RNF187 RNA-Seq in HepG2

General Information


RBP	RNF187
Cell_Line	HepG2
Method	CRISPR
Exp_Name	RNF187-BGHcLV20-HepG2
ENCODE_series_ID	ENCSR927AOM
Batch_ID	BGHcLV20
Pool ID	Pool-200928
Local_Set_Name	set45_H
ENCODE_KD_Exp_ID	ENCSR637CZY
ENCODE_CN_Exp_ID	ENCSR306EWE
Rep1	RNF187-BGHcLV20-27
Rep2	RNF187-BGHcLV20-28
CN1	NT-BGHcLV20-1
CN2	NT-BGHcLV20-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	95.3
Rep2_WB	98.7
Antibody Cat#	PA5-56340
Antibody Lot#	Lot# UF2796809A
Antibody DCC ID	ENCAB212BNU
Status	Released
Project	ENCODE4
ID	78

Experiment Information (Status: Released)

	BGHcLV20-27	BGHcLV20-28
idx	577	578
TRCN#_or_BGC#	BGC#0000486	BGC#0000486
shRNA_or_gRNA_sequence	AGCAGTCGTCGGCGCACTCG	AGCAGTCGTCGGCGCACTCG
PAM	GGG	GGG
Name	RNF187_97	RNF187_97
Sample_ID	BGHcLV20-27	BGHcLV20-28
transduction_Date	12/10/19	12/10/19
days	D6	D6
RBP_name	RNF187	RNF187
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ggttgtggggaccataactg
RT-qPCR_primer-R	tggtcgaaagtgaggatcttg
protein_conc	4844	5157
WB_result	95.3	98.7
Ave_WB	97.0
WB_DONE_date	8/31/20	JESS
MW	26kDa
IP	Rabbit / I
antibody_Cat#	PA5-56340	Lot# UF2796809A
Antibody DCC ID	ENCAB212BNU
submitted_to_DCC_date	11/16/20
Rep1_TPM	102	0
Rep2_TPM	54	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	6732	6733

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RNF187	Product_ID: PA5-56340 Lot_ID: UF2796809A Source: Thermo Fisher Target Name: RNF187-human

Experiment Status

	BGHcLV20-27	BGHcLV20-28
Sample_ID	BGHcLV20-27	BGHcLV20-28
Sample Name
Sample Name	RNF187-BGHcLV20-27	RNF187-BGHcLV20-28
RBP	RNF187	RNF187
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5817	5818

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV20-27	BGHcLV20-28
Sample #	67	68
Sample Name	RNF187-BGHcLV20-27	RNF187-BGHcLV20-28
Sample_Name_Alias
Index Well Position	E08	F08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	310	321
Peak_Molarity	146.00	86.20
libSampleQC_DNA_Well	DNA_Library_set45/set1/E8.png	DNA_Library_set45/set1/F8.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_set45/set1/E8.png	RNA_Library_set45/set2/D11.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGHcLV20-27	BGHcLV20-28
RBP	RNF187	RNF187
Batch_ID	BGHcLV20	BGHcLV20
WB_result	95.300	98.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	841	842

Sequencing Information

	BGHcLV20-27	BGHcLV20-28
Sample_ID	BGHcLV20-27	BGHcLV20-28
Sample Name	RNF187-BGHcLV20-27	RNF187-BGHcLV20-28
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_H	set45_H
total_reads	93,441,750	132,974,724
total_aligned_reads	90,218,756	128,909,908
unique_aligned_reads	85,011,124	121,542,454
percent_uniqueAligned	0.90978	0.91403
correlation_replicates	0.993198	0.993198
spikein_reads	41,018	53,992
percent_spikeins	0.00044	0.00041
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	472	473

Data Submission Information

	BGHcLV20-27	BGHcLV20-27	BGHcLV20-27	BGHcLV20-27	BGHcLV20-27	BGHcLV20-27	BGHcLV20-28	BGHcLV20-28	BGHcLV20-28	BGHcLV20-28
ENCODE_alias	brenton-graveley:RNF187-BGHcLV20	brenton-graveley:RNF187-BGHcLV20-27	brenton-graveley:L-RNF187-BGHcLV20-27	brenton-graveley:RNF187-BGHcLV20-27_S61_R1_001.fastq.gz	brenton-graveley:RNF187-BGHcLV20-27_S61_R2_001.fastq.gz	brenton-graveley:RNF187-BGHcLV20-HepG2	brenton-graveley:RNF187-BGHcLV20-28	brenton-graveley:L-RNF187-BGHcLV20-28	brenton-graveley:RNF187-BGHcLV20-28_S62_R1_001.fastq.gz	brenton-graveley:RNF187-BGHcLV20-28_S62_R2_001.fastq.gz
ENCODE_accession	ENCSR637CZY	ENCBS320HYP	ENCLB162TCY	ENCFF635YVX	ENCFF822TPK	ENCSR927AOM	ENCBS493TQZ	ENCLB649YCQ	ENCFF395QIG	ENCFF813WSB
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	BGHcLV20-27	BGHcLV20-27	BGHcLV20-27	BGHcLV20-27	BGHcLV20-27	BGHcLV20-27	BGHcLV20-28	BGHcLV20-28	BGHcLV20-28	BGHcLV20-28
Sample Name	RNF187-BGHcLV20-27	RNF187-BGHcLV20-27	RNF187-BGHcLV20-27	RNF187-BGHcLV20-27	RNF187-BGHcLV20-27	RNF187-BGHcLV20-27	RNF187-BGHcLV20-28	RNF187-BGHcLV20-28	RNF187-BGHcLV20-28	RNF187-BGHcLV20-28
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45H_biosample_protocol	LV45H_library_protocol				LV45H_biosample_protocol	LV45H_library_protocol
protocol_URL		RNF187-BGHcLV20-27.pdf	L-RNF187-BGHcLV20-27.pdf				RNF187-BGHcLV20-28.pdf	L-RNF187-BGHcLV20-28.pdf
ID	2085	2125	2195	2265	2335	7301	2126	2196	2266	2336

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
RNF187-BGHcLV20-27_S61_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	472	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1318
RNF187-BGHcLV20-27_S61_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	472	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1338
RNF187-BGHcLV20-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	472					GRCh38	V40	RNF187-BGHcLV20-27_S61_R1_001.filtered.trimmed.paired.fastq.gz,RNF187-BGHcLV20-27_S61_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24859
RNF187-BGHcLV20-27_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	472					GRCh38	V40	RNF187-BGHcLV20-27_S61_R1_001.filtered.trimmed.paired.fastq.gz,RNF187-BGHcLV20-27_S61_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24879
RNF187-BGHcLV20-27_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	472					GRCh38	V40	RNF187-BGHcLV20-27/Aligned.sortedByCoord.out.bam		ENCORE2	25929
RNF187-BGHcLV20-27_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	472					GRCh38	V40	RNF187-BGHcLV20-27/Aligned.sortedByCoord.out.bam		ENCORE2	25949
RNF187-BGHcLV20-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	472					GRCh38	V40	RNF187-BGHcLV20-27/Aligned.sortedByCoord.out.bam		ENCORE2	25969
RNF187-BGHcLV20-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	472					GRCh38	V40	RNF187-BGHcLV20-27/Aligned.sortedByCoord.out.bam		ENCORE2	25989
RNF187-BGHcLV20-28_S62_R1_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	473	NovaSeq6000	100	paired-ended	1				NT-BGHcLV20-1_S51_R1_001.fastq.gz,NT-BGHcLV20-2_S52_R1_001.fastq.gz	ENCODE4	1319
RNF187-BGHcLV20-28_S62_R2_001.fastq.gz	ENCODE_DATA/set45_H/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	473	NovaSeq6000	100	paired-ended	2				NT-BGHcLV20-1_S51_R2_001.fastq.gz,NT-BGHcLV20-2_S52_R2_001.fastq.gz	ENCODE4	1339
RNF187-BGHcLV20-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	473					GRCh38	V40	RNF187-BGHcLV20-28_S62_R1_001.filtered.trimmed.paired.fastq.gz,RNF187-BGHcLV20-28_S62_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24860
RNF187-BGHcLV20-28_quant.sf	ENCODE_DATA/set45_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	473					GRCh38	V40	RNF187-BGHcLV20-28_S62_R1_001.filtered.trimmed.paired.fastq.gz,RNF187-BGHcLV20-28_S62_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24880
RNF187-BGHcLV20-28_Signal.Unique.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	473					GRCh38	V40	RNF187-BGHcLV20-28/Aligned.sortedByCoord.out.bam		ENCORE2	25930
RNF187-BGHcLV20-28_Signal.Unique.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	473					GRCh38	V40	RNF187-BGHcLV20-28/Aligned.sortedByCoord.out.bam		ENCORE2	25950
RNF187-BGHcLV20-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	473					GRCh38	V40	RNF187-BGHcLV20-28/Aligned.sortedByCoord.out.bam		ENCORE2	25970
RNF187-BGHcLV20-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	473					GRCh38	V40	RNF187-BGHcLV20-28/Aligned.sortedByCoord.out.bam		ENCORE2	25990