DCPS RNA-Seq in HepG2

General Information


RBP	DCPS
Cell_Line	HepG2
Method	CRISPR
Exp_Name	DCPS-BGHcLV29-HepG2
ENCODE_series_ID	ENCSR158AHF
Batch_ID	BGHcLV29
Pool ID	Pool-211117
Local_Set_Name	set50_H
ENCODE_KD_Exp_ID	ENCSR524NOZ
ENCODE_CN_Exp_ID	ENCSR462MFN
Rep1	DCPS-BGHcLV29-63
Rep2	DCPS-BGHcLV29-64
CN1	NT-BGHcLV29-1
CN2	NT-BGHcLV29-2
Rep1_qPCR	38.7
Rep2_qPCR	33
Rep1_WB	70.8
Rep2_WB	71.4
Antibody Cat#	A305-444A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB554JMA
Status	Submitted
Project	ENCODE4
ID	863

Experiment Information (Status: Released)

	BGHcLV29-63	BGHcLV29-64
idx	904	905
TRCN#_or_BGC#	BGC#0000739	BGC#0000739
shRNA_or_gRNA_sequence	CTCCCGTCTCTCGGATCAGG	CTCCCGTCTCTCGGATCAGG
PAM	CGG	CGG
Name	DCPS_92	DCPS_92
Sample_ID	BGHcLV29-63	BGHcLV29-64
transduction_Date	7/20	7/20
days	D6	D6
RBP_name	DCPS	DCPS
qPCR_result	38.7	33
Ave_qPCR	35.85
RT-qPCR_primer-F	cagatccctacgcgacctta
RT-qPCR_primer-R	agtgcacatgcaggtggtag
protein_conc	4877	4249
WB_result	70.8	71.4
Ave_WB	71.1
WB_DONE_date	8/26/21
MW	39KD
IP	Rabbit / I
antibody_Cat#	A305-444A	LOT #1
Antibody DCC ID	ENCAB554JMA
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/5/21	11/5/21
repeat_library
Note
ID	7083	7084

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
DCPS	Product_ID: A305-444A Lot_ID: 1 Source: Bethyl Labs Target Name: DCPS-human

Experiment Status

	BGHcLV29-63	BGHcLV29-64
Sample_ID	BGHcLV29-63	BGHcLV29-64
Sample Name
Sample Name	DCPS-BGHcLV29-63	DCPS-BGHcLV29-64
RBP	DCPS	DCPS
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10011	10012

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV29-63	BGHcLV29-64
Sample #	39	40
Sample Name	DCPS-BGHcLV29-63	DCPS-BGHcLV29-64
Sample_Name_Alias
Index Well Position	G05	H05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101	Lib-211101
Tecan_Location
Tecan
Tecan_date
Size_bp	294	294
Peak_Molarity	38.20	36.50
libSampleQC_DNA_Well	DNA_Library_set50/set1/G5.png	DNA_Library_set50/set1/H5.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_set50/set1/G11.png	RNA_Library_set50/set1/H11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGHcLV29-63	BGHcLV29-64
RBP	DCPS	DCPS
Batch_ID	BGHcLV29	BGHcLV29
WB_result	70.800	71.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3126	3127

Sequencing Information

	BGHcLV29-63	BGHcLV29-64
Sample_ID	BGHcLV29-63	BGHcLV29-64
Sample Name	DCPS-BGHcLV29-63	DCPS-BGHcLV29-64
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_H	set50_H
total_reads	87,948,312	70,021,326
total_aligned_reads	82,574,896	64,987,330
unique_aligned_reads	77,910,256	61,270,298
percent_uniqueAligned	0.88586	0.87502
correlation_replicates	0.994579	0.994579
spikein_reads	12,832	9,910
percent_spikeins	0.00015	0.00014
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1907	1908

Data Submission Information

	BGHcLV29-63	BGHcLV29-63	BGHcLV29-63	BGHcLV29-63	BGHcLV29-63	BGHcLV29-63	BGHcLV29-64	BGHcLV29-64	BGHcLV29-64	BGHcLV29-64
ENCODE_alias	brenton-graveley:DCPS-BGHcLV29	brenton-graveley:DCPS-BGHcLV29-63	brenton-graveley:L-DCPS-BGHcLV29-63	brenton-graveley:DCPS-BGHcLV29-63_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCPS-BGHcLV29-63_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCPS-BGHcLV29-HepG2	brenton-graveley:DCPS-BGHcLV29-64	brenton-graveley:L-DCPS-BGHcLV29-64	brenton-graveley:DCPS-BGHcLV29-64_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:DCPS-BGHcLV29-64_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR524NOZ	ENCBS330HJH	ENCLB202NGF	ENCFF813HXN	ENCFF373NGD	ENCSR158AHF	ENCBS055NUJ	ENCLB468DVU	ENCFF294UQR	ENCFF237MIU
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	BGHcLV29-63	BGHcLV29-63	BGHcLV29-63	BGHcLV29-63	BGHcLV29-63	BGHcLV29-63	BGHcLV29-64	BGHcLV29-64	BGHcLV29-64	BGHcLV29-64
Sample Name	DCPS-BGHcLV29-63	DCPS-BGHcLV29-63	DCPS-BGHcLV29-63	DCPS-BGHcLV29-63	DCPS-BGHcLV29-63	DCPS-BGHcLV29-63	DCPS-BGHcLV29-64	DCPS-BGHcLV29-64	DCPS-BGHcLV29-64	DCPS-BGHcLV29-64
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50H_biosample_protocol	LV50H_library_protocol				LV50H_biosample_protocol	LV50H_library_protocol
protocol_URL		DCPS-BGHcLV29-63.pdf	L-DCPS-BGHcLV29-63.pdf				DCPS-BGHcLV29-64.pdf	L-DCPS-BGHcLV29-64.pdf
ID	5861	5915	5987	6059	6131	6184	5916	5988	6060	6132

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-BGHcLV29-63_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1907	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5795
DCPS-BGHcLV29-63_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1907	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5837
DCPS-BGHcLV29-63_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1907					GRCh38	V40	DCPS-BGHcLV29-63_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCPS-BGHcLV29-63_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18962
DCPS-BGHcLV29-63_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1907					GRCh38	V40	DCPS-BGHcLV29-63/Aligned.sortedByCoord.out.bam		ENCORE2	19020
DCPS-BGHcLV29-63_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1907					GRCh38	V40	DCPS-BGHcLV29-63/Aligned.sortedByCoord.out.bam		ENCORE2	19066
DCPS-BGHcLV29-63_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1907					GRCh38	V40	DCPS-BGHcLV29-63/Aligned.sortedByCoord.out.bam		ENCORE2	19112
DCPS-BGHcLV29-63_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1907					GRCh38	V40	DCPS-BGHcLV29-63/Aligned.sortedByCoord.out.bam		ENCORE2	19158
DCPS-BGHcLV29-63_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1907					GRCh38	V40	DCPS-BGHcLV29-63_S37_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCPS-BGHcLV29-63_S37_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19204
DCPS-BGHcLV29-64_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1908	NovaSeq6000	100	paired-ended	1				NT-BGHcLV29-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5796
DCPS-BGHcLV29-64_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1908	NovaSeq6000	100	paired-ended	2				NT-BGHcLV29-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV29-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5838
DCPS-BGHcLV29-64_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1908					GRCh38	V40	DCPS-BGHcLV29-64_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCPS-BGHcLV29-64_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18963
DCPS-BGHcLV29-64_Signal.Unique.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1908					GRCh38	V40	DCPS-BGHcLV29-64/Aligned.sortedByCoord.out.bam		ENCORE2	19021
DCPS-BGHcLV29-64_Signal.Unique.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1908					GRCh38	V40	DCPS-BGHcLV29-64/Aligned.sortedByCoord.out.bam		ENCORE2	19067
DCPS-BGHcLV29-64_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1908					GRCh38	V40	DCPS-BGHcLV29-64/Aligned.sortedByCoord.out.bam		ENCORE2	19113
DCPS-BGHcLV29-64_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1908					GRCh38	V40	DCPS-BGHcLV29-64/Aligned.sortedByCoord.out.bam		ENCORE2	19159
DCPS-BGHcLV29-64_quant.sf	ENCODE_DATA/set50_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1908					GRCh38	V40	DCPS-BGHcLV29-64_S38_L001_R1_001.filtered.trimmed.paired.fastq.gz,DCPS-BGHcLV29-64_S38_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	19205