ANXA2 RNA-Seq in HepG2

General Information


RBP	ANXA2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	ANXA2-BGHcLV12-HepG2
ENCODE_series_ID	ENCSR992VVQ
Batch_ID	BGHcLV12
Pool ID	Pool-190423
Local_Set_Name	set42
ENCODE_KD_Exp_ID	ENCSR862BCF
ENCODE_CN_Exp_ID	ENCSR827PII
Rep1	ANXA2-BGHcLV12-3
Rep2	ANXA2-BGHcLV12-4
CN1	NT-BGHcLV12-1
CN2	NT-BGHcLV12-2
Rep1_qPCR	97.6
Rep2_qPCR	97.9
Rep1_WB	54.2
Rep2_WB	62.5
Antibody Cat#	GTX100046
Antibody Lot#
Antibody DCC ID	ENCAB049MLI
Status	Released
Project	ENCODE4
ID	162

Experiment Information (Status: Released)

	BGHcLV12-3	BGHcLV12-4
idx	263	264
TRCN#_or_BGC#	BGC#0000242	BGC#0000242
shRNA_or_gRNA_sequence	GGTCCTTCTCTGGTAGGCGA	GGTCCTTCTCTGGTAGGCGA
PAM	agg	agg
Name	ANXA2_66	ANXA2_66
Sample_ID	BGHcLV12-3	BGHcLV12-4
transduction_Date	8/17/18	8/17/18
days	D6	D6
RBP_name	ANXA2	ANXA2
qPCR_result	97.6	97.9
Ave_qPCR	97.8
RT-qPCR_primer-F	caggatattgccttcgccta
RT-qPCR_primer-R	caaaatcaccgtctccaggt
protein_conc	4018	4140
WB_result	54.2	62.5
Ave_WB	58.3
WB_DONE_date	2/14/19
MW	40 kDa
IP
antibody_Cat#	GTX100046
Antibody DCC ID	ENCAB049MLI
submitted_to_DCC_date	2/22/19
Rep1_TPM	59	0
Rep2_TPM	40	0
Action	Ready	Ready
Library_start_date	03/13/19	03/13/19
repeat_library
Note
ID	6406	6407

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
ANXA2	Product_ID: GTX100046 Lot_ID: 39476 Source: GeneTex Target Name: ANXA2-human

Experiment Status

	BGHcLV12-3	BGHcLV12-4
Sample_ID	BGHcLV12-3	BGHcLV12-4
Sample Name	ANXA2-BGHcLV12-3	ANXA2-BGHcLV12-4
Sample Name	ANXA2-BGHcLV12-3	ANXA2-BGHcLV12-4
RBP	ANXA2	ANXA2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	2803	2804

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV12-3	BGHcLV12-4
Sample #	33	34
Sample Name	ANXA2-BGHcLV12-3	ANXA2-BGHcLV12-4
Sample_Name_Alias
Index Well Position	A05	B05
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2019-03-13	2019-03-13
Lib_ID	Lib-190313	Lib-190313
Tecan_Location	3-A1	3-B1
Tecan	61.98	77.32
Tecan_date	2019-03-13	2019-03-13
Size_bp	296	290
Peak_Molarity	43.30	100.00
libSampleQC_DNA_Well	DNA_Library_set42/set1/A5.png	DNA_Library_set42/set1/B5.png
RIN	9.3	9.6
libSample_RNA_Well	RNA_Library_set42/set1/A5.png	RNA_Library_set42/set1/B5.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2019-03-13	2019-03-13
Sample_ID	BGHcLV12-3	BGHcLV12-4
RBP	ANXA2	ANXA2
Batch_ID	BGHcLV12	BGHcLV12
WB_result	54.200	62.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	33	34

Sequencing Information

	BGHcLV12-3	BGHcLV12-4
Sample_ID	BGHcLV12-3	BGHcLV12-4
Sample Name	ANXA2-BGHcLV12-3	ANXA2-BGHcLV12-4
Pool ID	Pool-190423	Pool-190423
LocalServer_folder	set42	set42
total_reads	43,809,730	61,810,786
total_aligned_reads	40,129,202	58,830,230
unique_aligned_reads	37,766,830	55,342,768
percent_uniqueAligned	0.86206	0.89536
correlation_replicates	0.992734	0.992734
spikein_reads	48,996	37,380
percent_spikeins	0.00112	0.00060
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	3	4

Data Submission Information

	BGHcLV12-3	BGHcLV12-3	BGHcLV12-3	BGHcLV12-3	BGHcLV12-3	BGHcLV12-3	BGHcLV12-4	BGHcLV12-4	BGHcLV12-4	BGHcLV12-4
ENCODE_alias	brenton-graveley:ANXA2-BGHcLV12	brenton-graveley:ANXA2-BGHcLV12-3	brenton-graveley:L-ANXA2-BGHcLV12-3	brenton-graveley:ANXA2-BGHcLV12-3_TACCGAGG+CCTGAACT_HK3H2DSXX_S33_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ANXA2-BGHcLV12-3_TACCGAGG+CCTGAACT_HK3H2DSXX_S33_L004_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ANXA2-BGHcLV12-HepG2	brenton-graveley:ANXA2-BGHcLV12-4	brenton-graveley:L-ANXA2-BGHcLV12-4	brenton-graveley:ANXA2-BGHcLV12-4_CGTTAGAA+TTCAGGTC_HK3H2DSXX_S34_L004_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:ANXA2-BGHcLV12-4_CGTTAGAA+TTCAGGTC_HK3H2DSXX_S34_L004_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR862BCF	ENCBS857FJC	ENCLB085GFH	ENCFF630JEP	ENCFF775ALW	ENCSR992VVQ	ENCBS951TYV	ENCLB353EKL	ENCFF185GDC	ENCFF429KZL
object_type	experiment	biosample	library	file_fastq1	file_fastq2	gene_silencing_series	biosample	library	file_fastq1	file_fastq2
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHcLV12-3	BGHcLV12-3	BGHcLV12-3	BGHcLV12-3	BGHcLV12-3	BGHcLV12-3	BGHcLV12-4	BGHcLV12-4	BGHcLV12-4	BGHcLV12-4
Sample Name	ANXA2-BGHcLV12-3	ANXA2-BGHcLV12-3	ANXA2-BGHcLV12-3	ANXA2-BGHcLV12-3	ANXA2-BGHcLV12-3	ANXA2-BGHcLV12-3	ANXA2-BGHcLV12-4	ANXA2-BGHcLV12-4	ANXA2-BGHcLV12-4	ANXA2-BGHcLV12-4
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2020-11-20	2022-03-02	2020-11-20	2020-11-20	2020-11-20	2020-11-20
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV42_biosample_protocol	LV42_library_protocol				LV42_biosample_protocol	LV42_library_protocol
protocol_URL		ANXA2-BGHcLV12-3.pdf	L-ANXA2-BGHcLV12-3.pdf				ANXA2-BGHcLV12-4.pdf	L-ANXA2-BGHcLV12-4.pdf
ID	746	787	869	953	1035	7083	788	870	954	1036

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
ANXA2-BGHcLV12-3_TACCGAGG+CCTGAACT_HK3H2DSXX_S33_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	335
ANXA2-BGHcLV12-3_TACCGAGG+CCTGAACT_HK3H2DSXX_S33_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	3	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	417
ANXA2-BGHcLV12-3_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	3					GRCh38	V40	ANXA2-BGHcLV12-3_TACCGAGG+CCTGAACT_HK3H2DSXX_S33_L004_R1_001.filtered.trimmed.paired.fastq.gz,ANXA2-BGHcLV12-3_TACCGAGG+CCTGAACT_HK3H2DSXX_S33_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23674
ANXA2-BGHcLV12-3_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3					GRCh38	V40	ANXA2-BGHcLV12-3/Aligned.sortedByCoord.out.bam		ENCORE2	23756
ANXA2-BGHcLV12-3_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	3					GRCh38	V40	ANXA2-BGHcLV12-3/Aligned.sortedByCoord.out.bam		ENCORE2	23838
ANXA2-BGHcLV12-3_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3					GRCh38	V40	ANXA2-BGHcLV12-3/Aligned.sortedByCoord.out.bam		ENCORE2	23920
ANXA2-BGHcLV12-3_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	3					GRCh38	V40	ANXA2-BGHcLV12-3/Aligned.sortedByCoord.out.bam		ENCORE2	24002
ANXA2-BGHcLV12-3_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	3					GRCh38	V40	ANXA2-BGHcLV12-3_TACCGAGG+CCTGAACT_HK3H2DSXX_S33_L004_R1_001.filtered.trimmed.paired.fastq.gz,ANXA2-BGHcLV12-3_TACCGAGG+CCTGAACT_HK3H2DSXX_S33_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24084
ANXA2-BGHcLV12-4_CGTTAGAA+TTCAGGTC_HK3H2DSXX_S34_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	4	NovaSeq6000	100	paired-ended	1				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	336
ANXA2-BGHcLV12-4_CGTTAGAA+TTCAGGTC_HK3H2DSXX_S34_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set42/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	4	NovaSeq6000	100	paired-ended	2				NT-BGHcLV12-1_GGCATTCT+CTAGCTTG_HK3H2DSXX_S31_L004_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV12-2_AATGCCTC+TCGATCCA_HK3H2DSXX_S32_L004_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	418
ANXA2-BGHcLV12-4_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	4					GRCh38	V40	ANXA2-BGHcLV12-4_CGTTAGAA+TTCAGGTC_HK3H2DSXX_S34_L004_R1_001.filtered.trimmed.paired.fastq.gz,ANXA2-BGHcLV12-4_CGTTAGAA+TTCAGGTC_HK3H2DSXX_S34_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	23675
ANXA2-BGHcLV12-4_Signal.Unique.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	4					GRCh38	V40	ANXA2-BGHcLV12-4/Aligned.sortedByCoord.out.bam		ENCORE2	23757
ANXA2-BGHcLV12-4_Signal.Unique.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	4					GRCh38	V40	ANXA2-BGHcLV12-4/Aligned.sortedByCoord.out.bam		ENCORE2	23839
ANXA2-BGHcLV12-4_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	4					GRCh38	V40	ANXA2-BGHcLV12-4/Aligned.sortedByCoord.out.bam		ENCORE2	23921
ANXA2-BGHcLV12-4_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set42/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	4					GRCh38	V40	ANXA2-BGHcLV12-4/Aligned.sortedByCoord.out.bam		ENCORE2	24003
ANXA2-BGHcLV12-4_quant.sf	ENCODE_DATA/set42/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	4					GRCh38	V40	ANXA2-BGHcLV12-4_CGTTAGAA+TTCAGGTC_HK3H2DSXX_S34_L004_R1_001.filtered.trimmed.paired.fastq.gz,ANXA2-BGHcLV12-4_CGTTAGAA+TTCAGGTC_HK3H2DSXX_S34_L004_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	24085