LSM7 RNA-Seq in K562

General Information


RBP	LSM7
Cell_Line	K562
Method	CRISPR
Exp_Name	LSM7-BGKcLV21-K562
ENCODE_series_ID	ENCSR545ARH
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR307KLI
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	LSM7-BGKcLV21-27
Rep2	LSM7-BGKcLV21-28
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	67.9
Rep2_WB	71.0
Antibody Cat#	A305-097A
Antibody Lot#	lot# 1
Antibody DCC ID	ENCAB362WTJ
Status	Released
Project	ENCODE4
ID	70

Experiment Information (Status: Released)

	BGKcLV21-27	BGKcLV21-28
idx	760	761
TRCN#_or_BGC#	BGC#0000522	BGC#0000522
shRNA_or_gRNA_sequence	CGTGGTGCTAATCTGCCCGC	CGTGGTGCTAATCTGCCCGC
PAM	AGG	AGG
Name	LSM7_95	LSM7_95
Sample_ID	BGKcLV21-27	BGKcLV21-28
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	LSM7	LSM7
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4943	5428
WB_result	67.9	71.0
Ave_WB	69.4
WB_DONE_date	8/20/20
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	09/24/20	09/24/20
repeat_library
Note
ID	4880	4881

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

	BGKcLV21-27	BGKcLV21-28
Sample_ID	BGKcLV21-27	BGKcLV21-28
Sample Name
Sample Name	LSM7-BGKcLV21-27	LSM7-BGKcLV21-28
RBP	LSM7	LSM7
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6131	6132

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-27	BGKcLV21-28
Sample #	49	50
Sample Name	LSM7-BGKcLV21-27	LSM7-BGKcLV21-28
Sample_Name_Alias
Index Well Position	C06	D06
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2020-09-24	2020-09-24
Lib_ID	Lib-200924	Lib-200924
Tecan_Location
Tecan
Tecan_date
Size_bp	314	316
Peak_Molarity	170.00	118.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/C6.png	DNA_Library_set45/set1/D6.png
RIN	9.9	9.5
libSample_RNA_Well	RNA_Library_set45/set2/E10.png	RNA_Library_set45/set1/D6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV21-27	BGKcLV21-28
RBP	LSM7	LSM7
Batch_ID	BGKcLV21	BGKcLV21
WB_result	67.900	71.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	823	824

Sequencing Information

	BGKcLV21-27	BGKcLV21-28
Sample_ID	BGKcLV21-27	BGKcLV21-28
Sample Name	LSM7-BGKcLV21-27	LSM7-BGKcLV21-28
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	160,827,658	165,150,398
total_aligned_reads	157,832,102	161,768,526
unique_aligned_reads	144,295,284	147,471,702
percent_uniqueAligned	0.89720	0.89295
correlation_replicates	0.987180	0.987180
spikein_reads	105,070	72,976
percent_spikeins	0.00065	0.00044
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	454	455

Data Submission Information

	BGKcLV21-27	BGKcLV21-27	BGKcLV21-27	BGKcLV21-27	BGKcLV21-27	BGKcLV21-27	BGKcLV21-28	BGKcLV21-28	BGKcLV21-28	BGKcLV21-28
ENCODE_alias	brenton-graveley:LSM7-BGKcLV21	brenton-graveley:LSM7-BGKcLV21-27	brenton-graveley:L-LSM7-BGKcLV21-27	brenton-graveley:LSM7-BGKcLV21-27_S43_R1_001.fastq.gz	brenton-graveley:LSM7-BGKcLV21-27_S43_R2_001.fastq.gz	brenton-graveley:LSM7-BGKcLV21-K562	brenton-graveley:LSM7-BGKcLV21-28	brenton-graveley:L-LSM7-BGKcLV21-28	brenton-graveley:LSM7-BGKcLV21-28_S44_R1_001.fastq.gz	brenton-graveley:LSM7-BGKcLV21-28_S44_R2_001.fastq.gz
ENCODE_accession	ENCSR307KLI	ENCBS783NZF	ENCLB259SFH	ENCFF875FEV	ENCFF366POV	ENCSR545ARH	ENCBS643NSH	ENCLB500HRS	ENCFF117AAD	ENCFF329JVE
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	BGKcLV21-27	BGKcLV21-27	BGKcLV21-27	BGKcLV21-27	BGKcLV21-27	BGKcLV21-27	BGKcLV21-28	BGKcLV21-28	BGKcLV21-28	BGKcLV21-28
Sample Name	LSM7-BGKcLV21-27	LSM7-BGKcLV21-27	LSM7-BGKcLV21-27	LSM7-BGKcLV21-27	LSM7-BGKcLV21-27	LSM7-BGKcLV21-27	LSM7-BGKcLV21-28	LSM7-BGKcLV21-28	LSM7-BGKcLV21-28	LSM7-BGKcLV21-28
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2021-03-18	2022-03-02	2021-03-18	2021-03-18	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV45K_biosample_protocol	LV45K_library_protocol				LV45K_biosample_protocol	LV45K_library_protocol
protocol_URL		LSM7-BGKcLV21-27.pdf	L-LSM7-BGKcLV21-27.pdf				LSM7-BGKcLV21-28.pdf	L-LSM7-BGKcLV21-28.pdf
ID	2111	2177	2247	2317	2387	7249	2178	2248	2318	2388

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-BGKcLV21-27_S43_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	454	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1226
LSM7-BGKcLV21-27_S43_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	454	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1276
LSM7-BGKcLV21-27_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	454					GRCh38	V40	LSM7-BGKcLV21-27_S43_R1_001.filtered.trimmed.paired.fastq.gz,LSM7-BGKcLV21-27_S43_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25219
LSM7-BGKcLV21-27_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	454					GRCh38	V40	LSM7-BGKcLV21-27_S43_R1_001.filtered.trimmed.paired.fastq.gz,LSM7-BGKcLV21-27_S43_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27173
LSM7-BGKcLV21-27_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	454					GRCh38	V40	LSM7-BGKcLV21-27/Aligned.sortedByCoord.out.bam		ENCORE2	27223
LSM7-BGKcLV21-27_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	454					GRCh38	V40	LSM7-BGKcLV21-27/Aligned.sortedByCoord.out.bam		ENCORE2	27273
LSM7-BGKcLV21-27_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	454					GRCh38	V40	LSM7-BGKcLV21-27/Aligned.sortedByCoord.out.bam		ENCORE2	27323
LSM7-BGKcLV21-27_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	454					GRCh38	V40	LSM7-BGKcLV21-27/Aligned.sortedByCoord.out.bam		ENCORE2	27373
LSM7-BGKcLV21-28_S44_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	455	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1227
LSM7-BGKcLV21-28_S44_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	455	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1277
LSM7-BGKcLV21-28_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2_file_links	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	455					GRCh38	V40	LSM7-BGKcLV21-28_S44_R1_001.filtered.trimmed.paired.fastq.gz,LSM7-BGKcLV21-28_S44_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25220
LSM7-BGKcLV21-28_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	455					GRCh38	V40	LSM7-BGKcLV21-28_S44_R1_001.filtered.trimmed.paired.fastq.gz,LSM7-BGKcLV21-28_S44_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27174
LSM7-BGKcLV21-28_Signal.Unique.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	455					GRCh38	V40	LSM7-BGKcLV21-28/Aligned.sortedByCoord.out.bam		ENCORE2	27224
LSM7-BGKcLV21-28_Signal.Unique.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	455					GRCh38	V40	LSM7-BGKcLV21-28/Aligned.sortedByCoord.out.bam		ENCORE2	27274
LSM7-BGKcLV21-28_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	455					GRCh38	V40	LSM7-BGKcLV21-28/Aligned.sortedByCoord.out.bam		ENCORE2	27324
LSM7-BGKcLV21-28_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	455					GRCh38	V40	LSM7-BGKcLV21-28/Aligned.sortedByCoord.out.bam		ENCORE2	27374