FYTTD1 RNA-Seq in K562

General Information


RBP	FYTTD1
Cell_Line	K562
Method	CRISPR
Exp_Name	FYTTD1-BGKcLV21-K562
ENCODE_series_ID	ENCSR611TFA
Batch_ID	BGKcLV21
Pool ID	Pool-200928
Local_Set_Name	set45_K
ENCODE_KD_Exp_ID	ENCSR832XLB
ENCODE_CN_Exp_ID	ENCSR854OFV
Rep1	FYTTD1-BGKcLV21-25
Rep2	FYTTD1-BGKcLV21-26
CN1	NT-BGKcLV21-1
CN2	NT-BGKcLV21-2
Rep1_qPCR	0.0
Rep2_qPCR	0.0
Rep1_WB	67.2
Rep2_WB	71.5
Antibody Cat#	A303-525A
Antibody Lot#	lot# 1
Antibody DCC ID	ENCAB933RZK
Status	Released
Project	ENCODE4
ID	69

Experiment Information (Status: Released)

	BGKcLV21-25	BGKcLV21-26
idx	758	759
TRCN#_or_BGC#	BGC#0000520	BGC#0000520
shRNA_or_gRNA_sequence	CTTGCAGCTAGGAAAACGAC	CTTGCAGCTAGGAAAACGAC
PAM	TGG	TGG
Name	FYTTD1_91	FYTTD1_91
Sample_ID	BGKcLV21-25	BGKcLV21-26
transduction_Date	8/4/20	8/4/20
days	Day 6	Day 6
RBP_name	FYTTD1	FYTTD1
qPCR_result	0.0	0.0
Ave_qPCR	0.0
RT-qPCR_primer-F
RT-qPCR_primer-R
protein_conc	4349	4769
WB_result	67.2	71.5
Ave_WB	69.4
WB_DONE_date	8/10/20
MW	35.8kDa
IP	Rabbit / I
antibody_Cat#	A303-525A	lot# 1
Antibody DCC ID	ENCAB933RZK
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	4878	4879

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
FYTTD1	Product_ID: A303-525A Lot_ID: 1 Source: Bethyl Labs Target Name: FYTTD1-human

Experiment Status

	BGKcLV21-25	BGKcLV21-26
Sample_ID	BGKcLV21-25	BGKcLV21-26
Sample Name
Sample Name	FYTTD1-BGKcLV21-25	FYTTD1-BGKcLV21-26
RBP	FYTTD1	FYTTD1
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2021-03-18	2021-03-18
Project	ENCODE4	ENCODE4
Note
ID	6129	6130

Library-Prep
Sequencing

Library-Prep Information

	BGKcLV21-25	BGKcLV21-26
Sample #	47	48
Sample Name	FYTTD1-BGKcLV21-25	FYTTD1-BGKcLV21-26
Sample_Name_Alias
Index Well Position	A06	B06
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	318	322
Peak_Molarity	107.00	143.00
libSampleQC_DNA_Well	DNA_Library_set45/set1/A6.png	DNA_Library_set45/set1/B6.png
RIN	9.8	9.7
libSample_RNA_Well	RNA_Library_set45/set1/A6.png	RNA_Library_set45/set1/B6.png
SampleQC_method	TapeStation	TapeStation
SampleQC_date	2020-09-22	2020-09-22
Sample_ID	BGKcLV21-25	BGKcLV21-26
RBP	FYTTD1	FYTTD1
Batch_ID	BGKcLV21	BGKcLV21
WB_result	67.200	71.500
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE4	ENCODE4
ID	821	822

Sequencing Information

	BGKcLV21-25	BGKcLV21-26
Sample_ID	BGKcLV21-25	BGKcLV21-26
Sample Name	FYTTD1-BGKcLV21-25	FYTTD1-BGKcLV21-26
Pool ID	Pool-200928	Pool-200928
LocalServer_folder	set45_K	set45_K
total_reads	96,361,510	155,068,998
total_aligned_reads	94,928,824	149,986,650
unique_aligned_reads	86,763,680	137,190,906
percent_uniqueAligned	0.90040	0.88471
correlation_replicates	0.990287	0.990287
spikein_reads	92,336	116,200
percent_spikeins	0.00096	0.00075
original_ReadLength	101	101
QC_Status	Submitted	Submitted
ID	452	453

Data Submission Information

	BGKcLV21-25	BGKcLV21-25	BGKcLV21-25	BGKcLV21-25	BGKcLV21-25	BGKcLV21-25	BGKcLV21-26	BGKcLV21-26	BGKcLV21-26	BGKcLV21-26
ENCODE_alias	brenton-graveley:FYTTD1-BGKcLV21	brenton-graveley:FYTTD1-BGKcLV21-25	brenton-graveley:L-FYTTD1-BGKcLV21-25	brenton-graveley:FYTTD1-BGKcLV21-25_S41_R1_001.fastq.gz	brenton-graveley:FYTTD1-BGKcLV21-25_S41_R2_001.fastq.gz	brenton-graveley:FYTTD1-BGKcLV21-K562	brenton-graveley:FYTTD1-BGKcLV21-26	brenton-graveley:L-FYTTD1-BGKcLV21-26	brenton-graveley:FYTTD1-BGKcLV21-26_S42_R1_001.fastq.gz	brenton-graveley:FYTTD1-BGKcLV21-26_S42_R2_001.fastq.gz
ENCODE_accession	ENCSR832XLB	ENCBS108QSS	ENCLB089THP	ENCFF755QIW	ENCFF649APN	ENCSR611TFA	ENCBS496EAG	ENCLB205BGV	ENCFF783UUV	ENCFF009FMP
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	BGKcLV21-25	BGKcLV21-25	BGKcLV21-25	BGKcLV21-25	BGKcLV21-25	BGKcLV21-25	BGKcLV21-26	BGKcLV21-26	BGKcLV21-26	BGKcLV21-26
Sample Name	FYTTD1-BGKcLV21-25	FYTTD1-BGKcLV21-25	FYTTD1-BGKcLV21-25	FYTTD1-BGKcLV21-25	FYTTD1-BGKcLV21-25	FYTTD1-BGKcLV21-25	FYTTD1-BGKcLV21-26	FYTTD1-BGKcLV21-26	FYTTD1-BGKcLV21-26	FYTTD1-BGKcLV21-26
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		FYTTD1-BGKcLV21-25.pdf	L-FYTTD1-BGKcLV21-25.pdf				FYTTD1-BGKcLV21-26.pdf	L-FYTTD1-BGKcLV21-26.pdf
ID	2110	2175	2245	2315	2385	7226	2176	2246	2316	2386

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
FYTTD1-BGKcLV21-25_S41_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	452	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1224
FYTTD1-BGKcLV21-25_S41_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	452	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1274
FYTTD1-BGKcLV21-25_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	452					GRCh38	V40	FYTTD1-BGKcLV21-25_S41_R1_001.filtered.trimmed.paired.fastq.gz,FYTTD1-BGKcLV21-25_S41_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25217
FYTTD1-BGKcLV21-25_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	452					GRCh38	V40	FYTTD1-BGKcLV21-25_S41_R1_001.filtered.trimmed.paired.fastq.gz,FYTTD1-BGKcLV21-25_S41_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27171
FYTTD1-BGKcLV21-25_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	452					GRCh38	V40	FYTTD1-BGKcLV21-25/Aligned.sortedByCoord.out.bam		ENCORE2	27221
FYTTD1-BGKcLV21-25_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	452					GRCh38	V40	FYTTD1-BGKcLV21-25/Aligned.sortedByCoord.out.bam		ENCORE2	27271
FYTTD1-BGKcLV21-25_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	452					GRCh38	V40	FYTTD1-BGKcLV21-25/Aligned.sortedByCoord.out.bam		ENCORE2	27321
FYTTD1-BGKcLV21-25_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	452					GRCh38	V40	FYTTD1-BGKcLV21-25/Aligned.sortedByCoord.out.bam		ENCORE2	27371
FYTTD1-BGKcLV21-26_S42_R1_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	453	NovaSeq6000	100	paired-ended	1				NT-BGKcLV21-1_S25_R1_001.fastq.gz,NT-BGKcLV21-2_S26_R1_001.fastq.gz	ENCODE4	1225
FYTTD1-BGKcLV21-26_S42_R2_001.fastq.gz	ENCODE_DATA/set45_K/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	453	NovaSeq6000	100	paired-ended	2				NT-BGKcLV21-1_S25_R2_001.fastq.gz,NT-BGKcLV21-2_S26_R2_001.fastq.gz	ENCODE4	1275
FYTTD1-BGKcLV21-26_quant.sf	ENCODE_DATA/set45_K/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	453					GRCh38	V40	FYTTD1-BGKcLV21-26_S42_R1_001.filtered.trimmed.paired.fastq.gz,FYTTD1-BGKcLV21-26_S42_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	25218
FYTTD1-BGKcLV21-26_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set45_K/STAR_ENCORE2_trimmed_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	453					GRCh38	V40	FYTTD1-BGKcLV21-26_S42_R1_001.filtered.trimmed.paired.fastq.gz,FYTTD1-BGKcLV21-26_S42_R2_001.filtered.trimmed.paired.fastq.gz		ENCORE2	27172
FYTTD1-BGKcLV21-26_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	453					GRCh38	V40	FYTTD1-BGKcLV21-26/Aligned.sortedByCoord.out.bam		ENCORE2	27222
FYTTD1-BGKcLV21-26_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	453					GRCh38	V40	FYTTD1-BGKcLV21-26/Aligned.sortedByCoord.out.bam		ENCORE2	27272
FYTTD1-BGKcLV21-26_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	453					GRCh38	V40	FYTTD1-BGKcLV21-26/Aligned.sortedByCoord.out.bam		ENCORE2	27322
FYTTD1-BGKcLV21-26_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	453					GRCh38	V40	FYTTD1-BGKcLV21-26/Aligned.sortedByCoord.out.bam		ENCORE2	27372