DBNL RNA-Seq in K562

General Information


RBP	DBNL
Cell_Line	K562
Method	CRISPR
Exp_Name	DBNL-BGKcLV28-K562
ENCODE_series_ID	ENCSR523OQC
Batch_ID	BGKcLV28
Pool ID	Pool-210929
Local_Set_Name	set49
ENCODE_KD_Exp_ID	ENCSR593NFA
ENCODE_CN_Exp_ID	ENCSR220DTX
Rep1	DBNL-BGKcLV28-59
Rep2	DBNL-BGKcLV28-60
CN1	NT-BGKcLV28-1
CN2	NT-BGKcLV28-2
Rep1_qPCR	80.0
Rep2_qPCR	71.5
Rep1_WB	57.4
Rep2_WB	57.6
Antibody Cat#	A303-351A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB188XWI
Status	Released
Project	ENCODE4
ID	839

Experiment Information (Status: Released)

	BGKcLV28-59	BGKcLV28-59	BGKcLV28-60	BGKcLV28-60
idx	1005	1007	1006	1008
TRCN#_or_BGC#	BGC#0000735	BGC#0000735	BGC#0000735	BGC#0000735
shRNA_or_gRNA_sequence	TTTAATCTCAGACACGGCAT	TTTAATCTCAGACACGGCAT	TTTAATCTCAGACACGGCAT	TTTAATCTCAGACACGGCAT
PAM	TGG	TGG	TGG	TGG
Name	DBNL_91	DBNL_91	DBNL_91	DBNL_91
Sample_ID	BGKcLV28-59	BGKcLV28-59	BGKcLV28-60	BGKcLV28-60
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	DBNL	DBNL	DBNL	DBNL
qPCR_result	80.0	80.0	71.5	71.5
Ave_qPCR	75.8	75.8
RT-qPCR_primer-F	acctccagagcaggagacct	acctccagagcaggagacct
RT-qPCR_primer-R	gaatgtggtggtcaatgtgc	gaatgtggtggtcaatgtgc
protein_conc	2640	2640	2564	2564
WB_result	57.4	74.8	57.6	72.9045829
Ave_WB	57.5	73.9
WB_DONE_date	7/9/21	2/22/22	JESS
MW	48KD	48KD
IP
antibody_Cat#	A303-351A	A303-352A	LOT #1	LOT #1
Antibody DCC ID	ENCAB188XWI
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	5139	5141	5140	5142

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DBNL	Product_ID: A303-351A Lot_ID: 1 Source: Bethyl Labs Target Name: DBNL-human

Experiment Status

	BGKcLV28-59	BGKcLV28-60
Sample_ID	BGKcLV28-59	BGKcLV28-60
Sample Name
Sample Name	DBNL-BGKcLV28-59	DBNL-BGKcLV28-60
RBP	DBNL	DBNL
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-01-29	2022-01-29
Project	ENCODE4	ENCODE4
Note
ID	9937	9938

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV28-59	BGKcLV28-60
Sample #	45	46
Sample Name	DBNL-BGKcLV28-59	DBNL-BGKcLV28-60
Sample_Name_Alias
Index Well Position	E10	F10
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	327	328
Peak_Molarity	99.00	104.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set3/E6.png	DNA_Library_set48-49/set3/F6.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set48-49/set2/E6.png	RNA_Library_set48-49/set2/F6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-27	2021-09-27
Sample_ID	BGKcLV28-59	BGKcLV28-60
RBP	DBNL	DBNL
Batch_ID	BGKcLV28	BGKcLV28
WB_result	57.400	57.600
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	2106	2107

Sequencing Information

	BGKcLV28-59	BGKcLV28-60
Sample_ID	BGKcLV28-59	BGKcLV28-60
Sample Name	DBNL-BGKcLV28-59	DBNL-BGKcLV28-60
Pool ID	Pool-210929	Pool-210929
LocalServer_folder	set49	set49
total_reads	112,528,608	137,753,814
total_aligned_reads	109,707,082	134,722,692
unique_aligned_reads	101,197,278	124,449,376
percent_uniqueAligned	0.89930	0.90342
correlation_replicates	0.996706	0.996706
spikein_reads	21,756	20,778
percent_spikeins	0.00019	0.00015
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1857	1858

Data Submission Information

	BGKcLV28-59	BGKcLV28-59	BGKcLV28-59	BGKcLV28-59	BGKcLV28-59	BGKcLV28-59	BGKcLV28-60	BGKcLV28-60	BGKcLV28-60	BGKcLV28-60
ENCODE_alias	brenton-graveley:DBNL-BGKcLV28	brenton-graveley:DBNL-BGKcLV28-59	brenton-graveley:L-DBNL-BGKcLV28-59	brenton-graveley:DBNL-BGKcLV28-59_S127_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DBNL-BGKcLV28-59_S127_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DBNL-BGKcLV28-K562	brenton-graveley:DBNL-BGKcLV28-60	brenton-graveley:L-DBNL-BGKcLV28-60	brenton-graveley:DBNL-BGKcLV28-60_S128_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DBNL-BGKcLV28-60_S128_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR593NFA	ENCBS859OJC	ENCLB250EKU	ENCFF734GFW	ENCFF498GFG	ENCSR523OQC	ENCBS969WVP	ENCLB726REY	ENCFF057DUJ	ENCFF389MZM
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	BGKcLV28-59	BGKcLV28-59	BGKcLV28-59	BGKcLV28-59	BGKcLV28-59	BGKcLV28-59	BGKcLV28-60	BGKcLV28-60	BGKcLV28-60	BGKcLV28-60
Sample Name	DBNL-BGKcLV28-59	DBNL-BGKcLV28-59	DBNL-BGKcLV28-59	DBNL-BGKcLV28-59	DBNL-BGKcLV28-59	DBNL-BGKcLV28-59	DBNL-BGKcLV28-60	DBNL-BGKcLV28-60	DBNL-BGKcLV28-60	DBNL-BGKcLV28-60
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		DBNL-BGKcLV28-59.pdf	L-DBNL-BGKcLV28-59.pdf				DBNL-BGKcLV28-60.pdf	L-DBNL-BGKcLV28-60.pdf
ID	3493	3620	3754	3888	4022	7168	3621	3755	3889	4023

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
DBNL-BGKcLV28-59_S127_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1857	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	3974
DBNL-BGKcLV28-59_S127_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1857	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	4032
DBNL-BGKcLV28-59_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1857					GRCh38	V40	DBNL-BGKcLV28-59_S127_L004_R1_001.filtered.trimmed.paired.fastq.gz,DBNL-BGKcLV28-59_S127_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19256
DBNL-BGKcLV28-59_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	1857					GRCh38	V40	DBNL-BGKcLV28-59/Aligned.sortedByCoord.out.bam		ENCORE2	19314
DBNL-BGKcLV28-59_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	1857					GRCh38	V40	DBNL-BGKcLV28-59/Aligned.sortedByCoord.out.bam		ENCORE2	19372
DBNL-BGKcLV28-59_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	1857					GRCh38	V40	DBNL-BGKcLV28-59/Aligned.sortedByCoord.out.bam		ENCORE2	19430
DBNL-BGKcLV28-59_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	1857					GRCh38	V40	DBNL-BGKcLV28-59/Aligned.sortedByCoord.out.bam		ENCORE2	19488
DBNL-BGKcLV28-59_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1857					GRCh38	V40	DBNL-BGKcLV28-59_S127_L004_R1_001.filtered.trimmed.paired.fastq.gz,DBNL-BGKcLV28-59_S127_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19546
DBNL-BGKcLV28-60_S128_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1858	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	3975
DBNL-BGKcLV28-60_S128_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set49/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1858	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	4033
DBNL-BGKcLV28-60_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set49/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1858					GRCh38	V40	DBNL-BGKcLV28-60_S128_L004_R1_001.filtered.trimmed.paired.fastq.gz,DBNL-BGKcLV28-60_S128_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19257
DBNL-BGKcLV28-60_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	1858					GRCh38	V40	DBNL-BGKcLV28-60/Aligned.sortedByCoord.out.bam		ENCORE2	19315
DBNL-BGKcLV28-60_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	1858					GRCh38	V40	DBNL-BGKcLV28-60/Aligned.sortedByCoord.out.bam		ENCORE2	19373
DBNL-BGKcLV28-60_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	1858					GRCh38	V40	DBNL-BGKcLV28-60/Aligned.sortedByCoord.out.bam		ENCORE2	19431
DBNL-BGKcLV28-60_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	1858					GRCh38	V40	DBNL-BGKcLV28-60/Aligned.sortedByCoord.out.bam		ENCORE2	19489
DBNL-BGKcLV28-60_quant.sf	ENCODE_DATA/set49/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1858					GRCh38	V40	DBNL-BGKcLV28-60_S128_L004_R1_001.filtered.trimmed.paired.fastq.gz,DBNL-BGKcLV28-60_S128_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19547