DCP1A RNA-Seq in K562

General Information


RBP	DCP1A
Cell_Line	K562
Method	CRISPR
Exp_Name	DCP1A-BGKcLV28-K562
ENCODE_series_ID	ENCSR582NNR
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR911ITT
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	DCP1A-BGKcLV28-61
Rep2	DCP1A-BGKcLV28-62
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	35.6
Rep2_qPCR	27.7
Rep1_WB	68.7
Rep2_WB	70.6
Antibody Cat#	A303-590A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB935HMJ
Status	Released
Project	ENCODE4
ID	840

Experiment Information (Status: Released)

	BGKcLV28-61	BGKcLV28-61	BGKcLV28-62	BGKcLV28-62
idx	1009	1011	1010	1012
TRCN#_or_BGC#	BGC#0000737	BGC#0000737	BGC#0000737	BGC#0000737
shRNA_or_gRNA_sequence	ACAGAGCGACCTGGCCCGTG	ACAGAGCGACCTGGCCCGTG	ACAGAGCGACCTGGCCCGTG	ACAGAGCGACCTGGCCCGTG
PAM	AGG	AGG	AGG	AGG
Name	DCP1A_90	DCP1A_90	DCP1A_90	DCP1A_90
Sample_ID	BGKcLV28-61	BGKcLV28-61	BGKcLV28-62	BGKcLV28-62
transduction_Date	7/12/21	7/12/21	7/12/21	7/12/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	DCP1A	DCP1A	DCP1A	DCP1A
qPCR_result	35.6	35.6	27.7	27.7
Ave_qPCR	31.7	31.7
RT-qPCR_primer-F	ggtgttatccagtgccatcc	ggtgttatccagtgccatcc
RT-qPCR_primer-R	gccagcaggactgaagaca	gccagcaggactgaagaca
protein_conc	2981	2981	2908	2908
WB_result	68.7	65.5	70.6	60.7
Ave_WB	69.7	63.1
WB_DONE_date	7/7/21	8/25/21	JESS	JESS
MW	63KD	63KD
IP
antibody_Cat#	A303-590A	A303-591A	LOT #1	LOT #1
Antibody DCC ID	ENCAB935HMJ	ENCAB984AGC
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/23/21		09/23/21
repeat_library
Note
ID	5143	5145	5144	5146

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DCP1A	Product_ID: A303-590A Lot_ID: 1 Source: Bethyl Labs Target Name: DCP1A-human
DCP1A	Product_ID: A303-591A Lot_ID: 1 Source: Bethyl Labs Target Name: DCP1A-human

Experiment Status

	BGKcLV28-61	BGKcLV28-61	BGKcLV28-62	BGKcLV28-62
Sample_ID	BGKcLV28-61	BGKcLV28-61	BGKcLV28-62	BGKcLV28-62
Sample Name
Sample Name	DCP1A-BGKcLV28-61		DCP1A-BGKcLV28-62
RBP	DCP1A	DCP1A	DCP1A	DCP1A
Cell_Line	K562	K562	K562	K562
Exp UID
Status	Released	NotSatisfied	Released	NotSatisfied
Status_date	2022-01-29	2021-09-16	2022-01-29	2021-09-16
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4
Note
ID	9939	9969	9940	9970

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-61	BGKcLV28-62
Sample #	47	48
Sample Name	DCP1A-BGKcLV28-61	DCP1A-BGKcLV28-62
Sample_Name_Alias
Index Well Position	G10	H10
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-09-21	2021-09-21
Lib_ID	Lib-210921	Lib-210921
Tecan_Location
Tecan
Tecan_date
Size_bp	319	329
Peak_Molarity	89.50	95.10
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/G6.png	DNA_Library_set48-49/set3/H6.png
RIN	9.8	9.8
libSample_RNA_Well	RNA_Library_set48-49/set2/G6.png	RNA_Library_set48-49/set2/H6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-61	BGKcLV28-62
RBP	DCP1A	DCP1A
Batch_ID	BGKcLV28	BGKcLV28
WB_result	68.700	70.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2108	2109

Sequencing Information

	BGKcLV28-61	BGKcLV28-62
Sample_ID	BGKcLV28-61	BGKcLV28-62
Sample Name	DCP1A-BGKcLV28-61	DCP1A-BGKcLV28-62
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	132,051,394	136,981,802
total_aligned_reads	128,987,818	128,606,514
unique_aligned_reads	118,997,102	118,276,492
percent_uniqueAligned	0.90114	0.86345
correlation_replicates	0.991354	0.991354
spikein_reads	20,944	23,698
percent_spikeins	0.00016	0.00017
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1859	1860

Data Submission Information

	BGKcLV28-61	BGKcLV28-61	BGKcLV28-61	BGKcLV28-61	BGKcLV28-61	BGKcLV28-61	BGKcLV28-62	BGKcLV28-62	BGKcLV28-62	BGKcLV28-62
ENCODE_alias	brenton-graveley:DCP1A-BGKcLV28	brenton-graveley:DCP1A-BGKcLV28-61	brenton-graveley:L-DCP1A-BGKcLV28-61	brenton-graveley:DCP1A-BGKcLV28-61_S129_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCP1A-BGKcLV28-61_S129_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCP1A-BGKcLV28-K562	brenton-graveley:DCP1A-BGKcLV28-62	brenton-graveley:L-DCP1A-BGKcLV28-62	brenton-graveley:DCP1A-BGKcLV28-62_S130_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCP1A-BGKcLV28-62_S130_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR911ITT	ENCBS002VIT	ENCLB346SFO	ENCFF877GEJ	ENCFF709RTJ	ENCSR582NNR	ENCBS844MEQ	ENCLB273GZE	ENCFF442VAD	ENCFF630HBY
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	BGKcLV28-61	BGKcLV28-61	BGKcLV28-61	BGKcLV28-61	BGKcLV28-61	BGKcLV28-61	BGKcLV28-62	BGKcLV28-62	BGKcLV28-62	BGKcLV28-62
Sample Name	DCP1A-BGKcLV28-61	DCP1A-BGKcLV28-61	DCP1A-BGKcLV28-61	DCP1A-BGKcLV28-61	DCP1A-BGKcLV28-61	DCP1A-BGKcLV28-61	DCP1A-BGKcLV28-62	DCP1A-BGKcLV28-62	DCP1A-BGKcLV28-62	DCP1A-BGKcLV28-62
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-01-29	2022-03-02	2022-01-29	2022-01-29	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV49_biosample_protocol	LV49_library_protocol				LV49_biosample_protocol	LV49_library_protocol
protocol_URL		DCP1A-BGKcLV28-61.pdf	L-DCP1A-BGKcLV28-61.pdf				DCP1A-BGKcLV28-62.pdf	L-DCP1A-BGKcLV28-62.pdf
ID	3494	3622	3756	3890	4024	7169	3623	3757	3891	4025

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
DCP1A-BGKcLV28-61_S129_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1859	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3976
DCP1A-BGKcLV28-61_S129_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1859	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4034
DCP1A-BGKcLV28-61_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1859					GRCh38	V40	DCP1A-BGKcLV28-61_S129_L004_R1_001.filtered.trimmed.paired.fastq.gz,DCP1A-BGKcLV28-61_S129_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19258
DCP1A-BGKcLV28-61_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1859					GRCh38	V40	DCP1A-BGKcLV28-61/Aligned.sortedByCoord.out.bam		ENCORE2	19316
DCP1A-BGKcLV28-61_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1859					GRCh38	V40	DCP1A-BGKcLV28-61/Aligned.sortedByCoord.out.bam		ENCORE2	19374
DCP1A-BGKcLV28-61_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1859					GRCh38	V40	DCP1A-BGKcLV28-61/Aligned.sortedByCoord.out.bam		ENCORE2	19432
DCP1A-BGKcLV28-61_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1859					GRCh38	V40	DCP1A-BGKcLV28-61/Aligned.sortedByCoord.out.bam		ENCORE2	19490
DCP1A-BGKcLV28-61_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1859					GRCh38	V40	DCP1A-BGKcLV28-61_S129_L004_R1_001.filtered.trimmed.paired.fastq.gz,DCP1A-BGKcLV28-61_S129_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19548
DCP1A-BGKcLV28-62_S130_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1860	NovaSeq6000	100	paired-ended	1				NT-BGKcLV28-1_S83_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3977
DCP1A-BGKcLV28-62_S130_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1860	NovaSeq6000	100	paired-ended	2				NT-BGKcLV28-1_S83_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV28-2_S84_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	4035
DCP1A-BGKcLV28-62_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1860					GRCh38	V40	DCP1A-BGKcLV28-62_S130_L004_R1_001.filtered.trimmed.paired.fastq.gz,DCP1A-BGKcLV28-62_S130_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19259
DCP1A-BGKcLV28-62_Signal.Unique.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1860					GRCh38	V40	DCP1A-BGKcLV28-62/Aligned.sortedByCoord.out.bam		ENCORE2	19317
DCP1A-BGKcLV28-62_Signal.Unique.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1860					GRCh38	V40	DCP1A-BGKcLV28-62/Aligned.sortedByCoord.out.bam		ENCORE2	19375
DCP1A-BGKcLV28-62_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1860					GRCh38	V40	DCP1A-BGKcLV28-62/Aligned.sortedByCoord.out.bam		ENCORE2	19433
DCP1A-BGKcLV28-62_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1860					GRCh38	V40	DCP1A-BGKcLV28-62/Aligned.sortedByCoord.out.bam		ENCORE2	19491
DCP1A-BGKcLV28-62_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1860					GRCh38	V40	DCP1A-BGKcLV28-62_S130_L004_R1_001.filtered.trimmed.paired.fastq.gz,DCP1A-BGKcLV28-62_S130_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19549