RBM17 RNA-Seq in K562

General Information


RBP	RBM17
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM17-BGKcLV30-K562
ENCODE_series_ID	ENCSR284AXZ
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR012YIL
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RBM17-BGKcLV30-9
Rep2	RBM17-BGKcLV30-10
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	52.6
Rep2_WB	53.2
Antibody Cat#	A302-497A
Antibody Lot#	LOT #2
Antibody DCC ID	ENCAB724GMW
Status	Submitted
Project	ENCODE4
ID	867

Experiment Information (Status: Released)

	BGKcLV30-9	BGKcLV30-10
idx	1034	1035
TRCN#_or_BGC#	BGC#0000757	BGC#0000757
shRNA_or_gRNA_sequence	CACTCCTAGGTCATCGTACA	CACTCCTAGGTCATCGTACA
PAM	GGG	GGG
Name	RBM17_97	RBM17_97
Sample_ID	BGKcLV30-9	BGKcLV30-10
transduction_Date	8/30/21	8/30/21
days	D6	D6
RBP_name	RBM17	RBM17
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	TGGAAGTTGAAACCAAGGAAG
RT-qPCR_primer-R	ATCCGTACTGCTTCATCATC
protein_conc	2294	2738
WB_result	52.6	53.2
Ave_WB	52.9
WB_DONE_date	10/1/21
MW	45KD
IP
antibody_Cat#	A302-497A	LOT #2
Antibody DCC ID	ENCAB724GMW
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/10/21	11/10/21
repeat_library
Note
ID	5172	5173

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM17	Product_ID: A302-497A Lot_ID: 2 Source: Bethyl Labs Target Name: RBM17-human

Experiment Status

	BGKcLV30-9	BGKcLV30-10
Sample_ID	BGKcLV30-9	BGKcLV30-10
Sample Name
Sample Name	RBM17-BGKcLV30-9	RBM17-BGKcLV30-10
RBP	RBM17	RBM17
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10059	10060

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-9	BGKcLV30-10
Sample #	49	50
Sample Name	RBM17-BGKcLV30-9	RBM17-BGKcLV30-10
Sample_Name_Alias
Index Well Position	E07	F07
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101A	Lib-211101A
Tecan_Location
Tecan
Tecan_date
Size_bp	307	289
Peak_Molarity	40.80	39.00
libSampleQC_DNA_Well	DNA_Library_set50/set2/E9.png	DNA_Library_set50/set2/F9.png
RIN	9.5	9.4
libSample_RNA_Well	RNA_Library_set50/set2/E9.png	RNA_Library_set50/set2/F9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-9	BGKcLV30-10
RBP	RBM17	RBM17
Batch_ID	BGKcLV30	BGKcLV30
WB_result	52.600	53.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3136	3137

Sequencing Information

	BGKcLV30-9	BGKcLV30-10
Sample_ID	BGKcLV30-9	BGKcLV30-10
Sample Name	RBM17-BGKcLV30-9	RBM17-BGKcLV30-10
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	67,769,358	101,576,954
total_aligned_reads	61,991,838	96,030,602
unique_aligned_reads	56,854,882	88,002,868
percent_uniqueAligned	0.83895	0.86637
correlation_replicates	0.992819	0.992819
spikein_reads	17,484	27,650
percent_spikeins	0.00026	0.00027
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1921	1922

Data Submission Information

	BGKcLV30-9	BGKcLV30-9	BGKcLV30-9	BGKcLV30-9	BGKcLV30-9	BGKcLV30-9	BGKcLV30-10	BGKcLV30-10	BGKcLV30-10	BGKcLV30-10
ENCODE_alias	brenton-graveley:RBM17-BGKcLV30	brenton-graveley:RBM17-BGKcLV30-9	brenton-graveley:L-RBM17-BGKcLV30-9	brenton-graveley:RBM17-BGKcLV30-9_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM17-BGKcLV30-9_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM17-BGKcLV30-K562	brenton-graveley:RBM17-BGKcLV30-10	brenton-graveley:L-RBM17-BGKcLV30-10	brenton-graveley:RBM17-BGKcLV30-10_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM17-BGKcLV30-10_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR012YIL	ENCBS969UOM	ENCLB728YSO	ENCFF852OJP	ENCFF583DKY	ENCSR284AXZ	ENCBS379JXB	ENCLB230HET	ENCFF985WEJ	ENCFF521NRM
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	BGKcLV30-9	BGKcLV30-9	BGKcLV30-9	BGKcLV30-9	BGKcLV30-9	BGKcLV30-9	BGKcLV30-10	BGKcLV30-10	BGKcLV30-10	BGKcLV30-10
Sample Name	RBM17-BGKcLV30-9	RBM17-BGKcLV30-9	RBM17-BGKcLV30-9	RBM17-BGKcLV30-9	RBM17-BGKcLV30-9	RBM17-BGKcLV30-9	RBM17-BGKcLV30-10	RBM17-BGKcLV30-10	RBM17-BGKcLV30-10	RBM17-BGKcLV30-10
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50K_biosample_protocol	LV50K_library_protocol				LV50K_biosample_protocol	LV50K_library_protocol
protocol_URL		RBM17-BGKcLV30-9.pdf	L-RBM17-BGKcLV30-9.pdf				RBM17-BGKcLV30-10.pdf	L-RBM17-BGKcLV30-10.pdf
ID	5866	5925	5997	6069	6141	6188	5926	5998	6070	6142

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
RBM17-BGKcLV30-9_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1921	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5850
RBM17-BGKcLV30-9_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1921	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5880
RBM17-BGKcLV30-9_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1921					GRCh38	V40	RBM17-BGKcLV30-9_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM17-BGKcLV30-9_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18751
RBM17-BGKcLV30-9_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1921					GRCh38	V40	RBM17-BGKcLV30-9/Aligned.sortedByCoord.out.bam		ENCORE2	18781
RBM17-BGKcLV30-9_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1921					GRCh38	V40	RBM17-BGKcLV30-9/Aligned.sortedByCoord.out.bam		ENCORE2	18811
RBM17-BGKcLV30-9_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1921					GRCh38	V40	RBM17-BGKcLV30-9/Aligned.sortedByCoord.out.bam		ENCORE2	18841
RBM17-BGKcLV30-9_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1921					GRCh38	V40	RBM17-BGKcLV30-9/Aligned.sortedByCoord.out.bam		ENCORE2	18871
RBM17-BGKcLV30-9_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1921					GRCh38	V40	RBM17-BGKcLV30-9_S51_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM17-BGKcLV30-9_S51_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18901
RBM17-BGKcLV30-10_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1922	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5849
RBM17-BGKcLV30-10_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1922	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5879
RBM17-BGKcLV30-10_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1922					GRCh38	V40	RBM17-BGKcLV30-10_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM17-BGKcLV30-10_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18750
RBM17-BGKcLV30-10_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1922					GRCh38	V40	RBM17-BGKcLV30-10/Aligned.sortedByCoord.out.bam		ENCORE2	18780
RBM17-BGKcLV30-10_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1922					GRCh38	V40	RBM17-BGKcLV30-10/Aligned.sortedByCoord.out.bam		ENCORE2	18810
RBM17-BGKcLV30-10_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1922					GRCh38	V40	RBM17-BGKcLV30-10/Aligned.sortedByCoord.out.bam		ENCORE2	18840
RBM17-BGKcLV30-10_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1922					GRCh38	V40	RBM17-BGKcLV30-10/Aligned.sortedByCoord.out.bam		ENCORE2	18870
RBM17-BGKcLV30-10_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1922					GRCh38	V40	RBM17-BGKcLV30-10_S52_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM17-BGKcLV30-10_S52_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18900