title: Plate9-215-Liver

description: Plate 9_LIVER_F11


title: Plate9-213-Liver

status: Public on Sep 15 2022

type: SRA

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

country: USA

institute: Division of the National Toxicology Program at NIEHS

description: Plate 9_LIVER_H10

library_source: transcriptomic

data_processing: Data were processed using the Tempo-SeqR software package

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Male and female SD rats were placed on NTP-2000 diet and housed up to 5 animals per cage. After a 10-14 day quarantine, 8-10 week old animals were randomly assigned to treatment and control groups.

extract_protocol: All animals were euthanized the day after the last dose of chemical was administered and the liver and kidney were removed during necropsy. Two samples from each the left liver lobe and right kidney were collected within five minutes of termination for toxicogenomic evaluation. Tissue samples were cut into approximately 5 cubic mm pieces, aliquoted into screw-cap tubes, flash frozen in liquid nitrogen, and stored at -80 degreees C. RNA was extracted from one of the two collected samples and the extraction batch information recorded in the metadata along with the quantity and quality of each RNA sample. The RNA samples and metadata file were sent to BioSpyder for evaluation using the whole transcriptome TempOSeq platform with a minimum of 10 million reads/sample.

treatment_protocol: Each of six chemicals was given at nine doses (5 mL/kg dosing volume) to the treatment groups. A vehicle control group was also included for each treatment group. Rats received the test formulations via gavage for five consecutive days.

tag: strain

value: Sprague Dawley (SD)

tag: Sex

value: Male

tag: tissue

value: Liver

tag: chemical

value: 10:2 FTOH

tag: concentration

tag: unit

value: mg/kg

tag: vehicle

value: water/tween

tag: duration

value: day

tag: platfrom

value: TempO-Seq


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell113

city: Boston

first: Joana

middle: Graca

last: Marques

state: MA

address: 360 Longwood Avenue

institute: Dana-Farber Cancer Institute

description:
SMART-seq2
BT869AAVSID4R4-P1-B05

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were aligned by bowtie, and gene counts were quantified using RSEM as transcript-per-million, or TPM.
Expression levels were calculated as Ei,j = log2(TPMi,j/10 + 1) for gene i in sample j. TPM values were divided by 10 for better approximation of the estimated complexity of single-cell libraries.
We filtered out low quality cells with less than 2,500 detected genes or an average housekeeping expression level below 2.5 and removed low expressed genes with TPM greater than 16 in less than 5 cells.
We defined relative expression as centered expression levels, Eri,j = Ei,j − average[Ei,1...n] for the remaining cells and genes.
Assembly: hg19
Supplementary files format and content: TPM values for each gene in each cell and in every condition. Control AAVS1 (CTRL) and SMARCA4 knockout (SM4KO) TPM data are gathered in one csv file per replicate.

organism: Homo sapiens

growth_protocol: BT869 cells were grown as neurospheres in tumor stem media base supplemented with B27 minus vitamin A (Thermo Fisher Scientific), human growth factors (EGF, FGF, PDGF-AA, PDGF-BB [Shenandoah Biotechnology]) and heparin (Stemcell Technologies) in ultra-low attachment flasks  in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Live cells were FACS sorted into 96-well plates containing TCL lysis buffer (Qiagen) and plates were frozen prior to processing for Smart-seq2
SMART-seq2

tag: cell line

tag: cell type

tag: genotype

value: AAVS1 control knockout

tag: treatment

value: nucleofection

tag: time

value: 4 days


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell104

description:
SMART-seq2
BT869AAVSID4R4-P1-A08


title: Plate8-517-Kidney

description: Plate 8_KIDNEY_E02

source_name: Kidney

value: Female

value: Kidney

value: corn oil


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell102

description:
SMART-seq2
BT869AAVSID4R4-P1-A06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell101

description:
SMART-seq2
BT869AAVSID4R4-P1-A05


title: Plate9-264-Liver

description: Plate 9_LIVER_F05


title: Plate8-516-Kidney

description: Plate 8_KIDNEY_C04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell100

description:
SMART-seq2
BT869AAVSID4R4-P1-A04


title: Plate8-513-Kidney

description: Plate 8_KIDNEY_F03


title: Plate8-512-Kidney

description: Plate 8_KIDNEY_D03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell99

description:
SMART-seq2
BT869AAVSID4R4-P1-A03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell97

description:
SMART-seq2
BT869AAVSID4R4-P1-A01


title: Plate8-506-Kidney

description: Plate 8_KIDNEY_G02


title: Plate8-500-Kidney

description: Plate 8_KIDNEY_D02


title: Plate8-494-Kidney

description: Plate 8_KIDNEY_C02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell96

description:
SMART-seq2
AAVS1-P2-H12


title: Plate8-499-Kidney

description: Plate 8_KIDNEY_G03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell95

description:
SMART-seq2
AAVS1-P2-H11


title: Plate8-493-Kidney

description: Plate 8_KIDNEY_A04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell103

description:
SMART-seq2
BT869AAVSID4R4-P1-A07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell92

description:
SMART-seq2
AAVS1-P2-H08


title: Plate8-474-Kidney

description: Plate 8_KIDNEY_A02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell94

description:
SMART-seq2
AAVS1-P2-H10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell93

description:
SMART-seq2
AAVS1-P2-H09


title: Plate8-452-Kidney

description: Plate 8_KIDNEY_H02


title: Plate8-490-Kidney

description: Plate 8_KIDNEY_H03


title: Plate8-450-Kidney

description: Plate 8_KIDNEY_F02


title: Plate8-467-Kidney

description: Plate 8_KIDNEY_E03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell90

description:
SMART-seq2
AAVS1-P2-H06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell91

description:
SMART-seq2
AAVS1-P2-H07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell89

description:
SMART-seq2
AAVS1-P2-H05


title: Plate8-449-Kidney

description: Plate 8_KIDNEY_B04


title: Plate8-436-Kidney

description: Plate 8_KIDNEY_B03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell87

description:
SMART-seq2
AAVS1-P2-H03


title: Plate8-435-Kidney

description: Plate 8_KIDNEY_B02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell98

description:
SMART-seq2
BT869AAVSID4R4-P1-A02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell85

description:
SMART-seq2
AAVS1-P2-H01


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell86

description:
SMART-seq2
AAVS1-P2-H02


title: Plate8-432-Kidney

description: Plate 8_KIDNEY_A03


title: Plate8-421-Kidney

description: Plate 8_KIDNEY_F07

value: 6:1 FTOH


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell84

description:
SMART-seq2
AAVS1-P2-G12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell83

description:
SMART-seq2
AAVS1-P2-G11


title: Plate8-419-Kidney

description: Plate 8_KIDNEY_B06


title: Plate8-418-Kidney

description: Plate 8_KIDNEY_A07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell81

description:
SMART-seq2
AAVS1-P2-G09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell82

description:
SMART-seq2
AAVS1-P2-G10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell79

description:
SMART-seq2
AAVS1-P2-G07


title: Plate8-412-Kidney

description: Plate 8_KIDNEY_D07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell80

description:
SMART-seq2
AAVS1-P2-G08


title: Plate8-396-Kidney

description: Plate 8_KIDNEY_H06


title: Plate8-409-Kidney

description: Plate 8_KIDNEY_F06


title: Plate8-375-Kidney

description: Plate 8_KIDNEY_D06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell88

description:
SMART-seq2
AAVS1-P2-H04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell76

description:
SMART-seq2
AAVS1-P2-G04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell75

description:
SMART-seq2
AAVS1-P2-G03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell78

description:
SMART-seq2
AAVS1-P2-G06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell77

description:
SMART-seq2
AAVS1-P2-G05


title: Plate8-363-Kidney

description: Plate 8_KIDNEY_G06


title: Plate8-371-Kidney

description: Plate 8_KIDNEY_E07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell73

description:
SMART-seq2
AAVS1-P2-G01


title: Plate8-359-Kidney

description: Plate 8_KIDNEY_H07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell74

description:
SMART-seq2
AAVS1-P2-G02


title: Plate8-357-Kidney

description: Plate 8_KIDNEY_C06


title: Plate8-434-Kidney

description: Plate 8_KIDNEY_C03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell72

description:
SMART-seq2
AAVS1-P2-F12


title: Plate8-356-Kidney

description: Plate 8_KIDNEY_E06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell71

description:
SMART-seq2
AAVS1-P2-F11


title: Plate8-348-Kidney

description: Plate 8_KIDNEY_B07


title: Plate8-335-Kidney

description: Plate 8_KIDNEY_C07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell70

description:
SMART-seq2
AAVS1-P2-F10


title: Plate8-334-Kidney

description: Plate 8_KIDNEY_G07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell68

description:
SMART-seq2
AAVS1-P2-F08


title: Plate7-540-Kidney

description: Plate 7_KIDNEY_F08


title: Plate8-395-Kidney

description: Plate 8_KIDNEY_A06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell69

description:
SMART-seq2
AAVS1-P2-F09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell67

description:
SMART-seq2
AAVS1-P2-F07


title: Plate7-539-Kidney

description: Plate 7_KIDNEY_E09


title: Plate7-538-Kidney

description: Plate 7_KIDNEY_D10


title: Plate7-536-Kidney

description: Plate 7_KIDNEY_H02


title: Plate7-535-Kidney

description: Plate 7_KIDNEY_G02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell65

description:
SMART-seq2
AAVS1-P2-F05


title: Plate7-534-Kidney

description: Plate 7_KIDNEY_G07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell63

description:
SMART-seq2
AAVS1-P2-F03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell61

description:
SMART-seq2
AAVS1-P2-F01


title: Plate7-533-Kidney

description: Plate 7_KIDNEY_D05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell62

description:
SMART-seq2
AAVS1-P2-F02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell60

description:
SMART-seq2
AAVS1-P2-E12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell64

description:
SMART-seq2
AAVS1-P2-F04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell59

description:
SMART-seq2
AAVS1-P2-E11


title: Plate7-531-Kidney

description: Plate 7_KIDNEY_C06


title: Plate7-530-Kidney

description: Plate 7_KIDNEY_C05


title: Plate7-528-Kidney

description: Plate 7_KIDNEY_E04


title: Plate7-529-Kidney

description: Plate 7_KIDNEY_H06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell58

description:
SMART-seq2
AAVS1-P2-E10


title: Plate7-532-Kidney

description: Plate 7_KIDNEY_D02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell56

description:
SMART-seq2
AAVS1-P2-E08


title: Plate7-526-Kidney

description: Plate 7_KIDNEY_A02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell54

description:
SMART-seq2
AAVS1-P2-E06


title: Plate7-527-Kidney

description: Plate 7_KIDNEY_E03


title: Plate7-525-Kidney

description: Plate 7_KIDNEY_G10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell52

description:
SMART-seq2
AAVS1-P2-E04


title: Plate7-524-Kidney

description: Plate 7_KIDNEY_B12


title: Plate7-522-Kidney

description: Plate 7_KIDNEY_D03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell50

description:
SMART-seq2
AAVS1-P2-E02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell51

description:
SMART-seq2
AAVS1-P2-E03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell49

description:
SMART-seq2
AAVS1-P2-E01


title: Plate7-521-Kidney

description: Plate 7_KIDNEY_A11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell53

description:
SMART-seq2
AAVS1-P2-E05


title: Plate7-519-Kidney

description: Plate 7_KIDNEY_B05


title: Plate7-515-Kidney

description: Plate 7_KIDNEY_C07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell46

description:
SMART-seq2
AAVS1-P2-D10


title: Plate7-523-Kidney

description: Plate 7_KIDNEY_C04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell57

description:
SMART-seq2
AAVS1-P2-E09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell43

description:
SMART-seq2
AAVS1-P2-D07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell48

description:
SMART-seq2
AAVS1-P2-D12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell44

description:
SMART-seq2
AAVS1-P2-D08


title: Plate7-518-Kidney

description: Plate 7_KIDNEY_G12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell55

description:
SMART-seq2
AAVS1-P2-E07


title: Plate7-514-Kidney

description: Plate 7_KIDNEY_A08


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell45

description:
SMART-seq2
AAVS1-P2-D09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell42

description:
SMART-seq2
AAVS1-P2-D06


title: Plate7-511-Kidney

description: Plate 7_KIDNEY_C03


title: Plate7-509-Kidney

description: Plate 7_KIDNEY_E12


title: Plate7-508-Kidney

description: Plate 7_KIDNEY_G09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell40

description:
SMART-seq2
AAVS1-P2-D04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell47

description:
SMART-seq2
AAVS1-P2-D11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell39

description:
SMART-seq2
AAVS1-P2-D03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell66

description:
SMART-seq2
AAVS1-P2-F06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell38

description:
SMART-seq2
AAVS1-P2-D02


title: Plate7-505-Kidney

description: Plate 7_KIDNEY_F05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell41

description:
SMART-seq2
AAVS1-P2-D05


title: Plate7-504-Kidney

description: Plate 7_KIDNEY_H07


title: Plate7-507-Kidney

description: Plate 7_KIDNEY_A06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell37

description:
SMART-seq2
AAVS1-P2-D01


title: Plate7-503-Kidney

description: Plate 7_KIDNEY_B04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell35

description:
SMART-seq2
AAVS1-P2-C11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell34

description:
SMART-seq2
AAVS1-P2-C10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell36

description:
SMART-seq2
AAVS1-P2-C12


title: Plate7-502-Kidney

description: Plate 7_KIDNEY_D04


title: Plate7-510-Kidney

description: Plate 7_KIDNEY_H09


title: Plate7-501-Kidney

description: Plate 7_KIDNEY_G06


title: Plate7-498-Kidney

description: Plate 7_KIDNEY_G05


title: Plate7-497-Kidney

description: Plate 7_KIDNEY_H03


title: Plate7-496-Kidney

description: Plate 7_KIDNEY_F02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell32

description:
SMART-seq2
AAVS1-P2-C08


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell31

description:
SMART-seq2
AAVS1-P2-C07


title: Plate7-492-Kidney

description: Plate 7_KIDNEY_G08


title: Plate7-495-Kidney

description: Plate 7_KIDNEY_F04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell28

description:
SMART-seq2
AAVS1-P2-C04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell29

description:
SMART-seq2
AAVS1-P2-C05


title: Plate7-520-Kidney

description: Plate 7_KIDNEY_B07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell26

description:
SMART-seq2
AAVS1-P2-C02


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell33

description:
SMART-seq2
AAVS1-P2-C09


title: Plate7-486-Kidney

description: Plate 7_KIDNEY_A05


title: Plate7-487-Kidney

description: Plate 7_KIDNEY_H04


title: Plate7-489-Kidney

description: Plate 7_KIDNEY_E07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell27

description:
SMART-seq2
AAVS1-P2-C03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell25

description:
SMART-seq2
AAVS1-P2-C01


title: Plate7-488-Kidney

description: Plate 7_KIDNEY_G01


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell24

description:
SMART-seq2
AAVS1-P2-B12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell23

description:
SMART-seq2
AAVS1-P2-B11


title: Plate7-485-Kidney

description: Plate 7_KIDNEY_A12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell20

description:
SMART-seq2
AAVS1-P2-B08


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell21

description:
SMART-seq2
AAVS1-P2-B09


title: Plate7-491-Kidney

description: Plate 7_KIDNEY_F11


title: Plate7-479-Kidney

description: Plate 7_KIDNEY_E05


title: Plate7-483-Kidney

description: Plate 7_KIDNEY_G03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell22

description:
SMART-seq2
AAVS1-P2-B10


title: Plate7-481-Kidney

description: Plate 7_KIDNEY_C12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell18

description:
SMART-seq2
AAVS1-P2-B06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell19

description:
SMART-seq2
AAVS1-P2-B07


title: Plate7-480-Kidney

description: Plate 7_KIDNEY_D08


title: Plate7-482-Kidney

description: Plate 7_KIDNEY_E11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell17

description:
SMART-seq2
AAVS1-P2-B05


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell30

description:
SMART-seq2
AAVS1-P2-C06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell16

description:
SMART-seq2
AAVS1-P2-B04


title: Plate7-477-Kidney

description: Plate 7_KIDNEY_E10


title: Plate7-478-Kidney

description: Plate 7_KIDNEY_G04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell15

description:
SMART-seq2
AAVS1-P2-B03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell13

description:
SMART-seq2
AAVS1-P2-B01


title: Plate7-476-Kidney

description: Plate 7_KIDNEY_A09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell14

description:
SMART-seq2
AAVS1-P2-B02


title: Plate7-484-Kidney

description: Plate 7_KIDNEY_B09


title: Plate7-473-Kidney

description: Plate 7_KIDNEY_A07


title: Plate7-475-Kidney

description: Plate 7_KIDNEY_A03


title: Plate7-472-Kidney

description: Plate 7_KIDNEY_H10


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell11

description:
SMART-seq2
AAVS1-P2-A11


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell12

description:
SMART-seq2
AAVS1-P2-A12


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell10

description:
SMART-seq2
AAVS1-P2-A10


title: Plate7-470-Kidney

description: Plate 7_KIDNEY_H05


title: Plate7-471-Kidney

description: Plate 7_KIDNEY_D07


title: Plate7-469-Kidney

description: Plate 7_KIDNEY_C09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell5

description:
SMART-seq2
AAVS1-P2-A05


title: Plate7-466-Kidney

description: Plate 7_KIDNEY_F09


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell7

description:
SMART-seq2
AAVS1-P2-A07


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell6

description:
SMART-seq2
AAVS1-P2-A06


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell8

description:
SMART-seq2
AAVS1-P2-A08


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell9

description:
SMART-seq2
AAVS1-P2-A09


title: Plate7-468-Kidney

description: Plate 7_KIDNEY_D12


title: Plate7-465-Kidney

description: Plate 7_KIDNEY_B11


title: Plate7-464-Kidney

description: Plate 7_KIDNEY_C11


title: Plate7-462-Kidney

description: Plate 7_KIDNEY_H08


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell4

description:
SMART-seq2
AAVS1-P2-A04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell2

description:
SMART-seq2
AAVS1-P2-A02


title: Plate7-463-Kidney

description: Plate 7_KIDNEY_A04


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell3

description:
SMART-seq2
AAVS1-P2-A03


title: scRNAseq_BT869_AAVS1ko_d4_rep2_cell1

description:
SMART-seq2
AAVS1-P2-A01


title: Plate7-461-Kidney

description: Plate 7_KIDNEY_D06


title: Plate7-459-Kidney

description: Plate 7_KIDNEY_H11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell191

description:
SMART-seq2
D4SM4R1-P2-H11

value: SMARCA4 knockout


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell192

description:
SMART-seq2
D4SM4R1-P2-H12


title: Plate7-458-Kidney

description: Plate 7_KIDNEY_E06


title: Plate7-457-Kidney

description: Plate 7_KIDNEY_G11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell190

description:
SMART-seq2
D4SM4R1-P2-H10


title: Plate7-460-Kidney

description: Plate 7_KIDNEY_D11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell189

description:
SMART-seq2
D4SM4R1-P2-H09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell188

description:
SMART-seq2
D4SM4R1-P2-H08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell187

description:
SMART-seq2
D4SM4R1-P2-H07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell186

description:
SMART-seq2
D4SM4R1-P2-H06


title: Plate7-455-Kidney

description: Plate 7_KIDNEY_C10


title: Plate7-454-Kidney

description: Plate 7_KIDNEY_F12


title: Plate7-453-Kidney

description: Plate 7_KIDNEY_B03


title: Plate7-448-Kidney

description: Plate 7_KIDNEY_B10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell184

description:
SMART-seq2
D4SM4R1-P2-H04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell183

description:
SMART-seq2
D4SM4R1-P2-H03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell181

description:
SMART-seq2
D4SM4R1-P2-H01


title: Plate7-446-Kidney

description: Plate 7_KIDNEY_C08


title: Plate7-447-Kidney

description: Plate 7_KIDNEY_E08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell179

description:
SMART-seq2
D4SM4R1-P2-G11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell180

description:
SMART-seq2
D4SM4R1-P2-G12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell182

description:
SMART-seq2
D4SM4R1-P2-H02


title: Plate7-456-Kidney

description: Plate 7_KIDNEY_F03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell176

description:
SMART-seq2
D4SM4R1-P2-G08


title: Plate7-441-Kidney

description: Plate 7_KIDNEY_A10


title: Plate7-440-Kidney

description: Plate 7_KIDNEY_E02


title: Plate7-442-Kidney

description: Plate 7_KIDNEY_B02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell185

description:
SMART-seq2
D4SM4R1-P2-H05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell177

description:
SMART-seq2
D4SM4R1-P2-G09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell175

description:
SMART-seq2
D4SM4R1-P2-G07


title: Plate7-451-Kidney

description: Plate 7_KIDNEY_C02


title: Plate7-439-Kidney

description: Plate 7_KIDNEY_B08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell174

description:
SMART-seq2
D4SM4R1-P2-G06


title: Plate7-443-Kidney

description: Plate 7_KIDNEY_H12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell173

description:
SMART-seq2
D4SM4R1-P2-G05


title: Plate7-444-Kidney

description: Plate 7_KIDNEY_B06


title: Plate7-445-Kidney

description: Plate 7_KIDNEY_H01


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell172

description:
SMART-seq2
D4SM4R1-P2-G04


title: Plate7-437-Kidney

description: Plate 7_KIDNEY_D09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell171

description:
SMART-seq2
D4SM4R1-P2-G03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell169

description:
SMART-seq2
D4SM4R1-P2-G01


title: Plate7-433-Kidney

description: Plate 7_KIDNEY_F10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell178

description:
SMART-seq2
D4SM4R1-P2-G10


title: Plate7-431-Kidney

description: Plate 7_KIDNEY_F07


title: Plate6-429-Kidney

description: Plate 6_KIDNEY_A03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell168

description:
SMART-seq2
D4SM4R1-P2-F12


title: Plate6-427-Kidney

description: Plate 6_KIDNEY_H10


title: Plate6-428-Kidney

description: Plate 6_KIDNEY_D05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell166

description:
SMART-seq2
D4SM4R1-P2-F10


title: Plate6-426-Kidney

description: Plate 6_KIDNEY_D06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell164

description:
SMART-seq2
D4SM4R1-P2-F08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell165

description:
SMART-seq2
D4SM4R1-P2-F09


title: Plate6-416-Kidney

description: Plate 6_KIDNEY_G11


title: Plate6-420-Kidney

description: Plate 6_KIDNEY_D08


title: Plate6-417-Kidney

description: Plate 6_KIDNEY_A02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell170

description:
SMART-seq2
D4SM4R1-P2-G02


title: Plate7-438-Kidney

description: Plate 7_KIDNEY_F06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell162

description:
SMART-seq2
D4SM4R1-P2-F06


title: Plate6-430-Kidney

description: Plate 6_KIDNEY_H06


title: Plate6-415-Kidney

description: Plate 6_KIDNEY_H07


title: Plate6-413-Kidney

description: Plate 6_KIDNEY_D03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell159

description:
SMART-seq2
D4SM4R1-P2-F03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell161

description:
SMART-seq2
D4SM4R1-P2-F05


title: Plate6-414-Kidney

description: Plate 6_KIDNEY_B08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell167

description:
SMART-seq2
D4SM4R1-P2-F11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell157

description:
SMART-seq2
D4SM4R1-P2-F01


title: Plate6-411-Kidney

description: Plate 6_KIDNEY_F11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell158

description:
SMART-seq2
D4SM4R1-P2-F02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell156

description:
SMART-seq2
D4SM4R1-P2-E12


title: Plate6-407-Kidney

description: Plate 6_KIDNEY_G06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell155

description:
SMART-seq2
D4SM4R1-P2-E11


title: Plate6-408-Kidney

description: Plate 6_KIDNEY_F02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell154

description:
SMART-seq2
D4SM4R1-P2-E10


title: Plate6-406-Kidney

description: Plate 6_KIDNEY_H12


title: Plate6-405-Kidney

description: Plate 6_KIDNEY_E07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell163

description:
SMART-seq2
D4SM4R1-P2-F07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell152

description:
SMART-seq2
D4SM4R1-P2-E08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell153

description:
SMART-seq2
D4SM4R1-P2-E09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell160

description:
SMART-seq2
D4SM4R1-P2-F04


title: Plate6-404-Kidney

description: Plate 6_KIDNEY_H02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell150

description:
SMART-seq2
D4SM4R1-P2-E06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell151

description:
SMART-seq2
D4SM4R1-P2-E07


title: Plate6-401-Kidney

description: Plate 6_KIDNEY_C03


title: Plate6-402-Kidney

description: Plate 6_KIDNEY_D10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell149

description:
SMART-seq2
D4SM4R1-P2-E05


title: Plate6-410-Kidney

description: Plate 6_KIDNEY_F12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell147

description:
SMART-seq2
D4SM4R1-P2-E03


title: Plate6-397-Kidney

description: Plate 6_KIDNEY_F05


title: Plate6-400-Kidney

description: Plate 6_KIDNEY_B03


title: Plate6-399-Kidney

description: Plate 6_KIDNEY_G05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell148

description:
SMART-seq2
D4SM4R1-P2-E04


title: Plate6-398-Kidney

description: Plate 6_KIDNEY_C12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell146

description:
SMART-seq2
D4SM4R1-P2-E02


title: Plate6-394-Kidney

description: Plate 6_KIDNEY_D02


title: Plate6-393-Kidney

description: Plate 6_KIDNEY_H04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell145

description:
SMART-seq2
D4SM4R1-P2-E01


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell143

description:
SMART-seq2
D4SM4R1-P2-D11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell144

description:
SMART-seq2
D4SM4R1-P2-D12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell140

description:
SMART-seq2
D4SM4R1-P2-D08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell142

description:
SMART-seq2
D4SM4R1-P2-D10


title: Plate6-390-Kidney

description: Plate 6_KIDNEY_A06


title: Plate6-403-Kidney

description: Plate 6_KIDNEY_D11


title: Plate6-392-Kidney

description: Plate 6_KIDNEY_A09


title: Plate6-389-Kidney

description: Plate 6_KIDNEY_D09


title: Plate6-388-Kidney

description: Plate 6_KIDNEY_H01


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell139

description:
SMART-seq2
D4SM4R1-P2-D07


title: Plate6-387-Kidney

description: Plate 6_KIDNEY_C06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell138

description:
SMART-seq2
D4SM4R1-P2-D06


title: Plate6-386-Kidney

description: Plate 6_KIDNEY_A11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell137

description:
SMART-seq2
D4SM4R1-P2-D05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell136

description:
SMART-seq2
D4SM4R1-P2-D04


title: Plate6-385-Kidney

description: Plate 6_KIDNEY_E04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell134

description:
SMART-seq2
D4SM4R1-P2-D02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell135

description:
SMART-seq2
D4SM4R1-P2-D03


title: Plate6-383-Kidney

description: Plate 6_KIDNEY_H09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell132

description:
SMART-seq2
D4SM4R1-P2-C12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell133

description:
SMART-seq2
D4SM4R1-P2-D01


title: Plate6-384-Kidney

description: Plate 6_KIDNEY_C07


title: Plate6-381-Kidney

description: Plate 6_KIDNEY_A10


title: Plate6-382-Kidney

description: Plate 6_KIDNEY_G04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell129

description:
SMART-seq2
D4SM4R1-P2-C09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell131

description:
SMART-seq2
D4SM4R1-P2-C11


title: Plate6-380-Kidney

description: Plate 6_KIDNEY_G09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell130

description:
SMART-seq2
D4SM4R1-P2-C10


title: Plate6-377-Kidney

description: Plate 6_KIDNEY_A05


title: Plate6-391-Kidney

description: Plate 6_KIDNEY_G03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell128

description:
SMART-seq2
D4SM4R1-P2-C08


title: Plate6-379-Kidney

description: Plate 6_KIDNEY_E06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell141

description:
SMART-seq2
D4SM4R1-P2-D09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell127

description:
SMART-seq2
D4SM4R1-P2-C07


title: Plate6-376-Kidney

description: Plate 6_KIDNEY_A08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell126

description:
SMART-seq2
D4SM4R1-P2-C06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell125

description:
SMART-seq2
D4SM4R1-P2-C05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell124

description:
SMART-seq2
D4SM4R1-P2-C04


title: Plate6-374-Kidney

description: Plate 6_KIDNEY_B06


title: Plate6-373-Kidney

description: Plate 6_KIDNEY_H08


title: Plate6-370-Kidney

description: Plate 6_KIDNEY_B02


title: Plate6-369-Kidney

description: Plate 6_KIDNEY_F04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell122

description:
SMART-seq2
D4SM4R1-P2-C02


title: Plate6-372-Kidney

description: Plate 6_KIDNEY_F08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell121

description:
SMART-seq2
D4SM4R1-P2-C01


title: Plate6-378-Kidney

description: Plate 6_KIDNEY_A04


title: Plate6-368-Kidney

description: Plate 6_KIDNEY_C02


title: Plate6-366-Kidney

description: Plate 6_KIDNEY_E03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell120

description:
SMART-seq2
D4SM4R1-P2-B12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell119

description:
SMART-seq2
D4SM4R1-P2-B11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell118

description:
SMART-seq2
D4SM4R1-P2-B10


title: Plate6-367-Kidney

description: Plate 6_KIDNEY_E09


title: Plate6-364-Kidney

description: Plate 6_KIDNEY_G01


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell117

description:
SMART-seq2
D4SM4R1-P2-B09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell114

description:
SMART-seq2
D4SM4R1-P2-B06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell115

description:
SMART-seq2
D4SM4R1-P2-B07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell116

description:
SMART-seq2
D4SM4R1-P2-B08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell113

description:
SMART-seq2
D4SM4R1-P2-B05


title: Plate6-361-Kidney

description: Plate 6_KIDNEY_G10


title: Plate6-358-Kidney

description: Plate 6_KIDNEY_G02


title: Plate6-355-Kidney

description: Plate 6_KIDNEY_H05


title: Plate6-360-Kidney

description: Plate 6_KIDNEY_C10


title: Plate6-362-Kidney

description: Plate 6_KIDNEY_C04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell112

description:
SMART-seq2
D4SM4R1-P2-B04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell123

description:
SMART-seq2
D4SM4R1-P2-C03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell110

description:
SMART-seq2
D4SM4R1-P2-B02


title: Plate6-354-Kidney

description: Plate 6_KIDNEY_B04


title: Plate6-353-Kidney

description: Plate 6_KIDNEY_E11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell109

description:
SMART-seq2
D4SM4R1-P2-B01


title: Plate6-351-Kidney

description: Plate 6_KIDNEY_G12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell107

description:
SMART-seq2
D4SM4R1-P2-A11


title: Plate6-365-Kidney

description: Plate 6_KIDNEY_D12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell111

description:
SMART-seq2
D4SM4R1-P2-B03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell108

description:
SMART-seq2
D4SM4R1-P2-A12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell106

description:
SMART-seq2
D4SM4R1-P2-A10


title: Plate6-350-Kidney

description: Plate 6_KIDNEY_F06


title: Plate6-349-Kidney

description: Plate 6_KIDNEY_E10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell104

description:
SMART-seq2
D4SM4R1-P2-A08


title: Plate6-347-Kidney

description: Plate 6_KIDNEY_C09


title: Plate6-346-Kidney

description: Plate 6_KIDNEY_B09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell105

description:
SMART-seq2
D4SM4R1-P2-A09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell102

description:
SMART-seq2
D4SM4R1-P2-A06


title: Plate6-345-Kidney

description: Plate 6_KIDNEY_H03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell103

description:
SMART-seq2
D4SM4R1-P2-A07


title: Plate6-344-Kidney

description: Plate 6_KIDNEY_F10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell101

description:
SMART-seq2
D4SM4R1-P2-A05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell100

description:
SMART-seq2
D4SM4R1-P2-A04


title: Plate6-342-Kidney

description: Plate 6_KIDNEY_A07


title: Plate6-341-Kidney

description: Plate 6_KIDNEY_G08


title: Plate6-343-Kidney

description: Plate 6_KIDNEY_E05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell98

description:
SMART-seq2
D4SM4R1-P2-A02


title: Plate6-339-Kidney

description: Plate 6_KIDNEY_H11


title: Plate6-340-Kidney

description: Plate 6_KIDNEY_B10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell97

description:
SMART-seq2
D4SM4R1-P2-A01


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell96

description:
SMART-seq2
D4SM4R1-P1-H12


title: Plate6-352-Kidney

description: Plate 6_KIDNEY_G07


title: Plate6-336-Kidney

description: Plate 6_KIDNEY_F09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell95

description:
SMART-seq2
D4SM4R1-P1-H11


title: Plate6-338-Kidney

description: Plate 6_KIDNEY_E08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell93

description:
SMART-seq2
D4SM4R1-P1-H09


title: Plate6-333-Kidney

description: Plate 6_KIDNEY_C05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell94

description:
SMART-seq2
D4SM4R1-P1-H10


title: Plate6-337-Kidney

description: Plate 6_KIDNEY_B05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell91

description:
SMART-seq2
D4SM4R1-P1-H07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell90

description:
SMART-seq2
D4SM4R1-P1-H06


title: Plate6-331-Kidney

description: Plate 6_KIDNEY_E12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell92

description:
SMART-seq2
D4SM4R1-P1-H08


title: Plate6-332-Kidney

description: Plate 6_KIDNEY_F03


title: Plate6-330-Kidney

description: Plate 6_KIDNEY_C08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell99

description:
SMART-seq2
D4SM4R1-P2-A03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell89

description:
SMART-seq2
D4SM4R1-P1-H05


title: Plate6-328-Kidney

description: Plate 6_KIDNEY_F07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell88

description:
SMART-seq2
D4SM4R1-P1-H04


title: Plate6-327-Kidney

description: Plate 6_KIDNEY_B07


title: Plate6-326-Kidney

description: Plate 6_KIDNEY_D07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell85

description:
SMART-seq2
D4SM4R1-P1-H01


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell86

description:
SMART-seq2
D4SM4R1-P1-H02


title: Plate6-325-Kidney

description: Plate 6_KIDNEY_B11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell84

description:
SMART-seq2
D4SM4R1-P1-G12


title: Plate6-323-Kidney

description: Plate 6_KIDNEY_E02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell83

description:
SMART-seq2
D4SM4R1-P1-G11


title: Plate6-324-Kidney

description: Plate 6_KIDNEY_C11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell82

description:
SMART-seq2
D4SM4R1-P1-G10


title: Plate6-322-Kidney

description: Plate 6_KIDNEY_B12


title: Plate6-321-Kidney

description: Plate 6_KIDNEY_A12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell81

description:
SMART-seq2
D4SM4R1-P1-G09


title: Plate5-190-Kidney

description: Plate 5_KIDNEY_F05

value: PFHxSAm


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell80

description:
SMART-seq2
D4SM4R1-P1-G08


title: Plate5-189-Kidney

description: Plate 5_KIDNEY_G09

value: Sprague Dawley (SD)


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell77

description:
SMART-seq2
D4SM4R1-P1-G05


title: Plate5-187-Kidney

description: Plate 5_KIDNEY_C07


title: Plate5-186-Kidney

description: Plate 5_KIDNEY_D02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell79

description:
SMART-seq2
D4SM4R1-P1-G07


title: Plate5-188-Kidney

description: Plate 5_KIDNEY_F07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell78

description:
SMART-seq2
D4SM4R1-P1-G06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell87

description:
SMART-seq2
D4SM4R1-P1-H03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell75

description:
SMART-seq2
D4SM4R1-P1-G03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell76

description:
SMART-seq2
D4SM4R1-P1-G04


title: Plate6-329-Kidney

description: Plate 6_KIDNEY_D04

value: Male


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell74

description:
SMART-seq2
D4SM4R1-P1-G02


title: Plate5-182-Kidney

description: Plate 5_KIDNEY_E12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell71

description:
SMART-seq2
D4SM4R1-P1-F11


title: Plate5-183-Kidney

description: Plate 5_KIDNEY_E08


title: Plate5-185-Kidney

description: Plate 5_KIDNEY_A05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell73

description:
SMART-seq2
D4SM4R1-P1-G01


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell72

description:
SMART-seq2
D4SM4R1-P1-F12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell69

description:
SMART-seq2
D4SM4R1-P1-F09


title: Plate5-181-Kidney

description: Plate 5_KIDNEY_H09


title: Plate5-180-Kidney

description: Plate 5_KIDNEY_A11


title: Plate5-179-Kidney

description: Plate 5_KIDNEY_H01


title: Plate5-178-Kidney

description: Plate 5_KIDNEY_B11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell68

description:
SMART-seq2
D4SM4R1-P1-F08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell67

description:
SMART-seq2
D4SM4R1-P1-F07


title: Plate5-177-Kidney

description: Plate 5_KIDNEY_H06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell66

description:
SMART-seq2
D4SM4R1-P1-F06


title: Plate5-175-Kidney

description: Plate 5_KIDNEY_D04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell65

description:
SMART-seq2
D4SM4R1-P1-F05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell64

description:
SMART-seq2
D4SM4R1-P1-F04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell63

description:
SMART-seq2
D4SM4R1-P1-F03


title: Plate5-174-Kidney

description: Plate 5_KIDNEY_B05


title: Plate5-173-Kidney

description: Plate 5_KIDNEY_C06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell62

description:
SMART-seq2
D4SM4R1-P1-F02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell61

description:
SMART-seq2
D4SM4R1-P1-F01


title: Plate5-171-Kidney

description: Plate 5_KIDNEY_G10


title: Plate5-184-Kidney

description: Plate 5_KIDNEY_A12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell60

description:
SMART-seq2
D4SM4R1-P1-E12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell70

description:
SMART-seq2
D4SM4R1-P1-F10


title: Plate5-170-Kidney

description: Plate 5_KIDNEY_B08


title: Plate5-172-Kidney

description: Plate 5_KIDNEY_C05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell59

description:
SMART-seq2
D4SM4R1-P1-E11


title: Plate5-169-Kidney

description: Plate 5_KIDNEY_A04


title: Plate5-168-Kidney

description: Plate 5_KIDNEY_E04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell57

description:
SMART-seq2
D4SM4R1-P1-E09


title: Plate5-166-Kidney

description: Plate 5_KIDNEY_B09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell56

description:
SMART-seq2
D4SM4R1-P1-E08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell55

description:
SMART-seq2
D4SM4R1-P1-E07


title: Plate5-165-Kidney

description: Plate 5_KIDNEY_A02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell53

description:
SMART-seq2
D4SM4R1-P1-E05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell54

description:
SMART-seq2
D4SM4R1-P1-E06


title: Plate5-176-Kidney

description: Plate 5_KIDNEY_C10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell52

description:
SMART-seq2
D4SM4R1-P1-E04


title: Plate5-163-Kidney

description: Plate 5_KIDNEY_G07


title: Plate5-162-Kidney

description: Plate 5_KIDNEY_B06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell51

description:
SMART-seq2
D4SM4R1-P1-E03


title: Plate5-160-Kidney

description: Plate 5_KIDNEY_F10


title: Plate5-159-Kidney

description: Plate 5_KIDNEY_H11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell50

description:
SMART-seq2
D4SM4R1-P1-E02


title: Plate5-161-Kidney

description: Plate 5_KIDNEY_B12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell49

description:
SMART-seq2
D4SM4R1-P1-E01


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell47

description:
SMART-seq2
D4SM4R1-P1-D11


title: Plate5-157-Kidney

description: Plate 5_KIDNEY_B02


title: Plate5-158-Kidney

description: Plate 5_KIDNEY_F08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell48

description:
SMART-seq2
D4SM4R1-P1-D12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell46

description:
SMART-seq2
D4SM4R1-P1-D10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell58

description:
SMART-seq2
D4SM4R1-P1-E10


title: Plate5-156-Kidney

description: Plate 5_KIDNEY_A09


title: Plate5-167-Kidney

description: Plate 5_KIDNEY_C03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell45

description:
SMART-seq2
D4SM4R1-P1-D09


title: Plate5-155-Kidney

description: Plate 5_KIDNEY_H04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell43

description:
SMART-seq2
D4SM4R1-P1-D07


title: Plate5-154-Kidney

description: Plate 5_KIDNEY_H03


title: Plate5-152-Kidney

description: Plate 5_KIDNEY_E10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell42

description:
SMART-seq2
D4SM4R1-P1-D06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell44

description:
SMART-seq2
D4SM4R1-P1-D08


title: Plate5-164-Kidney

description: Plate 5_KIDNEY_F04


title: Plate5-153-Kidney

description: Plate 5_KIDNEY_B04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell41

description:
SMART-seq2
D4SM4R1-P1-D05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell40

description:
SMART-seq2
D4SM4R1-P1-D04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell39

description:
SMART-seq2
D4SM4R1-P1-D03


title: Plate5-150-Kidney

description: Plate 5_KIDNEY_D06


title: Plate5-151-Kidney

description: Plate 5_KIDNEY_A06


title: Plate5-149-Kidney

description: Plate 5_KIDNEY_E03


title: Plate5-147-Kidney

description: Plate 5_KIDNEY_A03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell36

description:
SMART-seq2
D4SM4R1-P1-C12


title: Plate5-146-Kidney

description: Plate 5_KIDNEY_H08


title: Plate5-145-Kidney

description: Plate 5_KIDNEY_D05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell38

description:
SMART-seq2
D4SM4R1-P1-D02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell34

description:
SMART-seq2
D4SM4R1-P1-C10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell37

description:
SMART-seq2
D4SM4R1-P1-D01


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell33

description:
SMART-seq2
D4SM4R1-P1-C09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell35

description:
SMART-seq2
D4SM4R1-P1-C11


title: Plate5-144-Kidney

description: Plate 5_KIDNEY_E05


title: Plate5-143-Kidney

description: Plate 5_KIDNEY_G12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell31

description:
SMART-seq2
D4SM4R1-P1-C07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell32

description:
SMART-seq2
D4SM4R1-P1-C08


title: Plate5-148-Kidney

description: Plate 5_KIDNEY_G04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell30

description:
SMART-seq2
D4SM4R1-P1-C06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell28

description:
SMART-seq2
D4SM4R1-P1-C04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell29

description:
SMART-seq2
D4SM4R1-P1-C05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell27

description:
SMART-seq2
D4SM4R1-P1-C03


title: Plate5-141-Kidney

description: Plate 5_KIDNEY_D03


title: Plate5-140-Kidney

description: Plate 5_KIDNEY_B03


title: Plate5-138-Kidney

description: Plate 5_KIDNEY_D11


title: Plate5-136-Kidney

description: Plate 5_KIDNEY_B10


title: Plate5-139-Kidney

description: Plate 5_KIDNEY_B07


title: Plate5-137-Kidney

description: Plate 5_KIDNEY_C09


title: Plate5-142-Kidney

description: Plate 5_KIDNEY_F06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell26

description:
SMART-seq2
D4SM4R1-P1-C02


title: Plate5-134-Kidney

description: Plate 5_KIDNEY_G03


title: Plate5-135-Kidney

description: Plate 5_KIDNEY_A08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell23

description:
SMART-seq2
D4SM4R1-P1-B11


title: Plate5-133-Kidney

description: Plate 5_KIDNEY_C12


title: Plate5-132-Kidney

description: Plate 5_KIDNEY_H02


title: Plate5-131-Kidney

description: Plate 5_KIDNEY_H12


title: Plate5-130-Kidney

description: Plate 5_KIDNEY_H07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell19

description:
SMART-seq2
D4SM4R1-P1-B07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell20

description:
SMART-seq2
D4SM4R1-P1-B08


title: Plate5-129-Kidney

description: Plate 5_KIDNEY_E02


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell17

description:
SMART-seq2
D4SM4R1-P1-B05


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell18

description:
SMART-seq2
D4SM4R1-P1-B06


title: Plate5-128-Kidney

description: Plate 5_KIDNEY_C04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell16

description:
SMART-seq2
D4SM4R1-P1-B04


title: Plate5-126-Kidney

description: Plate 5_KIDNEY_E09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell15

description:
SMART-seq2
D4SM4R1-P1-B03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell24

description:
SMART-seq2
D4SM4R1-P1-B12


title: Plate5-125-Kidney

description: Plate 5_KIDNEY_C11


title: Plate5-123-Kidney

description: Plate 5_KIDNEY_E07


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell12

description:
SMART-seq2
D4SM4R1-P1-A12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell10

description:
SMART-seq2
D4SM4R1-P1-A10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell13

description:
SMART-seq2
D4SM4R1-P1-B01


title: Plate5-120-Kidney

description: Plate 5_KIDNEY_H10


title: Plate5-122-Kidney

description: Plate 5_KIDNEY_F03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell14

description:
SMART-seq2
D4SM4R1-P1-B02


title: Plate5-121-Kidney

description: Plate 5_KIDNEY_E06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell22

description:
SMART-seq2
D4SM4R1-P1-B10


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell21

description:
SMART-seq2
D4SM4R1-P1-B09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell9

description:
SMART-seq2
D4SM4R1-P1-A09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell8

description:
SMART-seq2
D4SM4R1-P1-A08


title: Plate5-118-Kidney

description: Plate 5_KIDNEY_D07


title: Plate5-127-Kidney

description: Plate 5_KIDNEY_C08


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell6

description:
SMART-seq2
D4SM4R1-P1-A06


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell5

description:
SMART-seq2
D4SM4R1-P1-A05


title: Plate5-117-Kidney

description: Plate 5_KIDNEY_A07


title: Plate5-115-Kidney

description: Plate 5_KIDNEY_H05


title: Plate5-113-Kidney

description: Plate 5_KIDNEY_D09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell4

description:
SMART-seq2
D4SM4R1-P1-A04


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell3

description:
SMART-seq2
D4SM4R1-P1-A03


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell11

description:
SMART-seq2
D4SM4R1-P1-A11


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell1

description:
SMART-seq2
D4SM4R1-P1-A01


title: Plate5-111-Kidney

description: Plate 5_KIDNEY_C02


title: Plate5-112-Kidney

description: Plate 5_KIDNEY_F12


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell2

description:
SMART-seq2
D4SM4R1-P1-A02


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell191

description:
SMART-seq2
D4Cas9R1-P2-H11

value: Cas9 only control knockout


title: Plate5-124-Kidney

description: Plate 5_KIDNEY_G06


title: Plate5-110-Kidney

description: Plate 5_KIDNEY_E11


title: Plate5-109-Kidney

description: Plate 5_KIDNEY_A10


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell192

description:
SMART-seq2
D4Cas9R1-P2-H12


title: Plate5-119-Kidney

description: Plate 5_KIDNEY_D10


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell190

description:
SMART-seq2
D4Cas9R1-P2-H10


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell189

description:
SMART-seq2
D4Cas9R1-P2-H09


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell25

description:
SMART-seq2
D4SM4R1-P1-C01


title: scRNAseq_BT869_SMARCA4ko_d4_rep1_cell7

description:
SMART-seq2
D4SM4R1-P1-A07


title: Plate5-107-Kidney

description: Plate 5_KIDNEY_G05


title: Plate5-116-Kidney

description: Plate 5_KIDNEY_F09


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell186

description:
SMART-seq2
D4Cas9R1-P2-H06


title: Plate5-106-Kidney

description: Plate 5_KIDNEY_G11


title: Plate5-105-Kidney

description: Plate 5_KIDNEY_F02


title: Plate5-104-Kidney

description: Plate 5_KIDNEY_G01


title: Plate5-103-Kidney

description: Plate 5_KIDNEY_D12


title: Plate5-114-Kidney

description: Plate 5_KIDNEY_G02


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell184

description:
SMART-seq2
D4Cas9R1-P2-H04


title: Plate5-108-Kidney

description: Plate 5_KIDNEY_F11


title: Plate5-101-Kidney

description: Plate 5_KIDNEY_D08


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell179

description:
SMART-seq2
D4Cas9R1-P2-G11


title: Plate4-538-Liver

description: Plate 4_LIVER_H05

value: Liver


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell180

description:
SMART-seq2
D4Cas9R1-P2-G12


title: Plate4-531-Liver

description: Plate 4_LIVER_G06

value: mg/kg


title: Plate5-102-Kidney

description: Plate 5_KIDNEY_G08

value: water/tween


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell182

description:
SMART-seq2
D4Cas9R1-P2-H02


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell178

description:
SMART-seq2
D4Cas9R1-P2-G10


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell181

description:
SMART-seq2
D4Cas9R1-P2-H01


title: Plate4-532-Liver

description: Plate 4_LIVER_A07

value: day


title: Plate4-540-Liver

description: Plate 4_LIVER_B07

value: TempO-Seq


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell185

description:
SMART-seq2
D4Cas9R1-P2-H05


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell176

description:
SMART-seq2
D4Cas9R1-P2-G08


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell188

description:
SMART-seq2
D4Cas9R1-P2-H08


title: Plate4-504-Liver

description: Plate 4_LIVER_E06


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell177

description:
SMART-seq2
D4Cas9R1-P2-G09


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell175

description:
SMART-seq2
D4Cas9R1-P2-G07


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell183

description:
SMART-seq2
D4Cas9R1-P2-H03


title: Plate4-494-Liver

description: Plate 4_LIVER_A05


title: Plate4-502-Liver

description: Plate 4_LIVER_A06


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell174

description:
SMART-seq2
D4Cas9R1-P2-G06


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell173

description:
SMART-seq2
D4Cas9R1-P2-G05


title: Plate4-525-Liver

description: Plate 4_LIVER_D06


title: Plate4-491-Liver

description: Plate 4_LIVER_C06


title: Plate4-499-Liver

description: Plate 4_LIVER_B06


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell172

description:
SMART-seq2
D4Cas9R1-P2-G04


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell171

description:
SMART-seq2
D4Cas9R1-P2-G03


title: Plate4-489-Liver

description: Plate 4_LIVER_B05


title: Plate4-479-Liver

description: Plate 4_LIVER_C05


title: Plate4-471-Liver

description: Plate 4_LIVER_C07


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell169

description:
SMART-seq2
D4Cas9R1-P2-G01


title: Plate4-455-Liver

description: Plate 4_LIVER_D05


title: LiverC_Cattle [WGBS]

city: Beijing

first: Siqian

last: Chen

address: 2rd, Yuanmingyuan West Road

department: College of Animal Science and Technology

country: China

institute: China Agricultural University

library_source: genomic

data_processing:
FastQC v 0.11.2 and Trim Galore v 0.4.0 was used to assess the quality of the sequence data and filter low-quality reads (q < 30), respectively. The cleaned data were then mapped to the sscrofa11.1 genomes using bowtie2 under the Bismark software (0.14.5) with default parameters
Duplicated reads were removed using deduplicate_bismark
symmetric-cpgs was employed to obtain methyl CpG site information using methpipe software
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: CpG report files

molecule: genomic DNA

organism: Bos taurus

source_name: liver

extract_protocol:
DNA was extracted according to the TIANamp Genomic DNA Kit protocol
DNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: developmental stage

value: adult


title: LiverC_Cattle

data_processing:
The adapter sequences and low-quality bases were filtered using Trimmomatic v0.39
The trimmed reads were mapped to the Ensembl 103 version of reference genomes with annotated genes using STAR aligner v 2.7.6 with the following options: “--outFilterMismatchNmax 3 –outFilterType BySJout –quantMode GeneCounts –outFilterMismatchNoverLmax 0.04 –outSAMtype SAM SortedByCoordinate”.
Gene expression levels were quantified as counts using featureCounts
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

extract_protocol:
Total RNA were extracted using TRIzol method from frozen liver samples
mRNA were enriched using magnetic beads with Oligo(dT) and sheared. The cDNA was synthesized using random hexamers, end-repaired, and ligated to A base and sequencing adapters.

tag: development stage


title: LiverA_Cattle


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell167

description:
SMART-seq2
D4Cas9R1-P2-F11

value: nucleofection

value: 4 days


title: LiverB_Cattle


title: LiverB_Cattle [WGBS]


title: Plate4-447-Liver

description: Plate 4_LIVER_F06

value: Female


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell168

description:
SMART-seq2
D4Cas9R1-P2-F12


title: PCs, ADT-derived cDNA

city: Seattle

first: Rene

last: Cheng

state: WA

address: 1900 9th AVE

institute: Seattle children research institute

description:
TotalSeq-B0251 anti-human Hashtag 1 Antibody, TotalSeq™-B0251 anti-human Hashtag 2 Antibody, TotalSeq™-B0251 anti-human Hashtag 3 Antibody,TotalSeq™-B0251 anti-human Hashtag 4 Antibody, TotalSeq™-B0136 anti-human IgM Antibody, TotalSeq™-B0389 anti-human CD38 Antibody, TotalSeq™-B0055 anti-human CD138 (Syndecan-1) Antibody
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

data_processing:
cellranger demultiplex and mkfastq
cellranger gene count with GRCh38 library
hashsolo demultiplex by hashsolo python package.
Assembly: GRCh38
Supplementary files format and content: filtered gene count matrix in h5 generated by cellranger.
Supplementary files format and content: demultiplex with different HTO and removed doublets by hashsolo, gene count matrix in h5.

molecule: polyA RNA

source_name: PBMC

extract_protocol:
Ex vivo differentiated B cells/PC at day7, day 13  was removed debris by ficoll gradient and following CITEseq labeling protocol (CG000149). Sorting viable cells before loading on chromian controller.
10X CG00317 next gem single cell 3' (dual index) with feature barcode technology for surface protein
CITE-seq
Surface protein phenotyping: TotalSeq™-B0136 anti-human IgM Antibody, TotalSeq™-B0389 anti-human CD38 Antibody, TotalSeq™-B0055 anti-human CD138 (Syndecan-1) Antibody
DAY7: TotalSeq™-B0251 anti-human Hashtag 1 Antibody for bio rep 1, TotalSeq™-B0251 anti-human Hashtag 2 Antibody for bio rep 2.
DAY13: TotalSeq™-B0251 anti-human Hashtag 3 Antibody for bio rep 1 ,TotalSeq™-B0251 anti-human Hashtag 4 Antibody for bio rep 2.

value: PBMC

value: B cells

tag: library type

value: ADT


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell166

description:
SMART-seq2
D4Cas9R1-P2-F10


title: PCs, mRNA-derived cDNA

description:
none
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: Plate4-453-Liver

description: Plate 4_LIVER_E05

tag: strain

value: Sprague Dawley (SD)

value: corn oil


title: Plate4-446-Liver

description: Plate 4_LIVER_F05

tag: Sex


title: HaCaT cells, bleogen pB1, 1 uM, 24 h 2

city: Singapore

first: Antony

last: Kam

address: 03S-74, 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

data_processing:
SOAPnuke developed by BGI Version v1.5.2
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:
1) Remove the reads containing the adaptor(adaptor pollution);
2) Remove reads whose N content is greater than 5%;
3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: xls files include FPKM values for each Sample

source_name: HaCaT

growth_protocol: HaCaT cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by BGI. Briefly, 1)mRNA enrichment and purification: Oligo dT Selection to enrich the mRNA (For total RNA extracted from human whole blood, globin mRNA are depleted ); 2)RNA fragmentation and cDNA synthesis (second-strand cDNA synthesis with dUTP instead of dTTP); 3)End repair, add A and adaptor ligation; 4)PCR; 5)Circularization and make DNB; 6) Sequencing on DNBSEQ platform

treatment_protocol: Cells were treated with bleogen pB1 or EGF for 24 h  post confluent cells

value: HaCaT

value: keratinocyte

value: WT

value: bleogen pB1 (1 microM) in serum free media


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell165

description:
SMART-seq2
D4Cas9R1-P2-F09

value: Cas9 only control knockout


title: HaCaT cells, bleogen pB1, 1 uM, 24 h 3


title: HaCaT cells, EGF, 10 nM, 24 h 3

value: epidermal growth factor (EGF) (10 nM) in serum free media


title: Plate4-445-Liver

description: Plate 4_LIVER_G05

tag: tissue

value: Liver

value: mg/kg

value: day

value: TempO-Seq


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell170

description:
SMART-seq2
D4Cas9R1-P2-G02

value: nucleofection

value: 4 days


title: HaCaT cells, EGF, 10 nM, 24 h 2


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell164

description:
SMART-seq2
D4Cas9R1-P2-F08


title: HaCaT cells, EGF, 10 nM, 24 h 1


title: Plate4-443-Liver

description: Plate 4_LIVER_H06

value: Female

tag: chemical


title: LiverA_Cattle [WGBS]

value: liver

value: adult


title: HaCaT cells, control 3

value: Serum free media


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell163

description:
SMART-seq2
D4Cas9R1-P2-F07


title: HaCaT cells, control 2


title: HaCaT cells, bleogen pB1, 1 uM, 24 h 1


title: HaCaT cells, control 1


title: Plate4-429-Liver

description: Plate 4_LIVER_E02

value: Sprague Dawley (SD)

value: 6:1 FTOH

tag: concentration

value: water/tween


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell162

description:
SMART-seq2
D4Cas9R1-P2-F06


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell161

description:
SMART-seq2
D4Cas9R1-P2-F05


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell160

description:
SMART-seq2
D4Cas9R1-P2-F04


title: Plate4-415-Liver

description: Plate 4_LIVER_G03

value: Male

tag: unit


title: Plate4-401-Liver

description: Plate 4_LIVER_B02

tag: vehicle


title: Plate4-414-Liver

description: Plate 4_LIVER_G02

tag: duration


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell159

description:
SMART-seq2
D4Cas9R1-P2-F03


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell158

description:
SMART-seq2
D4Cas9R1-P2-F02


title: Plate4-399-Liver

description: Plate 4_LIVER_E03

tag: platfrom


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell157

description:
SMART-seq2
D4Cas9R1-P2-F01

tag: cell line


title: Plate4-395-Liver

description: Plate 4_LIVER_C02


title: Plate4-433-Liver

description: Plate 4_LIVER_D07

value: corn oil


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell156

description:
SMART-seq2
D4Cas9R1-P2-E12

tag: cell type

value: Cas9 only control knockout


title: Plate4-390-Liver

description: Plate 4_LIVER_C03


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell155

description:
SMART-seq2
D4Cas9R1-P2-E11

tag: genotype


title: Plate4-383-Liver

description: Plate 4_LIVER_D03


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell154

description:
SMART-seq2
D4Cas9R1-P2-E10

tag: treatment


title: Plate4-377-Liver

description: Plate 4_LIVER_F02


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell153

description:
SMART-seq2
D4Cas9R1-P2-E09

tag: time


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell152

description:
SMART-seq2
D4Cas9R1-P2-E08


title: Mag2_IP_rep1

city: Tokyo

first: Sihan

last: Li

address: Shirokanedai 4-6-1, Minato-ku

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

description:
Riboseq_count.txt
Riboseq_length.txt
Riboseq_aroundstart.txt
Riboseq_position.txt.gz
OTHER: Ribosome profiling (ribo-seq)

data_processing:
Reads from ribo-seq were trimmed, demultiplexed, and filtered, then mapped to non-coding RNA using bowtie v2.2.5. Reads that did not align to non-coding RNA were mapped to sacCer3 whole genome using tophat v2.1.1 or hisat2 v2.1.0. Reads aligned to each gene were counted using htseq-count 0.11.3.
Count percentages around the initiation codon were calculated using R package RiboProfiling in Rstudio 1.2.1578. Ribosome P-site position was estimated based on the distance between accumulated read 5' ends and the initiation codon. P-sites on each transcript were then counted using riboplot 0.3.1.
Genome_build: sacCer3
Supplementary_files_format_and_content: raw counts (genes); text file including raw counts for every gene and every ribo-seq sample
Supplementary_files_format_and_content: raw counts (read lengths); text file including raw counts for every read length and every ribo-seq sample
Supplementary_files_format_and_content: read coverage around initiation; text file including read percentages in a window (±100 nt) around the initiation codon for every read length and every ribo-seq sample; used for estimation of ribosome P-site position
Supplementary_files_format_and_content: raw counts (P-site position); text file with raw counts of P-sites for each position in coding sequence of each gene; some ribo-seq samples are included (see description)
Supplementary_files_format_and_content: Riboseq_count.txt: raw counts (genes)
Supplementary_files_format_and_content: Riboseq_length.txt: raw counts (read lengths)
Supplementary_files_format_and_content: Riboseq_aroundstart.txt: read coverage around initiation
Supplementary_files_format_and_content: Riboseq_position.txt.gz: raw counts (P-site position)

organism: Saccharomyces cerevisiae

source_name: Ribosomes from yeast cells

growth_protocol: Cells were grown in yeast extract peptone medium with 2% glucose exponentially at 30°C and harvested at OD600=0.8 to 1.0

extract_protocol:
Mag2-bound ribosomes were obtained by purification of Mag2. The purified fraction was treated with RNase, and RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) following manufacturer's instructions.
Libraries were prepared for sequencing using a customized protocol from Ingolia et al., 2012. In brief, ribosome-protected mRNA fragments were purified and ligated to a single-stranded linker that serves as a priming site for reverse transcription. The first-strand reverse transcription products were circularized and PCR-amplified to generate a deep-sequencing library.

treatment_protocol: untreated


title: Mag2_IP_rep2


title: Mag2_input_rep2

description:
Control for Mag2 purification
Riboseq_count.txt
Riboseq_length.txt
Riboseq_aroundstart.txt
Riboseq_position.txt.gz
OTHER: Ribosome profiling (ribo-seq)

extract_protocol:
Cell lysates were treated with RNase, and ribosomes were sedimented through sucrose cushion. RNA from the ribosome fraction was extracted using TRIzol reagent (Thermo Fisher Scientific) following manufacturer's instructions.
Libraries were prepared for sequencing using a customized protocol from Ingolia et al., 2012. In brief, ribosome-protected mRNA fragments were purified and ligated to a single-stranded linker that serves as a priming site for reverse transcription. The first-strand reverse transcription products were circularized and PCR-amplified to generate a deep-sequencing library.


title: HD7_CD8_CTRL

type: RNA

city: London

first: Federica

last: Marelli-Berg

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Centre for Biochemical Pharmacology  Heart Centre

hyb_protocol: The microarrays were hybridised for 16 hours at 45oC with rotation at 60rpm as per manufacturers protocol. After hybridisation the microarrays were washed and stained using the GeneChip Hybridization, Wash, and Stain Kit (ThermoFisher, UK)

scan_protocol: scanning was performed with the GeneChip Scanner 3000 (ThermoFisher, UK)

data_processing: CEL files were normalsied via RMA using the oligo v1.52.1 package in R. Affymetrix probe IDs were annotated via the clariomdhumantranscriptcluster.db v8.7.0 package. Differential expression analysis was performed via the limma v3.44.3 package. All analyses conducted in R v4.0.3

label: biotin

source_name: CD8 Tcells

label_protocol: First strand cDNA was prepared, cRNA synthesised and amplified and second strand cDNA synthesised, fragmented and labelled using the GeneChip WT Plus kit (ThermoFisher, UK)

growth_protocol: Purified CD4+ and CD8+ T cells from 12 individuals were purified and stimulated

extract_protocol: RNA was extracted with RNEasy (Qiagen)

treatment_protocol: T cells were stimulated in vitro with anti-CD3 and anti-CD28 antibodies

value: cMet-

tag: donor


title: HD7_CD4_CTRL

source_name: CD4 Tcells


title: HD6_CD8_cMet

value: cMet+


title: HD6_CD4_cMet


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell151

description:
SMART-seq2
D4Cas9R1-P2-E07


title: HD8_CD4_cMet


title: Plate4-359-Liver

description: Plate 4_LIVER_D02

value: Liver

value: mg/kg


title: HD9_CD4_CTRL


title: HD7_CD4_cMet


title: mutant_purified_rep2

growth_protocol: Cells were grown in yeast synthetic complete medium with 2% galactose exponentially at 30°C and harvested at OD600=0.6 to 0.8

extract_protocol:
Mutant (18S: A1492C) ribosomes were purified from yeast cells. The purified fraction was treated with RNase, and RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) following manufacturer's instructions.
Libraries were prepared for sequencing using a customized protocol from Ingolia et al., 2012. In brief, ribosome-protected mRNA fragments were purified and ligated to a single-stranded linker that serves as a priming site for reverse transcription. The first-strand reverse transcription products were circularized and PCR-amplified to generate a deep-sequencing library.

value: wild type expressing 18S:A1492C plasmid


title: Plate4-350-Liver

description: Plate 4_LIVER_H03

value: day

value: TempO-Seq


title: HD8_CD4_CTRL


title: Plate4-370-Liver

description: Plate 4_LIVER_F03

value: Female


title: HD6_CD4_CTRL


title: Mag2_input_rep1


title: HD6_CD8_CTRL


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell150

description:
SMART-seq2
D4Cas9R1-P2-E06

value: nucleofection

value: 4 days


title: mutant_purified_rep1


title: HD4_CD8_CTRL


title: HD4_CD8_cMet


title: WT_purified_rep2

extract_protocol:
Wild type (18S: WT) ribosomes were purified from yeast cells. The purified fraction was treated with RNase, and RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) following manufacturer's instructions.
Libraries were prepared for sequencing using a customized protocol from Ingolia et al., 2012. In brief, ribosome-protected mRNA fragments were purified and ligated to a single-stranded linker that serves as a priming site for reverse transcription. The first-strand reverse transcription products were circularized and PCR-amplified to generate a deep-sequencing library.

value: wild type expressing 18S:WT plasmid


title: Plate4-339-Liver

description: Plate 4_LIVER_H02

value: Sprague Dawley (SD)


title: WT_purified_rep1


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell187

description:
SMART-seq2
D4Cas9R1-P2-H07


title: HD7_CD8_cMet


title: HD9_CD4_cMet


title: HD10_CD4_cMet


title: HD10_CD8_cMet


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell149

description:
SMART-seq2
D4Cas9R1-P2-E05


title: mutant_input_rep2

description:
Control for 18S: A1492C purification
Riboseq_count.txt
Riboseq_length.txt
Riboseq_aroundstart.txt
OTHER: Ribosome profiling (ribo-seq)


title: Plate4-335-Liver

description: Plate 4_LIVER_B03

value: 6:1 FTOH


title: mutant_input_rep1


title: WT_input_rep2

description:
Control for 18S: WT purification
Riboseq_count.txt
Riboseq_length.txt
Riboseq_aroundstart.txt
OTHER: Ribosome profiling (ribo-seq)


title: WT_input_rep1


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell148

description:
SMART-seq2
D4Cas9R1-P2-E04


title: HD4_CD4_CTRL


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell147

description:
SMART-seq2
D4Cas9R1-P2-E03


title: HD4_CD4_cMet


title: Plate4-334-Liver

description: Plate 4_LIVER_A02

value: water/tween


title: Plate4-327-Liver

description: Plate 4_LIVER_A03

value: Male


title: wk36_longGC

city: La Jolla

first: Shane

last: Crotty

state: California

address: 9420 Athena

institute: La Jolla Institute For Immunology

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

extract_protocol:
Frozen FNA or PBMC samples were thawed and recovered in 50 % (v/v) FBS in RPMI. Recovered live cells were enumerated and stained with the appropriate staining panel. MD39 and MD39-base KO baits were prepared by mixing biotinylated MD39 with fluorophore-conjugated streptavidin (SA) in small increments at RT in an appropriate volume of 1X PBS over the course of 45 min. MD39:SA were added to the cells for 20 minutes, after which the antibody master mix was added for another 30 minutes at 4 ºC. Where KO baits were used, KO baits were added to the cells first for 20 minutes, then WT MD39:SA baits and were added for another 20 min, followed by the addition of the remainder of the staining panel for an additional 30 minutes at 4ºC, similar to previously described12. Fully supplemented RPMI (R10; 10 % (v/v) FBS, 1x pen/strep, 1x Glutamax) was used as FACS buffer. For sorting, anti-human hashtag antibodies (Biolegend) were individually added to each sample at a concentration of 2.5 µg/5 million cells at the time of addition of the master mix.
Library construction was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell V(D)J Reagent Kit v1.1, 10x Genomics for  LN FNA samples and Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index), 10x Genomics for PBMC samples ).

value: B cells

value: PBMC

value: Long Prime


title: wk16_control_MBC_rep1

description: 10x Genomics

value: Short Prime


title: wk16_control_MBC_rep2

description: 10x Genomics


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell146

description:
SMART-seq2
D4Cas9R1-P2-E02

value: Cas9 only control knockout


title: Plate3-539-Liver

description: Plate 3_LIVER_F04

value: Liver

value: mg/kg

value: corn oil


title: wk33_longGC

description: 10x Genomics

source_name: Inguinal lymph node

value: Inguinal lymph node


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell145

description:
SMART-seq2
D4Cas9R1-P2-E01


title: wk29_longGC

description: 10x Genomics


title: Plate3-537-Liver

description: Plate 3_LIVER_C02

value: Female

value: day

value: TempO-Seq


title: wk16_control_GC

description: 10x Genomics


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell144

description:
SMART-seq2
D4Cas9R1-P2-D12

value: nucleofection

value: 4 days


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell143

description:
SMART-seq2
D4Cas9R1-P2-D11


title: wk16_longGC_GC

description: 10x Genomics


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell142

description:
SMART-seq2
D4Cas9R1-P2-D10


title: wk10_longGC_Envpos

description: 10x Genomics


title: Plate3-535-Liver

description: Plate 3_LIVER_H11

value: Sprague Dawley (SD)


title: wk10_control_Envpos

description: 10x Genomics


title: wk7_longGC_Envneg

description: 10x Genomics


title: wk7_longGC_Envpos

description: 10x Genomics


title: Plate3-534-Liver

description: Plate 3_LIVER_F05


title: Plate3-533-Liver

description: Plate 3_LIVER_F07


title: wk10_longGC_Envneg

description: 10x Genomics


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell141

description:
SMART-seq2
D4Cas9R1-P2-D09


title: wk10_control_Envneg

description: 10x Genomics


title: wk13_control

description: 10x Genomics


title: Plate3-530-Liver

description: Plate 3_LIVER_G09


title: wk7_control_Envpos

description: 10x Genomics


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell139

description:
SMART-seq2
D4Cas9R1-P2-D07


title: Plate3-529-Liver

description: Plate 3_LIVER_G03


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell140

description:
SMART-seq2
D4Cas9R1-P2-D08


title: wk4_longGC_Envneg

description: 10x Genomics


title: wk7_control_Envneg

description: 10x Genomics


title: wk4_longGC_Envpos

description: 10x Genomics


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell138

description:
SMART-seq2
D4Cas9R1-P2-D06


title: wk4_control_Envpos

description: 10x Genomics


title: Plate3-528-Liver

description: Plate 3_LIVER_C05


title: Plate3-536-Liver

description: Plate 3_LIVER_F02


title: Plate3-527-Liver

description: Plate 3_LIVER_D04


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell137

description:
SMART-seq2
D4Cas9R1-P2-D05


title: wk3_longGC_Envneg

description: 10x Genomics


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell136

description:
SMART-seq2
D4Cas9R1-P2-D04


title: wk3_control_Envpos

description: 10x Genomics


title: Plate3-526-Liver

description: Plate 3_LIVER_B06


title: Yil161w_IP_rep2

extract_protocol:
Yil161w-bound ribosomes were obtained by purification of Yil161w. The purified fraction was treated with RNase, and RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) following manufacturer's instructions.
Libraries were prepared for sequencing using a customized protocol from Ingolia et al., 2012. In brief, ribosome-protected mRNA fragments were purified and ligated to a single-stranded linker that serves as a priming site for reverse transcription. The first-strand reverse transcription products were circularized and PCR-amplified to generate a deep-sequencing library.


title: Yil161w_input_rep2

description:
Control for Yil161w purification
Riboseq_count.txt
Riboseq_length.txt
Riboseq_aroundstart.txt
Riboseq_position.txt.gz
OTHER: Ribosome profiling (ribo-seq)


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell134

description:
SMART-seq2
D4Cas9R1-P2-D02


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell133

description:
SMART-seq2
D4Cas9R1-P2-D01


title: Yil161w_input_rep1


title: wk3_longGC_Envpos

description: 10x Genomics


title: Fap1_input_rep2

description:
Control for Fap1 purification
Riboseq_count.txt
Riboseq_length.txt
Riboseq_aroundstart.txt
Riboseq_position.txt.gz
OTHER: Ribosome profiling (ribo-seq)


title: Plate3-522-Liver

description: Plate 3_LIVER_D08


title: Yil161w_IP_rep1


title: Fap1_IP_rep1

extract_protocol:
Fap1-bound ribosomes were obtained by purification of Fap1. The purified fraction was treated with RNase, and RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) following manufacturer's instructions.
Libraries were prepared for sequencing using a customized protocol from Ingolia et al., 2012. In brief, ribosome-protected mRNA fragments were purified and ligated to a single-stranded linker that serves as a priming site for reverse transcription. The first-strand reverse transcription products were circularized and PCR-amplified to generate a deep-sequencing library.


title: Fap1_input_rep1


title: Plate3-521-Liver

description: Plate 3_LIVER_C06


title: wk4_control_Envneg

description: 10x Genomics


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell135

description:
SMART-seq2
D4Cas9R1-P2-D03


title: Plate3-524-Liver

description: Plate 3_LIVER_G04


title: Fap1_IP_rep2


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell132

description:
SMART-seq2
D4Cas9R1-P2-C12


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell130

description:
SMART-seq2
D4Cas9R1-P2-C10


title: RNAseq of A549 cells : siDDX42-4 Rep3

city: Evry-Courcouronnes

first: Emmanuel

last: Labaronne

address: Genopôle Campus  4 rue Pierre Fontaine - Pépinière du Génopôle

country: France

institute: ADLIN science

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastq v0.19.7 (parameters : --qualified_quality_phred 20  --disable_length_filtering  --detect_adapter_for_pe )
RNA expression is quantified with kallisto v0.44.0 (parameter : --bias --bootstrap-samples 100) against human mRNA transcriptome
Supplementary files format and content: tab-delimited text files include quantification values for each Sample

source_name: lung

growth_protocol: U87-MG/CD4/CXCR4 cells and A549-ACE2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the Rneasy mini plus kit (Qiagen) and RNA integrity numbers were determined using a 2100 Bioanalyzer (Agilent)
Ribosomal RNAs were depleted using the QIAseq FastSelect -rRNA HMR Kit (Qiagen) and libraries were prepared according to manufacturer’s instructions using the QIAseq Stranded Total RNA Lib Kit (Qiagen)

treatment_protocol: Cells were transfected with 44nM of indicated siRNA with lipofectamine RNAimax (Thermofisher Scientific). Three days post-transfection, cells were lysed for RNA extraction.

value: lung

value: epithelial cell


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell131

description:
SMART-seq2
D4Cas9R1-P2-C11


title: RNAseq of A549 cells : siDDX42-1 Rep3


title: RNAseq of A549 cells : siControl Rep3

value: siCTRL


title: Plate3-519-Liver

description: Plate 3_LIVER_G10


title: Plate3-523-Liver

description: Plate 3_LIVER_E12

value: Male


title: wk3_control_Envneg

description: 10x Genomics

value: B cells


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell129

description:
SMART-seq2
D4Cas9R1-P2-C09


title: RNAseq of A549 cells : siDDX42-4 Rep2


title: Plate3-518-Liver

description: Plate 3_LIVER_E05


title: RNAseq of A549 cells : siDDX42-1Rep2


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell128

description:
SMART-seq2
D4Cas9R1-P2-C08


title: RNAseq of A549 cells : siControl Rep2


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell127

description:
SMART-seq2
D4Cas9R1-P2-C07


title: RNAseq of A549 cells : siDDX42-1 Rep1


title: Plate3-517-Liver

description: Plate 3_LIVER_G07


title: Plate3-516-Liver

description: Plate 3_LIVER_B03


title: RNAseq of A549 cells : siDDX42-4 Rep1


title: RNAseq of U87MG cells : siDDX42-4 Rep3

source_name: brain

value: brain

value: Brain Likely Glioblastoma


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell126

description:
SMART-seq2
D4Cas9R1-P2-C06

value: Cas9 only control knockout


title: Plate3-520-Liver

description: Plate 3_LIVER_D02

value: Liver

value: mg/kg


title: Plate3-515-Liver

description: Plate 3_LIVER_D05

value: corn oil


title: RNAseq of U87MG cells : siDDX42-2 Rep3


title: RNAseq of A549 cells : siControl Rep1


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell125

description:
SMART-seq2
D4Cas9R1-P2-C05


title: RNAseq of U87MG cells : siDDX42-1 Rep3


title: Plate3-514-Liver

description: Plate 3_LIVER_G05


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell124

description:
SMART-seq2
D4Cas9R1-P2-C04


title: RNAseq of U87MG cells : siControl Rep3


title: RNAseq of U87MG cells : siDDX42-4 Rep2


title: RNAseq of U87MG cells : siDDX42-2 Rep2


title: Plate3-513-Liver

description: Plate 3_LIVER_B07


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell123

description:
SMART-seq2
D4Cas9R1-P2-C03


title: RNAseq of U87MG cells : siDDX42-2 Rep1


title: RNAseq of U87MG cells : siControl Rep2


title: RNAseq of U87MG cells : siDDX42-1Rep2


title: Plate3-511-Liver

description: Plate 3_LIVER_H10


title: RNAseq of U87MG cells : siDDX42-1 Rep1


title: RNAseq of U87MG cells : siControl Rep1


title: Plate3-510-Liver

description: Plate 3_LIVER_H04

value: Female


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell120

description:
SMART-seq2
D4Cas9R1-P2-B12


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell121

description:
SMART-seq2
D4Cas9R1-P2-C01


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell119

description:
SMART-seq2
D4Cas9R1-P2-B11


title: Plate3-512-Liver

description: Plate 3_LIVER_C08

value: day


title: Plate3-508-Liver

description: Plate 3_LIVER_G08

value: TempO-Seq


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell118

description:
SMART-seq2
D4Cas9R1-P2-B10

value: nucleofection


title: RNAseq of U87MG cells : siDDX42-4 Rep1


title: hPSC cardiomyocytes at Day 30 of differentiation (D30_G07)_miRNA

city: Sao Paulo

first: Jose Eduardo

last: Krieger

state: Sao Paulo

address: 44 Av. Dr. Enéas de Carvalho Aguiar

department: Medical School

country: Brazil

institute: University of Sao Paulo

hyb_protocol: Samples were hybridized with GeneChipTM    WT PLUS Reagent Kit (Affymetrix) and scanned at  GeneTitan ™ Microarray System

scan_protocol: The entire protocol for processing, running and scanning the samples followed the manufacturer's instruction [GeneChip ™ WT PLUS Reagent Kit Manual] at GeneTitan ™ Microarray System

data_processing: The .CEL files were analyzed using the Transcriptome Analysis Console software (TAC v4.0) from AppliedBiosystems

source_name: hPSC-derived cardiomyocytes

label_protocol: Samples were enzymatically fragmented and biotinylated using microRNA samples and hybridized to GeneChipTM miRNA 4.1 array plate (Thermo-Fisher, #902409)

growth_protocol: Prior to cardiac differentiation hPSC cells were maintained in E8:mTeSR [(1:1), Stemcell Technologies, #85850] with daily change. Established hPSC-CM were cultivated with RPMI-1640 supplemented with B27 and insulin until the end of protocol.

extract_protocol: We used the RNeasy Micro Kit (Qiagen) for total RNA isolation and followed microRNA isolation and purification with miRNeasy (Quiagen)

treatment_protocol: Cardiac cell differentiation protocol followed Burridge et al., 2014 specifications. No treatment was applied after cell differentiation.

value: hPSC-derived cardiomyocytes

tag: age

tag: cell lineage

value: Coriell Cell Repositories (AICS-0037-172)


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell117

description:
SMART-seq2
D4Cas9R1-P2-B09

value: 4 days


title: Plate3-506-Liver

description: Plate 3_LIVER_E03

tag: strain

value: Sprague Dawley (SD)


title: Plate3-507-Liver

description: Plate 3_LIVER_G06

tag: Sex


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell116

description:
SMART-seq2
D4Cas9R1-P2-B08


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell122

description:
SMART-seq2
D4Cas9R1-P2-C02


title: hPSC early cardiomyocytes at Day 8 of differentiation (D8_E07)_miRNA

source_name: hPSC-derived early cardiomyocytes

value: hPSC-derived early cardiomyocytes


title: hPSC progenitor cardiomyocytes at Day 4 of differentiation (D4_C07)_miRNA

source_name: hPSC-derived cardiac progenitors

value: hPSC-derived cardiac progenitors


title: hPSC cardiomyocytes at Day 15 of differentiation (D15_F07)_miRNA


title: hPSC progenitor cardiomyocytes at Day 2 of differentiation (D2_B07)_miRNA


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell115

description:
SMART-seq2
D4Cas9R1-P2-B07


title: Plate3-505-Liver

description: Plate 3_LIVER_G01

value: Male

tag: tissue


title: hPSC early cardiomyocytes at Day 6 of differentiation (D6_D07)_miRNA


title: Plate3-509-Liver

description: Plate 3_LIVER_H01

tag: chemical


title: hPSCs  at Day 0 of differentiation (D0_A07)_miRNA

source_name: hPSCs

value: hPSCs


title: Plate3-503-Liver

description: Plate 3_LIVER_C07

tag: concentration


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell114

description:
SMART-seq2
D4Cas9R1-P2-B06


title: Plate3-501-Liver

description: Plate 3_LIVER_H05

tag: unit


title: LiverC_Goat_H3K4me3

data_processing:
We used Trim Galore v0.4.0 and FastQC v0.11.2 software to trim the raw reads and obtain sequence quality reports.
The clean reads were mapping to the corresponding reference genome of each species using BWA-MEM software v0.7.17  with the default parameters,uplicated alignment reads were removed using the Picard Tools v2.25.0 with the parameter “REMOVE_DUPLICATES = true”.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
narrow peaks using MACS2 v2.1.1 with options “-q 0.01”.
bigWig files were generated using deepTools v3.1.1 with the follow parameters “--normalizeUsing CPM”.
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Capra hircus

extract_protocol: none provided by the submitter

value: liver

tag: chip antibody

value: H3K4me3 (Abcam ab85850)


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell113

description:
SMART-seq2
D4Cas9R1-P2-B05

value: Cas9 only control knockout


title: hPSC early cardiomyocytes at Day 8 of differentiation (D8_E05)_miRNA


title: hPSC progenitor cardiomyocytes at Day 4 of differentiation (D4_C05)_miRNA


title: hPSC early cardiomyocytes at Day 6 of differentiation (D6_D05)_miRNA


title: LiverC_Goat_H3K27ac

value: H3K27ac (Abcam ab4729)


title: hPSC cardiomyocytes at Day 15 of differentiation (D15_F05)_miRNA


title: Plate3-500-Liver

description: Plate 3_LIVER_H06

extract_protocol: All animals were euthanized the day after the last dose of chemical was administered and the liver and kidney were removed during necropsy. Two samples from each the left liver lobe and right kidney were collected within five minutes of termination for toxicogenomic evaluation. Tissue samples were cut into approximately 5 cubic mm pieces, aliquoted into screw-cap tubes, flash frozen in liquid nitrogen, and stored at -80 degreees C. RNA was extracted from one of the two collected samples and the extraction batch information recorded in the metadata along with the quantity and quality of each RNA sample. The RNA samples and metadata file were sent to BioSpyder for evaluation using the whole transcriptome TempOSeq platform with a minimum of 10 million reads/sample.

value: Liver

value: mg/kg

tag: vehicle

value: corn oil

tag: duration


title: Plate3-498-Liver

description: Plate 3_LIVER_D03

value: Female

value: day

tag: platfrom

value: TempO-Seq


title: hPSC progenitor cardiomyocytes at Day 2 of differentiation (D2_B05)_miRNA

tag: cell type

value: Coriell Cell Repositories (AICS-0037-172)


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell112

description:
SMART-seq2
D4Cas9R1-P2-B04

extract_protocol:
Live cells were FACS sorted into 96-well plates containing TCL lysis buffer (Qiagen) and plates were frozen prior to processing for Smart-seq2
SMART-seq2

tag: cell line

tag: genotype

value: nucleofection

value: 4 days


title: LiverB_Goat_H3K4me3


title: LiverB_Goat_input


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell111

description:
SMART-seq2
D4Cas9R1-P2-B03

tag: treatment

tag: time


title: hPSC cardiomyocytes at Day 30 of differentiation (D30_G05)_miRNA

value: hPSC-derived cardiomyocytes

tag: age


title: LiverB_Goat_H3K27ac


title: LiverA_Goat_input


title: Plate3-497-Liver

description: Plate 3_LIVER_H08

value: Sprague Dawley (SD)


title: Plate3-496-Liver

description: Plate 3_LIVER_C04


title: LiverA_Goat_H3K4me3


title: LiverC_Goat_input


title: Plate3-495-Liver

description: Plate 3_LIVER_D10

value: Male


title: LiverA_Goat_H3K27ac


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell110

description:
SMART-seq2
D4Cas9R1-P2-B02


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell109

description:
SMART-seq2
D4Cas9R1-P2-B01


title: Genomic DNA from Cervical cancer sample 1931 A T

type: genomic

first: Andy

last: Feber

address: 72 Huntley St

institute: University College London

description: Cervical cancer sample

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: Cy5 and Cy133

source_name: Tumour

label_protocol: standard Illumina protocol

tag: gender

tag: sample type

value: Cervical Cancer

tag: disease state

value: Tumour


title: Genomic DNA from Cervical cancer sample 2064 A T

description: Cervical cancer sample

label: Cy5 and Cy134


title: hPSCs  at Day 0 of differentiation (D0_A05)_miRNA

value: hPSCs

tag: cell lineage


title: Genomic DNA from Cervical cancer sample 2043 C T

description: Cervical cancer sample

label: Cy5 and Cy131


title: Plate3-493-Liver

description: Plate 3_LIVER_H03

tag: strain

tag: Sex

tag: tissue

tag: chemical


title: Genomic DNA from Cervical cancer sample 2059 A2 T

description: Cervical cancer sample

label: Cy5 and Cy129


title: Genomic DNA from Cervical cancer sample 2041 A T

description: Cervical cancer sample

label: Cy5 and Cy130


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell107

description:
SMART-seq2
D4Cas9R1-P2-A11

value: Cas9 only control knockout


title: Plate3-492-Liver

description: Plate 3_LIVER_F06

tag: concentration

tag: unit

tag: vehicle


title: Plate3-490-Liver

description: Plate 3_LIVER_C12

tag: duration

tag: platfrom


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell106

description:
SMART-seq2
D4Cas9R1-P2-A10

tag: cell line

tag: cell type

tag: genotype


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell105

description:
SMART-seq2
D4Cas9R1-P2-A09

tag: treatment

tag: time


title: Genomic DNA from Cervical cancer sample 1550 A T

description: Cervical cancer sample

label: Cy5 and Cy127

tag: gender

tag: sample type


title: Genomic DNA from Cervical cancer sample 1289 A T

description: Cervical cancer sample

label: Cy5 and Cy126

tag: disease state


title: Plate3-488-Liver

description: Plate 3_LIVER_F11

tag: strain


title: Genomic DNA from Cervical cancer sample 2003 B T

description: Cervical cancer sample

label: Cy5 and Cy125


title: Genomic DNA from Cervical cancer sample 1498 A T

description: Cervical cancer sample

label: Cy5 and Cy124


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell104

description:
SMART-seq2
D4Cas9R1-P2-A08


title: Genomic DNA from Cervical cancer sample 2051 A T

description: Cervical cancer sample

label: Cy5 and Cy132


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell108

description:
SMART-seq2
D4Cas9R1-P2-A12


title: Genomic DNA from Cervical cancer sample 2008 A T

description: Cervical cancer sample

label: Cy5 and Cy122


title: Genomic DNA from Normal Sample 2008 B N SQ

description: Normal Sample

label: Cy5 and Cy123

source_name: Normal

value: Histological Normal Cervix

value: Normal


title: Genomic DNA from Cervical cancer sample 1989 A T

description: Cervical cancer sample

label: Cy5 and Cy120


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell103

description:
SMART-seq2
D4Cas9R1-P2-A07


title: Plate3-486-Liver

description: Plate 3_LIVER_G11

source_name: Liver

tag: Sex

value: Liver

value: mg/kg


title: Genomic DNA from Cervical cancer sample 1777 A T

description: Cervical cancer sample

label: Cy5 and Cy121

value: Female


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell101

description:
SMART-seq2
D4Cas9R1-P2-A05


title: Plate3-485-Liver

description: Plate 3_LIVER_A12

tag: tissue

value: corn oil

value: day


title: Genomic DNA from Cervical cancer sample 1805 C T

description: Cervical cancer sample

label: Cy5 and Cy118


title: Plate3-484-Liver

description: Plate 3_LIVER_C09

tag: chemical

value: TempO-Seq


title: Genomic DNA from Cervical cancer sample 1994 A T

description: Cervical cancer sample

label: Cy5 and Cy116


title: Plate3-483-Liver

description: Plate 3_LIVER_A04

tag: concentration


title: Genomic DNA from Cervical cancer sample 1976 A T

description: Cervical cancer sample

label: Cy5 and Cy113


title: Genomic DNA from Cervical cancer sample 1880 A T

description: Cervical cancer sample

label: Cy5 and Cy128


title: Plate3-487-Liver

description: Plate 3_LIVER_B04

tag: unit


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell98

description:
SMART-seq2
D4Cas9R1-P2-A02

value: nucleofection


title: Genomic DNA from Cervical cancer sample 1797 A T

description: Cervical cancer sample

label: Cy5 and Cy117


title: Genomic DNA from Normal Sample 1560 B N SQ

description: Normal Sample

label: Cy5 and Cy111


title: Genomic DNA from Cervical cancer sample 1609 A T

description: Cervical cancer sample

label: Cy5 and Cy112


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell100

description:
SMART-seq2
D4Cas9R1-P2-A04

value: 4 days


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell97

description:
SMART-seq2
D4Cas9R1-P2-A01


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell102

description:
SMART-seq2
D4Cas9R1-P2-A06


title: Genomic DNA from Cervical cancer sample 1560 C T

description: Cervical cancer sample

label: Cy5 and Cy110


title: Genomic DNA from Normal Sample 1805 A N SQ

description: Normal Sample

label: Cy5 and Cy119


title: Genomic DNA from Cervical cancer sample 1688 C T

description: Cervical cancer sample

label: Cy5 and Cy108


title: Genomic DNA from Cervical cancer sample 399 A1 D

description: Cervical cancer sample

label: Cy5 and Cy107


title: Plate3-480-Liver

description: Plate 3_LIVER_A11

tag: vehicle


title: Plate3-478-Liver

description: Plate 3_LIVER_E11

tag: duration


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell95

description:
SMART-seq2
D4Cas9R1-P1-H11


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell96

description:
SMART-seq2
D4Cas9R1-P1-H12


title: Genomic DNA from Cervical cancer sample 98 B1 D

description: Cervical cancer sample

label: Cy5 and Cy106


title: Genomic DNA from Cervical cancer sample 2041 A1 Tc

description: Cervical cancer sample

label: Cy5 and Cy105


title: Plate3-477-Liver

description: Plate 3_LIVER_A09

tag: platfrom


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell99

description:
SMART-seq2
D4Cas9R1-P2-A03

tag: cell line


title: Plate3-482-Liver

description: Plate 3_LIVER_D06


title: Genomic DNA from Cervical cancer sample 1168 B Tc

description: Cervical cancer sample

label: Cy5 and Cy104


title: Genomic DNA from Cervical cancer sample 1778 C T

description: Cervical cancer sample

label: Cy5 and Cy114


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell94

description:
SMART-seq2
D4Cas9R1-P1-H10

tag: cell type


title: Plate3-481-Liver

description: Plate 3_LIVER_B02


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell93

description:
SMART-seq2
D4Cas9R1-P1-H09

tag: genotype


title: Genomic DNA from Cervical cancer sample 1378 A T

description: Cervical cancer sample

label: Cy5 and Cy100


title: Genomic DNA from Cervical cancer sample 1959 A T

description: Cervical cancer sample

label: Cy5 and Cy101


title: Plate3-474-Liver

description: Plate 3_LIVER_D09


title: Plate3-475-Liver

description: Plate 3_LIVER_G12


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell92

description:
SMART-seq2
D4Cas9R1-P1-H08

tag: treatment


title: Genomic DNA from Cervical cancer sample 2084 A T

description: Cervical cancer sample

label: Cy5 and Cy102


title: Genomic DNA from Cervical cancer sample 1960 A T

description: Cervical cancer sample

label: Cy5 and Cy109


title: Genomic DNA from Cervical cancer sample 1598 C T

description: Cervical cancer sample

label: Cy5 and Cy99


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell91

description:
SMART-seq2
D4Cas9R1-P1-H07

tag: time


title: Plate3-473-Liver

description: Plate 3_LIVER_A05


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell90

description:
SMART-seq2
D4Cas9R1-P1-H06


title: Genomic DNA from Cervical cancer sample 1316 A T

description: Cervical cancer sample

label: Cy5 and Cy98

tag: gender


title: Genomic DNA from Cervical cancer sample 984 A T

description: Cervical cancer sample

label: Cy5 and Cy96

tag: sample type


title: Genomic DNA from Normal Sample 984 A N Adeno.

description: Normal Sample

label: Cy5 and Cy97

tag: disease state


title: Genomic DNA from Cervical cancer sample 566 A T

description: Cervical cancer sample

label: Cy5 and Cy94


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell89

description:
SMART-seq2
D4Cas9R1-P1-H05


title: Plate3-476-Liver

description: Plate 3_LIVER_E02

tag: strain


title: Genomic DNA from Normal Sample 968 B N SQ

description: Normal Sample

label: Cy5 and Cy91


title: Genomic DNA from Normal Sample 292 A N SQ

description: Normal Sample

label: Cy5 and Cy93


title: Plate3-470-Liver

description: Plate 3_LIVER_D11

tag: Sex


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell87

description:
SMART-seq2
D4Cas9R1-P1-H03


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell88

description:
SMART-seq2
D4Cas9R1-P1-H04


title: Genomic DNA from Cervical cancer sample 292 A T

description: Cervical cancer sample

label: Cy5 and Cy92


title: Plate3-469-Liver

description: Plate 3_LIVER_C11

tag: tissue


title: Genomic DNA from Cervical cancer sample 968 A T

description: Cervical cancer sample

label: Cy5 and Cy90


title: Genomic DNA from Cervical cancer sample 434 A Tc

description: Cervical cancer sample

label: Cy5 and Cy103


title: Plate3-468-Liver

description: Plate 3_LIVER_F10

tag: chemical


title: Genomic DNA from Normal Sample 869 A3 N Adeno.

description: Normal Sample

label: Cy5 and Cy89


title: Genomic DNA from Normal Sample 564 A N SQ

description: Normal Sample

label: Cy5 and Cy87


title: Genomic DNA from Cervical cancer sample 869 A T

description: Cervical cancer sample

label: Cy5 and Cy88


title: Genomic DNA from Cervical cancer sample 564 A T

description: Cervical cancer sample

label: Cy5 and Cy86


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell86

description:
SMART-seq2
D4Cas9R1-P1-H02


title: Genomic DNA from Normal Sample 275 A N SQ

description: Normal Sample

label: Cy5 and Cy85


title: scRNAseq_BT869_Cas9onlyControl_d4_rep1_cell85

description:
SMART-seq2
D4Cas9R1-P1-H01


title: Plate3-467-Liver

description: Plate 3_LIVER_H07

tag: concentration


title: Genomic DNA from Cervical cancer sample 882 B T

description: Cervical cancer sample

label: Cy5 and Cy95


title: Plate3-466-Liver

description: Plate 3_LIVER_A03

tag: unit


title: Genomic DNA from Cervical cancer sample 275 A T

description: Cervical cancer sample

label: Cy5 and Cy84