RECQL5 RNA-Seq in K562

General Information


RBP	RECQL5
Cell_Line	K562
Method	CRISPR
Exp_Name	RECQL5-BGKcLV30-K562
ENCODE_series_ID	ENCSR127JDF
Batch_ID	BGKcLV30
Pool ID	Pool-211117
Local_Set_Name	set50_K
ENCODE_KD_Exp_ID	ENCSR632RWY
ENCODE_CN_Exp_ID	ENCSR347NKX
Rep1	RECQL5-BGKcLV30-29
Rep2	RECQL5-BGKcLV30-30
CN1	NT-BGKcLV30-1
CN2	NT-BGKcLV30-2
Rep1_qPCR	xx
Rep2_qPCR	xx
Rep1_WB	53.6
Rep2_WB	59.5
Antibody Cat#	A302-520A
Antibody Lot#	LOT #1
Antibody DCC ID	ENCAB159ICC
Status	Submitted
Project	ENCODE4
ID	872

Experiment Information (Status: Released)

	BGKcLV30-29	BGKcLV30-29	BGKcLV30-30	BGKcLV30-30
idx	1054	1056	1055	1057
TRCN#_or_BGC#	BGC#0000776	BGC#0000776	BGC#0000776	BGC#0000776
shRNA_or_gRNA_sequence	TACTCCGGACTCGCCGCTCA	TACTCCGGACTCGCCGCTCA	TACTCCGGACTCGCCGCTCA	TACTCCGGACTCGCCGCTCA
PAM	GGG	GGG	GGG	GGG
Name	RECQL5_97	RECQL5_97	RECQL5_97	RECQL5_97
Sample_ID	BGKcLV30-29	BGKcLV30-29	BGKcLV30-30	BGKcLV30-30
transduction_Date	8/30/21	8/30/21	8/30/21	8/30/21
days	D6	D6	D6	D6
RBP_name	RECQL5	RECQL5	RECQL5	RECQL5
qPCR_result	xx		xx
Ave_qPCR
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	2609	2609	2464	2464
WB_result	53.6	79.6	59.5	74.3
Ave_WB	56.5	77.0
WB_DONE_date	9/10/21	2/23/22	JESS
MW	109KD	109KD
IP
antibody_Cat#	A302-520A	A302-522A	LOT #1	LOT #1
Antibody DCC ID	ENCAB159ICC
submitted_to_DCC_date
Rep1_TPM	0	0	0	0
Rep2_TPM	0	0	0	0
Action	Ready		Ready
Library_start_date	11/10/21		11/10/21
repeat_library
Note
ID	5192	5194	5193	5195

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
RECQL5	Product_ID: A302-520A Lot_ID: 1 Source: Bethyl Labs Target Name: RECQL5-human

Experiment Status

	BGKcLV30-29	BGKcLV30-30
Sample_ID	BGKcLV30-29	BGKcLV30-30
Sample Name
Sample Name	RECQL5-BGKcLV30-29	RECQL5-BGKcLV30-30
RBP	RECQL5	RECQL5
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4
Note
ID	10069	10070

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV30-29	BGKcLV30-30
Sample #	59	60
Sample Name	RECQL5-BGKcLV30-29	RECQL5-BGKcLV30-30
Sample_Name_Alias
Index Well Position	G08	H08
Index_table	IDT_UniqueDualIndex_96	IDT_UniqueDualIndex_96
LibPrep_date	2021-11-01	2021-11-01
Lib_ID	Lib-211101A	Lib-211101A
Tecan_Location
Tecan
Tecan_date
Size_bp	279	275
Peak_Molarity	33.40	32.10
libSampleQC_DNA_Well	DNA_Library_set50/set2/G10.png	DNA_Library_set50/set2/H10.png
RIN	9.6	9.6
libSample_RNA_Well	RNA_Library_set50/set2/G10.png	RNA_Library_set50/set2/H10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2021-11-17	2021-11-17
Sample_ID	BGKcLV30-29	BGKcLV30-30
RBP	RECQL5	RECQL5
Batch_ID	BGKcLV30	BGKcLV30
WB_result	53.600	59.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	3146	3147

Sequencing Information

	BGKcLV30-29	BGKcLV30-30
Sample_ID	BGKcLV30-29	BGKcLV30-30
Sample Name	RECQL5-BGKcLV30-29	RECQL5-BGKcLV30-30
Pool ID	Pool-211117	Pool-211117
LocalServer_folder	set50_K	set50_K
total_reads	70,114,970	74,985,224
total_aligned_reads	65,610,368	69,972,066
unique_aligned_reads	59,777,572	63,658,080
percent_uniqueAligned	0.85257	0.84894
correlation_replicates	0.991905	0.991905
spikein_reads	9,436	10,186
percent_spikeins	0.00013	0.00014
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	1931	1932

Data Submission Information

	BGKcLV30-29	BGKcLV30-29	BGKcLV30-29	BGKcLV30-29	BGKcLV30-29	BGKcLV30-29	BGKcLV30-30	BGKcLV30-30	BGKcLV30-30	BGKcLV30-30
ENCODE_alias	brenton-graveley:RECQL5-BGKcLV30	brenton-graveley:RECQL5-BGKcLV30-29	brenton-graveley:L-RECQL5-BGKcLV30-29	brenton-graveley:RECQL5-BGKcLV30-29_S61_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RECQL5-BGKcLV30-29_S61_L001_R2_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RECQL5-BGKcLV30-K562	brenton-graveley:RECQL5-BGKcLV30-30	brenton-graveley:L-RECQL5-BGKcLV30-30	brenton-graveley:RECQL5-BGKcLV30-30_S62_L001_R1_001.filtered.trimmed.paired.fastq.gz	brenton-graveley:RECQL5-BGKcLV30-30_S62_L001_R2_001.filtered.trimmed.paired.fastq.gz
ENCODE_accession	ENCSR632RWY	ENCBS210FCU	ENCLB940CDV	ENCFF663OEM	ENCFF332VGL	ENCSR127JDF	ENCBS045SWE	ENCLB014SJZ	ENCFF621SQQ	ENCFF691OIW
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	BGKcLV30-29	BGKcLV30-29	BGKcLV30-29	BGKcLV30-29	BGKcLV30-29	BGKcLV30-29	BGKcLV30-30	BGKcLV30-30	BGKcLV30-30	BGKcLV30-30
Sample Name	RECQL5-BGKcLV30-29	RECQL5-BGKcLV30-29	RECQL5-BGKcLV30-29	RECQL5-BGKcLV30-29	RECQL5-BGKcLV30-29	RECQL5-BGKcLV30-29	RECQL5-BGKcLV30-30	RECQL5-BGKcLV30-30	RECQL5-BGKcLV30-30	RECQL5-BGKcLV30-30
Selected	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Status	Released	Released	Released	Released	Released	Released	Released	Released	Released	Released
Status_Date	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11	2022-02-11
Project	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4	ENCODE4
		LV50K_biosample_protocol	LV50K_library_protocol				LV50K_biosample_protocol	LV50K_library_protocol
protocol_URL		RECQL5-BGKcLV30-29.pdf	L-RECQL5-BGKcLV30-29.pdf				RECQL5-BGKcLV30-30.pdf	L-RECQL5-BGKcLV30-30.pdf
ID	5871	5935	6007	6079	6151	6193	5936	6008	6080	6152

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
RECQL5-BGKcLV30-29_S61_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1931	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5859
RECQL5-BGKcLV30-29_S61_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1931	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5889
RECQL5-BGKcLV30-29_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1931					GRCh38	V40	RECQL5-BGKcLV30-29_S61_L001_R1_001.filtered.trimmed.paired.fastq.gz,RECQL5-BGKcLV30-29_S61_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18760
RECQL5-BGKcLV30-29_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1931					GRCh38	V40	RECQL5-BGKcLV30-29/Aligned.sortedByCoord.out.bam		ENCORE2	18790
RECQL5-BGKcLV30-29_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1931					GRCh38	V40	RECQL5-BGKcLV30-29/Aligned.sortedByCoord.out.bam		ENCORE2	18820
RECQL5-BGKcLV30-29_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1931					GRCh38	V40	RECQL5-BGKcLV30-29/Aligned.sortedByCoord.out.bam		ENCORE2	18850
RECQL5-BGKcLV30-29_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1931					GRCh38	V40	RECQL5-BGKcLV30-29/Aligned.sortedByCoord.out.bam		ENCORE2	18880
RECQL5-BGKcLV30-29_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1931					GRCh38	V40	RECQL5-BGKcLV30-29_S61_L001_R1_001.filtered.trimmed.paired.fastq.gz,RECQL5-BGKcLV30-29_S61_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18910
RECQL5-BGKcLV30-30_S62_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1932	NovaSeq6000	100	paired-ended	1				NT-BGKcLV30-1_S47_L001_R1_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R1_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5860
RECQL5-BGKcLV30-30_S62_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE_DATA/set50_K/fastq_trimmed	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1932	NovaSeq6000	100	paired-ended	2				NT-BGKcLV30-1_S47_L001_R2_001.filtered.trimmed.paired.fastq.gz,NT-BGKcLV30-2_S48_L001_R2_001.filtered.trimmed.paired.fastq.gz	ENCODE4	5890
RECQL5-BGKcLV30-30_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1932					GRCh38	V40	RECQL5-BGKcLV30-30_S62_L001_R1_001.filtered.trimmed.paired.fastq.gz,RECQL5-BGKcLV30-30_S62_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18761
RECQL5-BGKcLV30-30_Signal.Unique.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1932					GRCh38	V40	RECQL5-BGKcLV30-30/Aligned.sortedByCoord.out.bam		ENCORE2	18791
RECQL5-BGKcLV30-30_Signal.Unique.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1932					GRCh38	V40	RECQL5-BGKcLV30-30/Aligned.sortedByCoord.out.bam		ENCORE2	18821
RECQL5-BGKcLV30-30_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1932					GRCh38	V40	RECQL5-BGKcLV30-30/Aligned.sortedByCoord.out.bam		ENCORE2	18851
RECQL5-BGKcLV30-30_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set50_K/STAR_ENCORE2_trimmed_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1932					GRCh38	V40	RECQL5-BGKcLV30-30/Aligned.sortedByCoord.out.bam		ENCORE2	18881
RECQL5-BGKcLV30-30_quant.sf	ENCODE_DATA/set50_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1932					GRCh38	V40	RECQL5-BGKcLV30-30_S62_L001_R1_001.filtered.trimmed.paired.fastq.gz,RECQL5-BGKcLV30-30_S62_L001_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	18911