RBM26 RNA-Seq in K562

General Information


RBP	RBM26
Cell_Line	K562
Method	CRISPR
Exp_Name	RBM26-BGKcLV30-K562
ENCODE_series_ID	ENCSR019AZZ
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR096JMV
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RBM26-BGKcLV30-13
Rep2	RBM26-BGKcLV30-14
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	23.0
Rep2_qPCR	7.3
Rep1_WB	56.9
Rep2_WB	55.4
Antibody Cat#	A301-216A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB870CGZ
Status	Submitted
Project	ENCODE4
ID	869

Experiment Information (Status: Released)

	BGKcLV30-13	BGKcLV30-14
idx	1038	1039
TRCN#_or_BGC#	BGC#0000760	BGC#0000760
shRNA_or_gRNA_sequence	ACCGGTACAATAGAAGACGA	ACCGGTACAATAGAAGACGA
PAM	GGG	GGG
Name	RBM26_95	RBM26_95
Sample_ID	BGKcLV30-13	BGKcLV30-14
transduction_Date	8/30/21	8/30/21
days	D6	D6
RBP_name	RBM26	RBM26
qPCR_result	23.0	7.3
Ave_qPCR	15.2
RT-qPCR_primer-F	catgccaaagaaacggtgta
RT-qPCR_primer-R	aaggcagcataccaggaaga
protein_conc	2332	2344
WB_result	56.9	55.4
Ave_WB	56.1
WB_DONE_date	9/27/21
MW	114KD
IP
antibody_Cat#	A301-216A	LOT #1
Antibody DCC ID	ENCAB870CGZ
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	5176	5177

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RBM26	Product_ID: A301-216A Lot_ID: 1 Source: Bethyl Labs Target Name: RBM26-human

Experiment Status

	BGKcLV30-13	BGKcLV30-14
Sample_ID	BGKcLV30-13	BGKcLV30-14
Sample Name
Sample Name	RBM26-BGKcLV30-13	RBM26-BGKcLV30-14
RBP	RBM26	RBM26
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10063	10064

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-13	BGKcLV30-14
Sample #	53	54
Sample Name	RBM26-BGKcLV30-13	RBM26-BGKcLV30-14
Sample_Name_Alias
Index Well Position	A08	B08
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	290
Peak_Molarity	41.40	40.60
libSampleQC_DNA_Well	DNA_Library_set50/set2/A10.png	DNA_Library_set50/set2/B10.png
RIN	9.5	9.6
libSample_RNA_Well	RNA_Library_set50/set2/A10.png	RNA_Library_set50/set2/B10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-13	BGKcLV30-14
RBP	RBM26	RBM26
Batch_ID	BGKcLV30	BGKcLV30
WB_result	56.900	55.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3140	3141

Sequencing Information

	BGKcLV30-13	BGKcLV30-14
Sample_ID	BGKcLV30-13	BGKcLV30-14
Sample Name	RBM26-BGKcLV30-13	RBM26-BGKcLV30-14
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	102,284,504	68,143,678
total_aligned_reads	96,945,142	63,598,332
unique_aligned_reads	88,574,030	58,176,430
percent_uniqueAligned	0.86596	0.85373
correlation_replicates	0.992552	0.992552
spikein_reads	31,620	12,684
percent_spikeins	0.00031	0.00019
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1925	1926

Data Submission Information

	BGKcLV30-13	BGKcLV30-13	BGKcLV30-13	BGKcLV30-13	BGKcLV30-13	BGKcLV30-13	BGKcLV30-14	BGKcLV30-14	BGKcLV30-14	BGKcLV30-14
ENCODE_alias	brenton-graveley:RBM26-BGKcLV30	brenton-graveley:RBM26-BGKcLV30-13	brenton-graveley:L-RBM26-BGKcLV30-13	brenton-graveley:RBM26-BGKcLV30-13_S55_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM26-BGKcLV30-13_S55_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM26-BGKcLV30-K562	brenton-graveley:RBM26-BGKcLV30-14	brenton-graveley:L-RBM26-BGKcLV30-14	brenton-graveley:RBM26-BGKcLV30-14_S56_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RBM26-BGKcLV30-14_S56_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR096JMV	ENCBS603SIB	ENCLB880XMT	ENCFF572LCY	ENCFF143HRS	ENCSR019AZZ	ENCBS384SFY	ENCLB852CBH	ENCFF489DCK	ENCFF382CFK
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	BGKcLV30-13	BGKcLV30-13	BGKcLV30-13	BGKcLV30-13	BGKcLV30-13	BGKcLV30-13	BGKcLV30-14	BGKcLV30-14	BGKcLV30-14	BGKcLV30-14
Sample Name	RBM26-BGKcLV30-13	RBM26-BGKcLV30-13	RBM26-BGKcLV30-13	RBM26-BGKcLV30-13	RBM26-BGKcLV30-13	RBM26-BGKcLV30-13	RBM26-BGKcLV30-14	RBM26-BGKcLV30-14	RBM26-BGKcLV30-14	RBM26-BGKcLV30-14
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		RBM26-BGKcLV30-13.pdf	L-RBM26-BGKcLV30-13.pdf				RBM26-BGKcLV30-14.pdf	L-RBM26-BGKcLV30-14.pdf
ID	5868	5929	6001	6073	6145	6190	5930	6002	6074	6146

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
RBM26-BGKcLV30-13_S55_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1925	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	5853
RBM26-BGKcLV30-13_S55_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1925	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	5883
RBM26-BGKcLV30-13_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1925					GRCh38	V40	RBM26-BGKcLV30-13_S55_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM26-BGKcLV30-13_S55_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18754
RBM26-BGKcLV30-13_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	1925					GRCh38	V40	RBM26-BGKcLV30-13/Aligned.sortedByCoord.out.bam		ENCORE2	18784
RBM26-BGKcLV30-13_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	1925					GRCh38	V40	RBM26-BGKcLV30-13/Aligned.sortedByCoord.out.bam		ENCORE2	18814
RBM26-BGKcLV30-13_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	1925					GRCh38	V40	RBM26-BGKcLV30-13/Aligned.sortedByCoord.out.bam		ENCORE2	18844
RBM26-BGKcLV30-13_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	1925					GRCh38	V40	RBM26-BGKcLV30-13/Aligned.sortedByCoord.out.bam		ENCORE2	18874
RBM26-BGKcLV30-13_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1925					GRCh38	V40	RBM26-BGKcLV30-13_S55_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM26-BGKcLV30-13_S55_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18904
RBM26-BGKcLV30-14_S56_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1926	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	5854
RBM26-BGKcLV30-14_S56_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1926	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	5884
RBM26-BGKcLV30-14_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1926					GRCh38	V40	RBM26-BGKcLV30-14_S56_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM26-BGKcLV30-14_S56_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18755
RBM26-BGKcLV30-14_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	1926					GRCh38	V40	RBM26-BGKcLV30-14/Aligned.sortedByCoord.out.bam		ENCORE2	18785
RBM26-BGKcLV30-14_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	1926					GRCh38	V40	RBM26-BGKcLV30-14/Aligned.sortedByCoord.out.bam		ENCORE2	18815
RBM26-BGKcLV30-14_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	1926					GRCh38	V40	RBM26-BGKcLV30-14/Aligned.sortedByCoord.out.bam		ENCORE2	18845
RBM26-BGKcLV30-14_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	1926					GRCh38	V40	RBM26-BGKcLV30-14/Aligned.sortedByCoord.out.bam		ENCORE2	18875
RBM26-BGKcLV30-14_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1926					GRCh38	V40	RBM26-BGKcLV30-14_S56_L001_R1_001.filtered.trimmed.paired.fastq.gz,RBM26-BGKcLV30-14_S56_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18905