RBM19 RNA-Seq in K562

General Information


RBP	RBM19
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM19-BGKcLV19-K562
ENCODE_series_ID	ENCSR987WYR
Batch_ID	BGKcLV19
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR129AAZ
ENCODE_CN_Exp_ID	ENCSR978MMZ
Rep1	RBM19-BGKcLV19-37
Rep2	RBM19-BGKcLV19-38
CN1	NT-BGKcLV19-1
CN2	NT-BGKcLV19-2
Rep1_qPCR	0
Rep2_qPCR	0
Rep1_WB	62.4
Rep2_WB	65.7095474
Antibody Cat#	PA5-58567
Antibody Lot#	LOT# UC2743817
Antibody DCC ID	ENCAB385QQI
Status	Released
Project	ENCODE4
ID	56

Experiment Information (Status: Released)

	BGKcLV19-37	BGKcLV19-38
idx	709	710
TRCN#_or_BGC#	BGC#0000484	BGC#0000484
shRNA_or_gRNA_sequence	CAGGCCATCATTCGCCCAAG	CAGGCCATCATTCGCCCAAG
PAM	TGG	TGG
Name	RBM19_94	RBM19_94
Sample_ID	BGKcLV19-37	BGKcLV19-38
transduction_Date	11/6/19	11/6/19
days	Day 6	Day 6
RBP_name	RBM19	RBM19
qPCR_result	0	0
Ave_qPCR	0.0
RT-qPCR_primer-F	TGAACTTCGACTCCGATTCTG
RT-qPCR_primer-R	CATGTCCGACAGCTCCTTCT
protein_conc	3969	4300
WB_result	62.4	65.7095474
Ave_WB	64.0
WB_DONE_date	8/20/20	jess
MW	107.3kDa
IP	Rabbit / I
antibody_Cat#	PA5-58567	LOT# UC2743817
Antibody DCC ID	ENCAB385QQI
submitted_to_DCC_date	11/16/20
Rep1_TPM	27.6	0
Rep2_TPM	25.7	0
Action	Ready	Ready
Library_start_date	09/24/20	09/24/20
repeat_library
Note
ID	4829	4830

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM19	Product_ID: PA5-58567 Lot_ID: UC2743817 Source: Thermo Fisher Target Name: RBM19-human

Experiment Status

	BGKcLV19-37	BGKcLV19-38
Sample_ID	BGKcLV19-37	BGKcLV19-38
Sample Name
Sample Name	RBM19-BGKcLV19-37	RBM19-BGKcLV19-38
RBP	RBM19	RBM19
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	5705	5706

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV19-37	BGKcLV19-38
Sample #	19	20
Sample Name	RBM19-BGKcLV19-37	RBM19-BGKcLV19-38
Sample_Name_Alias
Index Well Position	E02	F02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	304	290
Peak_Molarity	104.00	124.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/E2.png	DNA_Library_set45/set1/F2.png
RIN	9.7	9.8
libSample_RNA_Well	RNA_Library_set45/set1/E2.png	RNA_Library_set45/set1/F2.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV19-37	BGKcLV19-38
RBP	RBM19	RBM19
Batch_ID	BGKcLV19	BGKcLV19
WB_result	62.400	65.710
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	793	794

Sequencing Information

	BGKcLV19-37	BGKcLV19-38
Sample_ID	BGKcLV19-37	BGKcLV19-38
Sample Name	RBM19-BGKcLV19-37	RBM19-BGKcLV19-38
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	151,258,554	64,068,182
total_aligned_reads	132,649,810	59,821,846
unique_aligned_reads	120,645,460	54,647,708
percent_uniqueAligned	0.79761	0.85296
correlation_replicates	0.976274	0.976274
spikein_reads	139,840	40,934
percent_spikeins	0.00092	0.00064
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	424	425

Data Submission Information

	BGKcLV19-37	BGKcLV19-37	BGKcLV19-37	BGKcLV19-37	BGKcLV19-37	BGKcLV19-37	BGKcLV19-38	BGKcLV19-38	BGKcLV19-38	BGKcLV19-38
ENCODE_alias	brenton-graveley:RBM19-BGKcLV19	brenton-graveley:RBM19-BGKcLV19-37	brenton-graveley:L-RBM19-BGKcLV19-37	brenton-graveley:RBM19-BGKcLV19-37_S13_R1_001.fastq.gz	brenton-graveley:RBM19-BGKcLV19-37_S13_R2_001.fastq.gz	brenton-graveley:RBM19-BGKcLV19-K562	brenton-graveley:RBM19-BGKcLV19-38	brenton-graveley:L-RBM19-BGKcLV19-38	brenton-graveley:RBM19-BGKcLV19-38_S14_R1_001.fastq.gz	brenton-graveley:RBM19-BGKcLV19-38_S14_R2_001.fastq.gz
ENCODE_accession	ENCSR129AAZ	ENCBS358QBF	ENCLB212NDH	ENCFF742CGN	ENCFF602EQZ	ENCSR987WYR	ENCBS175FEQ	ENCLB093JIJ	ENCFF199WFM	ENCFF603QAD
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	BGKcLV19-37	BGKcLV19-37	BGKcLV19-37	BGKcLV19-37	BGKcLV19-37	BGKcLV19-37	BGKcLV19-38	BGKcLV19-38	BGKcLV19-38	BGKcLV19-38
Sample Name	RBM19-BGKcLV19-37	RBM19-BGKcLV19-37	RBM19-BGKcLV19-37	RBM19-BGKcLV19-37	RBM19-BGKcLV19-37	RBM19-BGKcLV19-37	RBM19-BGKcLV19-38	RBM19-BGKcLV19-38	RBM19-BGKcLV19-38	RBM19-BGKcLV19-38
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		RBM19-BGKcLV19-37.pdf	L-RBM19-BGKcLV19-37.pdf				RBM19-BGKcLV19-38.pdf	L-RBM19-BGKcLV19-38.pdf
ID	2096	2147	2217	2287	2357	7299	2148	2218	2288	2358

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
RBM19-BGKcLV19-37_S13_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	424	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1242
RBM19-BGKcLV19-37_S13_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	424	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1292
RBM19-BGKcLV19-37_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	424					GRCh38	V40	RBM19-BGKcLV19-37_S13_R1_001.filtered.trimmed.paired.fastq.gz,RBM19-BGKcLV19-37_S13_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25235
RBM19-BGKcLV19-37_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	424					GRCh38	V40	RBM19-BGKcLV19-37_S13_R1_001.filtered.trimmed.paired.fastq.gz,RBM19-BGKcLV19-37_S13_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27189
RBM19-BGKcLV19-37_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	424					GRCh38	V40	RBM19-BGKcLV19-37/Aligned.sortedByCoord.out.bam		ENCORE2	27239
RBM19-BGKcLV19-37_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	424					GRCh38	V40	RBM19-BGKcLV19-37/Aligned.sortedByCoord.out.bam		ENCORE2	27289
RBM19-BGKcLV19-37_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	424					GRCh38	V40	RBM19-BGKcLV19-37/Aligned.sortedByCoord.out.bam		ENCORE2	27339
RBM19-BGKcLV19-37_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	424					GRCh38	V40	RBM19-BGKcLV19-37/Aligned.sortedByCoord.out.bam		ENCORE2	27389
RBM19-BGKcLV19-38_S14_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	425	NovaSeq6000	100	paired-ended	1				NT-BGKcLV19-1_S1_R1_001.fastq.gz,NT-BGKcLV19-2_S2_R1_001.fastq.gz	ENCODE4	1243
RBM19-BGKcLV19-38_S14_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	425	NovaSeq6000	100	paired-ended	2				NT-BGKcLV19-1_S1_R2_001.fastq.gz,NT-BGKcLV19-2_S2_R2_001.fastq.gz	ENCODE4	1293
RBM19-BGKcLV19-38_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	425					GRCh38	V40	RBM19-BGKcLV19-38_S14_R1_001.filtered.trimmed.paired.fastq.gz,RBM19-BGKcLV19-38_S14_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25236
RBM19-BGKcLV19-38_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	425					GRCh38	V40	RBM19-BGKcLV19-38_S14_R1_001.filtered.trimmed.paired.fastq.gz,RBM19-BGKcLV19-38_S14_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27190
RBM19-BGKcLV19-38_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	425					GRCh38	V40	RBM19-BGKcLV19-38/Aligned.sortedByCoord.out.bam		ENCORE2	27240
RBM19-BGKcLV19-38_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	425					GRCh38	V40	RBM19-BGKcLV19-38/Aligned.sortedByCoord.out.bam		ENCORE2	27290
RBM19-BGKcLV19-38_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	425					GRCh38	V40	RBM19-BGKcLV19-38/Aligned.sortedByCoord.out.bam		ENCORE2	27340
RBM19-BGKcLV19-38_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	425					GRCh38	V40	RBM19-BGKcLV19-38/Aligned.sortedByCoord.out.bam		ENCORE2	27390