RNASEH2A RNA-Seq in K562

General Information


RBP	RNASEH2A
Cell_Line	K562
Method	CRISPR
Exp_Name	RNASEH2A-BGKcLV30-K562
ENCODE_series_ID	ENCSR541EAY
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR002JOW
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RNASEH2A-BGKcLV30-37
Rep2	RNASEH2A-BGKcLV30-38
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	77.7
Rep2_qPCR	69.5
Rep1_WB	68.3
Rep2_WB	66.9
Antibody Cat#	A304-149A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB029VMC
Status	Submitted
Project	ENCODE4
ID	875

Experiment Information (Status: Released)

	BGKcLV30-37	BGKcLV30-38
idx	1066	1067
TRCN#_or_BGC#	BGC#0000784	BGC#0000784
shRNA_or_gRNA_sequence	TTGCGTCCTGGGCGTCGATG	TTGCGTCCTGGGCGTCGATG
PAM	AGG	AGG
Name	RNASEH2A_97	RNASEH2A_97
Sample_ID	BGKcLV30-37	BGKcLV30-38
transduction_Date	8/30/21	8/30/21
days	D6	D6
RBP_name	RNASEH2A	RNASEH2A
qPCR_result	77.7	69.5
Ave_qPCR	73.6
RT-qPCR_primer-F	caagacaaaagcgtggttga
RT-qPCR_primer-R	gattctcggatgctgagtcc
protein_conc	2713	2538
WB_result	68.3	66.9
Ave_WB	67.6
WB_DONE_date	9/9/21
MW	33KD
IP
antibody_Cat#	A304-149A	LOT #1
Antibody DCC ID	ENCAB029VMC
submitted_to_DCC_date	8/16/22
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/10/21	11/10/21
repeat_library
Note
ID	5206	5207

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

	BGKcLV30-37	BGKcLV30-38
Sample_ID	BGKcLV30-37	BGKcLV30-38
Sample Name
Sample Name	RNASEH2A-BGKcLV30-37	RNASEH2A-BGKcLV30-38
RBP	RNASEH2A	RNASEH2A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10075	10076

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-37	BGKcLV30-38
Sample #	65	66
Sample Name	RNASEH2A-BGKcLV30-37	RNASEH2A-BGKcLV30-38
Sample_Name_Alias
Index Well Position	E09	F09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101A	Lib-211101A
Tecan_Location
Tecan
Tecan_date
Size_bp	291	289
Peak_Molarity	45.90	34.50
libSampleQC_DNA_Well	DNA_Library_set50/set2/E11.png	DNA_Library_set50/set2/F11.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set50/set2/E11.png	RNA_Library_set50/set2/F11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-37	BGKcLV30-38
RBP	RNASEH2A	RNASEH2A
Batch_ID	BGKcLV30	BGKcLV30
WB_result	68.300	66.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3152	3153

Sequencing Information

	BGKcLV30-37	BGKcLV30-38
Sample_ID	BGKcLV30-37	BGKcLV30-38
Sample Name	RNASEH2A-BGKcLV30-37	RNASEH2A-BGKcLV30-38
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	83,057,396	94,593,444
total_aligned_reads	74,260,126	90,003,240
unique_aligned_reads	67,874,248	82,263,318
percent_uniqueAligned	0.81720	0.86965
correlation_replicates	0.991539	0.991539
spikein_reads	10,266	14,420
percent_spikeins	0.00012	0.00015
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1937	1938

Data Submission Information

	BGKcLV30-37	BGKcLV30-37	BGKcLV30-37	BGKcLV30-37	BGKcLV30-37	BGKcLV30-37	BGKcLV30-38	BGKcLV30-38	BGKcLV30-38	BGKcLV30-38
ENCODE_alias	brenton-graveley:RNASEH2A-BGKcLV30	brenton-graveley:RNASEH2A-BGKcLV30-37	brenton-graveley:L-RNASEH2A-BGKcLV30-37	brenton-graveley:RNASEH2A-BGKcLV30-37_S67_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNASEH2A-BGKcLV30-37_S67_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNASEH2A-BGKcLV30-K562	brenton-graveley:RNASEH2A-BGKcLV30-38	brenton-graveley:L-RNASEH2A-BGKcLV30-38	brenton-graveley:RNASEH2A-BGKcLV30-38_S68_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNASEH2A-BGKcLV30-38_S68_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR002JOW	ENCBS759ZZR	ENCLB587UUT	ENCFF489WGO	ENCFF522FSF	ENCSR541EAY	ENCBS963CVP	ENCLB560ACR	ENCFF144DYI	ENCFF649YAR
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	BGKcLV30-37	BGKcLV30-37	BGKcLV30-37	BGKcLV30-37	BGKcLV30-37	BGKcLV30-37	BGKcLV30-38	BGKcLV30-38	BGKcLV30-38	BGKcLV30-38
Sample Name	RNASEH2A-BGKcLV30-37	RNASEH2A-BGKcLV30-37	RNASEH2A-BGKcLV30-37	RNASEH2A-BGKcLV30-37	RNASEH2A-BGKcLV30-37	RNASEH2A-BGKcLV30-37	RNASEH2A-BGKcLV30-38	RNASEH2A-BGKcLV30-38	RNASEH2A-BGKcLV30-38	RNASEH2A-BGKcLV30-38
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
		LV50K_biosample_protocol	LV50K_library_protocol				LV50K_biosample_protocol	LV50K_library_protocol
protocol_URL		RNASEH2A-BGKcLV30-37.pdf	L-RNASEH2A-BGKcLV30-37.pdf				RNASEH2A-BGKcLV30-38.pdf	L-RNASEH2A-BGKcLV30-38.pdf
ID	5874	5941	6013	6085	6157	6196	5942	6014	6086	6158

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-BGKcLV30-37_S67_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1937	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5865
RNASEH2A-BGKcLV30-37_S67_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1937	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5895
RNASEH2A-BGKcLV30-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1937					GRCh38	V40	RNASEH2A-BGKcLV30-37_S67_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNASEH2A-BGKcLV30-37_S67_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18766
RNASEH2A-BGKcLV30-37_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1937					GRCh38	V40	RNASEH2A-BGKcLV30-37/Aligned.sortedByCoord.out.bam		ENCORE2	18796
RNASEH2A-BGKcLV30-37_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1937					GRCh38	V40	RNASEH2A-BGKcLV30-37/Aligned.sortedByCoord.out.bam		ENCORE2	18826
RNASEH2A-BGKcLV30-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1937					GRCh38	V40	RNASEH2A-BGKcLV30-37/Aligned.sortedByCoord.out.bam		ENCORE2	18856
RNASEH2A-BGKcLV30-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1937					GRCh38	V40	RNASEH2A-BGKcLV30-37/Aligned.sortedByCoord.out.bam		ENCORE2	18886
RNASEH2A-BGKcLV30-37_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1937					GRCh38	V40	RNASEH2A-BGKcLV30-37_S67_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNASEH2A-BGKcLV30-37_S67_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18916
RNASEH2A-BGKcLV30-38_S68_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1938	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5866
RNASEH2A-BGKcLV30-38_S68_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1938	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5896
RNASEH2A-BGKcLV30-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1938					GRCh38	V40	RNASEH2A-BGKcLV30-38_S68_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNASEH2A-BGKcLV30-38_S68_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18767
RNASEH2A-BGKcLV30-38_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1938					GRCh38	V40	RNASEH2A-BGKcLV30-38/Aligned.sortedByCoord.out.bam		ENCORE2	18797
RNASEH2A-BGKcLV30-38_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1938					GRCh38	V40	RNASEH2A-BGKcLV30-38/Aligned.sortedByCoord.out.bam		ENCORE2	18827
RNASEH2A-BGKcLV30-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1938					GRCh38	V40	RNASEH2A-BGKcLV30-38/Aligned.sortedByCoord.out.bam		ENCORE2	18857
RNASEH2A-BGKcLV30-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1938					GRCh38	V40	RNASEH2A-BGKcLV30-38/Aligned.sortedByCoord.out.bam		ENCORE2	18887
RNASEH2A-BGKcLV30-38_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1938					GRCh38	V40	RNASEH2A-BGKcLV30-38_S68_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNASEH2A-BGKcLV30-38_S68_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18917