RBM8A RNA-Seq in K562

General Information


RBP	RBM8A
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM8A-BGKcLV30-K562
ENCODE_series_ID	ENCSR107CWG
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR163RXI
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RBM8A-BGKcLV30-23
Rep2	RBM8A-BGKcLV30-24
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	86.5
Rep2_WB	88.1
Antibody Cat#	A301-033A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB121MYB
Status	Submitted
Project	ENCODE4
ID	871

Experiment Information (Status: Released)

	BGKcLV30-23	BGKcLV30-24
idx	1048	1049
TRCN#_or_BGC#	BGC#0000770	BGC#0000770
shRNA_or_gRNA_sequence	ACATTCATCTCAACCTCGAC	ACATTCATCTCAACCTCGAC
PAM	AGG	AGG
Name	RBM8A_91	RBM8A_91
Sample_ID	BGKcLV30-23	BGKcLV30-24
transduction_Date	8/30/21	8/30/21
days	D6	D6
RBP_name	RBM8A	RBM8A
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	ttcgcagaatatggggaaat
RT-qPCR_primer-R	atcaaatcctggccattgag
protein_conc	2295	2153
WB_result	86.5	88.1
Ave_WB	87.3
WB_DONE_date	9/9/21
MW	20KD
IP
antibody_Cat#	A301-033A	LOT #1
Antibody DCC ID	ENCAB121MYB
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	5186	5187

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM8A	Product_ID: A301-033A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM8A-human

Experiment Status

	BGKcLV30-23	BGKcLV30-24
Sample_ID	BGKcLV30-23	BGKcLV30-24
Sample Name
Sample Name	RBM8A-BGKcLV30-23	RBM8A-BGKcLV30-24
RBP	RBM8A	RBM8A
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10067	10068

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-23	BGKcLV30-24
Sample #	57	58
Sample Name	RBM8A-BGKcLV30-23	RBM8A-BGKcLV30-24
Sample_Name_Alias
Index Well Position	E08	F08
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	288	293
Peak_Molarity	36.60	43.40
libSampleQC_DNA_Well	DNA_Library_set50/set2/E10.png	DNA_Library_set50/set2/F10.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set50/set2/E10.png	RNA_Library_set50/set2/F10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-23	BGKcLV30-24
RBP	RBM8A	RBM8A
Batch_ID	BGKcLV30	BGKcLV30
WB_result	86.500	88.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3144	3145

Sequencing Information

	BGKcLV30-23	BGKcLV30-24
Sample_ID	BGKcLV30-23	BGKcLV30-24
Sample Name	RBM8A-BGKcLV30-23	RBM8A-BGKcLV30-24
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	108,974,396	101,847,830
total_aligned_reads	104,093,438	97,065,314
unique_aligned_reads	94,960,368	88,470,904
percent_uniqueAligned	0.87140	0.86866
correlation_replicates	0.999474	0.999474
spikein_reads	20,868	15,820
percent_spikeins	0.00019	0.00016
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1929	1930

Data Submission Information

	BGKcLV30-23	BGKcLV30-23	BGKcLV30-23	BGKcLV30-23	BGKcLV30-23	BGKcLV30-23	BGKcLV30-24	BGKcLV30-24	BGKcLV30-24	BGKcLV30-24
ENCODE_alias	brenton-graveley:RBM8A-BGKcLV30	brenton-graveley:RBM8A-BGKcLV30-23	brenton-graveley:L-RBM8A-BGKcLV30-23	brenton-graveley:RBM8A-BGKcLV30-23_S59_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM8A-BGKcLV30-23_S59_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM8A-BGKcLV30-K562	brenton-graveley:RBM8A-BGKcLV30-24	brenton-graveley:L-RBM8A-BGKcLV30-24	brenton-graveley:RBM8A-BGKcLV30-24_S60_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM8A-BGKcLV30-24_S60_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR163RXI	ENCBS374GUN	ENCLB741YNX	ENCFF698INM	ENCFF049JUV	ENCSR107CWG	ENCBS978UDJ	ENCLB999ZXT	ENCFF208CFA	ENCFF670GJO
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	BGKcLV30-23	BGKcLV30-23	BGKcLV30-23	BGKcLV30-23	BGKcLV30-23	BGKcLV30-23	BGKcLV30-24	BGKcLV30-24	BGKcLV30-24	BGKcLV30-24
Sample Name	RBM8A-BGKcLV30-23	RBM8A-BGKcLV30-23	RBM8A-BGKcLV30-23	RBM8A-BGKcLV30-23	RBM8A-BGKcLV30-23	RBM8A-BGKcLV30-23	RBM8A-BGKcLV30-24	RBM8A-BGKcLV30-24	RBM8A-BGKcLV30-24	RBM8A-BGKcLV30-24
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		RBM8A-BGKcLV30-23.pdf	L-RBM8A-BGKcLV30-23.pdf				RBM8A-BGKcLV30-24.pdf	L-RBM8A-BGKcLV30-24.pdf
ID	5870	5933	6005	6077	6149	6192	5934	6006	6078	6150

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
RBM8A-BGKcLV30-23_S59_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1929	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	5857
RBM8A-BGKcLV30-23_S59_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1929	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	5887
RBM8A-BGKcLV30-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1929					GRCh38	V40	RBM8A-BGKcLV30-23_S59_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM8A-BGKcLV30-23_S59_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18758
RBM8A-BGKcLV30-23_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	1929					GRCh38	V40	RBM8A-BGKcLV30-23/Aligned.sortedByCoord.out.bam		ENCORE2	18788
RBM8A-BGKcLV30-23_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	1929					GRCh38	V40	RBM8A-BGKcLV30-23/Aligned.sortedByCoord.out.bam		ENCORE2	18818
RBM8A-BGKcLV30-23_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	1929					GRCh38	V40	RBM8A-BGKcLV30-23/Aligned.sortedByCoord.out.bam		ENCORE2	18848
RBM8A-BGKcLV30-23_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	1929					GRCh38	V40	RBM8A-BGKcLV30-23/Aligned.sortedByCoord.out.bam		ENCORE2	18878
RBM8A-BGKcLV30-23_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1929					GRCh38	V40	RBM8A-BGKcLV30-23_S59_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM8A-BGKcLV30-23_S59_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18908
RBM8A-BGKcLV30-24_S60_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1930	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	5858
RBM8A-BGKcLV30-24_S60_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1930	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	5888
RBM8A-BGKcLV30-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1930					GRCh38	V40	RBM8A-BGKcLV30-24_S60_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM8A-BGKcLV30-24_S60_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18759
RBM8A-BGKcLV30-24_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	1930					GRCh38	V40	RBM8A-BGKcLV30-24/Aligned.sortedByCoord.out.bam		ENCORE2	18789
RBM8A-BGKcLV30-24_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	1930					GRCh38	V40	RBM8A-BGKcLV30-24/Aligned.sortedByCoord.out.bam		ENCORE2	18819
RBM8A-BGKcLV30-24_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	1930					GRCh38	V40	RBM8A-BGKcLV30-24/Aligned.sortedByCoord.out.bam		ENCORE2	18849
RBM8A-BGKcLV30-24_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	1930					GRCh38	V40	RBM8A-BGKcLV30-24/Aligned.sortedByCoord.out.bam		ENCORE2	18879
RBM8A-BGKcLV30-24_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1930					GRCh38	V40	RBM8A-BGKcLV30-24_S60_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM8A-BGKcLV30-24_S60_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18909