DICER1 RNA-Seq in K562

General Information


RBP	DICER1
Cell_Line	K562
Method	CRISPR
Exp_Name	DICER1-BGKcLV15-K562
ENCODE_series_ID	ENCSR345FBJ
Batch_ID	BGKcLV15
Pool ID	Pool-200102
Local_Set_Name	set43_K
ENCODE_KD_Exp_ID	ENCSR715XCS
ENCODE_CN_Exp_ID	ENCSR404OHQ
Rep1	DICER1-BGKcLV15-11
Rep2	DICER1-BGKcLV15-12
CN1	NT-BGKcLV15-1
CN2	NT-BGKcLV15-2
Rep1_qPCR	46.3
Rep2_qPCR	58.5
Rep1_WB	78.0
Rep2_WB	71.9
Antibody Cat#	PA5-17021
Antibody Lot#	LOT# TL2693039
Antibody DCC ID	ENCAB330RCK
Status	Released
Project	ENCODE4
ID	123

Experiment Information (Status: Released)

	BGKcLV15-11	BGKcLV15-12
idx	539	540
TRCN#_or_BGC#	BGC#0000342	BGC#0000342
shRNA_or_gRNA_sequence	TGAATAGTGTCTGTCGTACC	TGAATAGTGTCTGTCGTACC
PAM	AGG	AGG
Name	DICER1-94	DICER1-94
Sample_ID	BGKcLV15-11	BGKcLV15-12
transduction_Date	4/2/19	4/2/19
days	Day 6	Day 6
RBP_name	DICER1	DICER1
qPCR_result	46.3	58.5
Ave_qPCR	52.4
RT-qPCR_primer-F	ACAAAAGCAACACAGATAAATGGG
RT-qPCR_primer-R	ACATCAGGCTCTCCTCCTCC
protein_conc	4205	4569
WB_result	78.0	71.9
Ave_WB	75.0
WB_DONE_date	4/25/19
MW	219KD
IP	Rabbit / I
antibody_Cat#	PA5-17021	LOT# TL2693039
Antibody DCC ID	ENCAB330RCK
submitted_to_DCC_date	4/17/19
Rep1_TPM	8.4	0
Rep2_TPM	27	0
Action	Ready	Ready
Library_start_date	05/30/19	05/30/19
repeat_library
Note
ID	4649	4650

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DICER1	Product_ID: PA5-17021 Lot_ID: TL2693039 Source: Thermo Fisher Target Name: DICER1-human

Experiment Status

	BGKcLV15-11	BGKcLV15-12
Sample_ID	BGKcLV15-11	BGKcLV15-12
Sample Name
Sample Name	DICER1-BGKcLV15-11	DICER1-BGKcLV15-12
RBP	DICER1	DICER1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-12-01	2020-12-01
Project	ENCODE4	ENCODE4
Note
ID	5335	5336

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV15-11	BGKcLV15-12
Sample #	5	6
Sample Name	DICER1-BGKcLV15-11	DICER1-BGKcLV15-12
Sample_Name_Alias
Index Well Position	E01	F01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-08-30	2020-08-30
Lib_ID	Lib-200830	Lib-200830
Tecan_Location	1-E1	1-F1
Tecan	23.95	24.96
Tecan_date	2019-12-10	2019-12-10
Size_bp	265	269
Peak_Molarity	21.40	14.60
libSampleQC_DNA_Well	DNA_Library_set43-44/set1/E1.png	DNA_Library_set43-44/set1/F1.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set43-44/set1/E1.png	RNA_Library_set43-44/set1/F1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-12-11	2019-12-11
Sample_ID	BGKcLV15-11	BGKcLV15-12
RBP	DICER1	DICER1
Batch_ID	BGKcLV15	BGKcLV15
WB_result	87.000	96.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	581	582

Sequencing Information

	BGKcLV15-11	BGKcLV15-12
Sample_ID	BGKcLV15-11	BGKcLV15-12
Sample Name	DICER1-BGKcLV15-11	DICER1-BGKcLV15-12
Pool ID	Pool-200102	Pool-200102
LocalServer_folder	set43_K	set43_K
total_reads	167,072,540	154,083,506
total_aligned_reads	135,677,220	99,743,548
unique_aligned_reads	123,763,402	90,886,340
percent_uniqueAligned	0.74078	0.58985
correlation_replicates	0.996459	0.996459
spikein_reads	69,152	74,204
percent_spikeins	0.00041	0.00048
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	87	88

Data Submission Information

	BGKcLV15-11	BGKcLV15-11	BGKcLV15-11	BGKcLV15-11	BGKcLV15-11	BGKcLV15-11	BGKcLV15-12	BGKcLV15-12	BGKcLV15-12	BGKcLV15-12
ENCODE_alias	brenton-graveley:DICER1-BGKcLV15	brenton-graveley:DICER1-BGKcLV15-11	brenton-graveley:L-DICER1-BGKcLV15-11	brenton-graveley:DICER1-BGKcLV15-11_S5_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DICER1-BGKcLV15-11_S5_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DICER1-BGKcLV15-K562	brenton-graveley:DICER1-BGKcLV15-12	brenton-graveley:L-DICER1-BGKcLV15-12	brenton-graveley:DICER1-BGKcLV15-12_S6_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DICER1-BGKcLV15-12_S6_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR715XCS	ENCBS524HOB	ENCLB645LGN	ENCFF463PLC	ENCFF843ZZY	ENCSR345FBJ	ENCBS629GVA	ENCLB754TSN	ENCFF974PKZ	ENCFF960GUL
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	BGKcLV15-11	BGKcLV15-11	BGKcLV15-11	BGKcLV15-11	BGKcLV15-11	BGKcLV15-11	BGKcLV15-12	BGKcLV15-12	BGKcLV15-12	BGKcLV15-12
Sample Name	DICER1-BGKcLV15-11	DICER1-BGKcLV15-11	DICER1-BGKcLV15-11	DICER1-BGKcLV15-11	DICER1-BGKcLV15-11	DICER1-BGKcLV15-11	DICER1-BGKcLV15-12	DICER1-BGKcLV15-12	DICER1-BGKcLV15-12	DICER1-BGKcLV15-12
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV43K_biosample_protocol	LV43K_library_protocol				LV43K_biosample_protocol	LV43K_library_protocol
protocol_URL		DICER1-BGKcLV15-11.pdf	L-DICER1-BGKcLV15-11.pdf				DICER1-BGKcLV15-12.pdf	L-DICER1-BGKcLV15-12.pdf
ID	19	120	284	482	534	7189	121	285	483	535

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
DICER1-BGKcLV15-11_S5_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	87	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	77
DICER1-BGKcLV15-11_S5_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	87	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	129
DICER1-BGKcLV15-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	87					GRCh38	V40	DICER1-BGKcLV15-11_S5_R1_001.filtered.trimmed.paired.fastq.gz,DICER1-BGKcLV15-11_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24368
DICER1-BGKcLV15-11_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	87					GRCh38	V40	DICER1-BGKcLV15-11/Aligned.sortedByCoord.out.bam		ENCORE2	24420
DICER1-BGKcLV15-11_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	87					GRCh38	V40	DICER1-BGKcLV15-11/Aligned.sortedByCoord.out.bam		ENCORE2	24472
DICER1-BGKcLV15-11_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	87					GRCh38	V40	DICER1-BGKcLV15-11/Aligned.sortedByCoord.out.bam		ENCORE2	24524
DICER1-BGKcLV15-11_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	87					GRCh38	V40	DICER1-BGKcLV15-11/Aligned.sortedByCoord.out.bam		ENCORE2	24576
DICER1-BGKcLV15-11_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	87					GRCh38	V40	DICER1-BGKcLV15-11_S5_R1_001.filtered.trimmed.paired.fastq.gz,DICER1-BGKcLV15-11_S5_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24628
DICER1-BGKcLV15-12_S6_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	88	NovaSeq6000	100	paired-ended	1				NT-BGKcLV15-1_S1_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	78
DICER1-BGKcLV15-12_S6_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set43_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	88	NovaSeq6000	100	paired-ended	2				NT-BGKcLV15-1_S1_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV15-2_S2_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	130
DICER1-BGKcLV15-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	88					GRCh38	V40	DICER1-BGKcLV15-12_S6_R1_001.filtered.trimmed.paired.fastq.gz,DICER1-BGKcLV15-12_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24369
DICER1-BGKcLV15-12_Signal.Unique.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	88					GRCh38	V40	DICER1-BGKcLV15-12/Aligned.sortedByCoord.out.bam		ENCORE2	24421
DICER1-BGKcLV15-12_Signal.Unique.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	88					GRCh38	V40	DICER1-BGKcLV15-12/Aligned.sortedByCoord.out.bam		ENCORE2	24473
DICER1-BGKcLV15-12_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	88					GRCh38	V40	DICER1-BGKcLV15-12/Aligned.sortedByCoord.out.bam		ENCORE2	24525
DICER1-BGKcLV15-12_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set43_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	88					GRCh38	V40	DICER1-BGKcLV15-12/Aligned.sortedByCoord.out.bam		ENCORE2	24577
DICER1-BGKcLV15-12_quant.sf	ENCODE_DATA/set43_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	88					GRCh38	V40	DICER1-BGKcLV15-12_S6_R1_001.filtered.trimmed.paired.fastq.gz,DICER1-BGKcLV15-12_S6_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24629