RNASEH2A RNA-Seq in HepG2

General Information


RBP	RNASEH2A
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RNASEH2A-BGHcLV32-HepG2
ENCODE_series_ID	ENCSR816VZJ
Batch_ID	BGHcLV32
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR703FPC
ENCODE_CN_Exp_ID	ENCSR232ERY
Rep1	RNASEH2A-BGHcLV32-35
Rep2	RNASEH2A-BGHcLV32-36
CN1	NT-BGHcLV32-1
CN2	NT-BGHcLV32-2
Rep1_qPCR	63.9
Rep2_qPCR	41.3
Rep1_WB	93.8
Rep2_WB	94.7
Antibody Cat#	A304-149A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB029VMC
Status	Submitted
Project	ENCODE4
ID	934

Experiment Information (Status: Released)

	BGHcLV32-35	BGHcLV32-36
idx	1034	1035
TRCN#_or_BGC#	BGC#0000784	BGC#0000784
shRNA_or_gRNA_sequence	TTGCGTCCTGGGCGTCGATG	TTGCGTCCTGGGCGTCGATG
PAM	AGG	AGG
Name	RNASEH2A_97	RNASEH2A_97
Sample_ID	BGHcLV32-35	BGHcLV32-36
transduction_Date	10/28/21	10/28/21
days	D6	D6
RBP_name	RNASEH2A	RNASEH2A
qPCR_result	63.9	41.3
Ave_qPCR	52.6
RT-qPCR_primer-F	caagacaaaagcgtggttga
RT-qPCR_primer-R	gattctcggatgctgagtcc
protein_conc	5337	3910
WB_result	93.8	94.7
Ave_WB	94.2
WB_DONE_date	12/15/21
MW	33KD
IP
antibody_Cat#	A304-149A	LOT #1
Antibody DCC ID	ENCAB029VMC	8/4/22
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	2/9/22	2/9/22
repeat_library
Note
ID	9261	9262

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RNASEH2A	Product_ID: A304-149A Lot_ID: 1 Source: Bethyl Labs Target Name: RNASEH2A-human

Experiment Status

	BGHcLV32-35	BGHcLV32-36
Sample_ID	BGHcLV32-35	BGHcLV32-36
Sample Name
Sample Name	RNASEH2A-BGHcLV32-35	RNASEH2A-BGHcLV32-36
RBP	RNASEH2A	RNASEH2A
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10367	10368

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV32-35	BGHcLV32-36
Sample #	41	42
Sample Name	RNASEH2A-BGHcLV32-35	RNASEH2A-BGHcLV32-36
Sample_Name_Alias
Index Well Position	A06	B06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2022-02-01	2022-02-01
Lib_ID	Lib-220201	Lib-220201
Tecan_Location
Tecan
Tecan_date
Size_bp	352	299
Peak_Molarity	78.90	60.10
libSampleQC_DNA_Well	DNA_Library_set52/set2/A6.png	DNA_Library_set52/set2/B6.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set52/set2/E8.png	RNA_Library_set52/set2/F8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-02-16	2022-02-16
Sample_ID	BGHcLV32-35	BGHcLV32-36
RBP	RNASEH2A	RNASEH2A
Batch_ID	BGHcLV32	BGHcLV32
WB_result	93.800	94.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3218	3219

Sequencing Information

	BGHcLV32-35	BGHcLV32-36
Sample_ID	BGHcLV32-35	BGHcLV32-36
Sample Name	RNASEH2A-BGHcLV32-35	RNASEH2A-BGHcLV32-36
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	101,741,600	84,933,870
total_aligned_reads	90,677,430	69,070,614
unique_aligned_reads	85,467,448	64,961,282
percent_uniqueAligned	0.84004	0.76485
correlation_replicates	0.996202	0.996202
spikein_reads	17,416	11,890
percent_spikeins	0.00017	0.00014
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2013	2014

Data Submission Information

	BGHcLV32-35	BGHcLV32-35	BGHcLV32-35	BGHcLV32-35	BGHcLV32-35	BGHcLV32-35	BGHcLV32-36	BGHcLV32-36	BGHcLV32-36	BGHcLV32-36
ENCODE_alias	brenton-graveley:RNASEH2A-BGHcLV32	brenton-graveley:RNASEH2A-BGHcLV32-35	brenton-graveley:L-RNASEH2A-BGHcLV32-35	brenton-graveley:RNASEH2A-BGHcLV32-35_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNASEH2A-BGHcLV32-35_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNASEH2A-BGHcLV32-HepG2	brenton-graveley:RNASEH2A-BGHcLV32-36	brenton-graveley:L-RNASEH2A-BGHcLV32-36	brenton-graveley:RNASEH2A-BGHcLV32-36_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNASEH2A-BGHcLV32-36_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR703FPC	ENCBS559VPJ	ENCLB413MRS	ENCFF937QIR	ENCFF782CTV	ENCSR816VZJ	ENCBS083RVQ	ENCLB648GDT	ENCFF951NUA	ENCFF832LNF
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	BGHcLV32-35	BGHcLV32-35	BGHcLV32-35	BGHcLV32-35	BGHcLV32-35	BGHcLV32-35	BGHcLV32-36	BGHcLV32-36	BGHcLV32-36	BGHcLV32-36
Sample Name	RNASEH2A-BGHcLV32-35	RNASEH2A-BGHcLV32-35	RNASEH2A-BGHcLV32-35	RNASEH2A-BGHcLV32-35	RNASEH2A-BGHcLV32-35	RNASEH2A-BGHcLV32-35	RNASEH2A-BGHcLV32-36	RNASEH2A-BGHcLV32-36	RNASEH2A-BGHcLV32-36	RNASEH2A-BGHcLV32-36
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		RNASEH2A-BGHcLV32-35.pdf	L-RNASEH2A-BGHcLV32-35.pdf				RNASEH2A-BGHcLV32-36.pdf	L-RNASEH2A-BGHcLV32-36.pdf
ID	7464	7535	7647	7755	7865	7954	7536	7648	7756	7866

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
RNASEH2A-BGHcLV32-35_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2013	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6513
RNASEH2A-BGHcLV32-35_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2013	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6567
RNASEH2A-BGHcLV32-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2013					GRCh38	V40	RNASEH2A-BGHcLV32-35_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNASEH2A-BGHcLV32-35_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18434
RNASEH2A-BGHcLV32-35_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2013					GRCh38	V40	RNASEH2A-BGHcLV32-35/Aligned.sortedByCoord.out.bam		ENCORE2	18488
RNASEH2A-BGHcLV32-35_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2013					GRCh38	V40	RNASEH2A-BGHcLV32-35/Aligned.sortedByCoord.out.bam		ENCORE2	18542
RNASEH2A-BGHcLV32-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2013					GRCh38	V40	RNASEH2A-BGHcLV32-35/Aligned.sortedByCoord.out.bam		ENCORE2	18596
RNASEH2A-BGHcLV32-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2013					GRCh38	V40	RNASEH2A-BGHcLV32-35/Aligned.sortedByCoord.out.bam		ENCORE2	18650
RNASEH2A-BGHcLV32-35_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2013					GRCh38	V40	RNASEH2A-BGHcLV32-35_S39_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNASEH2A-BGHcLV32-35_S39_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18704
RNASEH2A-BGHcLV32-36_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2014	NovaSeq6000	100	paired-ended	1				NT-BGHcLV32-1_S33_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6514
RNASEH2A-BGHcLV32-36_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2014	NovaSeq6000	100	paired-ended	2				NT-BGHcLV32-1_S33_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV32-2_S34_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6568
RNASEH2A-BGHcLV32-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2014					GRCh38	V40	RNASEH2A-BGHcLV32-36_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNASEH2A-BGHcLV32-36_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18435
RNASEH2A-BGHcLV32-36_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2014					GRCh38	V40	RNASEH2A-BGHcLV32-36/Aligned.sortedByCoord.out.bam		ENCORE2	18489
RNASEH2A-BGHcLV32-36_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	2014					GRCh38	V40	RNASEH2A-BGHcLV32-36/Aligned.sortedByCoord.out.bam		ENCORE2	18543
RNASEH2A-BGHcLV32-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2014					GRCh38	V40	RNASEH2A-BGHcLV32-36/Aligned.sortedByCoord.out.bam		ENCORE2	18597
RNASEH2A-BGHcLV32-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	2014					GRCh38	V40	RNASEH2A-BGHcLV32-36/Aligned.sortedByCoord.out.bam		ENCORE2	18651
RNASEH2A-BGHcLV32-36_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2014					GRCh38	V40	RNASEH2A-BGHcLV32-36_S40_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNASEH2A-BGHcLV32-36_S40_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18705