PCBP3 RNA-Seq in K562

General Information


RBP	PCBP3
Cell_Line	K562
Method	CRISPR
Exp_Name	PCBP3-BGKcLV06-K562
ENCODE_series_ID	ENCSR494SZR
Batch_ID	BGKcLV06
Pool ID	Pool-170911
Local_Set_Name	set39_K
ENCODE_KD_Exp_ID	ENCSR105LOV
ENCODE_CN_Exp_ID	ENCSR341TTW
Rep1	PCBP3-BGKcLV06-23
Rep2	PCBP3-BGKcLV06-24
CN1	NT-BGKcLV06-1
CN2	NT-BGKcLV06-2
Rep1_qPCR	no good primers
Rep2_qPCR
Rep1_WB	48.6
Rep2_WB	56.1
Antibody Cat#	RN054PW
Antibody Lot#
Antibody DCC ID	ENCAB823NUI
Status	Released
Project	ENCODE3
ID	774

Experiment Information (Status: Released)

	BGKcLV06-23	BGKcLV06-24
idx	199	200
TRCN#_or_BGC#	BGC#0000086	BGC#0000086
shRNA_or_gRNA_sequence	ACCATCCGCCTGCTGATGCA	ACCATCCGCCTGCTGATGCA
PAM
Name	PCBP3_78	PCBP3_78
Sample_ID	BGKcLV06-23	BGKcLV06-24
transduction_Date	6/9/17	6/9/17
days	Day 6	Day 6
RBP_name	PCBP3	PCBP3
qPCR_result	no good primers
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	1870	1527
WB_result	48.6	56.1
Ave_WB	52.4
WB_DONE_date	6/23/17
MW	39kD
IP
antibody_Cat#	RN054PW
Antibody DCC ID	ENCAB823NUI	ENCAB823NUI
submitted_to_DCC_date	9/29/17
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	8/3/17	8/3/17
repeat_library
Note
ID	4297	4298

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PCBP3	Product_ID: RN054PW Lot_ID: 1 Source: MBLI Target Name: PCBP3-human

Experiment Status

	BGKcLV06-23	BGKcLV06-24
Sample_ID	BGKcLV06-23	BGKcLV06-24
Sample Name	PCBP3-BGKcLV06-23	PCBP3-BGKcLV06-24
Sample Name	PCBP3-BGKcLV06-23	PCBP3-BGKcLV06-24
RBP	PCBP3	PCBP3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2017-11-20	2017-11-20
Project	ENCODE3	ENCODE3
Note
ID	1365	1366

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV06-23	BGKcLV06-24
Sample #
Sample Name	PCBP3-BGKcLV06-23	PCBP3-BGKcLV06-24
Sample_Name_Alias	PCBP3-BGKcLV06-23	PCBP3-BGKcLV06-24
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2017-08-03	2017-08-03
Lib_ID	Lib-170803	Lib-170803
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_set39/set2/G1.png	DNA_Library_set39/set2/H1.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set39/set3/H1.png	RNA_Library_set39/set1/G1.png
SampleQC_method
SampleQC_date
Sample_ID	BGKcLV06-23	BGKcLV06-24
RBP	PCBP3	PCBP3
Batch_ID	BGKcLV06	BGKcLV06
WB_result	48.600	56.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	3060	3061

Sequencing Information

	BGKcLV06-23	BGKcLV06-24
Sample_ID	BGKcLV06-23	BGKcLV06-24
Sample Name	PCBP3-BGKcLV06-23	PCBP3-BGKcLV06-24
Pool ID	Pool-170911	Pool-170911
LocalServer_folder	set39_K	set39_K
total_reads	92,653,638	80,072,806
total_aligned_reads	82,272,354	69,517,052
unique_aligned_reads	73,556,740	62,697,586
percent_uniqueAligned	0.79389	0.78301
correlation_replicates	0.995660	0.995660
spikein_reads	58,470	30,786
percent_spikeins	0.00063	0.00038
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1711	1712

Data Submission Information

	BGKcLV06-23	BGKcLV06-23
ENCODE_alias	brenton-graveley:PCBP3-BGKcLV06	brenton-graveley:PCBP3-BGKcLV06-K562
ENCODE_accession	ENCSR105LOV	ENCSR494SZR
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKcLV06-23	BGKcLV06-23
Sample Name	PCBP3-BGKcLV06-23	PCBP3-BGKcLV06-23
Selected	Yes	Yes
Status	Released	Released
Status_Date	2017-11-15	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3222	6852

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
PCBP3-BGKcLV06-23_ATGTCA_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1711	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22476
PCBP3-BGKcLV06-23_ATGTCA_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1711	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22512
PCBP3-BGKcLV06-23_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1711					GRCh38	V40	PCBP3-BGKcLV06-23_ATGTCA_ACBE67ANXX_L005_001.R1.fastq.gz,PCBP3-BGKcLV06-23_ATGTCA_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22548
PCBP3-BGKcLV06-23_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1711					GRCh38	V40	PCBP3-BGKcLV06-23/Aligned.sortedByCoord.out.bam		ENCORE2	22584
PCBP3-BGKcLV06-23_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1711					GRCh38	V40	PCBP3-BGKcLV06-23/Aligned.sortedByCoord.out.bam		ENCORE2	22620
PCBP3-BGKcLV06-23_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1711					GRCh38	V40	PCBP3-BGKcLV06-23/Aligned.sortedByCoord.out.bam		ENCORE2	22656
PCBP3-BGKcLV06-23_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1711					GRCh38	V40	PCBP3-BGKcLV06-23/Aligned.sortedByCoord.out.bam		ENCORE2	22692
PCBP3-BGKcLV06-23_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1711					GRCh38	V40	PCBP3-BGKcLV06-23_ATGTCA_ACBE67ANXX_L005_001.R1.fastq.gz,PCBP3-BGKcLV06-23_ATGTCA_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22728
PCBP3-BGKcLV06-24_CCGTCC_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1712	HiSeq2500	100	paired-ended	1				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R1.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R1.fastq.gz	ENCODE3	22477
PCBP3-BGKcLV06-24_CCGTCC_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE_DATA/set39_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1712	HiSeq2500	100	paired-ended	2				NT-BGKcLV06-1_GATCAG_ACBE67ANXX_L005_001.R2.fastq.gz,NT-BGKcLV06-2_TAGCTT_ACBE67ANXX_L005_001.R2.fastq.gz	ENCODE3	22513
PCBP3-BGKcLV06-24_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1712					GRCh38	V40	PCBP3-BGKcLV06-24_CCGTCC_ACBE67ANXX_L005_001.R1.fastq.gz,PCBP3-BGKcLV06-24_CCGTCC_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22549
PCBP3-BGKcLV06-24_Signal.Unique.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1712					GRCh38	V40	PCBP3-BGKcLV06-24/Aligned.sortedByCoord.out.bam		ENCORE2	22585
PCBP3-BGKcLV06-24_Signal.Unique.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1712					GRCh38	V40	PCBP3-BGKcLV06-24/Aligned.sortedByCoord.out.bam		ENCORE2	22621
PCBP3-BGKcLV06-24_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1712					GRCh38	V40	PCBP3-BGKcLV06-24/Aligned.sortedByCoord.out.bam		ENCORE2	22657
PCBP3-BGKcLV06-24_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set39_K/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1712					GRCh38	V40	PCBP3-BGKcLV06-24/Aligned.sortedByCoord.out.bam		ENCORE2	22693
PCBP3-BGKcLV06-24_quant.sf	ENCODE_DATA/set39_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1712					GRCh38	V40	PCBP3-BGKcLV06-24_CCGTCC_ACBE67ANXX_L005_001.R1.fastq.gz,PCBP3-BGKcLV06-24_CCGTCC_ACBE67ANXX_L005_001.R2.fastq.gz		ENCORE2	22729