CALR RNA-Seq in HepG2

General Information


RBP	CALR
Cell_Line	HepG2
Method	shRNA
Exp_Name	CALR-BGHLV23-HepG2
ENCODE_series_ID	ENCSR300GZP
Batch_ID	BGHLV23
Pool ID	Pool-151215B
Local_Set_Name	set23
ENCODE_KD_Exp_ID	ENCSR040WAK
ENCODE_CN_Exp_ID	ENCSR364GRM
Rep1	CALR_BGHLV23-5B
Rep2	CALR_BGHLV23-6B
CN1	NT_BGHLV23-1B
CN2	NT_BGHLV23-2B
Rep1_qPCR	84.5
Rep2_qPCR	86.5
Rep1_WB	48.2
Rep2_WB	64.8
Antibody Cat#	A301-130A
Antibody Lot#	A301-130A
Antibody DCC ID	ENCAB210ATY
Status	Released
Project	ENCODE3
ID	600

Experiment Information (Status: NotSatisfied)

	BGHLV23-5	BGHLV23-6
idx	497	498
TRCN#_or_BGC#	TRCN0000019990	TRCN0000019990
shRNA_or_gRNA_sequence	GCACGGAGACTCAGAATACAA	GCACGGAGACTCAGAATACAA
PAM
Name	CALR_90	CALR_90
Sample_ID	BGHLV23-5	BGHLV23-6
transduction_Date	10/29/2014	10/29/2014
days
RBP_name	CALR	CALR
qPCR_result	84.5	86.5
Ave_qPCR	85.5
RT-qPCR_primer-F	ccgttgcaaggatgatgagt
RT-qPCR_primer-R	cacctggctgttgtcaatctt
protein_conc	4644	4891
WB_result	48.2	64.8
Ave_WB	56.5
WB_DONE_date	4/16/2015
MW	48kDa
IP	1	1
antibody_Cat#	A301-130A	A301-130A
Antibody DCC ID	ENCAB210ATY	ENCAB210ATY
submitted_to_DCC_date	5/4/2015
Rep1_TPM	479.7	0
Rep2_TPM	518	0
Action
Library_start_date	6/10/2015	6/10/2015
repeat_library
Note
ID	2572	2573

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CALR	Product_ID: A301-130A Lot_ID: 1 Source: Bethyl Labs Target Name: CALR-human

Experiment Status

	BGHLV23-5	BGHLV23-5	BGHLV23-6	BGHLV23-6
Sample_ID	BGHLV23-5	BGHLV23-5	BGHLV23-6	BGHLV23-6
Sample Name	CALR-BGHLV23-5	CALR_BGHLV23-5B	CALR-BGHLV23-6	CALR_BGHLV23-6B
Sample Name	CALR-BGHLV23-5	CALR_BGHLV23-5B	CALR-BGHLV23-6	CALR_BGHLV23-6B
RBP	CALR	CALR	CALR	CALR
Cell_Line	HepG2	HepG2	HepG2	HepG2
Exp UID
Status	NotSatisfied	Released	NotSatisfied	Released
Status_date	2015-08-13	2016-03-04	2015-08-13	2016-03-04
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
Note	Bad Correlation between replicates		Bad Correlation between replicates
ID	22	1072	23	1073

Library-Prep
Sequencing

Library-Prep Information

	BGHLV23-5	BGHLV23-5	BGHLV23-6	BGHLV23-6
Sample #
Sample Name	CALR-BGHLV23-5	CALR-BGHLV23-5B	CALR-BGHLV23-6	CALR-BGHLV23-6B
Sample_Name_Alias	CALR-BGHLV23-5	CALR_BGHLV23-5B	CALR-BGHLV23-6	CALR_BGHLV23-6B
Index Well Position	S20	S15	S21	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-06-10	2015-11-03	2015-06-10	2015-11-03
Lib_ID	Lib-150610	Lib-151103	Lib-150610	Lib-151103
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV20-22-23/set2/A2.png	DNA_Library_LV28-29-30/set1/G8.png	DNA_Library_LV20-22-23/set1/D11.png	DNA_Library_LV28-29-30/set1/H8.png
RIN	9.6	10.0	9.5	9.7
libSample_RNA_Well	RNA_Library_LV22-23-25/set1/G4.png	RNA_Library_LV22-23-25/set1/G4.png	RNA_Library_LV22-23-25/set1/H4.png	RNA_Library_LV22-23-25/set1/H4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV23-5	BGHLV23-5	BGHLV23-6	BGHLV23-6
RBP	CALR	CALR	CALR	CALR
Batch_ID	BGHLV23	BGHLV23	BGHLV23	BGHLV23
WB_result	48.200	48.200	64.800	64.800
Library Description	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix		B		B
Lib_Status	SendToSequence	SendToSequence	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3	ENCODE3	ENCODE3
ID	2500	2764	2501	2765

Sequencing Information

	BGHLV23-5	BGHLV23-5	BGHLV23-6	BGHLV23-6
Sample_ID	BGHLV23-5	BGHLV23-5	BGHLV23-6	BGHLV23-6
Sample Name	CALR-BGHLV23-5	CALR_BGHLV23-5B	CALR-BGHLV23-6	CALR_BGHLV23-6B
Pool ID	Pool-150701	Pool-151215B	Pool-150701	Pool-151215B
LocalServer_folder	set23	set23	set23	set23
total_reads	59,490,000	66,326,608	50,690,000	55,074,082
total_aligned_reads	53,428,662	54,837,428	35,514,438	45,547,794
unique_aligned_reads	50,463,256	51,952,008	33,765,344	43,149,564
percent_uniqueAligned	0.84826	0.78328	0.66611	0.78348
correlation_replicates	0.592657	0.998950	0.592657	0.998950
spikein_reads	413,702	128,940	24,700	121,026
percent_spikeins	0.00695	0.00194	0.00049	0.00220
original_ReadLength	100	100	100	100
QC_Status	BadCorrelation	Submitted	BadCorrelation	Submitted
ID	1122	1413	1123	1414

Data Submission Information

	BGHLV23-5	BGHLV23-5
ENCODE_alias	brenton-graveley:CALR_BGHLV23	brenton-graveley:CALR-BGHLV23-HepG2
ENCODE_accession	ENCSR040WAK	ENCSR300GZP
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV23-5	BGHLV23-5
Sample Name	CALR_BGHLV23-5B	CALR_BGHLV23-5B
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3085	6608

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
CALR_BGHLV23-5B_ATGTCA_L008_001.R1.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1413	HiSeq2000	100	paired-ended	1				NT_BGHLV23-1B_AGTCAA_L007_001.R1.fastq.gz,NT_BGHLV23-2B_AGTTCC_L007_001.R1.fastq.gz	ENCODE3	16650
CALR_BGHLV23-5B_ATGTCA_L008_001.R2.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1413	HiSeq2000	100	paired-ended	2				NT_BGHLV23-1B_AGTCAA_L007_001.R2.fastq.gz,NT_BGHLV23-2B_AGTTCC_L007_001.R2.fastq.gz	ENCODE3	16688
CALR_BGHLV23-5B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1413					GRCh38	V40	CALR_BGHLV23-5B_ATGTCA_L008_001.R1.fastq.gz,CALR_BGHLV23-5B_ATGTCA_L008_001.R2.fastq.gz		ENCORE2	16726
CALR_BGHLV23-5B_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	1413					GRCh38	V40	CALR_BGHLV23-5B/Aligned.sortedByCoord.out.bam		ENCORE2	16764
CALR_BGHLV23-5B_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	1413					GRCh38	V40	CALR_BGHLV23-5B/Aligned.sortedByCoord.out.bam		ENCORE2	16802
CALR_BGHLV23-5B_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	1413					GRCh38	V40	CALR_BGHLV23-5B/Aligned.sortedByCoord.out.bam		ENCORE2	16840
CALR_BGHLV23-5B_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	1413					GRCh38	V40	CALR_BGHLV23-5B/Aligned.sortedByCoord.out.bam		ENCORE2	16878
CALR_BGHLV23-5B_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1413					GRCh38	V40	CALR_BGHLV23-5B_ATGTCA_L008_001.R1.fastq.gz,CALR_BGHLV23-5B_ATGTCA_L008_001.R2.fastq.gz		ENCORE2	16916
CALR_BGHLV23-6B_CCGTCC_L008_001.R1.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1414	HiSeq2000	100	paired-ended	1				NT_BGHLV23-1B_AGTCAA_L007_001.R1.fastq.gz,NT_BGHLV23-2B_AGTTCC_L007_001.R1.fastq.gz	ENCODE3	16651
CALR_BGHLV23-6B_CCGTCC_L008_001.R2.fastq.gz	ENCODE_DATA/set23/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1414	HiSeq2000	100	paired-ended	2				NT_BGHLV23-1B_AGTCAA_L007_001.R2.fastq.gz,NT_BGHLV23-2B_AGTTCC_L007_001.R2.fastq.gz	ENCODE3	16689
CALR_BGHLV23-6B_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set23/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1414					GRCh38	V40	CALR_BGHLV23-6B_CCGTCC_L008_001.R1.fastq.gz,CALR_BGHLV23-6B_CCGTCC_L008_001.R2.fastq.gz		ENCORE2	16727
CALR_BGHLV23-6B_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	1414					GRCh38	V40	CALR_BGHLV23-6B/Aligned.sortedByCoord.out.bam		ENCORE2	16765
CALR_BGHLV23-6B_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	1414					GRCh38	V40	CALR_BGHLV23-6B/Aligned.sortedByCoord.out.bam		ENCORE2	16803
CALR_BGHLV23-6B_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	1414					GRCh38	V40	CALR_BGHLV23-6B/Aligned.sortedByCoord.out.bam		ENCORE2	16841
CALR_BGHLV23-6B_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	1414					GRCh38	V40	CALR_BGHLV23-6B/Aligned.sortedByCoord.out.bam		ENCORE2	16879
CALR_BGHLV23-6B_quant.sf	ENCODE_DATA/set23/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1414					GRCh38	V40	CALR_BGHLV23-6B_CCGTCC_L008_001.R1.fastq.gz,CALR_BGHLV23-6B_CCGTCC_L008_001.R2.fastq.gz		ENCORE2	16917