RPUSD2 RNA-Seq in HepG2

General Information


RBP	RPUSD2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RPUSD2-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR764UVM
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR235JSA
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	RPUSD2-BGHcLV31-13
Rep2	RPUSD2-BGHcLV31-14
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	83.9
Rep2_WB	81.2
Antibody Cat#	A305-209A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB305MHJ
Status	Submitted
Project	ENCODE4
ID	919

Experiment Information (Status: Released)

	BGHcLV31-13	BGHcLV31-14
idx	929	930
TRCN#_or_BGC#	BGC#0000829	BGC#0000829
shRNA_or_gRNA_sequence	TGACGCTGGTGGCGACGCGA	TGACGCTGGTGGCGACGCGA
PAM	AGG	AGG
Name	RPUSD2_97	RPUSD2_97
Sample_ID	BGHcLV31-13	BGHcLV31-14
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	RPUSD2	RPUSD2
qPCR_result	xx
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4155	4394
WB_result	83.9	81.2
Ave_WB	82.6
WB_DONE_date	11/4/21
MW	61kd
IP
antibody_Cat#	A305-209A	LOT #1
Antibody DCC ID	ENCAB305MHJ
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7108	7109

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RPUSD2	Product_ID: A305-209A Lot_ID: 1 Source: Bethyl Labs Target Name: RPUSD2-human

Experiment Status

	BGHcLV31-13	BGHcLV31-14
Sample_ID	BGHcLV31-13	BGHcLV31-14
Sample Name
Sample Name	RPUSD2-BGHcLV31-13	RPUSD2-BGHcLV31-14
RBP	RPUSD2	RPUSD2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10293	10294

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-13	BGHcLV31-14
Sample #	7	8
Sample Name	RPUSD2-BGHcLV31-13	RPUSD2-BGHcLV31-14
Sample_Name_Alias
Index Well Position	G01	H01
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	282	283
Peak_Molarity	74.70	77.80
libSampleQC_DNA_Well	DNA_Library_set52/set1/G8.png	DNA_Library_set52/set1/H8.png
RIN	9.6	9.7
libSample_RNA_Well	RNA_Library_set52/set1/G1.png	RNA_Library_set52/set1/H1.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-13	BGHcLV31-14
RBP	RPUSD2	RPUSD2
Batch_ID	BGHcLV31	BGHcLV31
WB_result	83.900	81.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3184	3185

Sequencing Information

	BGHcLV31-13	BGHcLV31-14
Sample_ID	BGHcLV31-13	BGHcLV31-14
Sample Name	RPUSD2-BGHcLV31-13	RPUSD2-BGHcLV31-14
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	92,979,592	84,119,742
total_aligned_reads	79,771,736	73,435,040
unique_aligned_reads	75,034,930	69,088,132
percent_uniqueAligned	0.80700	0.82131
correlation_replicates	0.994544	0.994544
spikein_reads	6,900	8,604
percent_spikeins	0.00007	0.00010
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1981	1982

Data Submission Information

	BGHcLV31-13	BGHcLV31-13	BGHcLV31-13	BGHcLV31-13	BGHcLV31-13	BGHcLV31-13	BGHcLV31-14	BGHcLV31-14	BGHcLV31-14	BGHcLV31-14
ENCODE_alias	brenton-graveley:RPUSD2-BGHcLV31	brenton-graveley:RPUSD2-BGHcLV31-13	brenton-graveley:L-RPUSD2-BGHcLV31-13	brenton-graveley:RPUSD2-BGHcLV31-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPUSD2-BGHcLV31-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPUSD2-BGHcLV31-HepG2	brenton-graveley:RPUSD2-BGHcLV31-14	brenton-graveley:L-RPUSD2-BGHcLV31-14	brenton-graveley:RPUSD2-BGHcLV31-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RPUSD2-BGHcLV31-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR235JSA	ENCBS417HWB	ENCLB529HTX	ENCFF374NSH	ENCFF588DHI	ENCSR764UVM	ENCBS711EJM	ENCLB034HDS	ENCFF455BJO	ENCFF132YUC
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	BGHcLV31-13	BGHcLV31-13	BGHcLV31-13	BGHcLV31-13	BGHcLV31-13	BGHcLV31-13	BGHcLV31-14	BGHcLV31-14	BGHcLV31-14	BGHcLV31-14
Sample Name	RPUSD2-BGHcLV31-13	RPUSD2-BGHcLV31-13	RPUSD2-BGHcLV31-13	RPUSD2-BGHcLV31-13	RPUSD2-BGHcLV31-13	RPUSD2-BGHcLV31-13	RPUSD2-BGHcLV31-14	RPUSD2-BGHcLV31-14	RPUSD2-BGHcLV31-14	RPUSD2-BGHcLV31-14
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		RPUSD2-BGHcLV31-13.pdf	L-RPUSD2-BGHcLV31-13.pdf				RPUSD2-BGHcLV31-14.pdf	L-RPUSD2-BGHcLV31-14.pdf
ID	7447	7505	7613	7723	7833	7939	7506	7614	7724	7834

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
RPUSD2-BGHcLV31-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1981	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6527
RPUSD2-BGHcLV31-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1981	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6581
RPUSD2-BGHcLV31-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1981					GRCh38	V40	RPUSD2-BGHcLV31-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPUSD2-BGHcLV31-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18448
RPUSD2-BGHcLV31-13_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	1981					GRCh38	V40	RPUSD2-BGHcLV31-13/Aligned.sortedByCoord.out.bam		ENCORE2	18502
RPUSD2-BGHcLV31-13_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	1981					GRCh38	V40	RPUSD2-BGHcLV31-13/Aligned.sortedByCoord.out.bam		ENCORE2	18556
RPUSD2-BGHcLV31-13_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	1981					GRCh38	V40	RPUSD2-BGHcLV31-13/Aligned.sortedByCoord.out.bam		ENCORE2	18610
RPUSD2-BGHcLV31-13_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	1981					GRCh38	V40	RPUSD2-BGHcLV31-13/Aligned.sortedByCoord.out.bam		ENCORE2	18664
RPUSD2-BGHcLV31-13_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1981					GRCh38	V40	RPUSD2-BGHcLV31-13_S7_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPUSD2-BGHcLV31-13_S7_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18718
RPUSD2-BGHcLV31-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1982	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6528
RPUSD2-BGHcLV31-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1982	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6582
RPUSD2-BGHcLV31-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1982					GRCh38	V40	RPUSD2-BGHcLV31-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPUSD2-BGHcLV31-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18449
RPUSD2-BGHcLV31-14_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	1982					GRCh38	V40	RPUSD2-BGHcLV31-14/Aligned.sortedByCoord.out.bam		ENCORE2	18503
RPUSD2-BGHcLV31-14_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	1982					GRCh38	V40	RPUSD2-BGHcLV31-14/Aligned.sortedByCoord.out.bam		ENCORE2	18557
RPUSD2-BGHcLV31-14_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	1982					GRCh38	V40	RPUSD2-BGHcLV31-14/Aligned.sortedByCoord.out.bam		ENCORE2	18611
RPUSD2-BGHcLV31-14_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	1982					GRCh38	V40	RPUSD2-BGHcLV31-14/Aligned.sortedByCoord.out.bam		ENCORE2	18665
RPUSD2-BGHcLV31-14_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1982					GRCh38	V40	RPUSD2-BGHcLV31-14_S8_L001_R1_001.filtered.trimmed.paired.fastq.gz,RPUSD2-BGHcLV31-14_S8_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18719