CHTOP RNA-Seq in K562

General Information


RBP	CHTOP
Cell_Line	K562
Method	CRISPR
Exp_Name	CHTOP-BGKcLV21-K562
ENCODE_series_ID	ENCSR574VQZ
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR913OZW
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	CHTOP-BGKcLV21-5
Rep2	CHTOP-BGKcLV21-6
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	78.5
Rep2_WB	73.9
Antibody Cat#	A303-411A
Antibody Lot#	Lot# 1
Antibody DCC ID	ENCAB775SVW
Status	Released
Project	ENCODE4
ID	62

Experiment Information (Status: Released)

	BGKcLV21-5	BGKcLV21-6
idx	738	739
TRCN#_or_BGC#	BGC#0000498	BGC#0000498
shRNA_or_gRNA_sequence	ACGGTTAGGCCGACCCATAG	ACGGTTAGGCCGACCCATAG
PAM	GGG	GGG
Name	CHTOP _98	CHTOP _98
Sample_ID	BGKcLV21-5	BGKcLV21-6
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	CHTOP	CHTOP
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F	CGCCGAAAGTTGTGCTAAAA
RT-qPCR_primer-R	CGAAGCCCGAATATTCACTG
protein_conc	4416	3476
WB_result	78.5	73.9
Ave_WB	76.2
WB_DONE_date	8/5/20
MW	26.4kDa
IP	Rabbit / I
antibody_Cat#	A303-411A	Lot# 1
Antibody DCC ID	ENCAB775SVW
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	4858	4859

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
CHTOP	Product_ID: A303-411A Lot_ID: 1 Source: Bethyl Labs Target Name: CHTOP-human

Experiment Status

	BGKcLV21-5	BGKcLV21-6
Sample_ID	BGKcLV21-5	BGKcLV21-6
Sample Name
Sample Name	CHTOP-BGKcLV21-5	CHTOP-BGKcLV21-6
RBP	CHTOP	CHTOP
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6115	6116

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-5	BGKcLV21-6
Sample #	33	34
Sample Name	CHTOP-BGKcLV21-5	CHTOP-BGKcLV21-6
Sample_Name_Alias
Index Well Position	C04	D04
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	315	326
Peak_Molarity	211.00	196.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/C4.png	DNA_Library_set45/set1/D4.png
RIN	10.0	9.9
libSample_RNA_Well	RNA_Library_set45/set1/C4.png	RNA_Library_set45/set2/C10.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-25	2020-09-25
Sample_ID	BGKcLV21-5	BGKcLV21-6
RBP	CHTOP	CHTOP
Batch_ID	BGKcLV21	BGKcLV21
WB_result	78.500	73.900
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	807	808

Sequencing Information

	BGKcLV21-5	BGKcLV21-6
Sample_ID	BGKcLV21-5	BGKcLV21-6
Sample Name	CHTOP-BGKcLV21-5	CHTOP-BGKcLV21-6
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	200,831,156	196,219,678
total_aligned_reads	195,859,946	186,800,478
unique_aligned_reads	178,287,908	170,227,294
percent_uniqueAligned	0.88775	0.86753
correlation_replicates	0.993745	0.993745
spikein_reads	120,212	71,832
percent_spikeins	0.00060	0.00037
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	438	439

Data Submission Information

	BGKcLV21-5	BGKcLV21-5	BGKcLV21-5	BGKcLV21-5	BGKcLV21-5	BGKcLV21-5	BGKcLV21-6	BGKcLV21-6	BGKcLV21-6	BGKcLV21-6
ENCODE_alias	brenton-graveley:CHTOP-BGKcLV21	brenton-graveley:CHTOP-BGKcLV21-5	brenton-graveley:L-CHTOP-BGKcLV21-5	brenton-graveley:CHTOP-BGKcLV21-5_S27_R1_001.fastq.gz	brenton-graveley:CHTOP-BGKcLV21-5_S27_R2_001.fastq.gz	brenton-graveley:CHTOP-BGKcLV21-K562	brenton-graveley:CHTOP-BGKcLV21-6	brenton-graveley:L-CHTOP-BGKcLV21-6	brenton-graveley:CHTOP-BGKcLV21-6_S28_R1_001.fastq.gz	brenton-graveley:CHTOP-BGKcLV21-6_S28_R2_001.fastq.gz
ENCODE_accession	ENCSR913OZW	ENCBS278CHX	ENCLB678HRR	ENCFF264AEH	ENCFF589DSD	ENCSR574VQZ	ENCBS608XTN	ENCLB317XMX	ENCFF664FRL	ENCFF850CIA
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	BGKcLV21-5	BGKcLV21-5	BGKcLV21-5	BGKcLV21-5	BGKcLV21-5	BGKcLV21-5	BGKcLV21-6	BGKcLV21-6	BGKcLV21-6	BGKcLV21-6
Sample Name	CHTOP-BGKcLV21-5	CHTOP-BGKcLV21-5	CHTOP-BGKcLV21-5	CHTOP-BGKcLV21-5	CHTOP-BGKcLV21-5	CHTOP-BGKcLV21-5	CHTOP-BGKcLV21-6	CHTOP-BGKcLV21-6	CHTOP-BGKcLV21-6	CHTOP-BGKcLV21-6
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		CHTOP-BGKcLV21-5.pdf	L-CHTOP-BGKcLV21-5.pdf				CHTOP-BGKcLV21-6.pdf	L-CHTOP-BGKcLV21-6.pdf
ID	2103	2161	2231	2301	2371	7137	2162	2232	2302	2372

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
CHTOP-BGKcLV21-5_S27_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	438	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1208
CHTOP-BGKcLV21-5_S27_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	438	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1258
CHTOP-BGKcLV21-5_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	438					GRCh38	V40	CHTOP-BGKcLV21-5_S27_R1_001.filtered.trimmed.paired.fastq.gz,CHTOP-BGKcLV21-5_S27_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25201
CHTOP-BGKcLV21-5_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	438					GRCh38	V40	CHTOP-BGKcLV21-5_S27_R1_001.filtered.trimmed.paired.fastq.gz,CHTOP-BGKcLV21-5_S27_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27155
CHTOP-BGKcLV21-5_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	438					GRCh38	V40	CHTOP-BGKcLV21-5/Aligned.sortedByCoord.out.bam		ENCORE2	27205
CHTOP-BGKcLV21-5_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	438					GRCh38	V40	CHTOP-BGKcLV21-5/Aligned.sortedByCoord.out.bam		ENCORE2	27255
CHTOP-BGKcLV21-5_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	438					GRCh38	V40	CHTOP-BGKcLV21-5/Aligned.sortedByCoord.out.bam		ENCORE2	27305
CHTOP-BGKcLV21-5_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	438					GRCh38	V40	CHTOP-BGKcLV21-5/Aligned.sortedByCoord.out.bam		ENCORE2	27355
CHTOP-BGKcLV21-6_S28_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	439	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1209
CHTOP-BGKcLV21-6_S28_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	439	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1259
CHTOP-BGKcLV21-6_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	439					GRCh38	V40	CHTOP-BGKcLV21-6_S28_R1_001.filtered.trimmed.paired.fastq.gz,CHTOP-BGKcLV21-6_S28_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25202
CHTOP-BGKcLV21-6_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	439					GRCh38	V40	CHTOP-BGKcLV21-6_S28_R1_001.filtered.trimmed.paired.fastq.gz,CHTOP-BGKcLV21-6_S28_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27156
CHTOP-BGKcLV21-6_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	439					GRCh38	V40	CHTOP-BGKcLV21-6/Aligned.sortedByCoord.out.bam		ENCORE2	27206
CHTOP-BGKcLV21-6_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	439					GRCh38	V40	CHTOP-BGKcLV21-6/Aligned.sortedByCoord.out.bam		ENCORE2	27256
CHTOP-BGKcLV21-6_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	439					GRCh38	V40	CHTOP-BGKcLV21-6/Aligned.sortedByCoord.out.bam		ENCORE2	27306
CHTOP-BGKcLV21-6_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	439					GRCh38	V40	CHTOP-BGKcLV21-6/Aligned.sortedByCoord.out.bam		ENCORE2	27356