RBM25 RNA-Seq in K562

General Information


RBP	RBM25
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM25-BGKcLV30-K562
ENCODE_series_ID	ENCSR435FMG
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR041IXV
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RBM25-BGKcLV30-11
Rep2	RBM25-BGKcLV30-12
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	49.2
Rep2_qPCR	50.6
Rep1_WB	83.3
Rep2_WB	90.3
Antibody Cat#	A301-067A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB042ILI
Status	Submitted
Project	ENCODE4
ID	868

Experiment Information (Status: Released)

	BGKcLV30-11	BGKcLV30-12
idx	1036	1037
TRCN#_or_BGC#	BGC#0000759	BGC#0000759
shRNA_or_gRNA_sequence	CATTTGAATCGCCCTCCCAT	CATTTGAATCGCCCTCCCAT
PAM	GGG	GGG
Name	RBM25_89	RBM25_89
Sample_ID	BGKcLV30-11	BGKcLV30-12
transduction_Date	8/30/21	8/30/21
days	D6	D6
RBP_name	RBM25	RBM25
qPCR_result	49.2	50.6
Ave_qPCR	49.9
RT-qPCR_primer-F	GAATTCTTAGAAGACTATGATGATGA
RT-qPCR_primer-R	TTTCTCTATCACGCAACCTTT
protein_conc	2397	2530
WB_result	83.3	90.3
Ave_WB	86.8
WB_DONE_date	9/22/21
MW	100KD
IP
antibody_Cat#	A301-067A	LOT #1
Antibody DCC ID	ENCAB042ILI
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	5174	5175

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM25	Product_ID: A301-067A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM25-human

Experiment Status

	BGKcLV30-11	BGKcLV30-12
Sample_ID	BGKcLV30-11	BGKcLV30-12
Sample Name
Sample Name	RBM25-BGKcLV30-11	RBM25-BGKcLV30-12
RBP	RBM25	RBM25
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10061	10062

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-11	BGKcLV30-12
Sample #	51	52
Sample Name	RBM25-BGKcLV30-11	RBM25-BGKcLV30-12
Sample_Name_Alias
Index Well Position	G07	H07
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	282	277
Peak_Molarity	61.20	25.80
libSampleQC_DNA_Well	DNA_Library_set50/set2/G9.png	DNA_Library_set50/set2/H9.png
RIN	9.6	9.5
libSample_RNA_Well	RNA_Library_set50/set2/G9.png	RNA_Library_set50/set2/H9.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-11	BGKcLV30-12
RBP	RBM25	RBM25
Batch_ID	BGKcLV30	BGKcLV30
WB_result	83.300	90.300
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3138	3139

Sequencing Information

	BGKcLV30-11	BGKcLV30-12
Sample_ID	BGKcLV30-11	BGKcLV30-12
Sample Name	RBM25-BGKcLV30-11	RBM25-BGKcLV30-12
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	98,109,070	63,180,726
total_aligned_reads	91,211,242	56,935,080
unique_aligned_reads	83,120,572	51,546,634
percent_uniqueAligned	0.84723	0.81586
correlation_replicates	0.994639	0.994639
spikein_reads	26,050	11,110
percent_spikeins	0.00027	0.00018
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1923	1924

Data Submission Information

	BGKcLV30-11	BGKcLV30-11	BGKcLV30-11	BGKcLV30-11	BGKcLV30-11	BGKcLV30-11	BGKcLV30-12	BGKcLV30-12	BGKcLV30-12	BGKcLV30-12
ENCODE_alias	brenton-graveley:RBM25-BGKcLV30	brenton-graveley:RBM25-BGKcLV30-11	brenton-graveley:L-RBM25-BGKcLV30-11	brenton-graveley:RBM25-BGKcLV30-11_S53_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM25-BGKcLV30-11_S53_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM25-BGKcLV30-K562	brenton-graveley:RBM25-BGKcLV30-12	brenton-graveley:L-RBM25-BGKcLV30-12	brenton-graveley:RBM25-BGKcLV30-12_S54_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM25-BGKcLV30-12_S54_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR041IXV	ENCBS873CAZ	ENCLB230KGJ	ENCFF104IDO	ENCFF611HAX	ENCSR435FMG	ENCBS824XKV	ENCLB886YKI	ENCFF066PYO	ENCFF548GSX
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	BGKcLV30-11	BGKcLV30-11	BGKcLV30-11	BGKcLV30-11	BGKcLV30-11	BGKcLV30-11	BGKcLV30-12	BGKcLV30-12	BGKcLV30-12	BGKcLV30-12
Sample Name	RBM25-BGKcLV30-11	RBM25-BGKcLV30-11	RBM25-BGKcLV30-11	RBM25-BGKcLV30-11	RBM25-BGKcLV30-11	RBM25-BGKcLV30-11	RBM25-BGKcLV30-12	RBM25-BGKcLV30-12	RBM25-BGKcLV30-12	RBM25-BGKcLV30-12
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		RBM25-BGKcLV30-11.pdf	L-RBM25-BGKcLV30-11.pdf				RBM25-BGKcLV30-12.pdf	L-RBM25-BGKcLV30-12.pdf
ID	5867	5927	5999	6071	6143	6189	5928	6000	6072	6144

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-BGKcLV30-11_S53_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1923	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	5851
RBM25-BGKcLV30-11_S53_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1923	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	5881
RBM25-BGKcLV30-11_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1923					GRCh38	V40	RBM25-BGKcLV30-11_S53_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGKcLV30-11_S53_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18752
RBM25-BGKcLV30-11_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	1923					GRCh38	V40	RBM25-BGKcLV30-11/Aligned.sortedByCoord.out.bam		ENCORE2	18782
RBM25-BGKcLV30-11_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	1923					GRCh38	V40	RBM25-BGKcLV30-11/Aligned.sortedByCoord.out.bam		ENCORE2	18812
RBM25-BGKcLV30-11_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	1923					GRCh38	V40	RBM25-BGKcLV30-11/Aligned.sortedByCoord.out.bam		ENCORE2	18842
RBM25-BGKcLV30-11_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	1923					GRCh38	V40	RBM25-BGKcLV30-11/Aligned.sortedByCoord.out.bam		ENCORE2	18872
RBM25-BGKcLV30-11_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1923					GRCh38	V40	RBM25-BGKcLV30-11_S53_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGKcLV30-11_S53_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18902
RBM25-BGKcLV30-12_S54_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1924	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	5852
RBM25-BGKcLV30-12_S54_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1924	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	5882
RBM25-BGKcLV30-12_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1924					GRCh38	V40	RBM25-BGKcLV30-12_S54_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGKcLV30-12_S54_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18753
RBM25-BGKcLV30-12_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	1924					GRCh38	V40	RBM25-BGKcLV30-12/Aligned.sortedByCoord.out.bam		ENCORE2	18783
RBM25-BGKcLV30-12_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	1924					GRCh38	V40	RBM25-BGKcLV30-12/Aligned.sortedByCoord.out.bam		ENCORE2	18813
RBM25-BGKcLV30-12_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	1924					GRCh38	V40	RBM25-BGKcLV30-12/Aligned.sortedByCoord.out.bam		ENCORE2	18843
RBM25-BGKcLV30-12_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	1924					GRCh38	V40	RBM25-BGKcLV30-12/Aligned.sortedByCoord.out.bam		ENCORE2	18873
RBM25-BGKcLV30-12_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1924					GRCh38	V40	RBM25-BGKcLV30-12_S54_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM25-BGKcLV30-12_S54_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18903