RBM28 RNA-Seq in K562

General Information


RBP	RBM28
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM28-BGKcLV30-K562
ENCODE_series_ID	ENCSR409VAG
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR519LZD
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RBM28-BGKcLV30-17
Rep2	RBM28-BGKcLV30-18
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	12.9
Rep2_qPCR	9.0
Rep1_WB	53.0
Rep2_WB	53.0
Antibody Cat#	A303-925A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB217NYD
Status	Submitted
Project	ENCODE4
ID	870

Experiment Information (Status: Released)

	BGKcLV30-17	BGKcLV30-18
idx	1042	1043
TRCN#_or_BGC#	BGC#0000764	BGC#0000764
shRNA_or_gRNA_sequence	CTGCTTGACAGGCCGGACAG	CTGCTTGACAGGCCGGACAG
PAM	TGG	TGG
Name	RBM28_86	RBM28_86
Sample_ID	BGKcLV30-17	BGKcLV30-18
transduction_Date	8/30/21	8/30/21
days	D6	D6
RBP_name	RBM28	RBM28
qPCR_result	12.9	9.0
Ave_qPCR	11.0
RT-qPCR_primer-F	agttccaagagcacgagcat
RT-qPCR_primer-R	ctgcgctggatccttaattc
protein_conc	2130	2618
WB_result	53.0	53.0
Ave_WB	53.0
WB_DONE_date	10/14/21
MW	86KD
IP
antibody_Cat#	A303-925A	LOT #1
Antibody DCC ID	ENCAB217NYD
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	5180	5181

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM28	Product_ID: A303-925A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM28-human

Experiment Status

	BGKcLV30-17	BGKcLV30-18
Sample_ID	BGKcLV30-17	BGKcLV30-18
Sample Name
Sample Name	RBM28-BGKcLV30-17	RBM28-BGKcLV30-18
RBP	RBM28	RBM28
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10065	10066

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-17	BGKcLV30-18
Sample #	55	56
Sample Name	RBM28-BGKcLV30-17	RBM28-BGKcLV30-18
Sample_Name_Alias
Index Well Position	C08	D08
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	290	290
Peak_Molarity	52.00	38.10
libSampleQC_DNA_Well	DNA_Library_set50/set2/C10.png	DNA_Library_set50/set2/D10.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set50/set2/C10.png	RNA_Library_set50/set2/D10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-17	BGKcLV30-18
RBP	RBM28	RBM28
Batch_ID	BGKcLV30	BGKcLV30
WB_result	53.000	53.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3142	3143

Sequencing Information

	BGKcLV30-17	BGKcLV30-18
Sample_ID	BGKcLV30-17	BGKcLV30-18
Sample Name	RBM28-BGKcLV30-17	RBM28-BGKcLV30-18
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	113,481,358	112,538,264
total_aligned_reads	104,376,732	107,133,240
unique_aligned_reads	95,302,326	97,503,686
percent_uniqueAligned	0.83981	0.86640
correlation_replicates	0.991911	0.991911
spikein_reads	19,584	7,704
percent_spikeins	0.00017	0.00007
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1927	1928

Data Submission Information

	BGKcLV30-17	BGKcLV30-17	BGKcLV30-17	BGKcLV30-17	BGKcLV30-17	BGKcLV30-17	BGKcLV30-18	BGKcLV30-18	BGKcLV30-18	BGKcLV30-18
ENCODE_alias	brenton-graveley:RBM28-BGKcLV30	brenton-graveley:RBM28-BGKcLV30-17	brenton-graveley:L-RBM28-BGKcLV30-17	brenton-graveley:RBM28-BGKcLV30-17_S57_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM28-BGKcLV30-17_S57_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM28-BGKcLV30-K562	brenton-graveley:RBM28-BGKcLV30-18	brenton-graveley:L-RBM28-BGKcLV30-18	brenton-graveley:RBM28-BGKcLV30-18_S58_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM28-BGKcLV30-18_S58_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR519LZD	ENCBS539OCN	ENCLB903PYV	ENCFF863QPO	ENCFF986YST	ENCSR409VAG	ENCBS344KXS	ENCLB716LJJ	ENCFF299BXC	ENCFF730GJZ
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	BGKcLV30-17	BGKcLV30-17	BGKcLV30-17	BGKcLV30-17	BGKcLV30-17	BGKcLV30-17	BGKcLV30-18	BGKcLV30-18	BGKcLV30-18	BGKcLV30-18
Sample Name	RBM28-BGKcLV30-17	RBM28-BGKcLV30-17	RBM28-BGKcLV30-17	RBM28-BGKcLV30-17	RBM28-BGKcLV30-17	RBM28-BGKcLV30-17	RBM28-BGKcLV30-18	RBM28-BGKcLV30-18	RBM28-BGKcLV30-18	RBM28-BGKcLV30-18
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		RBM28-BGKcLV30-17.pdf	L-RBM28-BGKcLV30-17.pdf				RBM28-BGKcLV30-18.pdf	L-RBM28-BGKcLV30-18.pdf
ID	5869	5931	6003	6075	6147	6191	5932	6004	6076	6148

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
RBM28-BGKcLV30-17_S57_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1927	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	5855
RBM28-BGKcLV30-17_S57_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1927	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	5885
RBM28-BGKcLV30-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1927					GRCh38	V40	RBM28-BGKcLV30-17_S57_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM28-BGKcLV30-17_S57_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18756
RBM28-BGKcLV30-17_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	1927					GRCh38	V40	RBM28-BGKcLV30-17/Aligned.sortedByCoord.out.bam		ENCORE2	18786
RBM28-BGKcLV30-17_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	1927					GRCh38	V40	RBM28-BGKcLV30-17/Aligned.sortedByCoord.out.bam		ENCORE2	18816
RBM28-BGKcLV30-17_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	1927					GRCh38	V40	RBM28-BGKcLV30-17/Aligned.sortedByCoord.out.bam		ENCORE2	18846
RBM28-BGKcLV30-17_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	1927					GRCh38	V40	RBM28-BGKcLV30-17/Aligned.sortedByCoord.out.bam		ENCORE2	18876
RBM28-BGKcLV30-17_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1927					GRCh38	V40	RBM28-BGKcLV30-17_S57_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM28-BGKcLV30-17_S57_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18906
RBM28-BGKcLV30-18_S58_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1928	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	5856
RBM28-BGKcLV30-18_S58_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1928	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	5886
RBM28-BGKcLV30-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1928					GRCh38	V40	RBM28-BGKcLV30-18_S58_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM28-BGKcLV30-18_S58_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18757
RBM28-BGKcLV30-18_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	1928					GRCh38	V40	RBM28-BGKcLV30-18/Aligned.sortedByCoord.out.bam		ENCORE2	18787
RBM28-BGKcLV30-18_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	1928					GRCh38	V40	RBM28-BGKcLV30-18/Aligned.sortedByCoord.out.bam		ENCORE2	18817
RBM28-BGKcLV30-18_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	1928					GRCh38	V40	RBM28-BGKcLV30-18/Aligned.sortedByCoord.out.bam		ENCORE2	18847
RBM28-BGKcLV30-18_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	1928					GRCh38	V40	RBM28-BGKcLV30-18/Aligned.sortedByCoord.out.bam		ENCORE2	18877
RBM28-BGKcLV30-18_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1928					GRCh38	V40	RBM28-BGKcLV30-18_S58_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM28-BGKcLV30-18_S58_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18907