PUM2 RNA-Seq in HepG2

General Information


RBP	PUM2
Cell_Line	HepG2
Method	shRNA
Exp_Name	PUM2-BGHLV23-HepG2
ENCODE_series_ID	ENCSR721OFF
Batch_ID	BGHLV23
Pool ID	Pool-150701
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR210DML
ENCODE_CN_Exp_ID	ENCSR042QTH
Rep1	PUM2-BGHLV23-35
Rep2	PUM2-BGHLV23-36
CN1	non-target-BGHLV23-1
CN2	non-target-BGHLV23-2
Rep1_qPCR	51.8
Rep2_qPCR	65.2
Rep1_WB	72.4
Rep2_WB	53.2
Antibody Cat#	A300-202A
Antibody Lot#	A300-202A
Antibody DCC ID	ENCAB818JWN
Status	Released
Project	ENCODE3
ID	549

Experiment Information (Status: Released)

	BGHLV23-35	BGHLV23-36
idx	527	528
TRCN#_or_BGC#	TRCN0000296986	TRCN0000296986
shRNA_or_gRNA_sequence	TTGACTTTATTCATCCATTTG	TTGACTTTATTCATCCATTTG
PAM
Name	PUM2_86	PUM2_86
Sample_ID	BGHLV23-35	BGHLV23-36
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	PUM2	PUM2
qPCR_result	51.8	65.2
Ave_qPCR	58.5
RT-qPCR_primer-F	tgccaattacgtggttcaaa
RT-qPCR_primer-R	tgtgaggtcgaatcttgtgc
protein_conc	5738	5142
WB_result	72.4	53.2
Ave_WB	62.8
WB_DONE_date	6/10/2015
MW	114kDa
IP	1	1
antibody_Cat#	A300-202A	A300-202A
Antibody DCC ID	ENCAB818JWN	ENCAB818JWN
submitted_to_DCC_date	8/6/2015
Rep1_TPM	29.1	0
Rep2_TPM	24.3	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2608	2609

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
PUM2	Product_ID: A300-202A Lot_ID: 2 Source: Bethyl Labs Target Name: PUM2-human

Experiment Status

	BGHLV23-35	BGHLV23-36
Sample_ID	BGHLV23-35	BGHLV23-36
Sample Name	PUM2-BGHLV23-35	PUM2-BGHLV23-36
Sample Name	PUM2-BGHLV23-35	PUM2-BGHLV23-36
RBP	PUM2	PUM2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2015-08-13	2015-08-13
Project	ENCODE3	ENCODE3
Note
ID	836	837

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-35	BGHLV23-36
Sample #
Sample Name	PUM2-BGHLV23-35	PUM2-BGHLV23-36
Sample_Name_Alias	PUM2-BGHLV23-35	PUM2-BGHLV23-36
Index Well Position	S18	S19
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-06-10
Lib_ID	Lib-150610	Lib-150610
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set4/A2.png	DNA_Library_LV20-22-23/set4/B2.png
RIN	9.8	9.9
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/E7.png	RNA_Library_LV22-23-25/set1/F7.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-35	BGHLV23-36
RBP	PUM2	PUM2
Batch_ID	BGHLV23	BGHLV23
WB_result	72.400	53.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2524	2525

Sequencing Information

	BGHLV23-35	BGHLV23-36
Sample_ID	BGHLV23-35	BGHLV23-36
Sample Name	PUM2-BGHLV23-35	PUM2-BGHLV23-36
Pool ID	Pool-150701	Pool-150701
LocalServer_folder	set23	set23
total_reads	61,990,000	58,700,000
total_aligned_reads	55,183,612	53,235,820
unique_aligned_reads	51,984,312	50,153,052
percent_uniqueAligned	0.83859	0.85440
correlation_replicates	0.998365	0.998365
spikein_reads	272,532	290,220
percent_spikeins	0.00440	0.00494
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1146	1147

Data Submission Information

	BGHLV23-35	BGHLV23-35
ENCODE_alias	brenton-graveley:PUM2-BGHLV23	brenton-graveley:PUM2-BGHLV23-HepG2
ENCODE_accession	ENCSR210DML	ENCSR721OFF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-35	BGHLV23-35
Sample Name	PUM2-BGHLV23-35	PUM2-BGHLV23-35
Selected	Yes	Yes
Status	Released	Released
Status_Date	2015-08-11	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2950	6881

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
PUM2-BGHLV23-35_GTCCGC_L007_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1146	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16676
PUM2-BGHLV23-35_GTCCGC_L007_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1146	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16714
PUM2-BGHLV23-35_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1146					GRCh38	V40	PUM2-BGHLV23-35_GTCCGC_L007_R1_001.fastq.gz,PUM2-BGHLV23-35_GTCCGC_L007_R2_001.fastq.gz		ENCORE2	16752
PUM2-BGHLV23-35_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1146					GRCh38	V40	PUM2-BGHLV23-35/Aligned.sortedByCoord.out.bam		ENCORE2	16790
PUM2-BGHLV23-35_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1146					GRCh38	V40	PUM2-BGHLV23-35/Aligned.sortedByCoord.out.bam		ENCORE2	16828
PUM2-BGHLV23-35_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1146					GRCh38	V40	PUM2-BGHLV23-35/Aligned.sortedByCoord.out.bam		ENCORE2	16866
PUM2-BGHLV23-35_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1146					GRCh38	V40	PUM2-BGHLV23-35/Aligned.sortedByCoord.out.bam		ENCORE2	16904
PUM2-BGHLV23-35_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1146					GRCh38	V40	PUM2-BGHLV23-35_GTCCGC_L007_R1_001.fastq.gz,PUM2-BGHLV23-35_GTCCGC_L007_R2_001.fastq.gz		ENCORE2	16942
PUM2-BGHLV23-36_GTGAAA_L007_R1_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1147	HiSeq2000	100	paired-ended	1				non-target-BGHLV23-1_GTCCGC_L003_R1_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R1_001.fastq.gz	ENCODE3	16677
PUM2-BGHLV23-36_GTGAAA_L007_R2_001.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1147	HiSeq2000	100	paired-ended	2				non-target-BGHLV23-1_GTCCGC_L003_R2_001.fastq.gz,non-target-BGHLV23-2_GTGAAA_L004_R2_001.fastq.gz	ENCODE3	16715
PUM2-BGHLV23-36_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1147					GRCh38	V40	PUM2-BGHLV23-36_GTGAAA_L007_R1_001.fastq.gz,PUM2-BGHLV23-36_GTGAAA_L007_R2_001.fastq.gz		ENCORE2	16753
PUM2-BGHLV23-36_Signal.Unique.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1147					GRCh38	V40	PUM2-BGHLV23-36/Aligned.sortedByCoord.out.bam		ENCORE2	16791
PUM2-BGHLV23-36_Signal.Unique.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1147					GRCh38	V40	PUM2-BGHLV23-36/Aligned.sortedByCoord.out.bam		ENCORE2	16829
PUM2-BGHLV23-36_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1147					GRCh38	V40	PUM2-BGHLV23-36/Aligned.sortedByCoord.out.bam		ENCORE2	16867
PUM2-BGHLV23-36_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1147					GRCh38	V40	PUM2-BGHLV23-36/Aligned.sortedByCoord.out.bam		ENCORE2	16905
PUM2-BGHLV23-36_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1147					GRCh38	V40	PUM2-BGHLV23-36_GTGAAA_L007_R1_001.fastq.gz,PUM2-BGHLV23-36_GTGAAA_L007_R2_001.fastq.gz		ENCORE2	16943