PABPN1 RNA-Seq in K562

General Information


RBP	PABPN1
Cell_Line	K562
Method	shRNA
Exp_Name	PABPN1-BGKLV28-K562
ENCODE_series_ID	ENCSR017FFL
Batch_ID	BGKLV28
Pool ID	Pool-151215
Local_Set_Name	set28
ENCODE_KD_Exp_ID	ENCSR416ZJH
ENCODE_CN_Exp_ID	ENCSR164MUK
Rep1	PABPN1_BGKLV28-35
Rep2	PABPN1_BGKLV28-36
CN1	non-target_BGKLV28-1
CN2	non-target_BGKLV28-2
Rep1_qPCR	74.9
Rep2_qPCR	78.8
Rep1_WB	72.2
Rep2_WB	83.1
Antibody Cat#	RN023PW
Antibody Lot#	RN023PW
Antibody DCC ID	ENCAB032ZZR
Status	Released
Project	ENCODE3
ID	652

Experiment Information (Status: Released)

	BGKLV28-35	BGKLV28-36
idx	504	505
TRCN#_or_BGC#	TRCN0000000120	TRCN0000000120
shRNA_or_gRNA_sequence	CCCATAACTAACTGCTGAGGA	CCCATAACTAACTGCTGAGGA
PAM
Name	PABPN1	PABPN1
Sample_ID	BGKLV28-35	BGKLV28-36
transduction_Date	6/16/2015	6/16/2015
days
RBP_name	PABPN1	PABPN1
qPCR_result	74.9	78.8
Ave_qPCR	76.8
RT-qPCR_primer-F	tgtggttcagtcaaccgtgt
RT-qPCR_primer-R	aggccaaggaagtcctcact
protein_conc	2812	3401
WB_result	72.2	83.1
Ave_WB	77.6
WB_DONE_date	6/30/2015
MW	33kDa
IP	1MW	1MW
antibody_Cat#	RN023PW	RN023PW
Antibody DCC ID	ENCAB032ZZR	ENCAB032ZZR
submitted_to_DCC_date	8/6/2015
Rep1_TPM	77.5514457	0
Rep2_TPM	99.7755779	0
Action
Library_start_date	10/28/2015	10/28/2015
repeat_library
Note	x	x
ID	579	580

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PABPN1	Product_ID: RN023PW Lot_ID: 1 Source: MBLI Target Name: PABPN1-human

Experiment Status

	BGKLV28-35	BGKLV28-36
Sample_ID	BGKLV28-35	BGKLV28-36
Sample Name	PABPN1_BGKLV28-35	PABPN1_BGKLV28-36
Sample Name	PABPN1_BGKLV28-35	PABPN1_BGKLV28-36
RBP	PABPN1	PABPN1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-03-03	2016-03-03
Project	ENCODE3	ENCODE3
Note
ID	990	991

Library-Prep
Sequencing

Library-Prep Information

	BGKLV28-35	BGKLV28-36
Sample #
Sample Name	PABPN1-BGKLV28-35	PABPN1-BGKLV28-36
Sample_Name_Alias	PABPN1_BGKLV28-35	PABPN1_BGKLV28-36
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-10-28	2015-10-28
Lib_ID	Lib-151028	Lib-151028
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/C2.png	DNA_Library_LV28-29-30/set1/D2.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV26-27-28-29/set1/G7.png	RNA_Library_LV26-27-28-29/set1/H7.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV28-35	BGKLV28-36
RBP	PABPN1	PABPN1
Batch_ID	BGKLV28	BGKLV28
WB_result	72.200	83.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2682	2683

Sequencing Information

	BGKLV28-35	BGKLV28-36
Sample_ID	BGKLV28-35	BGKLV28-36
Sample Name	PABPN1_BGKLV28-35	PABPN1_BGKLV28-36
Pool ID	Pool-151215	Pool-151215
LocalServer_folder	set28	set28
total_reads	66,119,558	66,251,120
total_aligned_reads	56,436,246	57,678,522
unique_aligned_reads	51,536,120	52,395,040
percent_uniqueAligned	0.77944	0.79086
correlation_replicates	0.994766	0.994766
spikein_reads	263,088	224,972
percent_spikeins	0.00398	0.00340
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1324	1325

Data Submission Information

	BGKLV28-35	BGKLV28-35
ENCODE_alias	brenton-graveley:PABPN1_BGKLV28	brenton-graveley:PABPN1-BGKLV28-K562
ENCODE_accession	ENCSR416ZJH	ENCSR017FFL
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV28-35	BGKLV28-35
Sample Name	PABPN1_BGKLV28-35	PABPN1_BGKLV28-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3044	6845

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
PABPN1_BGKLV28-35_GGCTAC_L002_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1324	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20168
PABPN1_BGKLV28-35_GGCTAC_L002_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1324	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20200
PABPN1_BGKLV28-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1324					GRCh38	V40	PABPN1_BGKLV28-35_GGCTAC_L002_001.R1.fastq.gz,PABPN1_BGKLV28-35_GGCTAC_L002_001.R2.fastq.gz		ENCORE2	20232
PABPN1_BGKLV28-35_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1324					GRCh38	V40	PABPN1_BGKLV28-35/Aligned.sortedByCoord.out.bam		ENCORE2	20264
PABPN1_BGKLV28-35_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1324					GRCh38	V40	PABPN1_BGKLV28-35/Aligned.sortedByCoord.out.bam		ENCORE2	20296
PABPN1_BGKLV28-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1324					GRCh38	V40	PABPN1_BGKLV28-35/Aligned.sortedByCoord.out.bam		ENCORE2	20328
PABPN1_BGKLV28-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1324					GRCh38	V40	PABPN1_BGKLV28-35/Aligned.sortedByCoord.out.bam		ENCORE2	20360
PABPN1_BGKLV28-35_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1324					GRCh38	V40	PABPN1_BGKLV28-35_GGCTAC_L002_001.R1.fastq.gz,PABPN1_BGKLV28-35_GGCTAC_L002_001.R2.fastq.gz		ENCORE2	20392
PABPN1_BGKLV28-36_CTTGTA_L002_001.R1.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1325	HiSeq2500	100	paired-ended	1				non-target_BGKLV28-1_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R1.fastq.gz	ENCODE3	20169
PABPN1_BGKLV28-36_CTTGTA_L002_001.R2.fastq.gz	ENCODE_DATA/set28/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1325	HiSeq2500	100	paired-ended	2				non-target_BGKLV28-1_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV28-2_CGATGT_L001_001.R2.fastq.gz	ENCODE3	20201
PABPN1_BGKLV28-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1325					GRCh38	V40	PABPN1_BGKLV28-36_CTTGTA_L002_001.R1.fastq.gz,PABPN1_BGKLV28-36_CTTGTA_L002_001.R2.fastq.gz		ENCORE2	20233
PABPN1_BGKLV28-36_Signal.Unique.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1325					GRCh38	V40	PABPN1_BGKLV28-36/Aligned.sortedByCoord.out.bam		ENCORE2	20265
PABPN1_BGKLV28-36_Signal.Unique.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1325					GRCh38	V40	PABPN1_BGKLV28-36/Aligned.sortedByCoord.out.bam		ENCORE2	20297
PABPN1_BGKLV28-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1325					GRCh38	V40	PABPN1_BGKLV28-36/Aligned.sortedByCoord.out.bam		ENCORE2	20329
PABPN1_BGKLV28-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set28/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1325					GRCh38	V40	PABPN1_BGKLV28-36/Aligned.sortedByCoord.out.bam		ENCORE2	20361
PABPN1_BGKLV28-36_quant.sf	ENCODE_DATA/set28/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1325					GRCh38	V40	PABPN1_BGKLV28-36_CTTGTA_L002_001.R1.fastq.gz,PABPN1_BGKLV28-36_CTTGTA_L002_001.R2.fastq.gz		ENCORE2	20393