CAPRIN1 RNA-Seq in K562

General Information


RBP	CAPRIN1
Cell_Line	K562
Method	CRISPR
Exp_Name	CAPRIN1-BGKcLV26-K562
ENCODE_series_ID	ENCSR699ZDH
Batch_ID	BGKcLV26
Pool ID	Pool-210908
Local_Set_Name	set48_K
ENCODE_KD_Exp_ID	ENCSR633RMN
ENCODE_CN_Exp_ID	ENCSR900GQL
Rep1	CAPRIN1-BGKcLV26-53
Rep2	CAPRIN1-BGKcLV26-54
CN1	NT-BGKcLV26-1
CN2	NT-BGKcLV26-2
Rep1_qPCR
Rep2_qPCR
Rep1_WB	54.9
Rep2_WB	62.4
Antibody Cat#	A303-882A
Antibody Lot#	LOT# 1
Antibody DCC ID	ENCAB013NZM
Status	Released
Project	ENCODE4
ID	800

Experiment Information (Status: Released)

	BGKcLV26-53	BGKcLV26-53	BGKcLV26-54	BGKcLV26-54
idx	914	916	915	917
TRCN#_or_BGC#	BGC#0000661	BGC#0000661	BGC#0000661	BGC#0000661
shRNA_or_gRNA_sequence	AGTGCCAATATTGTCCGAAG	AGTGCCAATATTGTCCGAAG	AGTGCCAATATTGTCCGAAG	AGTGCCAATATTGTCCGAAG
PAM	AGG	AGG	AGG	AGG
Name	CAPRIN1_94	CAPRIN1_94	CAPRIN1_94	CAPRIN1_94
Sample_ID	BGKcLV26-53	BGKcLV26-53	BGKcLV26-54	BGKcLV26-54
transduction_Date	3/30/21	3/30/21	3/30/21	3/30/21
days	Day 6	Day 6	Day 6	Day 6
RBP_name	CAPRIN1	CAPRIN1	CAPRIN1	CAPRIN1
qPCR_result	0.0	0.0	0.0	0.0
Ave_qPCR	0.0	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4998	4998	5214	5214
WB_result	54.9	82.9	62.4	89.1046678
Ave_WB	58.6	86.0
WB_DONE_date	5/6/21	4/20/22	jess
MW	78kDa	78kDa
IP	Rabbit / I	Rabbit / I
antibody_Cat#	A303-881A	A303-882A	LOT# 1	LOT# 1
Antibody DCC ID	ENCAB944GEF
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	09/01/21		09/01/21
repeat_library
Note
ID	5046	5048	5047	5049

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CAPRIN1	Product_ID: A303-881A Lot_ID: 1 Source: Bethyl Labs Target Name: CAPRIN1-human

Experiment Status

	BGKcLV26-53	BGKcLV26-54
Sample_ID	BGKcLV26-53	BGKcLV26-54
Sample Name
Sample Name	CAPRIN1-BGKcLV26-53	CAPRIN1-BGKcLV26-54
RBP	CAPRIN1	CAPRIN1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4
Note
ID	9781	9782

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV26-53	BGKcLV26-54
Sample #	39	40
Sample Name	CAPRIN1-BGKcLV26-53	CAPRIN1-BGKcLV26-54
Sample_Name_Alias
Index Well Position	G05	H05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-07-22	2021-07-22
Lib_ID	Lib-210722	Lib-210722
Tecan_Location
Tecan
Tecan_date
Size_bp	291	289
Peak_Molarity	115.00	124.00
libSampleQC_DNA_Well	DNA_Library_set48-49/set1/G5.png	DNA_Library_set48-49/set1/H5.png
RIN	9.8	10.0
libSample_RNA_Well	RNA_Library_set48-49/set1/G5.png	RNA_Library_set48-49/set1/H5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-09-02	2021-09-02
Sample_ID	BGKcLV26-53	BGKcLV26-54
RBP	CAPRIN1	CAPRIN1
Batch_ID	BGKcLV26	BGKcLV26
WB_result	54.900	62.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1598	1599

Sequencing Information

	BGKcLV26-53	BGKcLV26-54
Sample_ID	BGKcLV26-53	BGKcLV26-54
Sample Name	CAPRIN1-BGKcLV26-53	CAPRIN1-BGKcLV26-54
Pool ID	Pool-210908	Pool-210908
LocalServer_folder	set48_K	set48_K
total_reads	81,799,062	64,556,238
total_aligned_reads	73,847,938	57,062,432
unique_aligned_reads	67,617,348	52,349,318
percent_uniqueAligned	0.82663	0.81091
correlation_replicates	0.999130	0.999130
spikein_reads	26,446	13,788
percent_spikeins	0.00032	0.00021
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	1775	1776

Data Submission Information

	BGKcLV26-53	BGKcLV26-53	BGKcLV26-53	BGKcLV26-53	BGKcLV26-53	BGKcLV26-53	BGKcLV26-54	BGKcLV26-54	BGKcLV26-54	BGKcLV26-54
ENCODE_alias	brenton-graveley:CAPRIN1-BGKcLV26	brenton-graveley:CAPRIN1-BGKcLV26-53	brenton-graveley:L-CAPRIN1-BGKcLV26-53	brenton-graveley:CAPRIN1-BGKcLV26-53_S45_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAPRIN1-BGKcLV26-53_S45_L003_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAPRIN1-BGKcLV26-K562	brenton-graveley:CAPRIN1-BGKcLV26-54	brenton-graveley:L-CAPRIN1-BGKcLV26-54	brenton-graveley:CAPRIN1-BGKcLV26-54_S46_L003_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:CAPRIN1-BGKcLV26-54_S46_L003_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR633RMN	ENCBS384UVR	ENCLB015LQY	ENCFF400UBN	ENCFF418KRT	ENCSR699ZDH	ENCBS897FOF	ENCLB216TII	ENCFF163FHN	ENCFF105BOW
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	BGKcLV26-53	BGKcLV26-53	BGKcLV26-53	BGKcLV26-53	BGKcLV26-53	BGKcLV26-53	BGKcLV26-54	BGKcLV26-54	BGKcLV26-54	BGKcLV26-54
Sample Name	CAPRIN1-BGKcLV26-53	CAPRIN1-BGKcLV26-53	CAPRIN1-BGKcLV26-53	CAPRIN1-BGKcLV26-53	CAPRIN1-BGKcLV26-53	CAPRIN1-BGKcLV26-53	CAPRIN1-BGKcLV26-54	CAPRIN1-BGKcLV26-54	CAPRIN1-BGKcLV26-54	CAPRIN1-BGKcLV26-54
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Submitted	Released	Released	Released	Released	Submitted	Released	Released	Released
Status_Date	2021-11-19	2022-02-04	2021-11-19	2021-11-19	2021-11-19	2022-03-02	2022-02-04	2021-11-19	2021-11-19	2021-11-19
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV48K_biosample_protocol	LV48K_library_protocol				LV48K_biosample_protocol	LV48K_library_protocol
protocol_URL		CAPRIN1-BGKcLV26-53.pdf	L-CAPRIN1-BGKcLV26-53.pdf				CAPRIN1-BGKcLV26-54.pdf	L-CAPRIN1-BGKcLV26-54.pdf
ID	3465	3564	3698	3832	3966	7112	3565	3699	3833	3967

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
CAPRIN1-BGKcLV26-53_S45_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1775	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3868
CAPRIN1-BGKcLV26-53_S45_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1775	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3918
CAPRIN1-BGKcLV26-53_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1775					GRCh38	V40	CAPRIN1-BGKcLV26-53_S45_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAPRIN1-BGKcLV26-53_S45_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25555
CAPRIN1-BGKcLV26-53_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1775					GRCh38	V40	CAPRIN1-BGKcLV26-53_S45_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAPRIN1-BGKcLV26-53_S45_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25605
CAPRIN1-BGKcLV26-53_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1775					GRCh38	V40	CAPRIN1-BGKcLV26-53/Aligned.sortedByCoord.out.bam		ENCORE2	26571
CAPRIN1-BGKcLV26-53_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1775					GRCh38	V40	CAPRIN1-BGKcLV26-53/Aligned.sortedByCoord.out.bam		ENCORE2	26621
CAPRIN1-BGKcLV26-53_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1775					GRCh38	V40	CAPRIN1-BGKcLV26-53/Aligned.sortedByCoord.out.bam		ENCORE2	26671
CAPRIN1-BGKcLV26-53_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1775					GRCh38	V40	CAPRIN1-BGKcLV26-53/Aligned.sortedByCoord.out.bam		ENCORE2	26721
CAPRIN1-BGKcLV26-54_S46_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1776	NovaSeq6000	100	paired-ended	1				NT-BGKcLV26-1_S7_L003_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3869
CAPRIN1-BGKcLV26-54_S46_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set48_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1776	NovaSeq6000	100	paired-ended	2				NT-BGKcLV26-1_S7_L003_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV26-2_S8_L003_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	3919
CAPRIN1-BGKcLV26-54_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1776					GRCh38	V40	CAPRIN1-BGKcLV26-54_S46_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAPRIN1-BGKcLV26-54_S46_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25556
CAPRIN1-BGKcLV26-54_quant.sf	ENCODE_DATA/set48_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1776					GRCh38	V40	CAPRIN1-BGKcLV26-54_S46_L003_R1_001.filtered.trimmed.paired.fastq.gz,CAPRIN1-BGKcLV26-54_S46_L003_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25606
CAPRIN1-BGKcLV26-54_Signal.Unique.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1776					GRCh38	V40	CAPRIN1-BGKcLV26-54/Aligned.sortedByCoord.out.bam		ENCORE2	26572
CAPRIN1-BGKcLV26-54_Signal.Unique.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1776					GRCh38	V40	CAPRIN1-BGKcLV26-54/Aligned.sortedByCoord.out.bam		ENCORE2	26622
CAPRIN1-BGKcLV26-54_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1776					GRCh38	V40	CAPRIN1-BGKcLV26-54/Aligned.sortedByCoord.out.bam		ENCORE2	26672
CAPRIN1-BGKcLV26-54_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set48_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1776					GRCh38	V40	CAPRIN1-BGKcLV26-54/Aligned.sortedByCoord.out.bam		ENCORE2	26722