SARNP RNA-Seq in HepG2

General Information


RBP	SARNP
Cell_Line	HepG2
Method	CRISPR
Exp_Name	SARNP-BGHcLV31-HepG2
ENCODE_series_ID	ENCSR048ILP
Batch_ID	BGHcLV31
Pool ID	Pool-220331
Local_Set_Name	set52
ENCODE_KD_Exp_ID	ENCSR207GTU
ENCODE_CN_Exp_ID	ENCSR452TFV
Rep1	SARNP-BGHcLV31-27
Rep2	SARNP-BGHcLV31-28
CN1	NT-BGHcLV31-1
CN2	NT-BGHcLV31-2
Rep1_qPCR	64.2
Rep2_qPCR	61.7
Rep1_WB	51.7
Rep2_WB	54.2
Antibody Cat#	A303-209A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB353OXX
Status	Submitted
Project	ENCODE4
ID	925

Experiment Information (Status: Released)

	BGHcLV31-27	BGHcLV31-28
idx	945	946
TRCN#_or_BGC#	BGC#0000843	BGC#0000843
shRNA_or_gRNA_sequence	CAAGATGGCGACCGAGACGG	CAAGATGGCGACCGAGACGG
PAM	TGG	TGG
Name	SARNP_80	SARNP_80
Sample_ID	BGHcLV31-27	BGHcLV31-28
transduction_Date	9/23/21	9/23/21
days	D6	D6
RBP_name	SARNP	SARNP
qPCR_result	64.2	61.7
Ave_qPCR	63.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4036	4202
WB_result	51.7	54.2
Ave_WB	53.0
WB_DONE_date	10/14/21
MW	24kd
IP
antibody_Cat#	A303-209A	LOT #1
Antibody DCC ID	ENCAB353OXX
submitted_to_DCC_date
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	12/16/21	12/16/21
repeat_library
Note
ID	7124	7125

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
SARNP	Product_ID: A303-209A Lot_ID: 1 Source: Bethyl Labs Target Name: SARNP-human

Experiment Status

	BGHcLV31-27	BGHcLV31-28
Sample_ID	BGHcLV31-27	BGHcLV31-28
Sample Name
Sample Name	SARNP-BGHcLV31-27	SARNP-BGHcLV31-28
RBP	SARNP	SARNP
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4
Note
ID	10305	10306

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV31-27	BGHcLV31-28
Sample #	19	20
Sample Name	SARNP-BGHcLV31-27	SARNP-BGHcLV31-28
Sample_Name_Alias
Index Well Position	C03	D03
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-12-16	2021-12-16
Lib_ID	Lib-211216	Lib-211216
Tecan_Location
Tecan
Tecan_date
Size_bp	289	296
Peak_Molarity	71.30	60.30
libSampleQC_DNA_Well	DNA_Library_set52/set1/C10.png	DNA_Library_set52/set1/D10.png
RIN	9.8	9.6
libSample_RNA_Well	RNA_Library_set52/set1/C3.png	RNA_Library_set52/set1/D3.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2022-01-04	2022-01-04
Sample_ID	BGHcLV31-27	BGHcLV31-28
RBP	SARNP	SARNP
Batch_ID	BGHcLV31	BGHcLV31
WB_result	51.700	54.200
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3196	3197

Sequencing Information

	BGHcLV31-27	BGHcLV31-28
Sample_ID	BGHcLV31-27	BGHcLV31-28
Sample Name	SARNP-BGHcLV31-27	SARNP-BGHcLV31-28
Pool ID	Pool-220331	Pool-220331
LocalServer_folder	set52	set52
total_reads	100,911,770	109,719,824
total_aligned_reads	90,325,756	100,285,104
unique_aligned_reads	85,167,828	94,460,098
percent_uniqueAligned	0.84398	0.86092
correlation_replicates	0.997254	0.997254
spikein_reads	4,574	2,636
percent_spikeins	0.00005	0.00002
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1993	1994

Data Submission Information

	BGHcLV31-27	BGHcLV31-27	BGHcLV31-27	BGHcLV31-27	BGHcLV31-27	BGHcLV31-27	BGHcLV31-28	BGHcLV31-28	BGHcLV31-28	BGHcLV31-28
ENCODE_alias	brenton-graveley:SARNP-BGHcLV31	brenton-graveley:SARNP-BGHcLV31-27	brenton-graveley:L-SARNP-BGHcLV31-27	brenton-graveley:SARNP-BGHcLV31-27_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SARNP-BGHcLV31-27_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SARNP-BGHcLV31-HepG2	brenton-graveley:SARNP-BGHcLV31-28	brenton-graveley:L-SARNP-BGHcLV31-28	brenton-graveley:SARNP-BGHcLV31-28_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:SARNP-BGHcLV31-28_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR207GTU	ENCBS621TYJ	ENCLB036MLA	ENCFF975KUC	ENCFF311GQG	ENCSR048ILP	ENCBS227PHU	ENCLB119ENP	ENCFF423TAZ	ENCFF501VVP
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	BGHcLV31-27	BGHcLV31-27	BGHcLV31-27	BGHcLV31-27	BGHcLV31-27	BGHcLV31-27	BGHcLV31-28	BGHcLV31-28	BGHcLV31-28	BGHcLV31-28
Sample Name	SARNP-BGHcLV31-27	SARNP-BGHcLV31-27	SARNP-BGHcLV31-27	SARNP-BGHcLV31-27	SARNP-BGHcLV31-27	SARNP-BGHcLV31-27	SARNP-BGHcLV31-28	SARNP-BGHcLV31-28	SARNP-BGHcLV31-28	SARNP-BGHcLV31-28
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28	2022-10-28
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV52_biosample_protocol	LV52_library_protocol				LV52_biosample_protocol	LV52_library_protocol
protocol_URL		SARNP-BGHcLV31-27.pdf	L-SARNP-BGHcLV31-27.pdf				SARNP-BGHcLV31-28.pdf	L-SARNP-BGHcLV31-28.pdf
ID	7453	7517	7625	7735	7845	7945	7518	7626	7736	7846

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
SARNP-BGHcLV31-27_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1993	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6539
SARNP-BGHcLV31-27_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1993	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6593
SARNP-BGHcLV31-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1993					GRCh38	V40	SARNP-BGHcLV31-27_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,SARNP-BGHcLV31-27_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18460
SARNP-BGHcLV31-27_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1993					GRCh38	V40	SARNP-BGHcLV31-27/Aligned.sortedByCoord.out.bam		ENCORE2	18514
SARNP-BGHcLV31-27_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1993					GRCh38	V40	SARNP-BGHcLV31-27/Aligned.sortedByCoord.out.bam		ENCORE2	18568
SARNP-BGHcLV31-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1993					GRCh38	V40	SARNP-BGHcLV31-27/Aligned.sortedByCoord.out.bam		ENCORE2	18622
SARNP-BGHcLV31-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1993					GRCh38	V40	SARNP-BGHcLV31-27/Aligned.sortedByCoord.out.bam		ENCORE2	18676
SARNP-BGHcLV31-27_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1993					GRCh38	V40	SARNP-BGHcLV31-27_S19_L001_R1_001.filtered.trimmed.paired.fastq.gz,SARNP-BGHcLV31-27_S19_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18730
SARNP-BGHcLV31-28_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1994	NovaSeq6000	100	paired-ended	1				NT-BGHcLV31-1_S1_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6540
SARNP-BGHcLV31-28_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set52/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1994	NovaSeq6000	100	paired-ended	2				NT-BGHcLV31-1_S1_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV31-2_S2_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	6594
SARNP-BGHcLV31-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1994					GRCh38	V40	SARNP-BGHcLV31-28_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,SARNP-BGHcLV31-28_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18461
SARNP-BGHcLV31-28_Signal.Unique.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1994					GRCh38	V40	SARNP-BGHcLV31-28/Aligned.sortedByCoord.out.bam		ENCORE2	18515
SARNP-BGHcLV31-28_Signal.Unique.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1994					GRCh38	V40	SARNP-BGHcLV31-28/Aligned.sortedByCoord.out.bam		ENCORE2	18569
SARNP-BGHcLV31-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1994					GRCh38	V40	SARNP-BGHcLV31-28/Aligned.sortedByCoord.out.bam		ENCORE2	18623
SARNP-BGHcLV31-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set52/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1994					GRCh38	V40	SARNP-BGHcLV31-28/Aligned.sortedByCoord.out.bam		ENCORE2	18677
SARNP-BGHcLV31-28_quant.sf	ENCODE_DATA/set52/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1994					GRCh38	V40	SARNP-BGHcLV31-28_S20_L001_R1_001.filtered.trimmed.paired.fastq.gz,SARNP-BGHcLV31-28_S20_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18731