAATG+CTTCACGG_HK3H2DSXX_S53_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23686
DNMT1-BGKcLV13-19_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	15					GRCh38	V40	DNMT1-BGKcLV13-19/Aligned.sortedByCoord.out.bam		ENCORE2	23768
DNMT1-BGKcLV13-19_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	15					GRCh38	V40	DNMT1-BGKcLV13-19/Aligned.sortedByCoord.out.bam		ENCORE2	23850
DNMT1-BGKcLV13-19_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	15					GRCh38	V40	DNMT1-BGKcLV13-19/Aligned.sortedByCoord.out.bam		ENCORE2	23932
DNMT1-BGKcLV13-19_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	15					GRCh38	V40	DNMT1-BGKcLV13-19/Aligned.sortedByCoord.out.bam		ENCORE2	24014
DNMT1-BGKcLV13-19_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	15					GRCh38	V40	DNMT1-BGKcLV13-19_CAACAATG+CTTCACGG_HK3H2DSXX_S53_L004_R1_001.filtered.trimmed.paired.fastq.gz,DNMT1-BGKcLV13-19_CAACAATG+CTTCACGG_HK3H2DSXX_S53_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24096
DNMT1-BGKcLV13-20_TGGTGGCA+TCCTGTAA_HK3H2DSXX_S54_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	16	NovaSeq6000	100	paired-ended	1				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	348
DNMT1-BGKcLV13-20_TGGTGGCA+TCCTGTAA_HK3H2DSXX_S54_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	16	NovaSeq6000	100	paired-ended	2				NT-BGKcLV13-1_ATATCTCG+ATCTTAGT_HK3H2DSXX_S49_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV13-2_GCGCTCTA+GCTCCGAC_HK3H2DSXX_S50_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	430
DNMT1-BGKcLV13-20_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	16					GRCh38	V40	DNMT1-BGKcLV13-20_TGGTGGCA+TCCTGTAA_HK3H2DSXX_S54_L004_R1_001.filtered.trimmed.paired.fastq.gz,DNMT1-BGKcLV13-20_TGGTGGCA+TCCTGTAA_HK3H2DSXX_S54_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23687
DNMT1-BGKcLV13-20_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	16					GRCh38	V40	DNMT1-BGKcLV13-20/Aligned.sortedByCoord.out.bam		ENCORE2	23769
DNMT1-BGKcLV13-20_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	16					GRCh38	V40	DNMT1-BGKcLV13-20/Aligned.sortedByCoord.out.bam		ENCORE2	23851
DNMT1-BGKcLV13-20_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	16					GRCh38	V40	DNMT1-BGKcLV13-20/Aligned.sortedByCoord.out.bam		ENCORE2	23933
DNMT1-BGKcLV13-20_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	16					GRCh38	V40	DNMT1-BGKcLV13-20/Aligned.sortedByCoord.out.bam		ENCORE2	24015
DNMT1-BGKcLV13-20_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	16					GRCh38	V40	DNMT1-BGKcLV13-20_TGGTGGCA+TCCTGTAA_HK3H2DSXX_S54_L004_R1_001.filtered.trimmed.paired.fastq.gz,DNMT1-BGKcLV13-20_TGGTGGCA+TCCTGTAA_HK3H2DSXX_S54_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24097