RBM25 RNA-Seq in K562

General Information


RBP	RBM25
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM25-BGKcLV11-K562
ENCODE_series_ID	ENCSR288XYD
Batch_ID	BGKcLV11
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR897BYR
ENCODE_CN_Exp_ID	ENCSR292PXV
Rep1	RBM25-BGKcLV11-83
Rep2	RBM25-BGKcLV11-84
CN1	NT-BGKcLV11-1
CN2	NT-BGKcLV11-2
Rep1_qPCR	60.5
Rep2_qPCR	53.4
Rep1_WB	49.9
Rep2_WB	60.3
Antibody Cat#	A301-068A
Antibody Lot#
Antibody DCC ID	ENCAB401CSY
Status	Archived
Project	ENCODE4
ID	187

Experiment Information (Status: Released)

	BGKcLV11-83	BGKcLV11-84
idx	399	400
TRCN#_or_BGC#	BGC#0000210	BGC#0000210
shRNA_or_gRNA_sequence	GAGTGGATAAGGGATCAGTG	GAGTGGATAAGGGATCAGTG
PAM	GGG	GGG
Name	RBM25-67F	RBM25-67F
Sample_ID	BGKcLV11-83	BGKcLV11-84
transduction_Date	8/3/18	8/3/18
days	Day 6	Day 6
RBP_name	RBM25	RBM25
qPCR_result	60.5	53.4
Ave_qPCR	57.0
RT-qPCR_primer-F	GAATTCTTAGAAGACTATGATGATGA
RT-qPCR_primer-R	TTTCTCTATCACGCAACCTTT
protein_conc	3786	4109
WB_result	49.9	60.3
Ave_WB	55.1
WB_DONE_date	9/11/18	WES
MW	100kDa
IP	1
antibody_Cat#	A301-068A
Antibody DCC ID	ENCAB401CSY
submitted_to_DCC_date	2/22/19
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	4501	4502

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM25	Product_ID: A301-068A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM25-human

Experiment Status

	BGKcLV11-83	BGKcLV11-84
Sample_ID	BGKcLV11-83	BGKcLV11-84
Sample Name	RBM25-BGKcLV11-83	RBM25-BGKcLV11-84
Sample Name	RBM25-BGKcLV11-83	RBM25-BGKcLV11-84
RBP	RBM25	RBM25
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2687	2688

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV11-83	BGKcLV11-84
Sample #	15	16
Sample Name	RBM25-BGKcLV11-83	RBM25-BGKcLV11-84
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	1-G2	1-H2
Tecan	30.54	40.39
Tecan_date	2019-03-13	2019-03-13
Size_bp	304	299
Peak_Molarity	33.10	189.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/G2.png	DNA_Library_set42/set1/H2.png
RIN	9.9	9.7
libSample_RNA_Well	RNA_Library_set42/set1/G2.png	RNA_Library_set42/set1/H2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGKcLV11-83	BGKcLV11-84
RBP	RBM25	RBM25
Batch_ID	BGKcLV11	BGKcLV11
WB_result	49.900	60.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	15	16

Sequencing Information

	BGKcLV11-83	BGKcLV11-84
Sample_ID	BGKcLV11-83	BGKcLV11-84
Sample Name	RBM25-BGKcLV11-83	RBM25-BGKcLV11-84
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	52,161,624	32,673,574
total_aligned_reads	47,673,056	30,640,558
unique_aligned_reads	43,366,906	27,849,828
percent_uniqueAligned	0.83139	0.85237
correlation_replicates	0.989430	0.989430
spikein_reads	95,116	42,028
percent_spikeins	0.00182	0.00129
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	61	62

Data Submission Information

	BGKcLV11-83	BGKcLV11-83	BGKcLV11-83	BGKcLV11-83	BGKcLV11-83	BGKcLV11-83	BGKcLV11-84	BGKcLV11-84	BGKcLV11-84	BGKcLV11-84
ENCODE_alias	brenton-graveley:RBM25-BGKcLV11	brenton-graveley:RBM25-BGKcLV11-83	brenton-graveley:L-RBM25-BGKcLV11-83	brenton-graveley:RBM25-BGKcLV11-83_GGCTTAAG+TCGTGACC_HK3H2DSXX_S15_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM25-BGKcLV11-83_GGCTTAAG+TCGTGACC_HK3H2DSXX_S15_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM25-BGKcLV11-K562	brenton-graveley:RBM25-BGKcLV11-84	brenton-graveley:L-RBM25-BGKcLV11-84	brenton-graveley:RBM25-BGKcLV11-84_AATCCGGA+CTACAGTT_HK3H2DSXX_S16_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM25-BGKcLV11-84_AATCCGGA+CTACAGTT_HK3H2DSXX_S16_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR897BYR	ENCBS697TKR	ENCLB649XWC	ENCFF588DCA	ENCFF559MEU	ENCSR288XYD	ENCBS339ZLL	ENCLB348LJW	ENCFF274QUG	ENCFF395YCC
object_type	experiment	biosample	library	file_fastq1	file_fastq2	experiment	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	BGKcLV11-83	BGKcLV11-83	BGKcLV11-83	BGKcLV11-83	BGKcLV11-83	BGKcLV11-83	BGKcLV11-84	BGKcLV11-84	BGKcLV11-84	BGKcLV11-84
Sample Name	RBM25-BGKcLV11-83	RBM25-BGKcLV11-83	RBM25-BGKcLV11-83	RBM25-BGKcLV11-83	RBM25-BGKcLV11-83	RBM25-BGKcLV11-83	RBM25-BGKcLV11-84	RBM25-BGKcLV11-84	RBM25-BGKcLV11-84	RBM25-BGKcLV11-84
Selected	Yes	Yes	Yes	Yes	Yes	No	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Archived	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		RBM25-BGKcLV11-83.pdf	L-RBM25-BGKcLV11-83.pdf				RBM25-BGKcLV11-84.pdf	L-RBM25-BGKcLV11-84.pdf
ID	768	831	913	1011	1093	7300	832	914	1012	1094

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
RBM25-BGKcLV11-83_GGCTTAAG+TCGTGACC_HK3H2DSXX_S15_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	61	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	393
RBM25-BGKcLV11-83_GGCTTAAG+TCGTGACC_HK3H2DSXX_S15_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	61	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	475
RBM25-BGKcLV11-83_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	61					GRCh38	V40	RBM25-BGKcLV11-83_GGCTTAAG+TCGTGACC_HK3H2DSXX_S15_L004_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGKcLV11-83_GGCTTAAG+TCGTGACC_HK3H2DSXX_S15_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23732
RBM25-BGKcLV11-83_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	61					GRCh38	V40	RBM25-BGKcLV11-83/Aligned.sortedByCoord.out.bam		ENCORE2	23814
RBM25-BGKcLV11-83_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	61					GRCh38	V40	RBM25-BGKcLV11-83/Aligned.sortedByCoord.out.bam		ENCORE2	23896
RBM25-BGKcLV11-83_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	61					GRCh38	V40	RBM25-BGKcLV11-83/Aligned.sortedByCoord.out.bam		ENCORE2	23978
RBM25-BGKcLV11-83_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	61					GRCh38	V40	RBM25-BGKcLV11-83/Aligned.sortedByCoord.out.bam		ENCORE2	24060
RBM25-BGKcLV11-83_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	61					GRCh38	V40	RBM25-BGKcLV11-83_GGCTTAAG+TCGTGACC_HK3H2DSXX_S15_L004_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGKcLV11-83_GGCTTAAG+TCGTGACC_HK3H2DSXX_S15_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24142
RBM25-BGKcLV11-84_AATCCGGA+CTACAGTT_HK3H2DSXX_S16_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	62	NovaSeq6000	100	paired-ended	1				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	394
RBM25-BGKcLV11-84_AATCCGGA+CTACAGTT_HK3H2DSXX_S16_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	62	NovaSeq6000	100	paired-ended	2				NT-BGKcLV11-1_CCGCGGTT+AGCGCTAG_HK3H2DSXX_S1_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV11-2_TTATAACC+GATATCGA_HK3H2DSXX_S2_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	476
RBM25-BGKcLV11-84_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	62					GRCh38	V40	RBM25-BGKcLV11-84_AATCCGGA+CTACAGTT_HK3H2DSXX_S16_L004_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGKcLV11-84_AATCCGGA+CTACAGTT_HK3H2DSXX_S16_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23733
RBM25-BGKcLV11-84_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	62					GRCh38	V40	RBM25-BGKcLV11-84/Aligned.sortedByCoord.out.bam		ENCORE2	23815
RBM25-BGKcLV11-84_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	62					GRCh38	V40	RBM25-BGKcLV11-84/Aligned.sortedByCoord.out.bam		ENCORE2	23897
RBM25-BGKcLV11-84_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	62					GRCh38	V40	RBM25-BGKcLV11-84/Aligned.sortedByCoord.out.bam		ENCORE2	23979
RBM25-BGKcLV11-84_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	62					GRCh38	V40	RBM25-BGKcLV11-84/Aligned.sortedByCoord.out.bam		ENCORE2	24061
RBM25-BGKcLV11-84_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	62					GRCh38	V40	RBM25-BGKcLV11-84_AATCCGGA+CTACAGTT_HK3H2DSXX_S16_L004_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGKcLV11-84_AATCCGGA+CTACAGTT_HK3H2DSXX_S16_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24143