DCPS RNA-Seq in K562

General Information


RBP	DCPS
Cell_Line	K562
Method	CRISPR
Exp_Name	DCPS-BGKcLV28-K562
ENCODE_series_ID	ENCSR123TYO
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR166VYI
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	DCPS-BGKcLV28-63
Rep2	DCPS-BGKcLV28-64
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	63.5
Rep2_qPCR	65.0
Rep1_WB	71.9
Rep2_WB	66.8
Antibody Cat#	A305-426A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB507CYA
Status	Released
Project	ENCODE4
ID	841

Experiment Information (Status: Released)

	BGKcLV28-63	BGKcLV28-64
idx	1013	1014
TRCN#_or_BGC#	BGC#0000739	BGC#0000739
shRNA_or_gRNA_sequence	CTCCCGTCTCTCGGATCAGG	CTCCCGTCTCTCGGATCAGG
PAM	CGG	CGG
Name	DCPS_92	DCPS_92
Sample_ID	BGKcLV28-63	BGKcLV28-64
transduction_Date	7/12/21	7/12/21
days	Day 6	Day 6
RBP_name	DCPS	DCPS
qPCR_result	63.5	65.0
Ave_qPCR	64.3
RT-qPCR_primer-F	cagatccctacgcgacctta
RT-qPCR_primer-R	agtgcacatgcaggtggtag
protein_conc	2723	2151
WB_result	71.9	66.8
Ave_WB	69.3
WB_DONE_date	8/26/21
MW	39KD
IP
antibody_Cat#	A305-426A	LOT #1
Antibody DCC ID	ENCAB507CYA
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	09/23/21	09/23/21
repeat_library
Note
ID	5147	5148

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DCPS	Product_ID: A305-426A Lot_ID: 1 Source: Bethyl Labs Target Name: DCPS-human

Experiment Status

	BGKcLV28-63	BGKcLV28-64
Sample_ID	BGKcLV28-63	BGKcLV28-64
Sample Name
Sample Name	DCPS-BGKcLV28-63	DCPS-BGKcLV28-64
RBP	DCPS	DCPS
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9941	9942

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-63	BGKcLV28-64
Sample #	49	50
Sample Name	DCPS-BGKcLV28-63	DCPS-BGKcLV28-64
Sample_Name_Alias
Index Well Position	A11	B11
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	313	324
Peak_Molarity	93.20	133.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/A7.png	DNA_Library_set48-49/set3/B7.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_set48-49/set2/A7.png	RNA_Library_set48-49/set2/B7.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-63	BGKcLV28-64
RBP	DCPS	DCPS
Batch_ID	BGKcLV28	BGKcLV28
WB_result	71.900	66.800
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2110	2111

Sequencing Information

	BGKcLV28-63	BGKcLV28-64
Sample_ID	BGKcLV28-63	BGKcLV28-64
Sample Name	DCPS-BGKcLV28-63	DCPS-BGKcLV28-64
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	157,030,618	127,205,984
total_aligned_reads	150,576,560	119,842,268
unique_aligned_reads	138,672,962	110,745,692
percent_uniqueAligned	0.88310	0.87060
correlation_replicates	0.998214	0.998214
spikein_reads	68,538	41,624
percent_spikeins	0.00044	0.00033
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1861	1862

Data Submission Information

	BGKcLV28-63	BGKcLV28-63	BGKcLV28-63	BGKcLV28-63	BGKcLV28-63	BGKcLV28-63	BGKcLV28-64	BGKcLV28-64	BGKcLV28-64	BGKcLV28-64
ENCODE_alias	brenton-graveley:DCPS-BGKcLV28	brenton-graveley:DCPS-BGKcLV28-63	brenton-graveley:L-DCPS-BGKcLV28-63	brenton-graveley:DCPS-BGKcLV28-63_S131_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCPS-BGKcLV28-63_S131_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCPS-BGKcLV28-K562	brenton-graveley:DCPS-BGKcLV28-64	brenton-graveley:L-DCPS-BGKcLV28-64	brenton-graveley:DCPS-BGKcLV28-64_S132_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCPS-BGKcLV28-64_S132_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR166VYI	ENCBS277ZLX	ENCLB713SIV	ENCFF465DNU	ENCFF195AKR	ENCSR123TYO	ENCBS771KWJ	ENCLB984FET	ENCFF038KRF	ENCFF985BVB
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	BGKcLV28-63	BGKcLV28-63	BGKcLV28-63	BGKcLV28-63	BGKcLV28-63	BGKcLV28-63	BGKcLV28-64	BGKcLV28-64	BGKcLV28-64	BGKcLV28-64
Sample Name	DCPS-BGKcLV28-63	DCPS-BGKcLV28-63	DCPS-BGKcLV28-63	DCPS-BGKcLV28-63	DCPS-BGKcLV28-63	DCPS-BGKcLV28-63	DCPS-BGKcLV28-64	DCPS-BGKcLV28-64	DCPS-BGKcLV28-64	DCPS-BGKcLV28-64
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		DCPS-BGKcLV28-63.pdf	L-DCPS-BGKcLV28-63.pdf				DCPS-BGKcLV28-64.pdf	L-DCPS-BGKcLV28-64.pdf
ID	3495	3624	3758	3892	4026	7171	3625	3759	3893	4027

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
DCPS-BGKcLV28-63_S131_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1861	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	3978
DCPS-BGKcLV28-63_S131_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1861	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	4036
DCPS-BGKcLV28-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1861					GRCh38	V40	DCPS-BGKcLV28-63_S131_L004_R1_001.filtered.trimmed.paired.fastq.gz,DCPS-BGKcLV28-63_S131_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19260
DCPS-BGKcLV28-63_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	1861					GRCh38	V40	DCPS-BGKcLV28-63/Aligned.sortedByCoord.out.bam		ENCORE2	19318
DCPS-BGKcLV28-63_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	1861					GRCh38	V40	DCPS-BGKcLV28-63/Aligned.sortedByCoord.out.bam		ENCORE2	19376
DCPS-BGKcLV28-63_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	1861					GRCh38	V40	DCPS-BGKcLV28-63/Aligned.sortedByCoord.out.bam		ENCORE2	19434
DCPS-BGKcLV28-63_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	1861					GRCh38	V40	DCPS-BGKcLV28-63/Aligned.sortedByCoord.out.bam		ENCORE2	19492
DCPS-BGKcLV28-63_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1861					GRCh38	V40	DCPS-BGKcLV28-63_S131_L004_R1_001.filtered.trimmed.paired.fastq.gz,DCPS-BGKcLV28-63_S131_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19550
DCPS-BGKcLV28-64_S132_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1862	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	3979
DCPS-BGKcLV28-64_S132_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1862	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	4037
DCPS-BGKcLV28-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1862					GRCh38	V40	DCPS-BGKcLV28-64_S132_L004_R1_001.filtered.trimmed.paired.fastq.gz,DCPS-BGKcLV28-64_S132_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19261
DCPS-BGKcLV28-64_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	1862					GRCh38	V40	DCPS-BGKcLV28-64/Aligned.sortedByCoord.out.bam		ENCORE2	19319
DCPS-BGKcLV28-64_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	1862					GRCh38	V40	DCPS-BGKcLV28-64/Aligned.sortedByCoord.out.bam		ENCORE2	19377
DCPS-BGKcLV28-64_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	1862					GRCh38	V40	DCPS-BGKcLV28-64/Aligned.sortedByCoord.out.bam		ENCORE2	19435
DCPS-BGKcLV28-64_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	1862					GRCh38	V40	DCPS-BGKcLV28-64/Aligned.sortedByCoord.out.bam		ENCORE2	19493
DCPS-BGKcLV28-64_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1862					GRCh38	V40	DCPS-BGKcLV28-64_S132_L004_R1_001.filtered.trimmed.paired.fastq.gz,DCPS-BGKcLV28-64_S132_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19551