RNF187 RNA-Seq in K562

General Information


RBP	RNF187
Cell_Line	K562
Method	CRISPR
Exp_Name	RNF187-BGKcLV19-K562
ENCODE_series_ID	ENCSR270YVR
Batch_ID	BGKcLV19
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR050ONB
ENCODE_CN_Exp_ID	ENCSR978MMZ
Rep1	RNF187-BGKcLV19-39
Rep2	RNF187-BGKcLV19-40
CN1	NT-BGKcLV19-1
CN2	NT-BGKcLV19-2
Rep1_qPCR	0
Rep2_qPCR	0
Rep1_WB	76.4
Rep2_WB	73.2
Antibody Cat#	PA5-56340
Antibody Lot#	Lot# UF2796809A
Antibody DCC ID	ENCAB212BNU
Status	Released
Project	ENCODE4
ID	57

Experiment Information (Status: Released)

	BGKcLV19-39	BGKcLV19-40
idx	711	712
TRCN#_or_BGC#	BGC#0000486	BGC#0000486
shRNA_or_gRNA_sequence	AGCAGTCGTCGGCGCACTCG	AGCAGTCGTCGGCGCACTCG
PAM	GGG	GGG
Name	RNF187_97	RNF187_97
Sample_ID	BGKcLV19-39	BGKcLV19-40
transduction_Date	11/6/19	11/6/19
days	Day 6	Day 6
RBP_name	RNF187	RNF187
qPCR_result	0	0
Ave_qPCR	0.0
RT-qPCR_primer-F	ggttgtggggaccataactg
RT-qPCR_primer-R	tggtcgaaagtgaggatcttg
protein_conc	4177	4149
WB_result	76.4	73.2
Ave_WB	74.8
WB_DONE_date	8/5/20
MW	26kDa
IP	Rabbit / I
antibody_Cat#	PA5-56340	Lot# UF2796809A
Antibody DCC ID	ENCAB212BNU
submitted_to_DCC_date	11/16/20
Rep1_TPM	91.1	0
Rep2_TPM	59.3	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4831	4832

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

	BGKcLV19-39	BGKcLV19-40
Sample_ID	BGKcLV19-39	BGKcLV19-40
Sample Name
Sample Name	RNF187-BGKcLV19-39	RNF187-BGKcLV19-40
RBP	RNF187	RNF187
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5707	5708

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV19-39	BGKcLV19-40
Sample #	21	22
Sample Name	RNF187-BGKcLV19-39	RNF187-BGKcLV19-40
Sample_Name_Alias
Index Well Position	G02	H02
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	299	300
Peak_Molarity	85.70	97.10
libSampleQC_DNA_Well	DNA_Library_set45/set1/G2.png	DNA_Library_set45/set1/H2.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set45/set1/G2.png	RNA_Library_set45/set2/B10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV19-39	BGKcLV19-40
RBP	RNF187	RNF187
Batch_ID	BGKcLV19	BGKcLV19
WB_result	76.400	73.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	795	796

Sequencing Information

	BGKcLV19-39	BGKcLV19-40
Sample_ID	BGKcLV19-39	BGKcLV19-40
Sample Name	RNF187-BGKcLV19-39	RNF187-BGKcLV19-40
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	94,936,288	97,648,270
total_aligned_reads	88,243,274	93,505,064
unique_aligned_reads	80,714,500	85,615,286
percent_uniqueAligned	0.85020	0.87677
correlation_replicates	0.983678	0.983678
spikein_reads	70,892	80,360
percent_spikeins	0.00075	0.00082
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	426	427

Data Submission Information

	BGKcLV19-39	BGKcLV19-39	BGKcLV19-39	BGKcLV19-39	BGKcLV19-39	BGKcLV19-39	BGKcLV19-40	BGKcLV19-40	BGKcLV19-40	BGKcLV19-40
ENCODE_alias	brenton-graveley:RNF187-BGKcLV19	brenton-graveley:RNF187-BGKcLV19-39	brenton-graveley:L-RNF187-BGKcLV19-39	brenton-graveley:RNF187-BGKcLV19-39_S15_R1_001.fastq.gz	brenton-graveley:RNF187-BGKcLV19-39_S15_R2_001.fastq.gz	brenton-graveley:RNF187-BGKcLV19-K562	brenton-graveley:RNF187-BGKcLV19-40	brenton-graveley:L-RNF187-BGKcLV19-40	brenton-graveley:RNF187-BGKcLV19-40_S16_R1_001.fastq.gz	brenton-graveley:RNF187-BGKcLV19-40_S16_R2_001.fastq.gz
ENCODE_accession	ENCSR050ONB	ENCBS823JJH	ENCLB814XIO	ENCFF064IPP	ENCFF565QAT	ENCSR270YVR	ENCBS828OWP	ENCLB601LGN	ENCFF449BGA	ENCFF125CIU
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	BGKcLV19-39	BGKcLV19-39	BGKcLV19-39	BGKcLV19-39	BGKcLV19-39	BGKcLV19-39	BGKcLV19-40	BGKcLV19-40	BGKcLV19-40	BGKcLV19-40
Sample Name	RNF187-BGKcLV19-39	RNF187-BGKcLV19-39	RNF187-BGKcLV19-39	RNF187-BGKcLV19-39	RNF187-BGKcLV19-39	RNF187-BGKcLV19-39	RNF187-BGKcLV19-40	RNF187-BGKcLV19-40	RNF187-BGKcLV19-40	RNF187-BGKcLV19-40
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
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		RNF187-BGKcLV19-39.pdf	L-RNF187-BGKcLV19-39.pdf				RNF187-BGKcLV19-40.pdf	L-RNF187-BGKcLV19-40.pdf
ID	2097	2149	2219	2289	2359	7302	2150	2220	2290	2360

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-BGKcLV19-39_S15_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	426	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1244
RNF187-BGKcLV19-39_S15_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	426	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1294
RNF187-BGKcLV19-39_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	426					GRCh38	V40	RNF187-BGKcLV19-39_S15_R1_001.filtered.trimmed.paired.fastq.gz,RNF187-BGKcLV19-39_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25237
RNF187-BGKcLV19-39_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	426					GRCh38	V40	RNF187-BGKcLV19-39_S15_R1_001.filtered.trimmed.paired.fastq.gz,RNF187-BGKcLV19-39_S15_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27191
RNF187-BGKcLV19-39_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	426					GRCh38	V40	RNF187-BGKcLV19-39/Aligned.sortedByCoord.out.bam		ENCORE2	27241
RNF187-BGKcLV19-39_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	426					GRCh38	V40	RNF187-BGKcLV19-39/Aligned.sortedByCoord.out.bam		ENCORE2	27291
RNF187-BGKcLV19-39_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	426					GRCh38	V40	RNF187-BGKcLV19-39/Aligned.sortedByCoord.out.bam		ENCORE2	27341
RNF187-BGKcLV19-39_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	426					GRCh38	V40	RNF187-BGKcLV19-39/Aligned.sortedByCoord.out.bam		ENCORE2	27391
RNF187-BGKcLV19-40_S16_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	427	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1245
RNF187-BGKcLV19-40_S16_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	427	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1295
RNF187-BGKcLV19-40_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	427					GRCh38	V40	RNF187-BGKcLV19-40_S16_R1_001.filtered.trimmed.paired.fastq.gz,RNF187-BGKcLV19-40_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25238
RNF187-BGKcLV19-40_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	427					GRCh38	V40	RNF187-BGKcLV19-40_S16_R1_001.filtered.trimmed.paired.fastq.gz,RNF187-BGKcLV19-40_S16_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27192
RNF187-BGKcLV19-40_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	427					GRCh38	V40	RNF187-BGKcLV19-40/Aligned.sortedByCoord.out.bam		ENCORE2	27242
RNF187-BGKcLV19-40_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	427					GRCh38	V40	RNF187-BGKcLV19-40/Aligned.sortedByCoord.out.bam		ENCORE2	27292
RNF187-BGKcLV19-40_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	427					GRCh38	V40	RNF187-BGKcLV19-40/Aligned.sortedByCoord.out.bam		ENCORE2	27342
RNF187-BGKcLV19-40_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	427					GRCh38	V40	RNF187-BGKcLV19-40/Aligned.sortedByCoord.out.bam		ENCORE2	27392