LSM7 RNA-Seq in HepG2

General Information


RBP	LSM7
Cell_Line	HepG2
Method	CRISPR
Exp_Name	LSM7-BGHcLV22-HepG2
ENCODE_series_ID	ENCSR098JWL
Batch_ID	BGHcLV22
Pool ID	Pool-201204
Local_Set_Name	set46_H
ENCODE_KD_Exp_ID	ENCSR120WNJ
ENCODE_CN_Exp_ID	ENCSR704VPL
Rep1	LSM7-BGHcLV22-29
Rep2	LSM7-BGHcLV22-30
CN1	NT-BGHcLV22-1
CN2	NT-BGHcLV22-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	73.4
Rep2_WB	71.4
Antibody Cat#	A305-097A
Antibody Lot#	lot# 1
Antibody DCC ID	ENCAB362WTJ
Status	Released
Project	ENCODE4
ID	43

Experiment Information (Status: Released)

	BGHcLV22-29	BGHcLV22-30
idx	622	623
TRCN#_or_BGC#	BGC#0000522	BGC#0000522
shRNA_or_gRNA_sequence	CGTGGTGCTAATCTGCCCGC	CGTGGTGCTAATCTGCCCGC
PAM	AGG	AGG
Name	LSM7_95	LSM7_95
Sample_ID	BGHcLV22-29	BGHcLV22-30
transduction_Date	8/22/20	8/22/20
days	D6	D6
RBP_name	LSM7	LSM7
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	GTACATCGACAAGACGATCCG
RT-qPCR_primer-R	AGCACAAGGTTGAGGAGTGG
protein_conc	2600	2485
WB_result	73.4	71.4
Ave_WB	72.4
WB_DONE_date	9/2/20-2	JESS
MW	35.8kDa
IP	Rabbit / I
antibody_Cat#	A305-097A	lot# 1
Antibody DCC ID	ENCAB362WTJ
submitted_to_DCC_date	11/16/20
Rep1_TPM	0	0
Rep2_TPM	0	0
Action	Ready	Ready
Library_start_date	11/24/20	11/24/20
repeat_library
Note
ID	6777	6778

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
LSM7	Product_ID: A305-097A Lot_ID: 1 Source: Bethyl Labs Target Name: LSM7-human

Experiment Status

	BGHcLV22-29	BGHcLV22-30
Sample_ID	BGHcLV22-29	BGHcLV22-30
Sample Name
Sample Name	LSM7-BGHcLV22-29	LSM7-BGHcLV22-30
RBP	LSM7	LSM7
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4
Note
ID	7379	7380

Library-Prep
Sequencing

Library-Prep Information

	BGHcLV22-29	BGHcLV22-30
Sample #	15	16
Sample Name	LSM7-BGHcLV22-29	LSM7-BGHcLV22-30
Sample_Name_Alias
Index Well Position	G02	H02
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-11-24	2020-11-24
Lib_ID	Lib-201124	Lib-201124
Tecan_Location
Tecan
Tecan_date
Size_bp	286	281
Peak_Molarity	80.20	76.70
libSampleQC_DNA_Well	DNA_Library_set46/set1/G2.png	DNA_Library_set46/set1/H2.png
RIN	9.7	9.7
libSample_RNA_Well	RNA_Library_set46/set1/G10.png	RNA_Library_set46/set1/H10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-12-04	2020-12-04
Sample_ID	BGHcLV22-29	BGHcLV22-30
RBP	LSM7	LSM7
Batch_ID	BGHcLV22	BGHcLV22
WB_result	73.400	71.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	1390	1391

Sequencing Information

	BGHcLV22-29	BGHcLV22-30
Sample_ID	BGHcLV22-29	BGHcLV22-30
Sample Name	LSM7-BGHcLV22-29	LSM7-BGHcLV22-30
Pool ID	Pool-201204	Pool-201204
LocalServer_folder	set46_H	set46_H
total_reads	190,785,508	223,086,922
total_aligned_reads	153,667,084	190,962,354
unique_aligned_reads	143,776,102	178,526,922
percent_uniqueAligned	0.75360	0.80026
correlation_replicates	0.986952	0.986952
spikein_reads	76,712	96,862
percent_spikeins	0.00040	0.00043
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	496	497

Data Submission Information

	BGHcLV22-29	BGHcLV22-29	BGHcLV22-29	BGHcLV22-29	BGHcLV22-29	BGHcLV22-29	BGHcLV22-30	BGHcLV22-30	BGHcLV22-30	BGHcLV22-30
ENCODE_alias	brenton-graveley:LSM7-BGHcLV22	brenton-graveley:LSM7-BGHcLV22-29	brenton-graveley:L-LSM7-BGHcLV22-29	brenton-graveley:LSM7-BGHcLV22-29_GGCTTAAG+GGTCACGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:LSM7-BGHcLV22-29_GGCTTAAG+GGTCACGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:LSM7-BGHcLV22-HepG2	brenton-graveley:LSM7-BGHcLV22-30	brenton-graveley:L-LSM7-BGHcLV22-30	brenton-graveley:LSM7-BGHcLV22-30_AATCCGGA+AACTGTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:LSM7-BGHcLV22-30_AATCCGGA+AACTGTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR120WNJ	ENCBS671YCK	ENCLB258RIU	ENCFF643YEM	ENCFF424RQP	ENCSR098JWL	ENCBS240ZAB	ENCLB366GGT	ENCFF365SZF	ENCFF412ZCN
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	BGHcLV22-29	BGHcLV22-29	BGHcLV22-29	BGHcLV22-29	BGHcLV22-29	BGHcLV22-29	BGHcLV22-30	BGHcLV22-30	BGHcLV22-30	BGHcLV22-30
Sample Name	LSM7-BGHcLV22-29	LSM7-BGHcLV22-29	LSM7-BGHcLV22-29	LSM7-BGHcLV22-29	LSM7-BGHcLV22-29	LSM7-BGHcLV22-29	LSM7-BGHcLV22-30	LSM7-BGHcLV22-30	LSM7-BGHcLV22-30	LSM7-BGHcLV22-30
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02	2022-03-02	2021-06-02	2021-06-02	2021-06-02	2021-06-02
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV46H_biosample_protocol	LV46H_library_protocol				LV46H_biosample_protocol	LV46H_library_protocol
protocol_URL		LSM7-BGHcLV22-29.pdf	L-LSM7-BGHcLV22-29.pdf				LSM7-BGHcLV22-30.pdf	L-LSM7-BGHcLV22-30.pdf
ID	2402	2441	2505	2569	2599	7248	2442	2506	2570	2600

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
LSM7-BGHcLV22-29_GGCTTAAG+GGTCACGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	496	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1360
LSM7-BGHcLV22-29_GGCTTAAG+GGTCACGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	496	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1424
LSM7-BGHcLV22-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	496					GRCh38	V40	LSM7-BGHcLV22-29_GGCTTAAG+GGTCACGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,LSM7-BGHcLV22-29_GGCTTAAG+GGTCACGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25263
LSM7-BGHcLV22-29_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	496					GRCh38	V40	LSM7-BGHcLV22-29_GGCTTAAG+GGTCACGA_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,LSM7-BGHcLV22-29_GGCTTAAG+GGTCACGA_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25361
LSM7-BGHcLV22-29_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	496					GRCh38	V40	LSM7-BGHcLV22-29/Aligned.sortedByCoord.out.bam		ENCORE2	26011
LSM7-BGHcLV22-29_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	496					GRCh38	V40	LSM7-BGHcLV22-29/Aligned.sortedByCoord.out.bam		ENCORE2	26041
LSM7-BGHcLV22-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	496					GRCh38	V40	LSM7-BGHcLV22-29/Aligned.sortedByCoord.out.bam		ENCORE2	26071
LSM7-BGHcLV22-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	496					GRCh38	V40	LSM7-BGHcLV22-29/Aligned.sortedByCoord.out.bam		ENCORE2	26101
LSM7-BGHcLV22-30_AATCCGGA+AACTGTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	497	NovaSeq6000	100	paired-ended	1				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1361
LSM7-BGHcLV22-30_AATCCGGA+AACTGTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set46_H/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	497	NovaSeq6000	100	paired-ended	2				NT-BGHcLV22-1_CCGCGGTT+CTAGCGCT_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGHcLV22-2_TTATAACC+TCGATATC_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	1425
LSM7-BGHcLV22-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	497					GRCh38	V40	LSM7-BGHcLV22-30_AATCCGGA+AACTGTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,LSM7-BGHcLV22-30_AATCCGGA+AACTGTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25264
LSM7-BGHcLV22-30_quant.sf	ENCODE_DATA/set46_H/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	497					GRCh38	V40	LSM7-BGHcLV22-30_AATCCGGA+AACTGTAG_HVKGLDSXY_L001_R1_001.filtered.trimmed.paired.fastq.gz,LSM7-BGHcLV22-30_AATCCGGA+AACTGTAG_HVKGLDSXY_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25362
LSM7-BGHcLV22-30_Signal.Unique.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	497					GRCh38	V40	LSM7-BGHcLV22-30/Aligned.sortedByCoord.out.bam		ENCORE2	26012
LSM7-BGHcLV22-30_Signal.Unique.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	497					GRCh38	V40	LSM7-BGHcLV22-30/Aligned.sortedByCoord.out.bam		ENCORE2	26042
LSM7-BGHcLV22-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	497					GRCh38	V40	LSM7-BGHcLV22-30/Aligned.sortedByCoord.out.bam		ENCORE2	26072
LSM7-BGHcLV22-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set46_H/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	497					GRCh38	V40	LSM7-BGHcLV22-30/Aligned.sortedByCoord.out.bam		ENCORE2	26102