STAU2 RNA-Seq in HepG2

General Information


RBP	STAU2
Cell_Line	HepG2
Method	CRISPR
Exp_Name	STAU2-BGHcLV10-HepG2
ENCODE_series_ID	ENCSR404DIU
Batch_ID	BGHcLV10
Pool ID	Pool-180901
Local_Set_Name	set41
ENCODE_KD_Exp_ID	ENCSR279MNU
ENCODE_CN_Exp_ID	ENCSR775ZWO
Rep1	STAU2-BGHcLV10-45
Rep2	STAU2-BGHcLV10-46
CN1	NT-BGHcLV10-1
CN2	NT-BGHcLV10-2
Rep1_qPCR	67.3
Rep2_qPCR	71.5
Rep1_WB	96.5
Rep2_WB	98.7
Antibody Cat#	RN013p
Antibody Lot#
Antibody DCC ID	ENCAB995HZA
Status	Released
Project	ENCODE4
ID	226

Experiment Information (Status: Released)

	BGHcLV10-45	BGHcLV10-46
idx	242	243
TRCN#_or_BGC#	BGC#0000227	BGC#0000227
shRNA_or_gRNA_sequence	TTCGGGGCATGTACAATCAG	TTCGGGGCATGTACAATCAG
PAM	AGG	AGG
Name	STAU2-90	STAU2-90
Sample_ID	BGHcLV10-45	BGHcLV10-46
transduction_Date	4/27/18	4/27/18
days	D6	D6
RBP_name	STAU2	STAU2
qPCR_result	67.3	71.5
Ave_qPCR	69.4
RT-qPCR_primer-F	ATCCAATCGATGGAGCAATG
RT-qPCR_primer-R	CCTGGTTATTGTCCGCTTTC
protein_conc	2563	2358
WB_result	96.5	98.7
Ave_WB	97.6
WB_DONE_date	6/4/18	WES
MW	63kd
IP
antibody_Cat#	RN013p
Antibody DCC ID	ENCAB995HZA
submitted_to_DCC_date	9/6/18
Rep1_TPM	14	0
Rep2_TPM	28	0
Action	Ready	Ready
Library_start_date	8/7/18	8/7/18
repeat_library
Note
ID	6385	6386

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
STAU2	Product_ID: RN013P Lot_ID: 1 Source: MBLI Target Name: STAU2-human

Experiment Status

	BGHcLV10-45	BGHcLV10-46
Sample_ID	BGHcLV10-45	BGHcLV10-46
Sample Name
Sample Name	STAU2-BGHcLV10-45	STAU2-BGHcLV10-46
RBP	STAU2	STAU2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2020-11-06	2020-11-06
Project	ENCODE4	ENCODE4
Note
ID	6303	6304

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV10-45	BGHcLV10-46
Sample #	63	64
Sample Name	STAU2-BGHcLV10-45	STAU2-BGHcLV10-46
Sample_Name_Alias
Index Well Position	C09	D09
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2018-10-01	2018-10-01
Lib_ID	Lib-181001	Lib-181001
Tecan_Location
Tecan
Tecan_date
Size_bp	273	281
Peak_Molarity	43.70	41.20
libSampleQC_DNA_Well	DNA_Library_set41/set5/C9.png	DNA_Library_set41/set5/D9.png
RIN	9.9	10.0
libSample_RNA_Well	RNA_Library_set41/set2/G11.png	RNA_Library_set41/set1/H8.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2018-08-08	2018-08-08
Sample_ID	BGHcLV10-45	BGHcLV10-46
RBP	STAU2	STAU2
Batch_ID	BGHcLV10	BGHcLV10
WB_result	96.500	98.700
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	913	914

Sequencing Information

	BGHcLV10-45	BGHcLV10-46
Sample_ID	BGHcLV10-45	BGHcLV10-46
Sample Name	STAU2-BGHcLV10-45	STAU2-BGHcLV10-46
Pool ID	Pool-180901	Pool-180901
LocalServer_folder	set41	set41
total_reads	165,598,308	122,773,418
total_aligned_reads	157,411,948	116,288,980
unique_aligned_reads	145,841,812	108,302,624
percent_uniqueAligned	0.88070	0.88213
correlation_replicates	0.991731	0.991731
spikein_reads	350,082	289,372
percent_spikeins	0.00211	0.00236
original_ReadLength	150	150
QC_Status	Submitted	Submitted
ID	319	320

Data Submission Information

	BGHcLV10-45	BGHcLV10-45	BGHcLV10-45	BGHcLV10-45	BGHcLV10-45	BGHcLV10-45	BGHcLV10-46	BGHcLV10-46	BGHcLV10-46	BGHcLV10-46
ENCODE_alias	brenton-graveley:STAU2-BGHcLV10	brenton-graveley:STAU2-BGHcLV10-45	brenton-graveley:L-STAU2-BGHcLV10-45	brenton-graveley:STAU2-BGHcLV10-45_TTCCTGTT+AGTATCTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:STAU2-BGHcLV10-45_TTCCTGTT+AGTATCTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:STAU2-BGHcLV10-HepG2	brenton-graveley:STAU2-BGHcLV10-46	brenton-graveley:L-STAU2-BGHcLV10-46	brenton-graveley:STAU2-BGHcLV10-46_CCTTCACC+GACGCTCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:STAU2-BGHcLV10-46_CCTTCACC+GACGCTCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR279MNU	ENCBS365HBD	ENCLB534DAK	ENCFF974POV	ENCFF535JKG	ENCSR404DIU	ENCBS219FEV	ENCLB274XXH	ENCFF184QFG	ENCFF021LRF
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	BGHcLV10-45	BGHcLV10-45	BGHcLV10-45	BGHcLV10-45	BGHcLV10-45	BGHcLV10-45	BGHcLV10-46	BGHcLV10-46	BGHcLV10-46	BGHcLV10-46
Sample Name	STAU2-BGHcLV10-45	STAU2-BGHcLV10-45	STAU2-BGHcLV10-45	STAU2-BGHcLV10-45	STAU2-BGHcLV10-45	STAU2-BGHcLV10-45	STAU2-BGHcLV10-46	STAU2-BGHcLV10-46	STAU2-BGHcLV10-46	STAU2-BGHcLV10-46
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
		LV41_biosample_protocol	LV41_library_protocol				LV41_biosample_protocol	LV41_library_protocol
protocol_URL		STAU2-BGHcLV10-45.pdf	L-STAU2-BGHcLV10-45.pdf				STAU2-BGHcLV10-46.pdf	L-STAU2-BGHcLV10-46.pdf
ID	1144	1208	1278	1348	1412	7339	1209	1279	1349	1413

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
STAU2-BGHcLV10-45_TTCCTGTT+AGTATCTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	319				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	555
STAU2-BGHcLV10-45_TTCCTGTT+AGTATCTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	319				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	625
STAU2-BGHcLV10-45_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	319	GRCh38	V40	STAU2-BGHcLV10-45_TTCCTGTT+AGTATCTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BGHcLV10-45_TTCCTGTT+AGTATCTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26793
STAU2-BGHcLV10-45_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	319	GRCh38	V40	STAU2-BGHcLV10-45/Aligned.sortedByCoord.out.bam		ENCORE2	26863
STAU2-BGHcLV10-45_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	319	GRCh38	V40	STAU2-BGHcLV10-45/Aligned.sortedByCoord.out.bam		ENCORE2	26933
STAU2-BGHcLV10-45_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	319	GRCh38	V40	STAU2-BGHcLV10-45/Aligned.sortedByCoord.out.bam		ENCORE2	27003
STAU2-BGHcLV10-45_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	319	GRCh38	V40	STAU2-BGHcLV10-45/Aligned.sortedByCoord.out.bam		ENCORE2	27073
STAU2-BGHcLV10-45_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	319	GRCh38	V40	STAU2-BGHcLV10-45_TTCCTGTT+AGTATCTT_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BGHcLV10-45_TTCCTGTT+AGTATCTT_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27143
STAU2-BGHcLV10-46_CCTTCACC+GACGCTCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	320				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	556
STAU2-BGHcLV10-46_CCTTCACC+GACGCTCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set41/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	320				NT-BGHcLV10-1_CAACAATG+CTTCACGG_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV10-2_TGGTGGCA+TCCTGTAA_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	626
STAU2-BGHcLV10-46_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	320	GRCh38	V40	STAU2-BGHcLV10-46_CCTTCACC+GACGCTCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BGHcLV10-46_CCTTCACC+GACGCTCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	26794
STAU2-BGHcLV10-46_Signal.Unique.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	320	GRCh38	V40	STAU2-BGHcLV10-46/Aligned.sortedByCoord.out.bam		ENCORE2	26864
STAU2-BGHcLV10-46_Signal.Unique.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	320	GRCh38	V40	STAU2-BGHcLV10-46/Aligned.sortedByCoord.out.bam		ENCORE2	26934
STAU2-BGHcLV10-46_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	320	GRCh38	V40	STAU2-BGHcLV10-46/Aligned.sortedByCoord.out.bam		ENCORE2	27004
STAU2-BGHcLV10-46_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set41/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	320	GRCh38	V40	STAU2-BGHcLV10-46/Aligned.sortedByCoord.out.bam		ENCORE2	27074
STAU2-BGHcLV10-46_quant.sf	ENCODE_DATA/set41/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	320	GRCh38	V40	STAU2-BGHcLV10-46_CCTTCACC+GACGCTCC_HGLMVDMXX_L001_R1_001.filtered.trimmed.paired.fastq.gz,STAU2-BGHcLV10-46_CCTTCACC+GACGCTCC_HGLMVDMXX_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27144