RBM14 RNA-Seq in K562

General Information


RBP	RBM14
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM14-BGKcLV30-K562
ENCODE_series_ID	ENCSR851LMI
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR821KIN
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RBM14-BGKcLV30-5
Rep2	RBM14-BGKcLV30-6
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	67.2
Rep2_WB	58.4
Antibody Cat#	A300-331A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB845NVZ
Status	Submitted
Project	ENCODE4
ID	866

Experiment Information (Status: Released)

	BGKcLV30-5	BGKcLV30-5	BGKcLV30-6	BGKcLV30-6
idx	1030	1030	1031	1031
TRCN#_or_BGC#	BGC#0000754	BGC#0000754	BGC#0000754	BGC#0000754
shRNA_or_gRNA_sequence	CGACGGGGCGGATACGACTC	CGACGGGGCGGATACGACTC	CGACGGGGCGGATACGACTC	CGACGGGGCGGATACGACTC
PAM	CGG	CGG	CGG	CGG
Name	RBM14_98	RBM14_98	RBM14_98	RBM14_98
Sample_ID	BGKcLV30-5	BGKcLV30-5	BGKcLV30-6	BGKcLV30-6
transduction_Date	8/30/21	8/30/21	8/30/21	8/30/21
days	D6	D6	D6	D6
RBP_name	RBM14	RBM14	RBM14	RBM14
qPCR_result	0.0	0.0	0.0	0.0
Ave_qPCR	0.0	0.0
RT-qPCR_primer-F	ACTTTGTTCCTTCGCCTCAG	ACTTTGTTCCTTCGCCTCAG
RT-qPCR_primer-R	AAACCGCAGATCTAGAGCCA	AAACCGCAGATCTAGAGCCA
protein_conc	2353	2353	2889	2889
WB_result	67.2	65.8	58.4	72.7637
Ave_WB	62.8	69.3
WB_DONE_date	9/22/21	6/28/22
MW	69KD	69KD
IP
antibody_Cat#	A300-331A	A300-845A	LOT #1	LOT # 2
Antibody DCC ID	ENCAB845NVZ	ENCAB835MEH
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	11/10/21		11/10/21
repeat_library
Note
ID	5166	5168	5167	5169

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM14	Product_ID: A300-331A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM14-human
RBM14	Product_ID: A300-845A Lot_ID: 2 Source: Bethyl Labs Target Name: RBM14-human

Experiment Status

	BGKcLV30-5	BGKcLV30-6
Sample_ID	BGKcLV30-5	BGKcLV30-6
Sample Name
Sample Name	RBM14-BGKcLV30-5	RBM14-BGKcLV30-6
RBP	RBM14	RBM14
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10057	10058

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-5	BGKcLV30-6
Sample #	47	48
Sample Name	RBM14-BGKcLV30-5	RBM14-BGKcLV30-6
Sample_Name_Alias
Index Well Position	C07	D07
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	309	297
Peak_Molarity	48.90	54.00
libSampleQC_DNA_Well	DNA_Library_set50/set2/C9.png	DNA_Library_set50/set2/D9.png
RIN	9.7	9.5
libSample_RNA_Well	RNA_Library_set50/set2/C9.png	RNA_Library_set50/set2/D9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-5	BGKcLV30-6
RBP	RBM14	RBM14
Batch_ID	BGKcLV30	BGKcLV30
WB_result	67.200	58.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3134	3135

Sequencing Information

	BGKcLV30-5	BGKcLV30-6
Sample_ID	BGKcLV30-5	BGKcLV30-6
Sample Name	RBM14-BGKcLV30-5	RBM14-BGKcLV30-6
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	58,892,904	99,037,940
total_aligned_reads	49,632,292	95,188,786
unique_aligned_reads	45,332,980	86,731,428
percent_uniqueAligned	0.76975	0.87574
correlation_replicates	0.971766	0.971766
spikein_reads	16,196	11,576
percent_spikeins	0.00028	0.00012
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1919	1920

Data Submission Information

	BGKcLV30-5	BGKcLV30-5	BGKcLV30-5	BGKcLV30-5	BGKcLV30-5	BGKcLV30-5	BGKcLV30-6	BGKcLV30-6	BGKcLV30-6	BGKcLV30-6
ENCODE_alias	brenton-graveley:RBM14-BGKcLV30	brenton-graveley:RBM14-BGKcLV30-5	brenton-graveley:L-RBM14-BGKcLV30-5	brenton-graveley:RBM14-BGKcLV30-5_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM14-BGKcLV30-5_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM14-BGKcLV30-K562	brenton-graveley:RBM14-BGKcLV30-6	brenton-graveley:L-RBM14-BGKcLV30-6	brenton-graveley:RBM14-BGKcLV30-6_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM14-BGKcLV30-6_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR821KIN	ENCBS334DIV	ENCLB280SXO	ENCFF199BHP	ENCFF770XHN	ENCSR851LMI	ENCBS590JCA	ENCLB118EXU	ENCFF579MFC	ENCFF255AXT
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	BGKcLV30-5	BGKcLV30-5	BGKcLV30-5	BGKcLV30-5	BGKcLV30-5	BGKcLV30-5	BGKcLV30-6	BGKcLV30-6	BGKcLV30-6	BGKcLV30-6
Sample Name	RBM14-BGKcLV30-5	RBM14-BGKcLV30-5	RBM14-BGKcLV30-5	RBM14-BGKcLV30-5	RBM14-BGKcLV30-5	RBM14-BGKcLV30-5	RBM14-BGKcLV30-6	RBM14-BGKcLV30-6	RBM14-BGKcLV30-6	RBM14-BGKcLV30-6
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		RBM14-BGKcLV30-5.pdf	L-RBM14-BGKcLV30-5.pdf				RBM14-BGKcLV30-6.pdf	L-RBM14-BGKcLV30-6.pdf
ID	5865	5923	5995	6067	6139	6187	5924	5996	6068	6140

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
RBM14-BGKcLV30-5_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1919	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	5847
RBM14-BGKcLV30-5_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1919	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	5877
RBM14-BGKcLV30-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1919					GRCh38	V40	RBM14-BGKcLV30-5_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM14-BGKcLV30-5_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18748
RBM14-BGKcLV30-5_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	1919					GRCh38	V40	RBM14-BGKcLV30-5/Aligned.sortedByCoord.out.bam		ENCORE2	18778
RBM14-BGKcLV30-5_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	1919					GRCh38	V40	RBM14-BGKcLV30-5/Aligned.sortedByCoord.out.bam		ENCORE2	18808
RBM14-BGKcLV30-5_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	1919					GRCh38	V40	RBM14-BGKcLV30-5/Aligned.sortedByCoord.out.bam		ENCORE2	18838
RBM14-BGKcLV30-5_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	1919					GRCh38	V40	RBM14-BGKcLV30-5/Aligned.sortedByCoord.out.bam		ENCORE2	18868
RBM14-BGKcLV30-5_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1919					GRCh38	V40	RBM14-BGKcLV30-5_S49_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM14-BGKcLV30-5_S49_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18898
RBM14-BGKcLV30-6_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1920	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	5848
RBM14-BGKcLV30-6_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1920	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	5878
RBM14-BGKcLV30-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1920					GRCh38	V40	RBM14-BGKcLV30-6_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM14-BGKcLV30-6_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18749
RBM14-BGKcLV30-6_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	1920					GRCh38	V40	RBM14-BGKcLV30-6/Aligned.sortedByCoord.out.bam		ENCORE2	18779
RBM14-BGKcLV30-6_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	1920					GRCh38	V40	RBM14-BGKcLV30-6/Aligned.sortedByCoord.out.bam		ENCORE2	18809
RBM14-BGKcLV30-6_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	1920					GRCh38	V40	RBM14-BGKcLV30-6/Aligned.sortedByCoord.out.bam		ENCORE2	18839
RBM14-BGKcLV30-6_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	1920					GRCh38	V40	RBM14-BGKcLV30-6/Aligned.sortedByCoord.out.bam		ENCORE2	18869
RBM14-BGKcLV30-6_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1920					GRCh38	V40	RBM14-BGKcLV30-6_S50_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM14-BGKcLV30-6_S50_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18899