PABPC1 RNA-Seq in HepG2

General Information


RBP	PABPC1
Cell_Line	HepG2
Method	shRNA
Exp_Name	PABPC1-BGHLV22-HepG2
ENCODE_series_ID	ENCSR494NLK
Batch_ID	BGHLV22
Pool ID	Pool-150701
Local_Set_Name	set22
ENCODE_KD_Exp_ID	ENCSR910YNJ
ENCODE_CN_Exp_ID	ENCSR279HMU
Rep1	PABPC1-BGHLV22-33
Rep2	PABPC1-BGHLV22-34
CN1	non-target-BGHLV22-1_17746
CN2	non-target-BGHLV22-2_17747
Rep1_qPCR	97.0
Rep2_qPCR	97.3
Rep1_WB	NO AB
Rep2_WB	NO AB
Antibody Cat#	NO AB
Antibody Lot#	NO AB
Antibody DCC ID
Status	Released
Project	ENCODE3
ID	524

Experiment Information (Status: Released)

	BGHLV22-33	BGHLV22-34
idx	461	462
TRCN#_or_BGC#	TRCN0000074639	TRCN0000074639
shRNA_or_gRNA_sequence	CCGCACCGTTCCACAGTATAA	CCGCACCGTTCCACAGTATAA
PAM
Name	PABPC1	PABPC1
Sample_ID	BGHLV22-33	BGHLV22-34
transduction_Date	10/16/2014	10/16/2014
days
RBP_name	PABPC1	PABPC1
qPCR_result	97.0	97.3
Ave_qPCR	97.2
RT-qPCR_primer-F	CAGGAGTTCGCAATCCTCAG
RT-qPCR_primer-R	GCAGTCAAAGGTTCCTGACC
protein_conc	7391	7658
WB_result	NO AB	NO AB
Ave_WB
WB_DONE_date
MW
IP
antibody_Cat#	NO AB	NO AB
Antibody DCC ID
submitted_to_DCC_date
Rep1_TPM	870.2	0
Rep2_TPM	726.8	0
Action
Library_start_date	6/5/2015	6/5/2015
repeat_library
Note
ID	2534	2535

Western Blot Western Blot info was not avaliable

Experiment Status

	BGHLV22-33	BGHLV22-34
Sample_ID	BGHLV22-33	BGHLV22-34
Sample Name	PABPC1-BGHLV22-33	PABPC1-BGHLV22-34
Sample Name	PABPC1-BGHLV22-33	PABPC1-BGHLV22-34
RBP	PABPC1	PABPC1
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	798	799

Library-Prep
Sequencing

Library-Prep Information

	BGHLV22-33	BGHLV22-34
Sample #
Sample Name	PABPC1-BGHLV22-33	PABPC1-BGHLV22-34
Sample_Name_Alias	PABPC1-BGHLV22-33	PABPC1-BGHLV22-34
Index Well Position	S22	S23
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-05	2015-06-05
Lib_ID	Lib-150605	Lib-150605
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set1/E8.png	DNA_Library_LV20-22-23/set2/G1.png
RIN	9.9	9.9
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/E2.png	RNA_Library_LV22-23-25/set1/F2.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV22-33	BGHLV22-34
RBP	PABPC1	PABPC1
Batch_ID	BGHLV22	BGHLV22
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2484	2485

Sequencing Information

	BGHLV22-33	BGHLV22-34
Sample_ID	BGHLV22-33	BGHLV22-34
Sample Name	PABPC1-BGHLV22-33	PABPC1-BGHLV22-34
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set22	set22
total_reads	60,690,000	53,750,000
total_aligned_reads	56,192,546	49,809,158
unique_aligned_reads	52,944,202	46,908,724
percent_uniqueAligned	0.87237	0.87272
correlation_replicates	0.996696	0.996696
spikein_reads	373,610	299,820
percent_spikeins	0.00616	0.00558
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1106	1107

Data Submission Information

	BGHLV22-33	BGHLV22-33
ENCODE_alias	brenton-graveley:PABPC1-BGHLV22	brenton-graveley:PABPC1-BGHLV22-HepG2
ENCODE_accession	ENCSR910YNJ	ENCSR494NLK
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV22-33	BGHLV22-33
Sample Name	PABPC1-BGHLV22-33	PABPC1-BGHLV22-33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2931	6841

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
PABPC1-BGHLV22-33_CGTACG_L001_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1106	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16296
PABPC1-BGHLV22-33_CGTACG_L001_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1106	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16336
PABPC1-BGHLV22-33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1106					GRCh38	V40	PABPC1-BGHLV22-33_CGTACG_L001_R1_001.fastq.gz,PABPC1-BGHLV22-33_CGTACG_L001_R2_001.fastq.gz		ENCORE2	16434
PABPC1-BGHLV22-33_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1106					GRCh38	V40	PABPC1-BGHLV22-33/Aligned.sortedByCoord.out.bam		ENCORE2	16474
PABPC1-BGHLV22-33_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1106					GRCh38	V40	PABPC1-BGHLV22-33/Aligned.sortedByCoord.out.bam		ENCORE2	16514
PABPC1-BGHLV22-33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1106					GRCh38	V40	PABPC1-BGHLV22-33/Aligned.sortedByCoord.out.bam		ENCORE2	16554
PABPC1-BGHLV22-33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1106					GRCh38	V40	PABPC1-BGHLV22-33/Aligned.sortedByCoord.out.bam		ENCORE2	16594
PABPC1-BGHLV22-33_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1106					GRCh38	V40	PABPC1-BGHLV22-33_CGTACG_L001_R1_001.fastq.gz,PABPC1-BGHLV22-33_CGTACG_L001_R2_001.fastq.gz		ENCORE2	16634
PABPC1-BGHLV22-34_GAGTGG_L001_R1_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1107	HiSeq2000	100	paired-ended	1				non-target-BGHLV22-1_17746_ATCACG_L006_R1_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R1_001.fastq.gz	ENCODE3	16297
PABPC1-BGHLV22-34_GAGTGG_L001_R2_001.fastq.gz	ENCODE_DATA/set22/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1107	HiSeq2000	100	paired-ended	2				non-target-BGHLV22-1_17746_ATCACG_L006_R2_001.fastq.gz,non-target-BGHLV22-2_17747_CGATGT_L006_R2_001.fastq.gz	ENCODE3	16337
PABPC1-BGHLV22-34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1107					GRCh38	V40	PABPC1-BGHLV22-34_GAGTGG_L001_R1_001.fastq.gz,PABPC1-BGHLV22-34_GAGTGG_L001_R2_001.fastq.gz		ENCORE2	16435
PABPC1-BGHLV22-34_Signal.Unique.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1107					GRCh38	V40	PABPC1-BGHLV22-34/Aligned.sortedByCoord.out.bam		ENCORE2	16475
PABPC1-BGHLV22-34_Signal.Unique.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1107					GRCh38	V40	PABPC1-BGHLV22-34/Aligned.sortedByCoord.out.bam		ENCORE2	16515
PABPC1-BGHLV22-34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1107					GRCh38	V40	PABPC1-BGHLV22-34/Aligned.sortedByCoord.out.bam		ENCORE2	16555
PABPC1-BGHLV22-34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set22/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1107					GRCh38	V40	PABPC1-BGHLV22-34/Aligned.sortedByCoord.out.bam		ENCORE2	16595
PABPC1-BGHLV22-34_quant.sf	ENCODE_DATA/set22/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1107					GRCh38	V40	PABPC1-BGHLV22-34_GAGTGG_L001_R1_001.fastq.gz,PABPC1-BGHLV22-34_GAGTGG_L001_R2_001.fastq.gz		ENCORE2	16635