PABPC1 RNA-Seq in K562

General Information


RBP	PABPC1
Cell_Line	K562
Method	shRNA
Exp_Name	PABPC1-BGKLV24-K562
ENCODE_series_ID	ENCSR448XEY
Batch_ID	BGKLV24
Pool ID	Pool-151101
Local_Set_Name	set24_2
ENCODE_KD_Exp_ID	ENCSR192GBD
ENCODE_CN_Exp_ID	ENCSR419JMU
Rep1	PABPC1_BGKLV24_41B
Rep2	PABPC1_BGKLV24_42B
CN1	non-target_BGKLV24_1B
CN2	non-target_BGKLV24_2B
Rep1_qPCR	86.9
Rep2_qPCR	87.4
Rep1_WB	no AB
Rep2_WB	no AB
Antibody Cat#	no AB
Antibody Lot#	no AB
Antibody DCC ID
Status	Released
Project	ENCODE3
ID	606

Experiment Information (Status: Released)

	BGKLV24-41	BGKLV24-42
idx	378	379
TRCN#_or_BGC#	TRCN0000074639	TRCN0000074639
shRNA_or_gRNA_sequence	CCGCACCGTTCCACAGTATAA	CCGCACCGTTCCACAGTATAA
PAM
Name	PABPC1	PABPC1
Sample_ID	BGKLV24-41	BGKLV24-42
transduction_Date	2/27/2015	2/27/2015
days
RBP_name	PABPC1	PABPC1
qPCR_result	86.9	87.4
Ave_qPCR	87.1
RT-qPCR_primer-F	CAGGAGTTCGCAATCCTCAG
RT-qPCR_primer-R	GCAGTCAAAGGTTCCTGACC
protein_conc	3718	3710
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	755.794981	0
Rep2_TPM	944.202095	0
Action
Library_start_date	9/2/2015	9/2/2015
repeat_library
Note	x	x
ID	435	436

Western Blot Western Blot info was not avaliable

Experiment Status

	BGKLV24-41	BGKLV24-42
Sample_ID	BGKLV24-41	BGKLV24-42
Sample Name	PABPC1_BGKLV24_41B	PABPC1_BGKLV24_42B
Sample Name	PABPC1_BGKLV24_41B	PABPC1_BGKLV24_42B
RBP	PABPC1	PABPC1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2015-12-08	2015-12-08
Project	ENCODE3	ENCODE3
Note
ID	894	895

Library-Prep
Sequencing

Library-Prep Information

	BGKLV24-41	BGKLV24-42
Sample #
Sample Name	PABPC1-BGKLV24-41B	PABPC1-BGKLV24-42B
Sample_Name_Alias	PABPC1_BGKLV24_41B	PABPC1_BGKLV24_42B
Index Well Position	S11	S12
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-09-02	2015-09-02
Lib_ID	Lib-150902	Lib-150902
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV24-25-26/set1/C6.png	DNA_Library_LV24-25-26/set1/D6.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV20-22-24/set1/G4.png	RNA_Library_LV20-22-24/set1/H4.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV24-41	BGKLV24-42
RBP	PABPC1	PABPC1
Batch_ID	BGKLV24	BGKLV24
WB_result	0.000	0.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix	B	B
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2582	2583

Sequencing Information

	BGKLV24-41	BGKLV24-42
Sample_ID	BGKLV24-41	BGKLV24-42
Sample Name	PABPC1_BGKLV24_41B	PABPC1_BGKLV24_42B
Pool ID	Pool-151101	Pool-151101
LocalServer_folder	set24_2	set24_2
total_reads	120,567,982	56,623,176
total_aligned_reads	118,359,830	55,933,120
unique_aligned_reads	107,978,174	51,282,196
percent_uniqueAligned	0.89558	0.90568
correlation_replicates	0.991729	0.991729
spikein_reads	460,154	233,506
percent_spikeins	0.00382	0.00412
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1224	1225

Data Submission Information

	BGKLV24-41	BGKLV24-41
ENCODE_alias	brenton-graveley:PABPC1_BGKLV24_B	brenton-graveley:PABPC1-BGKLV24-K562
ENCODE_accession	ENCSR192GBD	ENCSR448XEY
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV24-41	BGKLV24-41
Sample Name	PABPC1_BGKLV24_41B	PABPC1_BGKLV24_41B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-12-02	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2996	6842

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_BGKLV24_41B_GGCTAC_L002_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1224	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17480
PABPC1_BGKLV24_41B_GGCTAC_L002_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1224	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17504
PABPC1_BGKLV24_41B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1224					GRCh38	V40	PABPC1_BGKLV24_41B_GGCTAC_L002_001.R1.fastq.gz,PABPC1_BGKLV24_41B_GGCTAC_L002_001.R2.fastq.gz		ENCORE2	17528
PABPC1_BGKLV24_41B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1224					GRCh38	V40	PABPC1_BGKLV24_41B/Aligned.sortedByCoord.out.bam		ENCORE2	17552
PABPC1_BGKLV24_41B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1224					GRCh38	V40	PABPC1_BGKLV24_41B/Aligned.sortedByCoord.out.bam		ENCORE2	17576
PABPC1_BGKLV24_41B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1224					GRCh38	V40	PABPC1_BGKLV24_41B/Aligned.sortedByCoord.out.bam		ENCORE2	17600
PABPC1_BGKLV24_41B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1224					GRCh38	V40	PABPC1_BGKLV24_41B/Aligned.sortedByCoord.out.bam		ENCORE2	17624
PABPC1_BGKLV24_41B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1224					GRCh38	V40	PABPC1_BGKLV24_41B_GGCTAC_L002_001.R1.fastq.gz,PABPC1_BGKLV24_41B_GGCTAC_L002_001.R2.fastq.gz		ENCORE2	17648
PABPC1_BGKLV24_42B_CTTGTA_L002_001.R1.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1225	HiSeq2000	100	paired-ended	1				non-target_BGKLV24_1B_ATCACG_L001_001.R1.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R1.fastq.gz	ENCODE3	17481
PABPC1_BGKLV24_42B_CTTGTA_L002_001.R2.fastq.gz	ENCODE_DATA/set24_2/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1225	HiSeq2000	100	paired-ended	2				non-target_BGKLV24_1B_ATCACG_L001_001.R2.fastq.gz,non-target_BGKLV24_2B_CGATGT_L001_001.R2.fastq.gz	ENCODE3	17505
PABPC1_BGKLV24_42B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1225					GRCh38	V40	PABPC1_BGKLV24_42B_CTTGTA_L002_001.R1.fastq.gz,PABPC1_BGKLV24_42B_CTTGTA_L002_001.R2.fastq.gz		ENCORE2	17529
PABPC1_BGKLV24_42B_Signal.Unique.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1225					GRCh38	V40	PABPC1_BGKLV24_42B/Aligned.sortedByCoord.out.bam		ENCORE2	17553
PABPC1_BGKLV24_42B_Signal.Unique.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1225					GRCh38	V40	PABPC1_BGKLV24_42B/Aligned.sortedByCoord.out.bam		ENCORE2	17577
PABPC1_BGKLV24_42B_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1225					GRCh38	V40	PABPC1_BGKLV24_42B/Aligned.sortedByCoord.out.bam		ENCORE2	17601
PABPC1_BGKLV24_42B_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set24_2/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1225					GRCh38	V40	PABPC1_BGKLV24_42B/Aligned.sortedByCoord.out.bam		ENCORE2	17625
PABPC1_BGKLV24_42B_quant.sf	ENCODE_DATA/set24_2/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1225					GRCh38	V40	PABPC1_BGKLV24_42B_CTTGTA_L002_001.R1.fastq.gz,PABPC1_BGKLV24_42B_CTTGTA_L002_001.R2.fastq.gz		ENCORE2	17649