RNH1 RNA-Seq in HepG2

General Information


RBP	RNH1
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RNH1-BGHcLV32-HepG2
ENCODE_series_ID	ENCSR966HHU
Batch_ID	BGHcLV32
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR706QGC
ENCODE_CN_Exp_ID	ENCSR232ERY
Rep1	RNH1-BGHcLV32-37
Rep2	RNH1-BGHcLV32-38
CN1	NT-BGHcLV32-1
CN2	NT-BGHcLV32-2
Rep1_qPCR	70.9
Rep2_qPCR	79.8
Rep1_WB	59.9
Rep2_WB	56.4
Antibody Cat#	A305-356A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB513QMB
Status	Submitted
Project	ENCODE4
ID	935

Experiment Information (Status: Released)

	BGHcLV32-37	BGHcLV32-37	BGHcLV32-38	BGHcLV32-38
idx	1036	1038	1037	1039
TRCN#_or_BGC#	BGC#0000787	BGC#0000787	BGC#0000787	BGC#0000787
shRNA_or_gRNA_sequence	CGCGGAGATGACTCACCACA	CGCGGAGATGACTCACCACA	CGCGGAGATGACTCACCACA	CGCGGAGATGACTCACCACA
PAM	GGG	GGG	GGG	GGG
Name	RNH1_91	RNH1_91	RNH1_91	RNH1_91
Sample_ID	BGHcLV32-37	BGHcLV32-37	BGHcLV32-38	BGHcLV32-38
transduction_Date	10/28/21	10/28/21	10/28/21	10/28/21
days	D6	D6	D6	D6
RBP_name	RNH1	RNH1	RNH1	RNH1
qPCR_result	70.9	70.9	79.8	79.8
Ave_qPCR	75.4	75.4
RT-qPCR_primer-F	aaggagctcacggttagcaa	aaggagctcacggttagcaa
RT-qPCR_primer-R	cggcagttgtctgatgtcac	cggcagttgtctgatgtcac
protein_conc	4929	4929	5105	5105
WB_result	59.9	71.4	56.4	73.5
Ave_WB	58.1	72.4
WB_DONE_date	11/15/21	6/16/22	JESS
MW	50KD	50kd
IP
antibody_Cat#	A305-356A	A305-357A	LOT #1	LOT #1
Antibody DCC ID	ENCAB513QMB	ENCAB384YLR	8/4/22
submitted_to_DCC_date		8/16/22
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	2/9/22		2/9/22
repeat_library
Note
ID	7215	7217	7216	7218

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RNH1	Product_ID: A305-357A Lot_ID: 1 Source: Bethyl Labs Target Name: RNH1-human
RNH1	Product_ID: A305-356A Lot_ID: 1 Source: Bethyl Labs Target Name: RNH1-human

Experiment Status

	BGHcLV32-37	BGHcLV32-38
Sample_ID	BGHcLV32-37	BGHcLV32-38
Sample Name
Sample Name	RNH1-BGHcLV32-37	RNH1-BGHcLV32-38
RBP	RNH1	RNH1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10369	10370

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV32-37	BGHcLV32-38
Sample #	43	44
Sample Name	RNH1-BGHcLV32-37	RNH1-BGHcLV32-38
Sample_Name_Alias
Index Well Position	C06	D06
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	299	308
Peak_Molarity	74.70	58.90
libSampleQC_DNA_Well	DNA_Library_set52/set2/C6.png	DNA_Library_set52/set2/D6.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set52/set2/G8.png	RNA_Library_set52/set2/H8.png
SampleQC_method	TapeStation_2022	TapeStation_2022
SampleQC_date	2022-02-16	2022-02-16
Sample_ID	BGHcLV32-37	BGHcLV32-38
RBP	RNH1	RNH1
Batch_ID	BGHcLV32	BGHcLV32
WB_result	59.900	56.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3220	3221

Sequencing Information

	BGHcLV32-37	BGHcLV32-38
Sample_ID	BGHcLV32-37	BGHcLV32-38
Sample Name	RNH1-BGHcLV32-37	RNH1-BGHcLV32-38
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	96,424,764	94,395,340
total_aligned_reads	82,054,826	78,444,402
unique_aligned_reads	77,092,850	73,810,434
percent_uniqueAligned	0.79951	0.78193
correlation_replicates	0.998995	0.998995
spikein_reads	5,802	2,734
percent_spikeins	0.00006	0.00003
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	2015	2016

Data Submission Information

	BGHcLV32-37	BGHcLV32-37	BGHcLV32-37	BGHcLV32-37	BGHcLV32-37	BGHcLV32-37	BGHcLV32-38	BGHcLV32-38	BGHcLV32-38	BGHcLV32-38
ENCODE_alias	brenton-graveley:RNH1-BGHcLV32	brenton-graveley:RNH1-BGHcLV32-37	brenton-graveley:L-RNH1-BGHcLV32-37	brenton-graveley:RNH1-BGHcLV32-37_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNH1-BGHcLV32-37_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNH1-BGHcLV32-HepG2	brenton-graveley:RNH1-BGHcLV32-38	brenton-graveley:L-RNH1-BGHcLV32-38	brenton-graveley:RNH1-BGHcLV32-38_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RNH1-BGHcLV32-38_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR706QGC	ENCBS131BON	ENCLB570MZZ	ENCFF232LMZ	ENCFF016AYH	ENCSR966HHU	ENCBS428TND	ENCLB994JYJ	ENCFF102UGC	ENCFF488DWS
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	BGHcLV32-37	BGHcLV32-37	BGHcLV32-37	BGHcLV32-37	BGHcLV32-37	BGHcLV32-37	BGHcLV32-38	BGHcLV32-38	BGHcLV32-38	BGHcLV32-38
Sample Name	RNH1-BGHcLV32-37	RNH1-BGHcLV32-37	RNH1-BGHcLV32-37	RNH1-BGHcLV32-37	RNH1-BGHcLV32-37	RNH1-BGHcLV32-37	RNH1-BGHcLV32-38	RNH1-BGHcLV32-38	RNH1-BGHcLV32-38	RNH1-BGHcLV32-38
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	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		RNH1-BGHcLV32-37.pdf	L-RNH1-BGHcLV32-37.pdf				RNH1-BGHcLV32-38.pdf	L-RNH1-BGHcLV32-38.pdf
ID	7465	7537	7649	7757	7867	7955	7538	7650	7758	7868

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
RNH1-BGHcLV32-37_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2015	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	6515
RNH1-BGHcLV32-37_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2015	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	6569
RNH1-BGHcLV32-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2015					GRCh38	V40	RNH1-BGHcLV32-37_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNH1-BGHcLV32-37_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18436
RNH1-BGHcLV32-37_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	2015					GRCh38	V40	RNH1-BGHcLV32-37/Aligned.sortedByCoord.out.bam		ENCORE2	18490
RNH1-BGHcLV32-37_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	2015					GRCh38	V40	RNH1-BGHcLV32-37/Aligned.sortedByCoord.out.bam		ENCORE2	18544
RNH1-BGHcLV32-37_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	2015					GRCh38	V40	RNH1-BGHcLV32-37/Aligned.sortedByCoord.out.bam		ENCORE2	18598
RNH1-BGHcLV32-37_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	2015					GRCh38	V40	RNH1-BGHcLV32-37/Aligned.sortedByCoord.out.bam		ENCORE2	18652
RNH1-BGHcLV32-37_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2015					GRCh38	V40	RNH1-BGHcLV32-37_S41_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNH1-BGHcLV32-37_S41_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18706
RNH1-BGHcLV32-38_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2016	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	6516
RNH1-BGHcLV32-38_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	2016	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	6570
RNH1-BGHcLV32-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	2016					GRCh38	V40	RNH1-BGHcLV32-38_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNH1-BGHcLV32-38_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18437
RNH1-BGHcLV32-38_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	2016					GRCh38	V40	RNH1-BGHcLV32-38/Aligned.sortedByCoord.out.bam		ENCORE2	18491
RNH1-BGHcLV32-38_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	2016					GRCh38	V40	RNH1-BGHcLV32-38/Aligned.sortedByCoord.out.bam		ENCORE2	18545
RNH1-BGHcLV32-38_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	2016					GRCh38	V40	RNH1-BGHcLV32-38/Aligned.sortedByCoord.out.bam		ENCORE2	18599
RNH1-BGHcLV32-38_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	2016					GRCh38	V40	RNH1-BGHcLV32-38/Aligned.sortedByCoord.out.bam		ENCORE2	18653
RNH1-BGHcLV32-38_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	2016					GRCh38	V40	RNH1-BGHcLV32-38_S42_L001_R1_001.filtered.trimmed.paired.fastq.gz,RNH1-BGHcLV32-38_S42_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18707