title: 20160523_C51

city: Oxford

first: James

last: Kinchen

address: Weatherall Institute of Molecular Medicine, John Radcliffe Hospital

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description: processed data file header: WTCHG_288196_255231

data_processing:
Trimming of adaptor sequences (IlluminaP7, Nextera, SMARTer) - skewer (https://github.com/relipmoc/skewer)
Alignment to human genome (Ensembl GRCh38) - HISAT (v2.0.3b)
Gene count table assembly (Ensembl Release 84, March 2016 transcriptome annotation) - featureCounts (v1.5.0)
Genome_build: Ensembl GRCh38

source_name: colonic mucosa

extract_protocol:
Endoscopic forceps biopsies were dissociated using a combined enzymatic and mechanical approach. Depletion of non-stromal cell types was achieved by MACS separation. CD326 (EpCAM), CD45 and CD235a conjugated micro-beads were added to the cell suspension, Cells were incubated with microbeads, washed and loaded onto an LD column via a 35 µm pre-separation filter. The flow-through fraction was collected, and single cells pelleted by centrifugation at 500 G for 8 minutes. Biopsies from inflamed and non-inflamed bowel regions were collected separately from the same donor, and single cell isolation was performed for both sets of biopsies in parallel. The resulting single cell suspensions were counter-stained and mixed 1:1 immediately prior to loading onto the C1 IFC.
Nextera XT library prep kit (Illumina)

tag: disease

value: ulcerative colitis

value: single cell

value: Inflamed

value: DSP


title: 20160523_C95

status: Public on Sep 26 2018

type: SRA

description: processed data file header: WTCHG_288196_255232

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

value: Uninflamed


title: 20160523_C58

description: processed data file header: WTCHG_288196_256231

value: empty site control


title: BJ_MYO_R2_T24_B07_scRNA-seq

city: Seattle

first: Cole

middle: Bruce

last: Trapnell

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington

data_processing:
 Gene expression profiles for each cell were computed using TopHat (v 2.1.1) and Cufflinks (2.2.0) software packages, which were provided with the hg19 genomic reference and GENCODE v17 transcriptome index.
Genome_build: hg19
Supplementary_files_format_and_content: expression matrix in FPKM values (gene level)

molecule: total RNA

growth_protocol: Foreskin Human Fibroblasts obtained from commercial vendor (Stemgent) were expanded in alpha-mem supplemented with glutamax, 10% FBS and 16ng/ul of FGF-b (ThermoFisher Scientific).

extract_protocol:
To perform reprogramming and differentiation experiments HSMM and hFib-MYOD cells were plated in 24-well formats at a density of 50.000 cells per well. Gelatin was sometime used as a coating agent with no significant difference with respect to uncoated dishes. Differentiation and reprogramming was induced using a differentiation media containing alpha-mem supplemented with glutamax and 2% HS (ThermoFisher Scientific), supplemented with 2ug/ml of doxycycline to enact MYOD expression. When indicated, Insulin was used at 8ug/ml (ThermoFisher Scientific), BMP inhibitor LDN-193189 was used at 0.1uM (Stemgent), LSD1 inhibitor RN-1 was used at 1uM (EMD Millipore).
At the indicated time points, cells were harvested by gentle dissociation using TrypLE (ThermoFisher Scientific) and processed for full-length transcriptome sequencing using the Fluidigm C1 Single Cell or bulk mRNA sequencing as previously described ( Trapnell et al., 2014). Cells were loaded onto the microfluidic chip at a concentration of ~250 cells/μl to maximize the number of single cells captured and minimize the occurrence of doublets.  In some instances, cells were reloaded if the majority of capture sites were not occupied on the first attempt. As in Trapnell et al, 2014, captured cells were scored by manual on-chip microscopic inspection to determine if they were singletons and free of other debris.

treatment_protocol: The fibroblasts were then infected with a mixture of lentiviruses encoding hTERT (and Puromycin resistance gene), Tetracycline Repressor (and Geneticin resistance gene) and TR-controlled hMYOD (and Blasticidin resistance gene) (ThermoFisher Scientific). All the resistance genes are constitutively expressed and therefore triple selection was performed and maintained using 1ug/ml of Puromycin, 500ug/ml of Geneticin and 2ug/ml of Blasticidin to generate the hFib-MYOD line.

tag: cell type

value: Foreskin Human Fibroblasts

tag: cell line

value: hFib-MYOD line

tag: debris

value: FALSE

tag: clump

tag: control

tag: media

value: DM

tag: replicate

tag: time


title: BJ_MYO_R2_T24_B03_scRNA-seq


title: BJ_MYO_R2_T24_B04_scRNA-seq


title: 20160523_C91

description: processed data file header: WTCHG_288196_254232


title: 20160523_C47

description: processed data file header: WTCHG_288196_254231


title: BJ_MYO_R2_T24_B02_scRNA-seq


title: BJ_MYO_R2_T24_C05_scRNA-seq


title: BJ_MYO_R2_T24_B01_scRNA-seq


title: 20160523_C18

description: processed data file header: WTCHG_288196_254230


title: 20160523_C46

description: processed data file header: WTCHG_288196_253231


title: 20160523_C90

description: processed data file header: WTCHG_288196_253232


title: BJ_MYO_R2_T24_A12_scRNA-seq


title: BJ_MYO_R2_T24_A11_scRNA-seq


title: 20160523_C87

description: processed data file header: WTCHG_288196_252232


title: 20160523_C24

description: processed data file header: WTCHG_288196_256230


title: BJ_MYO_R2_T24_B05_scRNA-seq


title: BJ_MYO_R2_T24_A09_scRNA-seq


title: 20160523_C14

description: processed data file header: WTCHG_288196_252230


title: 20160523_Bulk2

description: processed data file header: WTCHG_288196_256232

value: bulk control


title: 20160523_C17

description: processed data file header: WTCHG_288196_253230


title: 20160523_C85

description: processed data file header: WTCHG_288196_251232


title: 20160523_C40

description: processed data file header: WTCHG_288196_251231


title: BJ_MYO_R2_T24_A07_scRNA-seq


title: BJ_MYO_R2_T24_A06_scRNA-seq


title: BJ_MYO_R2_T24_A08_scRNA-seq


title: BJ_MYO_R2_T24_A05_scRNA-seq


title: BJ_MYO_R2_T24_A03_scRNA-seq


title: BJ_MYO_R2_T24_A04_scRNA-seq


title: 20160523_C20

description: processed data file header: WTCHG_288196_255230


title: 20160523_C12

description: processed data file header: WTCHG_288196_251230


title: BJ_MYO_R2_T24_A10_scRNA-seq


title: 20160523_C09

description: processed data file header: WTCHG_288196_250230


title: 20160523_C83

description: processed data file header: WTCHG_288196_249232


title: 20160523_C84

description: processed data file header: WTCHG_288196_250232


title: 20160523_C39

description: processed data file header: WTCHG_288196_250231


title: BJ_MYO_R2_T24_A01_scRNA-seq


title: BJ_MYO_R1_T72_H12_scRNA-seq


title: 20160523_C45

description: processed data file header: WTCHG_288196_252231


title: BJ_MYO_R1_T72_H09_scRNA-seq


title: 20160523_C36

description: processed data file header: WTCHG_288196_249231


title: BJ_MYO_R2_T24_A02_scRNA-seq


title: BJ_MYO_R1_T72_H10_scRNA-seq


title: 20160523_C03

description: processed data file header: WTCHG_288196_249230


title: BJ_MYO_R1_T72_H07_scRNA-seq


title: 20160523_C34

description: processed data file header: WTCHG_288196_232231


title: 20160523_C81

description: processed data file header: WTCHG_288196_232232


title: 20160523_C02

description: processed data file header: WTCHG_288196_232230


title: 20160523_Bulk1

description: processed data file header: WTCHG_288196_232228


title: BJ_MYO_R1_T72_H05_scRNA-seq


title: 20160523_C74

description: processed data file header: WTCHG_288196_231232


title: BJ_MYO_R1_T72_H06_scRNA-seq


title: BJ_MYO_R1_T72_H03_scRNA-seq


title: 20160523_C01

description: processed data file header: WTCHG_288196_231230


title: 20160523_C33

description: processed data file header: WTCHG_288196_231231


title: BJ_MYO_R1_T72_H04_scRNA-seq


title: BJ_MYO_R1_T72_H08_scRNA-seq


title: 20160523_C72

description: processed data file header: WTCHG_288196_230232


title: BJ_MYO_R1_T72_G12_scRNA-seq


title: 20160523_C32

description: processed data file header: WTCHG_288196_230231


title: BJ_MYO_R1_T72_H01_scRNA-seq


title: 20160523_C60

description: processed data file header: WTCHG_288196_229232


title: BJ_MYO_R1_T72_H11_scRNA-seq


title: 20160523_C30

description: processed data file header: WTCHG_288196_229231


title: 20160519_C29

description: processed data file header: WTCHG_288196_256225


title: 20160519_C57

description: processed data file header: WTCHG_288196_256226


title: 20160519_C46

description: processed data file header: WTCHG_288196_255226


title: BJ_MYO_R1_T72_G11_scRNA-seq


title: 20160519_C28

description: processed data file header: WTCHG_288196_255225


title: BJ_MYO_R1_T72_G10_scRNA-seq


title: BJ_MYO_R1_T72_G09_scRNA-seq


title: 20160519_C94

description: processed data file header: WTCHG_288196_254227


title: BJ_MYO_R1_T72_H02_scRNA-seq


title: BJ_MYO_R1_T72_G06_scRNA-seq


title: BJ_MYO_R1_T72_G05_scRNA-seq


title: 20160519_C45

description: processed data file header: WTCHG_288196_254226


title: 20160519_C27

description: processed data file header: WTCHG_288196_254225


title: 20160519_C91

description: processed data file header: WTCHG_288196_253227


title: BJ_MYO_R1_T72_G02_scRNA-seq


title: BJ_MYO_R1_T72_G01_scRNA-seq


title: 20160519_C26

description: processed data file header: WTCHG_288196_253225


title: BJ_MYO_R1_T72_G03_scRNA-seq


title: BJ_MYO_R1_T72_F12_scRNA-seq


title: 20160519_C42

description: processed data file header: WTCHG_288196_252226


title: BJ_MYO_R1_T72_F11_scRNA-seq


title: 20160519_C25

description: processed data file header: WTCHG_288196_252225


title: BJ_MYO_R1_T72_G08_scRNA-seq


title: BJ_MYO_R1_T72_G07_scRNA-seq


title: 20160519_C87

description: processed data file header: WTCHG_288196_251227


title: BJ_MYO_R1_T72_F08_scRNA-seq


title: 20160519_C41

description: processed data file header: WTCHG_288196_251226


title: BJ_MYO_R1_T72_F07_scRNA-seq


title: BJ_MYO_R1_T72_F09_scRNA-seq


title: BJ_MYO_R1_T72_F06_scRNA-seq


title: 20160519_C86

description: processed data file header: WTCHG_288196_250227


title: BJ_MYO_R1_T72_G04_scRNA-seq


title: BJ_MYO_R1_T72_F05_scRNA-seq


title: 20160519_C22

description: processed data file header: WTCHG_288196_250225


title: 20160519_C44

description: processed data file header: WTCHG_288196_253226


title: BJ_MYO_R1_T72_F02_scRNA-seq


title: 20160519_C38

description: processed data file header: WTCHG_288196_250226


title: BJ_MYO_R1_T72_F04_scRNA-seq


title: 20160519_C23

description: processed data file header: WTCHG_288196_251225


title: 20160519_C82

description: processed data file header: WTCHG_288196_232227


title: 20160519_C21

description: processed data file header: WTCHG_288196_249225


title: 20160519_C20

description: processed data file header: WTCHG_288196_232225


title: 20160519_C83

description: processed data file header: WTCHG_288196_249227


title: 20160519_C90

description: processed data file header: WTCHG_288196_252227


title: 20160519_C34

description: processed data file header: WTCHG_288196_231226


title: BJ_MYO_R1_T72_E09_scRNA-seq


title: 20160519_C37

description: processed data file header: WTCHG_288196_249226


title: BJ_MYO_R1_T72_F01_scRNA-seq


title: BJ_MYO_R1_T72_E06_scRNA-seq


title: BJ_MYO_R1_T72_F03_scRNA-seq


title: BJ_MYO_R1_T72_E12_scRNA-seq


title: 20160519_C35

description: processed data file header: WTCHG_288196_232226


title: BJ_MYO_R1_T72_E04_scRNA-seq


title: BJ_MYO_R1_T72_E11_scRNA-seq


title: BJ_MYO_R1_T72_E03_scRNA-seq


title: BJ_MYO_R1_T72_E10_scRNA-seq


title: 20160519_C17

description: processed data file header: WTCHG_288196_231225


title: BJ_MYO_R1_T72_E07_scRNA-seq


title: BJ_MYO_R1_T72_E02_scRNA-seq


title: BJ_MYO_R1_T72_E05_scRNA-seq


title: BJ_MYO_R2_T24_B11_scRNA-seq


title: 20160519_C76

description: processed data file header: WTCHG_288196_230227


title: 20160519_C32

description: processed data file header: WTCHG_288196_230226


title: 20160519_Bulk1

description: processed data file header: WTCHG_288196_229228


title: BJ_MYO_R1_T72_D11_scRNA-seq


title: 20160519_C11

description: processed data file header: WTCHG_288196_227208


title: 20160519_C15

description: processed data file header: WTCHG_288196_230225


title: 20160519_C14

description: processed data file header: WTCHG_288196_229225


title: BJ_MYO_R1_T72_D06_scRNA-seq


title: BJ_MYO_R1_T72_D05_scRNA-seq


title: 20160519_C75

description: processed data file header: WTCHG_288196_229227


title: 20160519_C04

description: processed data file header: WTCHG_288196_207208


title: 20160519_C30

description: processed data file header: WTCHG_288196_229226


title: 20160519_C79

description: processed data file header: WTCHG_288196_231227


title: BJ_MYO_R1_T72_D04_scRNA-seq


title: 20160519_C13

description: processed data file header: WTCHG_288196_228208


title: BJ_MYO_R1_T72_D12_scRNA-seq


title: BJ_MYO_R1_T72_D10_scRNA-seq


title: BJ_MYO_R1_T72_D08_scRNA-seq


title: BJ_MYO_R1_T72_D09_scRNA-seq


title: 20160517_C37

description: processed data file header: WTCHG_288196_256228


title: BJ_MYO_R2_T24_C03_scRNA-seq


title: BJ_MYO_R1_T72_D02_scRNA-seq


title: 20160517_C23

description: processed data file header: WTCHG_288196_255228


title: 20160519_C10

description: processed data file header: WTCHG_288196_226208


title: BJ_MYO_R1_T72_D07_scRNA-seq

value: TRUE


title: 20160519_C09

description: processed data file header: WTCHG_288196_225208


title: 20160519_C02

description: processed data file header: WTCHG_288196_206208


title: 20160517_C20

description: processed data file header: WTCHG_288196_254228


title: BJ_MYO_R1_T72_C09_scRNA-seq


title: BJ_MYO_R1_T72_C10_scRNA-seq


title: BJ_MYO_R1_T72_C08_scRNA-seq


title: BJ_MYO_R1_T72_D01_scRNA-seq


title: 20160517_C77

description: processed data file header: WTCHG_288196_255229


title: BJ_MYO_R1_T72_C07_scRNA-seq


title: BJ_MYO_R1_T72_C11_scRNA-seq


title: BJ_MYO_R1_T72_C12_scRNA-seq


title: BJ_MYO_R1_T72_C05_scRNA-seq


title: BJ_MYO_R1_T72_C04_scRNA-seq


title: 20160519_C05

description: processed data file header: WTCHG_288196_208208


title: 20160517_C59

description: processed data file header: WTCHG_288196_251229


title: BJ_MYO_R1_T72_C03_scRNA-seq


title: 20160517_C12

description: processed data file header: WTCHG_288196_251228


title: 20160517_C74

description: processed data file header: WTCHG_288196_254229


title: 20160517_C19

description: processed data file header: WTCHG_288196_253228


title: 20160517_C62

description: processed data file header: WTCHG_288196_252229


title: 20160517_C79

description: processed data file header: WTCHG_288196_256229


title: 20160517_C64

description: processed data file header: WTCHG_288196_253229


title: BJ_MYO_R1_T72_C06_scRNA-seq


title: BJ_MYO_R1_T72_E01_scRNA-seq


title: 20160517_C08

description: processed data file header: WTCHG_288196_249228


title: BJ_MYO_R1_T72_B11_scRNA-seq


title: 20160517_C14

description: processed data file header: WTCHG_288196_252228


title: BJ_MYO_R1_T72_B10_scRNA-seq


title: BJ_MYO_R1_T72_B09_scRNA-seq


title: 20160517_C56

description: processed data file header: WTCHG_288196_250229


title: BJ_MYO_R1_T72_B08_scRNA-seq


title: 20160517_C11

description: processed data file header: WTCHG_288196_250228


title: BJ_MYO_R1_T72_B06_scRNA-seq


title: BJ_MYO_R1_T72_B12_scRNA-seq


title: 20160517_Bulk1

description: processed data file header: WTCHG_288196_230228


title: 20160517_C53

description: processed data file header: WTCHG_288196_249229


title: BJ_MYO_R1_T72_C02_scRNA-seq


title: 20160517_C52

description: processed data file header: WTCHG_288196_232229


title: BJ_MYO_R1_T72_B07_scRNA-seq


title: 20160517_C43

description: processed data file header: WTCHG_288196_230229


title: 20160517_C38

description: processed data file header: WTCHG_288196_229229


title: 20160517_C46

description: processed data file header: WTCHG_288196_231229


title: 20160517_C88

description: processed data file header: WTCHG_288196_229230


title: BJ_MYO_R1_T72_C01_scRNA-seq


title: BJ_MYO_R1_T72_B05_scRNA-seq


title: BJ_MYO_R1_T72_B02_scRNA-seq


title: BJ_MYO_R1_T72_B04_scRNA-seq


title: BJ_MYO_R1_T72_B03_scRNA-seq


title: 20160517_Bulk2

description: processed data file header: WTCHG_288196_231228


title: BJ_MYO_R1_T72_A12_scRNA-seq


title: BJ_MYO_R1_T72_D03_scRNA-seq


title: 20160513_Bulk1

description: processed data file header: WTCHG_288196_256227


title: BJ_MYO_R1_T72_A11_scRNA-seq


title: BJ_MYO_R1_T72_A10_scRNA-seq


title: 20160513_C85

description: processed data file header: WTCHG_288196_228207


title: 20160517_C89

description: processed data file header: WTCHG_288196_230230


title: 20160513_C44

description: processed data file header: WTCHG_288196_227205


title: BJ_MYO_R1_T72_B01_scRNA-seq


title: BJ_MYO_R1_T72_A07_scRNA-seq


title: 20160513_C81

description: processed data file header: WTCHG_288196_227207


title: 20160513_C20

description: processed data file header: WTCHG_288196_228204


title: BJ_MYO_R1_T72_A06_scRNA-seq


title: BJ_MYO_R1_T72_A08_scRNA-seq


title: BJ_MYO_R1_T72_A09_scRNA-seq


title: 20160513_C78

description: processed data file header: WTCHG_288196_226207


title: 20160513_C59

description: processed data file header: WTCHG_288196_226206


title: 20160513_C19

description: processed data file header: WTCHG_288196_227204


title: BJ_MYO_R1_T72_A04_scRNA-seq


title: 20160513_C41

description: processed data file header: WTCHG_288196_226205


title: 20160513_C17

description: processed data file header: WTCHG_288196_226204


title: 20160513_C47

description: processed data file header: WTCHG_288196_228205


title: BJ_MYO_R1_T72_A03_scRNA-seq


title: BJ_MYO_R1_T72_A05_scRNA-seq


title: BJ_MYO_R1_T72_A02_scRNA-seq


title: 20160513_C77

description: processed data file header: WTCHG_288196_225207


title: 20160513_C57

description: processed data file header: WTCHG_288196_225206


title: BJ_MYO_R1_T48_H12_scRNA-seq


title: 20160513_C38

description: processed data file header: WTCHG_288196_225205


title: 20160513_C16

description: processed data file header: WTCHG_288196_225204


title: BJ_MYO_R1_T48_H11_scRNA-seq


title: BJ_MYO_R1_T48_H09_scRNA-seq


title: 20160513_C65

description: processed data file header: WTCHG_288196_228206


title: 20160513_C62

description: processed data file header: WTCHG_288196_227206


title: 20160513_C14

description: processed data file header: WTCHG_288196_208204


title: 20160513_C76

description: processed data file header: WTCHG_288196_208207


title: 20160513_C56

description: processed data file header: WTCHG_288196_208206


title: BJ_MYO_R1_T48_H07_scRNA-seq


title: 20160513_C36

description: processed data file header: WTCHG_288196_208205


title: BJ_MYO_R1_T72_F10_scRNA-seq


title: BJ_MYO_R1_T48_H05_scRNA-seq


title: BJ_MYO_R1_T48_H06_scRNA-seq


title: 20160513_C55

description: processed data file header: WTCHG_288196_207206


title: 20160513_C75

description: processed data file header: WTCHG_288196_207207


title: BJ_MYO_R1_T48_G09_scRNA-seq


title: 20160513_C35

description: processed data file header: WTCHG_288196_207205


title: BJ_MYO_R1_T48_H03_scRNA-seq


title: BJ_MYO_R1_T48_H01_scRNA-seq


title: BJ_MYO_R1_T48_G08_scRNA-seq


title: 20160513_C72

description: processed data file header: WTCHG_288196_206207


title: BJ_MYO_R1_T48_H02_scRNA-seq


title: BJ_MYO_R1_T48_G11_scRNA-seq


title: 20160513_C54

description: processed data file header: WTCHG_288196_206206


title: BJ_MYO_R1_T48_G07_scRNA-seq


title: 20160513_C08

description: processed data file header: WTCHG_288196_206204

value: empty


title: 20160513_C32

description: processed data file header: WTCHG_288196_206205


title: BJ_MYO_R1_T48_H10_scRNA-seq


title: 20160513_C95

description: processed data file header: WTCHG_288196_205208


title: BJ_MYO_R1_T48_G06_scRNA-seq


title: 20160513_C71

description: processed data file header: WTCHG_288196_205207


title: 20160513_C53

description: processed data file header: WTCHG_288196_205206


title: 20160513_C30

description: processed data file header: WTCHG_288196_205205


title: BJ_MYO_R1_T48_G04_scRNA-seq


title: 20160513_C94

description: processed data file header: WTCHG_288196_204208


title: BJ_MYO_R1_T48_G05_scRNA-seq


title: BJ_MYO_R1_T48_H08_scRNA-seq


title: BJ_MYO_R1_T48_F12_scRNA-seq


title: BJ_MYO_R1_T48_G01_scRNA-seq


title: BJ_MYO_R1_T48_G03_scRNA-seq


title: BJ_MYO_R1_T48_G02_scRNA-seq


title: 20160513_C11

description: processed data file header: WTCHG_288196_207204


title: BJ_MYO_R1_T48_F11_scRNA-seq


title: 20160513_C52

description: processed data file header: WTCHG_288196_204206


title: 20160513_C06

description: processed data file header: WTCHG_288196_204204


title: 20160513_C26

description: processed data file header: WTCHG_288196_204205


title: BJ_MYO_R1_T48_F08_scRNA-seq


title: 20160513_C91

description: processed data file header: WTCHG_288196_203208


title: BJ_MYO_R1_T48_F06_scRNA-seq


title: BJ_MYO_R1_T48_F10_scRNA-seq


title: BJ_MYO_R1_T48_F09_scRNA-seq


title: BJ_MYO_R1_T48_F03_scRNA-seq


title: BJ_MYO_R1_T48_F04_scRNA-seq


title: 20160513_C24

description: processed data file header: WTCHG_288196_203205


title: 20160513_C50

description: processed data file header: WTCHG_288196_203206


title: 20160513_C68

description: processed data file header: WTCHG_288196_203207


title: BJ_MYO_R1_T48_F07_scRNA-seq


title: 20160513_C01

description: processed data file header: WTCHG_288196_203204


title: 20160513_C07

description: processed data file header: WTCHG_288196_205204


title: BJ_MYO_R1_T48_F02_scRNA-seq


title: 20160513_C90

description: processed data file header: WTCHG_288196_202208


title: 20160513_C69

description: processed data file header: WTCHG_288196_204207


title: 20160513_C49

description: processed data file header: WTCHG_288196_202206


title: BJ_MYO_R1_T48_E08_scRNA-seq


title: BJ_MYO_R1_T48_E10_scRNA-seq


title: 20160513_C86

description: processed data file header: WTCHG_288196_201208


title: BJ_MYO_R1_T48_E09_scRNA-seq


title: 20160513_C67

description: processed data file header: WTCHG_288196_202207


title: 20160513_C23

description: processed data file header: WTCHG_288196_202205


title: 20160513_C66

description: processed data file header: WTCHG_288196_201207


title: 20160513_C22

description: processed data file header: WTCHG_288196_201205


title: BJ_MYO_R1_T48_E06_scRNA-seq


title: BJ_MYO_R1_T48_E05_scRNA-seq


title: BJ_MYO_R1_T48_E07_scRNA-seq


title: BJ_MYO_R1_T48_E04_scRNA-seq


title: 20151130_C63

description: processed data file header: WTCHG_288196_228202


title: 20151130_C90

description: processed data file header: WTCHG_288196_228203


title: BJ_MYO_R1_T48_E02_scRNA-seq


title: 20151130_C87

description: processed data file header: WTCHG_288196_227203


title: 20151130_C26

description: processed data file header: WTCHG_288196_228201


title: BJ_MYO_R1_T48_D12_scRNA-seq


title: BJ_MYO_R1_T48_F01_scRNA-seq


title: BJ_MYO_R1_T48_E01_scRNA-seq


title: BJ_MYO_R1_T48_D10_scRNA-seq


title: 20151130_C22

description: processed data file header: WTCHG_288196_227201


title: BJ_MYO_R1_T48_E11_scRNA-seq


title: 20151130_C83

description: processed data file header: WTCHG_288196_226203


title: BJ_MYO_R1_T48_E12_scRNA-seq


title: BJ_MYO_R1_T48_D09_scRNA-seq


title: 20151130_C82

description: processed data file header: WTCHG_288196_225203


title: 20151130_C54

description: processed data file header: WTCHG_288196_226202


title: BJ_MYO_R1_T48_D08_scRNA-seq


title: 20151130_C52

description: processed data file header: WTCHG_288196_225202


title: 20151130_C16

description: processed data file header: WTCHG_288196_226201


title: BJ_MYO_R1_T48_D07_scRNA-seq


title: 20151130_Bulk1

description: processed data file header: WTCHG_288196_255227


title: 20151130_C15

description: processed data file header: WTCHG_288196_225201


title: BJ_MYO_R1_T48_E03_scRNA-seq


title: 20151130_C60

description: processed data file header: WTCHG_288196_227202


title: BJ_MYO_R1_T48_D05_scRNA-seq


title: BJ_MYO_R1_T48_D02_scRNA-seq


title: BJ_MYO_R1_T48_D03_scRNA-seq


title: 20151130_C12

description: processed data file header: WTCHG_288196_208201


title: 20151130_C81

description: processed data file header: WTCHG_288196_208203


title: 20151130_C49

description: processed data file header: WTCHG_288196_208202


title: 20151130_C80

description: processed data file header: WTCHG_288196_207203


title: 20151130_C48

description: processed data file header: WTCHG_288196_207202


title: BJ_MYO_R1_T48_D01_scRNA-seq


title: BJ_MYO_R1_T48_C11_scRNA-seq


title: BJ_MYO_R1_T48_C10_scRNA-seq


title: 20151130_C11

description: processed data file header: WTCHG_288196_207201


title: BJ_MYO_R1_T48_C08_scRNA-seq


title: BJ_MYO_R1_T48_D06_scRNA-seq


title: 20151130_C10

description: processed data file header: WTCHG_288196_206201


title: 20151130_C76

description: processed data file header: WTCHG_288196_205203


title: 20151130_C79

description: processed data file header: WTCHG_288196_206203


title: 20151130_C42

description: processed data file header: WTCHG_288196_205202


title: 20151130_C43

description: processed data file header: WTCHG_288196_206202


title: BJ_MYO_R1_T48_C03_scRNA-seq


title: BJ_MYO_R1_T48_C05_scRNA-seq


title: BJ_MYO_R1_T48_C04_scRNA-seq


title: 20151130_C73

description: processed data file header: WTCHG_288196_204203


title: BJ_MYO_R1_T48_C02_scRNA-seq


title: 20151130_C09

description: processed data file header: WTCHG_288196_205201


title: BJ_MYO_R1_T48_B12_scRNA-seq


title: BJ_MYO_R1_T48_C12_scRNA-seq


title: BJ_MYO_R1_T48_B11_scRNA-seq


title: BJ_MYO_R1_T48_B09_scRNA-seq


title: 20160513_C48

description: processed data file header: WTCHG_288196_201206


title: 20151130_C06

description: processed data file header: WTCHG_288196_203201


title: BJ_MYO_R1_T48_B08_scRNA-seq


title: 20151130_C69

description: processed data file header: WTCHG_288196_203203


title: 20151130_C35

description: processed data file header: WTCHG_288196_204202


title: BJ_MYO_R1_T48_B10_scRNA-seq


title: 20151130_C07

description: processed data file header: WTCHG_288196_204201


title: BJ_MYO_R1_T48_B07_scRNA-seq


title: 20151130_C34

description: processed data file header: WTCHG_288196_203202


title: BJ_MYO_R1_T48_B05_scRNA-seq


title: 20151130_C31

description: processed data file header: WTCHG_288196_202202


title: 20151130_C96

description: processed data file header: WTCHG_288196_202204


title: BJ_MYO_R1_T48_B04_scRNA-seq


title: BJ_MYO_R1_T48_B03_scRNA-seq


title: 20151130_C91

description: processed data file header: WTCHG_288196_201204


title: BJ_MYO_R1_T48_C01_scRNA-seq


title: BJ_MYO_R1_T48_B01_scRNA-seq


title: 20151130_C64

description: processed data file header: WTCHG_288196_201203


title: 20151130_C03

description: processed data file header: WTCHG_288196_202201


title: BJ_MYO_R1_T48_B02_scRNA-seq


title: 20151130_C27

description: processed data file header: WTCHG_288196_201202


title: 20151130_C02

description: processed data file header: WTCHG_288196_201201


title: BJ_MYO_R1_T48_A11_scRNA-seq


title: BJ_MYO_R1_T48_A10_scRNA-seq


title: BJ_MYO_R1_T48_A12_scRNA-seq


title: BJ_MYO_R1_T48_A09_scRNA-seq


title: BJ_MYO_R1_T48_B06_scRNA-seq


title: BJ_MYO_R1_T48_A08_scRNA-seq


title: BJ_MYO_R1_T48_A07_scRNA-seq


title: 20151130_C66

description: processed data file header: WTCHG_288196_202203


title: BJ_MYO_R1_T48_A06_scRNA-seq


title: BJ_MYO_R1_T48_A03_scRNA-seq


title: BJ_MYO_R1_T48_A04_scRNA-seq


title: BJ_MYO_R1_T48_A05_scRNA-seq


title: BJ_MYO_R1_T0_H12_scRNA-seq

value: GM


title: BJ_MYO_R1_T48_A01_scRNA-seq


title: BJ_MYO_R1_T0_H11_scRNA-seq


title: BJ_MYO_R1_T0_H08_scRNA-seq


title: BJ_MYO_R1_T0_H10_scRNA-seq


title: BJ_MYO_R1_T0_H07_scRNA-seq


title: BJ_MYO_R1_T0_H05_scRNA-seq


title: BJ_MYO_R1_T0_H04_scRNA-seq


title: BJ_MYO_R1_T0_H03_scRNA-seq


title: BJ_MYO_R1_T0_G10_scRNA-seq


title: BJ_MYO_R1_T0_G12_scRNA-seq


title: BJ_MYO_R1_T0_G11_scRNA-seq


title: BJ_MYO_R1_T0_H01_scRNA-seq


title: BJ_MYO_R1_T0_G09_scRNA-seq


title: BJ_MYO_R1_T0_G08_scRNA-seq


title: BJ_MYO_R1_T0_G07_scRNA-seq


title: BJ_MYO_R1_T0_H06_scRNA-seq


title: BJ_MYO_R1_T0_G06_scRNA-seq


title: BJ_MYO_R1_T0_G05_scRNA-seq


title: BJ_MYO_R1_T48_A02_scRNA-seq


title: BJ_MYO_R1_T0_G04_scRNA-seq


title: BJ_MYO_R1_T0_G03_scRNA-seq


title: BJ_MYO_R1_T0_H09_scRNA-seq


title: BJ_MYO_R1_T0_F09_scRNA-seq


title: BJ_MYO_R1_T0_F10_scRNA-seq


title: BJ_MYO_R1_T0_F12_scRNA-seq


title: BJ_MYO_R1_T0_F07_scRNA-seq


title: BJ_MYO_R1_T0_F05_scRNA-seq


title: BJ_MYO_R1_T0_F06_scRNA-seq


title: BJ_MYO_R1_T0_G02_scRNA-seq


title: BJ_MYO_R1_T0_F08_scRNA-seq


title: BJ_MYO_R1_T0_F11_scRNA-seq


title: BJ_MYO_R1_T0_H02_scRNA-seq


title: BJ_MYO_R1_T0_F03_scRNA-seq


title: BJ_MYO_R1_T0_F04_scRNA-seq


title: BJ_MYO_R1_T0_F02_scRNA-seq


title: BJ_MYO_R1_T0_E12_scRNA-seq


title: BJ_MYO_R1_T0_E11_scRNA-seq


title: BJ_MYO_R1_T0_E08_scRNA-seq


title: BJ_MYO_R1_T0_E09_scRNA-seq


title: BJ_MYO_R1_T0_E07_scRNA-seq


title: BJ_MYO_R1_T0_G01_scRNA-seq


title: BJ_MYO_R1_T0_E03_scRNA-seq


title: BJ_MYO_R1_T0_E05_scRNA-seq


title: BJ_MYO_R1_T0_E01_scRNA-seq


title: BJ_MYO_R1_T0_E02_scRNA-seq


title: BJ_MYO_R1_T0_E04_scRNA-seq


title: BJ_MYO_R1_T0_D12_scRNA-seq


title: BJ_MYO_R1_T0_D11_scRNA-seq


title: BJ_MYO_R1_T0_F01_scRNA-seq


title: BJ_MYO_R1_T0_D06_scRNA-seq


title: BJ_MYO_R1_T0_D05_scRNA-seq


title: BJ_MYO_R1_T0_D07_scRNA-seq


title: BJ_MYO_R1_T0_D09_scRNA-seq


title: BJ_MYO_R1_T0_D08_scRNA-seq


title: BJ_MYO_R1_T0_D10_scRNA-seq


title: BJ_MYO_R1_T0_D03_scRNA-seq


title: BJ_MYO_R1_T0_D02_scRNA-seq


title: BJ_MYO_R1_T0_C10_scRNA-seq


title: BJ_MYO_R1_T0_C11_scRNA-seq


title: BJ_MYO_R1_T0_D01_scRNA-seq


title: BJ_MYO_R1_T0_D04_scRNA-seq


title: BJ_MYO_R1_T0_E06_scRNA-seq


title: BJ_MYO_R1_T0_C04_scRNA-seq


title: BJ_MYO_R1_T0_C07_scRNA-seq


title: BJ_MYO_R1_T0_C09_scRNA-seq


title: BJ_MYO_R1_T0_C01_scRNA-seq


title: BJ_MYO_R1_T0_C06_scRNA-seq


title: BJ_MYO_R1_T0_C02_scRNA-seq


title: BJ_MYO_R1_T0_C12_scRNA-seq


title: BJ_MYO_R1_T0_C03_scRNA-seq


title: BJ_MYO_R1_T0_C05_scRNA-seq


title: BJ_MYO_R1_T0_B11_scRNA-seq


title: BJ_MYO_R1_T0_B10_scRNA-seq


title: BJ_MYO_R1_T0_B12_scRNA-seq


title: BJ_MYO_R1_T0_E10_scRNA-seq


title: 20150702_C19

description: processed data file header: WTCHG_209948_712517

extract_protocol:
Endoscopic forceps biopsies were dissociated using a combined enzymatic and mechanical approach. Depletion of non-stromal cell types was achieved by MACS separation. CD326 (EpCAM), CD45 and CD235a conjugated micro-beads were added to the cell suspension, Cells were incubated with microbeads, washed and loaded onto an LD column via a 35 µm pre-separation filter. The flow-through fraction was collected, and single cells pelleted by centrifugation at 500 G for 8 minutes.
Nextera XT library prep kit (Illumina)

value: healthy


title: 20150708_C23

description: processed data file header: WTCHG_209948_712508


title: BJ_MYO_R1_T0_B09_scRNA-seq


title: BJ_MYO_R1_T0_C08_scRNA-seq


title: 20150708_C45

description: processed data file header: WTCHG_209948_712506


title: 20150708_C80

description: processed data file header: WTCHG_209948_712507


title: BJ_MYO_R1_T0_B08_scRNA-seq


title: BJ_MYO_R1_T0_B06_scRNA-seq


title: BJ_MYO_R1_T0_B04_scRNA-seq


title: 20150702_C29

description: processed data file header: WTCHG_209948_712503


title: BJ_MYO_R1_T0_B05_scRNA-seq


title: BJ_MYO_R1_T0_B03_scRNA-seq


title: 20150708_C74

description: processed data file header: WTCHG_209948_711507


title: 20150708_C39

description: processed data file header: WTCHG_209948_711506


title: 20150702_C74

description: processed data file header: WTCHG_209948_712502


title: 20150708_C17

description: processed data file header: WTCHG_209948_711508


title: BJ_MYO_R1_T0_B02_scRNA-seq


title: 20150708_C9

description: processed data file header: WTCHG_209948_711505


title: BJ_MYO_R1_T0_A12_scRNA-seq


title: BJ_MYO_R1_T0_A11_scRNA-seq


title: 20150702_C84

description: processed data file header: WTCHG_209948_711504


title: 20150708_C21

description: processed data file header: WTCHG_209948_712505


title: 20150702_C13

description: processed data file header: WTCHG_209948_711517


title: 20150702_C23

description: processed data file header: WTCHG_209948_711503


title: 20150702_C68

description: processed data file header: WTCHG_209948_711502


title: BJ_MYO_R1_T0_B07_scRNA-seq


title: 20150702_C90

description: processed data file header: WTCHG_209948_712504


title: BJ_MYO_R1_T0_A05_scRNA-seq


title: BJ_MYO_R1_T0_A08_scRNA-seq


title: BJ_MYO_R1_T0_A06_scRNA-seq


title: 20150708_C46

description: processed data file header: WTCHG_209948_710508


title: BJ_MYO_R1_T0_A04_scRNA-seq


title: BJ_MYO_R1_T0_B01_scRNA-seq


title: BJ_MYO_R1_T0_A07_scRNA-seq


title: BJ_MYO_R1_T0_A02_scRNA-seq


title: BJ_MYO_R1_T0_A10_scRNA-seq


title: BJ_MYO_R1_T0_A03_scRNA-seq


title: 20150708_C3

description: processed data file header: WTCHG_209948_710505


title: 20150702_C78

description: processed data file header: WTCHG_209948_710504


title: 20150702_C1

description: processed data file header: WTCHG_209948_710517


title: BJ_MYO_R1_T0_A01_scRNA-seq


title: BJ_MYO_R1_T24_H11_scRNA-seq


title: 20150702_C62

description: processed data file header: WTCHG_209948_710502


title: 20150702_C17

description: processed data file header: WTCHG_209948_710503


title: BJ_MYO_R1_T24_H12_scRNA-seq


title: 20150708_C28

description: processed data file header: WTCHG_209948_709508


title: 20150702_C32

description: processed data file header: WTCHG_209948_709517


title: BJ_MYO_R1_T24_H09_scRNA-seq


title: BJ_MYO_R1_T24_H08_scRNA-seq


title: 20150708_C62

description: processed data file header: WTCHG_209948_710507


title: BJ_MYO_R1_T24_H05_scRNA-seq


title: 20150708_C13

description: processed data file header: WTCHG_209948_709506


title: 20150702_C88

description: processed data file header: WTCHG_209948_709505


title: BJ_MYO_R1_T24_H07_scRNA-seq


title: BJ_MYO_R1_T24_H06_scRNA-seq


title: 20150708_C56

description: processed data file header: WTCHG_209948_709507


title: 20150702_C70

description: processed data file header: WTCHG_209948_709504


title: 20150702_C5

description: processed data file header: WTCHG_209948_709503


title: 20150708_C27

description: processed data file header: WTCHG_209948_710506


title: 20150702_C26

description: processed data file header: WTCHG_209948_708517


title: 20150702_C56

description: processed data file header: WTCHG_209948_709502


title: 20150708_C12

description: processed data file header: WTCHG_209948_708508


title: 20150708_C50

description: processed data file header: WTCHG_209948_708507


title: BJ_MYO_R1_T24_H03_scRNA-seq


title: BJ_MYO_R1_T24_H02_scRNA-seq


title: BJ_MYO_R1_T24_H10_scRNA-seq


title: BJ_MYO_R1_T24_G12_scRNA-seq


title: BJ_MYO_R1_T24_G11_scRNA-seq


title: 20150708_C38

description: processed data file header: WTCHG_209948_708506


title: BJ_MYO_R1_T24_G10_scRNA-seq


title: 20150702_C64

description: processed data file header: WTCHG_209948_708504


title: BJ_MYO_R1_T24_H01_scRNA-seq


title: BJ_MYO_R1_T24_G08_scRNA-seq


title: 20150702_C34

description: processed data file header: WTCHG_209948_708503


title: 20150702_C76

description: processed data file header: WTCHG_209948_708505


title: BJ_MYO_R1_T48_C06_scRNA-seq


title: BJ_MYO_R1_T24_G07_scRNA-seq


title: BJ_MYO_R1_T24_H04_scRNA-seq


title: BJ_MYO_R1_T24_G09_scRNA-seq


title: 20150702_C20

description: processed data file header: WTCHG_209948_707517


title: BJ_MYO_R1_T24_G06_scRNA-seq


title: 20150708_C93

description: processed data file header: WTCHG_209948_707507


title: BJ_MYO_R1_T24_G05_scRNA-seq


title: BJ_MYO_R1_T24_G04_scRNA-seq


title: 20150708_C6

description: processed data file header: WTCHG_209948_707508


title: 20150702_C93

description: processed data file header: WTCHG_209948_708502


title: BJ_MYO_R1_T24_G03_scRNA-seq


title: BJ_MYO_R1_T24_G02_scRNA-seq


title: 20150702_C66

description: processed data file header: WTCHG_209948_707505


title: BJ_MYO_R1_T24_G01_scRNA-seq


title: 20150702_C58

description: processed data file header: WTCHG_209948_707504


title: BJ_MYO_R1_T24_F11_scRNA-seq


title: 20150702_C18

description: processed data file header: WTCHG_209948_707503


title: 20150702_C8

description: processed data file header: WTCHG_209948_706517


title: BJ_MYO_R1_T24_F10_scRNA-seq


title: BJ_MYO_R1_T24_F07_scRNA-seq


title: BJ_MYO_R1_T24_F09_scRNA-seq


title: 20150708_C81

description: processed data file header: WTCHG_209948_706507


title: BJ_MYO_R1_T24_F06_scRNA-seq


title: 20150702_C87

description: processed data file header: WTCHG_209948_707502


title: 20150708_C32

description: processed data file header: WTCHG_209948_707506


title: BJ_MYO_R1_T24_F08_scRNA-seq


title: 20150702_C89

description: processed data file header: WTCHG_209948_706505


title: BJ_MYO_R1_T24_F05_scRNA-seq


title: 20150702_C42

description: processed data file header: WTCHG_209948_706504


title: 20150702_C6

description: processed data file header: WTCHG_209948_706503


title: BJ_MYO_R1_T24_F12_scRNA-seq


title: 20150702_C75

description: processed data file header: WTCHG_209948_706502


title: BJ_MYO_R1_T24_F04_scRNA-seq


title: 20150708_C91

description: processed data file header: WTCHG_209948_706508


title: BJ_MYO_R1_T24_F01_scRNA-seq


title: 20150708_C26

description: processed data file header: WTCHG_209948_706506


title: BJ_MYO_R1_T24_F02_scRNA-seq


title: 20150702_C2

description: processed data file header: WTCHG_209948_705517


title: 20150708_C85

description: processed data file header: WTCHG_209948_705508


title: BJ_MYO_R1_T24_E12_scRNA-seq


title: 20150708_C75

description: processed data file header: WTCHG_209948_705507


title: 20150708_C20

description: processed data file header: WTCHG_209948_705506


title: BJ_MYO_R1_T24_E11_scRNA-seq


title: BJ_MYO_R1_T24_F03_scRNA-seq


title: BJ_MYO_R1_T24_E10_scRNA-seq


title: 20150702_C77

description: processed data file header: WTCHG_209948_705505


title: BJ_MYO_R1_T24_E09_scRNA-seq


title: BJ_MYO_R1_T24_E08_scRNA-seq


title: 20150702_C36

description: processed data file header: WTCHG_209948_705504


title: 20150702_C85

description: processed data file header: WTCHG_209948_705503


title: BJ_MYO_R1_T24_E06_scRNA-seq


title: 20150702_C37

description: processed data file header: WTCHG_209948_704517


title: 20150702_C67

description: processed data file header: WTCHG_209948_705502


title: BJ_MYO_R1_T24_E02_scRNA-seq


title: BJ_MYO_R1_T24_E04_scRNA-seq


title: 20150708_C67

description: processed data file header: WTCHG_209948_704507


title: BJ_MYO_R1_T24_E01_scRNA-seq


title: 20150702_C16

description: processed data file header: WTCHG_209948_704504


title: 20150702_C71

description: processed data file header: WTCHG_209948_704505


title: BJ_MYO_R1_T24_D12_scRNA-seq


title: BJ_MYO_R1_T24_E03_scRNA-seq


title: BJ_MYO_R1_T24_D11_scRNA-seq


title: 20150702_C21

description: processed data file header: WTCHG_209948_703517


title: 20150702_C79

description: processed data file header: WTCHG_209948_704503


title: BJ_MYO_R1_T24_D08_scRNA-seq


title: BJ_MYO_R1_T24_D07_scRNA-seq


title: BJ_MYO_R1_T24_D09_scRNA-seq


title: 20150708_C61

description: processed data file header: WTCHG_209948_703507


title: 20150708_C2

description: processed data file header: WTCHG_209948_703506


title: 20150702_C61

description: processed data file header: WTCHG_209948_704502


title: 20150708_C63

description: processed data file header: WTCHG_209948_704508


title: BJ_MYO_R1_T24_D06_scRNA-seq


title: BJ_MYO_R1_T24_D05_scRNA-seq


title: 20150708_C57

description: processed data file header: WTCHG_209948_703508


title: 20150702_C10

description: processed data file header: WTCHG_209948_703504


title: 20150702_C73

description: processed data file header: WTCHG_209948_703503


title: 20150702_C55

description: processed data file header: WTCHG_209948_703502


title: BJ_MYO_R1_T24_D02_scRNA-seq


title: BJ_MYO_R1_T24_D10_scRNA-seq


title: BJ_MYO_R1_T24_C12_scRNA-seq


title: 20150708_C55

description: processed data file header: WTCHG_209948_702507


title: BJ_MYO_R1_T24_D01_scRNA-seq


title: 20150708_C37

description: processed data file header: WTCHG_209948_702506


title: BJ_MYO_R1_T24_C10_scRNA-seq


title: BJ_MYO_R1_T24_C08_scRNA-seq


title: 20150702_C53

description: processed data file header: WTCHG_209948_702505


title: 20150702_C9

description: processed data file header: WTCHG_209948_702517


title: 20150708_C51

description: processed data file header: WTCHG_209948_702508


title: BJ_MYO_R1_T24_C11_scRNA-seq


title: 20150702_C41

description: processed data file header: WTCHG_209948_702504


title: BJ_MYO_R1_T24_E07_scRNA-seq


title: BJ_MYO_R1_T24_C07_scRNA-seq


title: BJ_MYO_R1_T24_D04_scRNA-seq


title: 20150702_C63

description: processed data file header: WTCHG_209948_702503


title: 20150702_C49

description: processed data file header: WTCHG_209948_702502


title: 20150702_C59

description: processed data file header: WTCHG_209948_703505


title: BJ_MYO_R1_T24_C05_scRNA-seq


title: BJ_MYO_R1_T24_C06_scRNA-seq


title: 20150702_C3

description: processed data file header: WTCHG_209948_701517


title: 20150708_C25

description: processed data file header: WTCHG_209948_701506


title: 20150708_C92

description: processed data file header: WTCHG_209948_701508


title: BJ_MYO_R1_T24_C04_scRNA-seq


title: BJ_MYO_R1_T24_C03_scRNA-seq


title: BJ_MYO_R1_T24_D03_scRNA-seq


title: BJ_MYO_R1_T24_B12_scRNA-seq


title: BJ_MYO_R1_T24_C02_scRNA-seq


title: 20150708_C49

description: processed data file header: WTCHG_209948_701507


title: 20150702_C45

description: processed data file header: WTCHG_209948_701502


title: 20150702_C35

description: processed data file header: WTCHG_209948_701504


title: BJ_MYO_R1_T24_B08_scRNA-seq


title: BJ_MYO_R1_T24_B10_scRNA-seq


title: BJ_MYO_R1_T24_B05_scRNA-seq


title: 20150702_C80

description: processed data file header: WTCHG_209948_701503


title: BJ_MYO_R1_T24_B11_scRNA-seq


title: BJ_MYO_R1_T24_B09_scRNA-seq


title: BJ_MYO_R1_T24_C09_scRNA-seq


title: 20150709_C89

description: processed data file header: WTCHG_207700_712507


title: 20150709_C52

description: processed data file header: WTCHG_207700_712506


title: 20150709_bulk2

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title: 20150702_C96

description: processed data file header: WTCHG_209948_701505


title: 20150709_C11

description: processed data file header: WTCHG_207700_712505


title: BJ_MYO_R1_T24_B02_scRNA-seq


title: BJ_MYO_R1_T24_B04_scRNA-seq


title: 20150709_C27

description: processed data file header: WTCHG_207700_712503


title: BJ_MYO_R1_T24_B01_scRNA-seq


title: BJ_MYO_R1_T24_A10_scRNA-seq


title: 20150709_C9

description: processed data file header: WTCHG_207700_712502


title: BJ_MYO_R1_T24_A09_scRNA-seq


title: 20150708_C84

description: processed data file header: WTCHG_207700_711517


title: 20150709_bulk1

description: processed data file header: WTCHG_207700_711508


title: BJ_MYO_R1_T24_B07_scRNA-seq


title: BJ_MYO_R1_T24_B06_scRNA-seq


title: 20150708_C90

description: processed data file header: WTCHG_207700_712517


title: 20150709_C48

description: processed data file header: WTCHG_207700_711506


title: 20150709_C34

description: processed data file header: WTCHG_207700_711505


title: BJ_MYO_R1_T24_A07_scRNA-seq


title: BJ_MYO_R1_T24_A05_scRNA-seq


title: BJ_MYO_R1_T24_A08_scRNA-seq


title: 20150709_C13

description: processed data file header: WTCHG_207700_711503


title: 20150709_C83

description: processed data file header: WTCHG_207700_711507


title: 20150709_C3

description: processed data file header: WTCHG_207700_711502


title: BJ_MYO_R1_T24_A04_scRNA-seq


title: BJ_MYO_R1_T24_A02_scRNA-seq


title: BJ_MYO_R1_T24_A06_scRNA-seq


title: BJ_MYO_R1_T24_A01_scRNA-seq


title: 20150708_bulk2

description: processed data file header: WTCHG_207700_710508


title: BJ_MYO_R1_T24_A12_scRNA-seq


title: 20150709_C42

description: processed data file header: WTCHG_207700_710506


title: 20150708_C64

description: processed data file header: WTCHG_207700_710517


title: 20150709_C56

description: processed data file header: WTCHG_207700_711504


title: BJ_MYO_R1_T24_A11_scRNA-seq


title: BJ_MYO_R1_T24_A03_scRNA-seq


title: 20150709_C62

description: processed data file header: WTCHG_207700_712504


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title: 20150709_C36

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title: 20150709_C1

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title: 20150709_C22

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title: 20150702_bulk1

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description: processed data file header: WTCHG_207700_701506


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title: 20150709_C33

description: processed data file header: WTCHG_207700_701504


title: 20150709_C68

description: processed data file header: WTCHG_207700_701505


title: 20150709_C21

description: processed data file header: WTCHG_207700_701503


title: 20150708_C65

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description: processed data file header: WTCHG_207700_701508


title: 20150709_C70

description: processed data file header: WTCHG_207700_701507


title: KDd3_B

city: Galveston

first: Allan

last: Brasier

state: TX

address: 301 Univ. Blvd

department: Medicine

institute: University Texas Medical Branch

data_processing:
Illumina bcl2fastq-1.8.4 used for base calling
Reads mapped to GRCh38 genome using STAR v2.5.1b with parameters --runThreadN 22 --outSAMtype BAM Unsorted SortedByCoordinate --outSAMstrandField intronMotif --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --alignMatesGapMax 1000000
Reads per gene counted using FeatureCounts v1.5.0-p1 with parameters -T 20 -p -s 2 with the Gencode GRch38 V24 basic annotation file
Log2 normalized counts obtained from DESeq2 v 1.12.1 using the rld function.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files containing read counts per gene and log2 normalized counts calculated by the DESeq2 rld function.

source_name: primary airway epithelial cells

extract_protocol:
Total cellular RNA was extracted using  RNAqueous™ phenol-free total RNA isolation kits (Life Technologies, CA) according to the manufacturer’s recommendations
Strand specific RNA libraries were prepared from 1 ug of total RNA using Illumina's RiboZero Gold kit using standard protocols

value: primary airway epithelial cells

tag: phenotype

value: RelA knockdown

tag: tgfb treatment

value: 3 days


title: KDd3_A


title: KDd3_C


title: 20150708_C96

description: processed data file header: WTCHG_207700_701502

value: single cell


title: KDd1_C

value: 1 day


title: KDd1_B


title: KDd0_C

value: 0 day


title: WTd1_C

value: RelA wildtype


title: KDd0_A


title: WTd1_B


title: KDd1_A


title: KDd0_B


title: WTd3_B


title: WTd3_A


title: WTd3_C


title: WTd1_A


title: WTd0_C


title: WTd0_A


title: WTd0_B


title: 20141119_C68

description: processed data file column header: WTCHG_168020_712517

extract_protocol:
Endoscopic forceps biopsies were incubated with 1mM EDTA with vigorous shaking to detach intact crypt units. Intact crypts separated from single cells and debris by centrifugation of the supernatant (150 G for 4 minutes). The crypt pellet was re-suspended in TrypLE Express (Thermo Fisher) supplemented with 50 ug/ml DNAse and incubated at 37C for 60 minutes, vortexing every 15 minutes. A pellet of dissociated single cells was obtained by passing the resultant suspension through a 35 um cell strainer and centrifugation of the filtrate at 500 G for 5 minutes.
Nextera XT library prep kit (Illumina)


title: 20141211_Bulk

description: processed data file column header: WTCHG_168020_712508


title: 20141211_C42

description: processed data file column header: WTCHG_168020_712507


title: 20141208_C27

description: processed data file column header: WTCHG_168020_712503


title: 20141208_C18

description: processed data file column header: WTCHG_168020_712504


title: 20141208_C72

description: processed data file column header: WTCHG_168020_712505


title: 20141208_Bulk

description: processed data file column header: WTCHG_168020_711508


title: 20141211_C56

description: processed data file column header: WTCHG_168020_712506


title: 20141119_C93

description: processed data file column header: WTCHG_168020_711517


title: 20141211_C10

description: processed data file column header: WTCHG_168020_711507


title: 20141208_C06

description: processed data file column header: WTCHG_168020_711504


title: 20141211_C81

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title: 20141119_C87

description: processed data file column header: WTCHG_168020_710517


title: 20141211_C49

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title: 20141211_C35

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title: 20141119_Bulk

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title: 20141119_C35

description: processed data file column header: WTCHG_168020_712502


title: 20141211_C82

description: processed data file column header: WTCHG_168020_709508

value: empty site control


title: 20141208_C26

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title: 20141211_C23

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title: 20141119_C01

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title: 20141119_C20

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title: 20141208_C17

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title: 20141211_C21

description: processed data file column header: WTCHG_168020_703506


title: 20141211_C83

description: processed data file column header: WTCHG_168020_705508


title: 20141119_C63

description: processed data file column header: WTCHG_168020_703502


title: 20141119_C90

description: processed data file column header: WTCHG_168020_703503


title: 20141119_C21

description: processed data file column header: WTCHG_168020_702517


title: 20141211_C80

description: processed data file column header: WTCHG_168020_702507


title: 20141208_C11

description: processed data file column header: WTCHG_168020_702505


title: 20141119_C15

description: processed data file column header: WTCHG_168020_701517


title: 20141211_C48

description: processed data file column header: WTCHG_168020_701508


title: 20141119_C16

description: processed data file column header: WTCHG_168020_702503


title: 20141211_C68

description: processed data file column header: WTCHG_168020_701507


title: 20141211_C15

description: processed data file column header: WTCHG_168020_702506


title: 20141208_C40

description: processed data file column header: WTCHG_168020_701505


title: 20141119_C57

description: processed data file column header: WTCHG_168020_702502


title: 20141208_C82

description: processed data file column header: WTCHG_168020_701506


title: 20141208_C39

description: processed data file column header: WTCHG_168020_701504


title: 20141119_C04

description: processed data file column header: WTCHG_168020_701503


title: 20141208_C49

description: processed data file column header: WTCHG_168020_702504


title: 20141119_C51

description: processed data file column header: WTCHG_168020_701502


title: GUT_REP1

city: medellin

first: Jean

middle: Paul

last: Delgado

state: antioquia

department: Biology

country: Colombia

institute: University of Atioquia

data_processing:
Sequenced reads were assembly using Trinity V 2.0.6 software pipeline, and default Trimmomatic parameters to remove sequence adapters and low quality reads (Phred score < 5), The reference transcriptome was assembled from all RNA samples and all contigs with length ≥ 200 nucleotides.
Sequence reads generated from limb tissue samples were aligned to the reference transcriptome using Bowtie2 (Langmead & Salzberg 2012) and RSEM (RNA-Seq by Expectation Maximization) was used to obtain estimates of transcript abundance for all transcripts (Li & Dewey 2011). Expression levels were calculated as transcripts per million (TPM) and Fragments Per Kilobase Million (FPKM)
transcript with the highest expression estimate was evaluated statistically using EBseq. Transcripts were considered differently expressed between control and post-amputation samples with FDR < 0.05, the fold change were calculate as condition 1 /condition 2, log2 of FC is provided
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include transcripts DEG calculated by Ebseq, the file include the normalized mean count value for each transcript at each condition and the log2 of the fold change of each time point over control

organism: Bolitoglossa ramosi

source_name: Gut

extract_protocol:
Total RNA from tissues were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of mRNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: days post amputation

value: Not apply

tag: developmental stage

value: Adult


title: SKIN_REP1

source_name: Dorsal and ventral skin


title: 20141211_C84

description: processed data file column header: WTCHG_168020_702508


title: PALETTA_70DPA_REP1

source_name: Regenerative tissue

value: 70 dpa


title: BLASTEMA_60DPA_REP2

value: 60 dpa


title: Mouse hippocampus 24h TBI1

city: Los Angeles

first: Douglas

last: Arneson

state: CA

address: 2000 Terasaki Life Sciences Bldg 610 Charles E Young Drive East

department: Integrative Biology and Physiology

institute: UCLA

description: Drop-Seq

data_processing:
Base calls performed with bcl2fastq2.15.
Read 2 was aligned with Star v2.5.0c.
Each aligned read was tagged with its mate-pair UMI and cell barcode.
Each aligned exonic read was tagged with a gene name.
A digital gene expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes.
Samples 1-6 -- prepared from both 24hr Sham and TBI mouse hippocampi on multiple separate days -- were merged together into a single matrix. Merged DGE file from all 6 samples generated. Entries contain raw UMI counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Digital gene expression matrices (genes x cells). Compressed, flat text files with tab delimiters.

organism: Mus musculus

source_name: Mus musculus hippocampus 24h 1.7atm TBI, 10 weeks

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads. Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.
Mouse hippocampus was dissected and dissociated into single-cell suspension, followed by drop-seq library preparation. Libraries were prepared following the latest drop-seq protcol.

tag: strain/background

tag: injury

value: 1.7atm TBI

tag: tissue

value: hippocampus

tag: age

value: 10 weeks


title: Mouse hippocampus 24h Sham1

description: Drop-Seq

source_name: Mus musculus hippocampus 24h Sham surgery, 10 weeks

value: Sham


title: Mouse hippocampus 24h Sham2

description: Drop-Seq


title: Mouse hippocampus 24h TBI3

description: Drop-Seq


title: Mouse hippocampus 24h Sham3

description: Drop-Seq


title: Mouse hippocampus 24h TBI2

description: Drop-Seq


title: BLASTEMA_20DPA_REP1

value: 20 dpa


title: BLASTEMA_40DPA_REP1

value: 40 dpa


title: LIMB_REP3

source_name: forelimb


title: IP WT unstimulated

city: Barcelona

first: Cristina

last: Lopez-Rodriguez

address: Carrer Dr. Aiguader, 88

department: Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

description: Antibodies were described in Lopez-Rodriguez et al., 1999, Proc Natl Acad Sci USA, vol 96: 7214-7219

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the reference genome using Bowtie2 aligner with default parameters
profile were calculated by using bedtools
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph profiles

molecule: genomic DNA

source_name: Unstimulated wild-type BMDM

growth_protocol: BMDM were generated by culturing bone marrow cell suspensions from wild-type and NFAT5-deficient mice in 25% (vol/vol) conditioned medium from M-CSF-producing L929 cells for 7 days.

extract_protocol:
Formaldehyde crosslinked chromatin was sonicated to fragments DNA to about 200-300 bp, the immunoprecipitated with anti-NFAT5 antibodies. Immunoprecipitated chromatin was purified and sequenced. Chromatin aliquots from the wild-type and NFAT5-deficient BMDMs sample were separated to use as a measure of chromatin input.
Libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs, Ref. E7370) according to the manufacturer's protocol from 5-10 ng of starting material. Final libraries were analyzed using the Agilent Bioanalyzer with a DNA High Sensitivity chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (KapaBiosystems, Ref. KK4835) prior to sequencing with Illumina HiSeq 2000

treatment_protocol: BMDM were immediately processed for ChIP-sequencing in unstimulated conditions (steady state BMDM)

value: BMDM

tag: genotype/variation

value: wild type

tag: mouse strain

tag: chip antibody

value: anti-NFAT5 antibodies were a mixture of two rabbit polyclonal antibodies to the amino-terminal or DNA binding domain regions of NFAT5


title: INPUT WT unstimulated

tag: cell type

value: Input total chromatin sample without immunoprecipitation


title: INPUT KO unstimulated

source_name: Unstimulated NFAT5-deficient BMDM


title: LIMB_REP1


title: LIMB_REP2


title: Gallbladder (5)

status: Public on Sep 25 2018

city: Leiden

first: Christiaan

last: Henkel

address: Sylviusweg 72

department: Institute of Biology

country: Netherlands

institute: University Leiden

description: Common Carp Sample 93

data_processing:
Illumina software used for basecalling.
tophat 2.0.5
htsec count
Genome_build: ASM127010v1 [GenBank assembly accession: GCA_001270105.1 & WGS Project: LHQP01]
Supplementary_files_format_and_content: Tab-delimited .tsv file for each Sample lists gene identifiers and raw counts.  For the gene identifiers' sequences, refer to the .gff linked as a supplementary file on the Series record.  The contigs listed in the .gff can be found at GenBank: LHQP00000000.1 (associated with BioProject PRJNA73579).

organism: Cyprinus carpio

source_name: Gallbladder

extract_protocol:
RNA Later
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gallbladder


title: Gallbladder (3)

description: Common Carp Sample 92


title: Gallbladder (2)

description: Common Carp Sample 91


title: Carp whole larvae control infected (1)

description: Common Carp Sample 86i

source_name: Embryo

value: Embryo


title: Carp whole larvae control infected (2)

description: Common Carp Sample 87i


title: Carp whole larvae control (1)

description: Common Carp Sample 86


title: ventricle

description: Common Carp Sample 84

source_name: Heart

value: Heart


title: Gallbladder (1)

description: Common Carp Sample 90


title: Bulbus

description: Common Carp Sample 85

source_name: Bulbus

value: Bulbus


title: BLASTEMA_60DPA_REP1

value: Adult


title: brain body (rear)

description: Common Carp Sample 82

source_name: Brain

value: Brain


title: vagal lobe

description: Common Carp Sample 78


title: mLN_SPF_resDC_6

city: Lausanne

first: Joern

last: Pezoldt

address: Station 19, SV 3818.A

department: SV

country: Switzerland

institute: EPFL

description: DESeq2_genes_diffexp_by_fc_Res_mLN_SPF_vs_Res_pLN_SPF.csv

data_processing:
Libraries were aligned versus the mouse reference genome (assembly: GRCm38) using the splice junction mapper Tophat2 v1.2.0 with default parameterization.
Reads aligned to annotated genes were quantified with the htseq-count program [Anders, Pyl, Huber, 2015, Bioinformatics 31, 166-169].
Determined read counts served as input to DESeq2 [Love, Huber, Anders, 2014, Genome Biology 15, 550] for pairwise detection and quantification of differential gene expression.
RPKM (reads per kilobase maximal transcript length per million mapped reads) values were computed for each library from the raw gene counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: .csv files include RPKM values, q-value and log2(FC) for each pair-wise comparison

growth_protocol: ex vivo

extract_protocol:
Total RNA was extracted from FACS‑sorted resident DCs using the RNeasy Plus Micro Kit (Qiagen).
cDNA was synthesized and amplified using template switching technology of the SMART‑Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories), followed by purification using the Agencourt AMPure XP Kit (Beckman Coulter). Library preparation was performed with Nextera XT DNA Library Prep Kit (Illumina). The Agilent Technologies 2100 Bioanalyzer was used to control quality and integrity of nucleic acids after each step.

treatment_protocol: For RNA‑seq analysis, CD45+ cells enriched with autoMACS were stained using fluorescence‑coupled antibodies and sorted for resident DCs by FACS (Aria II, 100 μm nozzle).

tag: ln

value: gut-draining

tag: transplanted

value: no

tag: strain

value: BALB/c


title: mLN_SPF_resDC_7


title: atrium

description: Common Carp Sample 83


title: mLN_SPF_resDC_4


title: mLN_SPF_resDC_5


title: mLN_SPF_resDC_3


title: pituitary

description: Common Carp Sample 80


title: IP KO unstimulated


title: brain body (front)

description: Common Carp Sample 81


title: Carp whole larvae control (2)

description: Common Carp Sample 87


title: corpus cerebelli

description: Common Carp Sample 77


title: medulla oblongata

description: Common Carp Sample 79


title: mLN_SPF_resDC_1


title: torus semicircularis (left)

description: Common Carp Sample 75


title: tectum opticum (right)

description: Common Carp Sample 74


title: mLN_SPF_Tx_resDC_4

description: DESeq2_genes_diffexp_by_fc_Res_mLN_SPF_Tx_vs_Res_pLN_SPF_Tx.csv

value: yes


title: mLN_SPF_Tx_resDC_5


title: telencephalon

description: Common Carp Sample 72


title: mLN_SPF_Tx_resDC_7


title: mLN_SPF_Tx_resDC_6


title: tectum opticum (left)

description: Common Carp Sample 73


title: optical nerve

description: Common Carp Sample 71


title: gut 3rd segment

description: Common Carp Sample 70

value: Gut


title: mLN_SPF_Tx_resDC_2


title: mLN_SPF_Tx_resDC_1


title: gallbladder

description: Common Carp Sample 69


title: pLN_SPF_resDC_5

value: skin-draining


title: swim bladder (rear)

description: Common Carp Sample 67

source_name: Swim bladder

value: Swim bladder


title: pLN_SPF_resDC_1


title: spleen (e)

description: Common Carp Sample 66

source_name: Spleen

value: Spleen


title: pLN_SPF_resDC_3


title: PBL

description: Common Carp Sample 68

source_name: Blood

value: Blood


title: hepatopancreas (e)

description: Common Carp Sample 62

source_name: Hepatopancreas

value: Hepatopancreas


title: pLN_SPF_Tx_resDC_4


title: spleen (a)

description: Common Carp Sample 63


title: spleen (d)

description: Common Carp Sample 65


title: mLN_SPF_resDC_2


title: pLN_SPF_resDC_4


title: spleen (b)

description: Common Carp Sample 64


title: pLN_SPF_resDC_2


title: pLN_SPF_Tx_resDC_3


title: torus semicircularis (right)

description: Common Carp Sample 76


title: hepatopancreas (d)

description: Common Carp Sample 61


title: hepatopancreas (c)

description: Common Carp Sample 60


title: hepatopancreas (b)

description: Common Carp Sample 59


title: pLN_SPF_Tx_resDC_1


title: hepatopancreas (a)

description: Common Carp Sample 58


title: mLN_SPF_Tx_resDC_3


title: mLN_GF_Tx_FSC_3

description: DESeq2_genes_diffexp_by_fc_mLN_GF_Tx_vs_pLN_SPF_Tx.csv

extract_protocol:
Total RNA was extracted from FACS‑sorted FSC using the RNeasy Plus Micro Kit (Qiagen).
cDNA was synthesized and amplified using template switching technology of the SMART‑Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories), followed by purification using the Agencourt AMPure XP Kit (Beckman Coulter). Library preparation was performed with Nextera XT DNA Library Prep Kit (Illumina). The Agilent Technologies 2100 Bioanalyzer was used to control quality and integrity of nucleic acids after each step.

treatment_protocol: For RNA‑seq analysis, CD45 cells depleted with autoMACS were stained using fluorescence‑coupled antibodies and sorted FSCs by FACS (Aria II, 100 μm nozzle; purity).


title: mLN_GF_Tx_FSC_2


title: mLN_GF_Tx_FSC_1


title: gonads male (a)

description: Common Carp Sample 56

source_name: Gonads

value: Gonads


title: mLN_SPF_FSC_8

description: DESeq2_genes_diffexp_by_fc_mLN_SPF_vs_pLN_SPF.csv


title: gonads male (b)

description: Common Carp Sample 57


title: ventral skin (e)

description: Common Carp Sample 55

source_name: Skin

value: Skin


title: mLN_SPF_FSC_6


title: mLN_SPF_FSC_4


title: ventral skin (a)

description: Common Carp Sample 51


title: mLN_SPF_FSC_5


title: ventral skin (b)

description: Common Carp Sample 52


title: mLN_SPF_FSC_2


title: mLN_SPF_FSC_3


title: ventral skin (c)

description: Common Carp Sample 53


title: pLN_SPF_Tx_resDC_2


title: mLN_SPF_Tx_FSC_6

description: DESeq2_genes_diffexp_by_fc_mLN_SPF_Tx_vs_pLN_SPF_Tx.csv


title: mLN_SPF_FSC_7


title: mLN_SPF_Tx_FSC_7


title: dorsal skin (d)

description: Common Carp Sample 49


title: dorsal skin (a)

description: Common Carp Sample 46


title: dorsal skin (b)

description: Common Carp Sample 47


title: mLN_SPF_Tx_FSC_4


title: right mid kidney (left)

description: Common Carp Sample 44

source_name: Kidney

value: Kidney


title: mLN_SPF_Tx_FSC_2


title: mLN_SPF_Tx_FSC_1


title: ventral skin (d)

description: Common Carp Sample 54


title: left mid kidney (left)

description: Common Carp Sample 42


title: mLN_SPF_Tx_FSC_3


title: pLN_SPF_FSC_7


title: left mid kidney (right)

description: Common Carp Sample 43


title: mLN_SPF_FSC_1


title: thymus dorsal (right)

description: Common Carp Sample 40

source_name: Thymus

value: Thymus


title: thymus ventral (right)

description: Common Carp Sample 41


title: dorsal skin (c)

description: Common Carp Sample 48


title: thymus ventral (left)

description: Common Carp Sample 39


title: thymus dorsal (left)

description: Common Carp Sample 38


title: dorsal skin (e)

description: Common Carp Sample 50


title: pLN_SPF_FSC_3


title: pLN_SPF_FSC_5


title: gill 3rd arch (right)

description: Common Carp Sample 37

source_name: Gill

value: Gill


title: pLN_SPF_FSC_4


title: mLN_SPF_Tx_FSC_5


title: gill 1st arch (right)

description: Common Carp Sample 35


title: pLN_SPF_FSC_2


title: pLN_SPF_Tx_FSC_4


title: gill 3rd arch (left)

description: Common Carp Sample 34


title: pLN_SPF_FSC_1


title: gill 2nd arch (right)

description: Common Carp Sample 36


title: gill 2nd arch (left)

description: Common Carp Sample 33


title: pLN_SPF_Tx_FSC_2


title: gill 1st arch (left)

description: Common Carp Sample 32


title: pLN_SPF_Tx_FSC_3


title: head kidney dorsal (left)

description: Common Carp Sample 28


title: pLN_SPF_Tx_FSC_1


title: head kidney ventral (right)

description: Common Carp Sample 31


title: pLN_SPF_FSC_6


title: head kidney ventral (left)

description: Common Carp Sample 29


title: ventral muscle (e)

description: Common Carp Sample 27

source_name: Muscle

value: Muscle


title: Reprogramming timecourse 2, timepoint 2

city: St Louis

first: Samantha

last: Morris

state: Missouri

address: Department of Developmental Biology, Washington University School of

institute: Washington University in St Louis

data_processing:
After sequencing, scRNA-seq libraries were processed, filtered, and aligned as previously described,  including correction of barcode synthesis errors. This process, and the required tools, are further  outlined online in the Drop-seq Alignment Cookbook (http://mccarrolllab.com/dropseq/). In an effort to  facilitate downstream analyses the reference genome used during alignment was modified to include  three transgenic sequences. The processed reads were aligned to the genome using STAR, default  settings were used. Following alignment, digital gene expression (DGE) matrices were then generated for each timepoint from both time courses. Cells which expressed 200 or more genes were selected  for inclusion in the matrices. For time course one this resulted in a combined 10,038 cells and 20,576  genes included in the digital expression matrix. The mean number of expressed genes in these cells  was 1,215.908, and the mean UMI count was 2,636.718. This matrix was then filtered to include only  cells with a UMI count of at least 1,000, cells in which the proportion of the UMI count attributable to  mitochondrial genes was less than or equal to 10%, resulting in an expression matrix with 5,932 cells  and 20,383 genes. This filtered expression matrix was used for all downstream analyses. The mean  UMI count of the filtered matrix was 4120.815, and the mean number of expressed genes was  1,801.648. The same was performed for the second time course, resulting in a combined gene  expression matrix of 8,335 cells and 21,023 genes. The mean UMI count and number of genes per  cell, for the combined matrix was 5,502.507 and 1820.732 respectively. After filtering the matrix  contained 5,414 cells and 20,934 genes, with a mean UMI count of 8,207.728 and a mean number of  genes per cell of 2635.565. These filtered matrices were used for all downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Digital Expression Matrix (Timecourse 1 combined)
Supplementary_files_format_and_content: Digital Expression Matrix (Timecourse 2 combined)

source_name: E13.5 Mouse Embryonic Fibroblasts

growth_protocol: Mouse embryonic fibroblasts were converted to iHeps/iEPs as in Sekiya and Suzuki (2011) 10 . Briefly,  fibroblasts were prepared from E13.5 embryos and serially transduced with polyethylene glycol  concentrated Hnf4a-t2a-Foxa1, followed by culture on gelatin for 2 weeks in hepato-medium  (DMEM:F-12, supplemented with 10% FBS, 1 mg/ml insulin (Sigma), dexamethasone (Sigma-Aldrich),  10 mM nicotinamide (Sigma-Aldrich), 2 mM L-glutamine, 50 mM b-mercaptoethanol (Life  Technologies), and penicillin/streptomycin, containing 20 ng/ml hepatocyte growth factor (Sigma-  Aldrich), and 20 ng/ml epidermal growth factor (Sigma-Aldrich), after which the emerging iEPs were  cultured on collagen.

extract_protocol:
Cells were dissociated using TrypLE Express (Gibco), washed in PBS containing 0.01% BSA and  diluted to 100 cells/μl. These cells were processed by Drop-seq within 15 minutes of their harvest.  Drop-seq was performed as previously described . In brief, cells and beads were diluted to an  estimated co-occupancy rate of 5% upon co-encapsulation. Two independent lots of beads  (Macosko201110, ChemGenes Corporation, Wilmington MA) were used: 091615 (Timecourse 1),  032516B (Timecourse 2).
Emulsions were collected and broken by perfluorooctanol (Sigma), followed  by bead harvest and reverse transcription. After ExonucleaseI treatment, aliquots of 2,000 beads  ( ∼ 100 cells) were amplified by PCR for 14 cycles. Following purification by addition of 0.6x AMPure  XP beads (Agencourt), cDNA from an estimated 5,000 cells was tagmented by Nextera XT using 600  pg of cDNA input, as assessed by Tapestation (Agilent) analysis. Following further purification, 1ng of  each library was used as input for GFP amplification for a further 12 cycles of PCR using the Drop-seq  P5-TSO_Hybrid primer (AATGATACGGCGACCACCGAGATCTACACGCCTGTCCGCGGAAGCAGT  GGTATCAACGCAGAGT ∗ A ∗ C) and a P7 hybrid primer complementary to the 3’ end of GFP  (P7/Seq2/GFP Hybrid: CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCT  TCCGATCTGGCATGGACGAGCTGTACAAGTAA). Following purification, the GFP amplicon was  spiked into the main library at 5% of the total concentration. Libraries were sequenced on an Illumina  HiSeq 2500 at 1.4pM, with custom priming (Read1CustSeqB Drop-seq primer).

value: Mouse fibroblast to induced endoderm progenitors


title: Reprogramming timecourse 2, timepoint 1


title: head kidney dorsal (right)

description: Common Carp Sample 30


title: ventral muscle (d)

description: Common Carp Sample 26


title: ventral muscle (c)

description: Common Carp Sample 25


title: Reprogramming timecourse 2, timepoint 0

value: Mouse fibroblasts


title: Reprogramming timecourse 1, timepoint 4


title: Reprogramming timecourse 1, timepoint 3


title: ventral muscle (a)

description: Common Carp Sample 23


title: ventral muscle (b)

description: Common Carp Sample 24


title: dorsal muscle (d)

description: Common Carp Sample 21


title: dorsal muscle (c)

description: Common Carp Sample 20


title: dorsal muscle (e)

description: Common Carp Sample 22


title: Reprogramming timecourse 2, timepoint 3


title: Reprogramming timecourse 1, timepoint 2


title: dorsal muscle (a)

description: Common Carp Sample 18


title: dorsal muscle (b)

description: Common Carp Sample 19


title: AP14.5NSC3

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

description: Matched location for all replicates

data_processing:
Sequenced reads were trimmed for adaptor sequence using Cutadapt and then mapped to mm10 whole genome using STAR 2.5.2b with parameters --chimSegmentMin 15 --chimJunctionOverhangMin 15 --twopassMode Basic --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outReadsUnmapped Fastx --outFilterMismatchNoverReadLmax 0.04 --outStd SAM --outSAMmode Full --outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within
Raw counts per gene model (ensembl 75) were extracted with featureCounts v1.4.4
Genome_build: mm10
Supplementary_files_format_and_content: Raw featureCounts-derived count data

source_name: Anterior nasal septum cartilage

extract_protocol:
Embryos were dissected and heads rapidly frozen in OCT. Frozen sections were cut onto Leica PEN membrane slides. Location-matched slides were stained and dehydrated for laser capture microdissection with a Leica LMD6500. RNA was prepared using an Arcturus Picopure RNA Isolation Kit with on-column DNase digestion as described by the manufacturer.
Library preparation was performed with an initial amplification step from 15 ng of RNA from each of the six samples with the NuGEN Ovation RNA-Seq System v2 to create double stranded cDNA. The Nextera XT DNA Sample Preparation Kit (Illumina) was used to create DNA library templates from the double stranded cDNA as described by the manufacturer. DNA sequencing was performed on an Illumina HiSeq 2500 instrument using standard protocols for paired end 100 bp sequencing.

tag: genotype

value: Fgfr2+/S252W; EIIA-Cre

value: nasal septum cartilage


title: Reprogramming timecourse 1, timepoint 0


title: lower tail

description: Common Carp Sample 17

source_name: Tail

value: Tail


title: Reprogramming timecourse 2, timepoint 4


title: anal fin

description: Common Carp Sample 15

source_name: Fin

value: Fin


title: WT14.5NSC3

description: Matched location for all replicates

value: WT


title: upper tail

description: Common Carp Sample 16


title: WT14.5NSC2

description: Matched location for all replicates


title: dorsal fin (rear)

description: Common Carp Sample 14


title: dorsal fin (front)

description: Common Carp Sample 13


title: pLN-GF2

data_processing:
Libraries were aligned versus the mouse reference genome (assembly: GRCm38) using the splice junction mapper Tophat2 v1.2.0 with default parameterization.
Reads aligned to annotated genes were quantified with the htseq-count program [Anders, Pyl, Huber, 2015, Bioinformatics 31, 166-169].
Determined read counts served as input to DESeq2 [Love, Huber, Anders, 2014, Genome Biology 15, 550] for pairwise detection and quantification of differential gene expression.
RPKM (reads per kilobase maximal transcript length per million mapped reads) values were computed for each library from the raw gene counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: skin-draining lymph node

extract_protocol:
RNA was isolated from ex vivo sorted FRCs via DNA/RNA AllPrep Kit (Qiagen) according to the manufacturer's protocols.
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer. Purification of poly A-containing mRNA was carried out via poly T oligo attached magnetic beads. Following purification, the mRNA was subjected to library preparation using Script Seq v2 Library preparation kit (Epicentre).

treatment_protocol: For stromal cell isolation, skin-draining pLNs (inguinal and axillary) or mLNs were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase P (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). In a first step, CD45- cells were enriched by autoMACS separation after indirect magnetic labeling of CD45+ cells using anti‑CD45-APC (30-F11, eBioscience) followed by anti‑APC microbeads (Miltenyi Biotec). Subsequently, the CD45- fraction was stained using fluorescence-coupled antibodies and either analyzed directly by flow cytometry or used to sort CD45-Ter119-CD31-gp38+ FRCs by FACS (Aria II, 100 μm nozzle; purity >91‑97 %) for RNA‑seq analysis.

value: fibroblastic reticular cell

value: skin

tag: organ

value: lymph node

tag: housing

value: germ-free

value: Balb/c


title: ZCCHC4-polysome profiling-KO-Polysome-repl.3

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: fragmented polyA RNA

data_processing:
Library strategy: Polysome Profiling
After removing adapters, reads were mapped to Human genome with tophat2. For ParCLIP, the data were analyzed by PARalyzer. For m6ASeq, the data were analyzed in the way descriped in Ma L's 2017 Genome Research paper(PMID:28052920). For  ploysome profiling data, cufflink were used to calculate the RPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Excel, peaks, RPKM

source_name: HepG2 ZCCHC4 knockout

extract_protocol: Illumina TruSeq Stranded mRNA Library Prep Kit

tag: cell line

value: HepG2 ZCCHC4 knockout

value: ZCCHC4 knockout


title: pelvic fin (left)

description: Common Carp Sample 11


title: ZCCHC4-polysome profiling-KO-Polysome-repl.1

description: fragmented polyA RNA


title: pLN-GF1


title: Reprogramming timecourse 1, timepoint 1


title: pectoral fin (right)

description: Common Carp Sample 10


title: mLN-GF-2

source_name: mesenteric lymph node

value: mesenteries


title: ZCCHC4-polysome profiling-KO-Polysome-repl.2

description: fragmented polyA RNA


title: ZCCHC4-polysome profiling-WT-Polysome-repl.3

description: fragmented polyA RNA

source_name: HepG2 wild-type

value: HepG2 wild-type

value: wild type


title: AP14.5NSC1

description: Matched location for all replicates


title: AP14.5NSC2

description: Matched location for all replicates


title: pLN-SPF-1

value: specific-pathogen-free


title: pLN-SPF-2


title: pectoral fin (left)

description: Common Carp Sample 9


title: crystalline (right)

description: Common Carp Sample 8

source_name: Eye

value: Eye


title: ZCCHC4-polysome profiling-KO-Input-repl.3

description: fragmented polyA RNA


title: ZCCHC4-polysome profiling-WT-Polysome-repl.1

description: fragmented polyA RNA


title: mLN-SPF-1


title: mLN-SPF-2


title: eye rear (right)

description: Common Carp Sample 6


title: eye front (right)

description: Common Carp Sample 5


title: ZCCHC4-polysome profiling-WT-Input-repl.3

description: fragmented polyA RNA


title: mLN-GF-1


title: ZCCHC4-polysome profiling-WT-Polysome-repl.2

description: fragmented polyA RNA


title: eye front (left)

description: Common Carp Sample 3


title: ZCCHC4-polysome profiling-WT-Input-repl.2

description: fragmented polyA RNA


title: pelvic fin (right)

description: Common Carp Sample 12


title: barb (right)

description: Common Carp Sample 2

source_name: Barb

value: Barb


title: WT14.5NSC1

description: Matched location for all replicates

value: nasal septum cartilage


title: ZCCHC4-m6Aseq-KO-Input-repl.2

description: fragmented polyA RNA

data_processing:
Library strategy: m6A-Seq
After removing adapters, reads were mapped to Human genome with tophat2. For ParCLIP, the data were analyzed by PARalyzer. For m6ASeq, the data were analyzed in the way descriped in Ma L's 2017 Genome Research paper(PMID:28052920). For  ploysome profiling data, cufflink were used to calculate the RPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Excel, peaks, RPKM


title: barb (left)

description: Common Carp Sample 1


title: ZCCHC4-m6Aseq-KO-IP-repl.2

description: fragmented polyA RNA immunoprecipitated with anti-m6A antibody


title: ZCCHC4-m6Aseq-KO-Input-repl.1

description: fragmented polyA RNA


title: ZCCHC4-m6Aseq-KO-IP-repl.1


title: crystalline (left)

description: Common Carp Sample 7


title: ZCCHC4-m6Aseq-WT-Input-repl.1

description: fragmented polyA RNA


title: ZCCHC4-m6Aseq-WT-Input-repl.2

description: fragmented polyA RNA


title: ZCCHC4-polysome profiling-WT-Input-repl.1

description: fragmented polyA RNA


title: IP_STAT3_OL

city: Rome

first: Matteo

last: Pallocca

address: Via Fermo Ognibene

country: Italy

institute: Italian National Cancer Institute "Regina Elena"

data_processing:
Mapping: Bowtie2
Peak calling: MACS2 (default parameters)
Bedgraph intermediate files for bigWig generation were generated using MACS2 bdgcmp command
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: IP_STAT3_OL, HepaRG

growth_protocol: Human hepatoma HepaRG cells were grown in William׳s E medium supplemented with 10% fetal bovine serum (FBS), 2 mM Glutamine, 20IU/ml of penicillin, 20 µg/ml of streptomycin and 5 mg/l insulin and 5 µM hydrocortisone hemisuccinate. After one week, HepaRG cells were transferred to the same medium supplemented with 2% dimethylsulfoxide (DMSO) for further two weeks in order to obtain confluent differentiated cultures containing both hepatocyte-like and progenitors/primitive biliary-like cells (around 50% of each type).

extract_protocol:
Chromatin was isolated from the nuclei of formaldehyde cross-linked cells, sonicated and immunoprecipated with anti-phospho-STAT3 antibody.
ChIP-Seq libraries were constructed from 10ng immunoprecipitated or original input chromatin using the ChIP-Seq Sample Prep Kit from Illumina, following the manufacturer's instructions.

treatment_protocol: Differentiated HepaRG cells were treated for 4 days with 250 µM of sodium oleate or vehicle as control.

value: hepatoma HepaRG cells

tag: agent

value: sodium oleate

value: Phospho-Stat3 (Tyr705) XP #9145 Cell Signaling


title: IP_STAT3_vehicle

source_name: IP_STAT3_vehicle, HepaRG

value: control


title: input_vehicle

source_name: input_vehicle, HepaRG


title: ZCCHC4-PARCLIP-repl.2

description: small RNA fragments crosslinked with ZCCHC4with 4SU

data_processing:
Library strategy: PARCLIP
After removing adapters, reads were mapped to Human genome with tophat2. For ParCLIP, the data were analyzed by PARalyzer. For m6ASeq, the data were analyzed in the way descriped in Ma L's 2017 Genome Research paper(PMID:28052920). For  ploysome profiling data, cufflink were used to calculate the RPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Excel, peaks, RPKM

source_name: HeLa

extract_protocol: NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

treatment_protocol: For PARCLIP treat the cell with 4SU at 100uM 24 hour

value: HeLa cells

value: N terminal Flag-HA tagged ZCCHC4 HeLa stable expression cell line


title: ZCCHC4-m6Aseq-WT-IP-repl.2


title: eye rear (left)

description: Common Carp Sample 4


title: L1700566

data_processing:
Library strategy: Drop-Seq
Data were analyzed using Cell Ranger™ v2.0 pipelines and were visualized by Loupe™ Cell Browser v1.0. Both are available in 10xGenomics website.
Genome_build: mm10
Supplementary_files_format_and_content: .csv files include mean UMI counts, log2 fold changes and adjusted p-values for the differentially expressed genes among the intentified cell clusters.

source_name: pLN-SPF

extract_protocol:
For stromal cell isolation, skin-draining pLNs (inguinal and axillary) or mLNs (small intestinal and colon/caecum-draining) were resected and digested in RPMI 1640 medium (Gibco) containing 0.2 mg/ml collagenase P (Roche), 0.15 U/ml dispase (Roche) and 0.2 mg/ml DNase I (Roche) as described previously (Fletcher et al., 2011, https://doi.org/10.3389/fimmu.2011.00035). After digestion, cells were kept at 4°C in PBS containing 0.2 % BSA and 5 mM EDTA (Roth). CD45- cells were enriched by MACS separation after direct magnetic labeling of CD45+ cells using  anti-CD45 Nanobeads (Biolegend). Subsequently, the CD45- fraction was stained using fluorescence-coupled antibodies and used to sort CD45‑CD24‑ cells by FACS (Aria II)) for single-cell mRNA‑seq analysis.
Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3’ reagent kit v2 for reverse transcription, cDNA amplification and library construction (10xGenomics). The detailed protocol was provided by 10xGenomics.

tag: antibody

value: TATGATTC,CCCACAGT,ATGCTGAA,GGATGCCG


title: input_OL

source_name: input_OL, HepaRG


title: ZCCHC4-m6Aseq-WT-IP-repl.1


title: Meis2Overexp3_39so

city: Madrid

first: Carlos

last: Torroja

state: Madrid

address: Melchor Fernandez Almagro, 3

department: Bioinformatics Unit

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description:
E3
pool of 2 embryos

data_processing:
Samples were sequenced in an Illumina GAIIx sequencer
Base calls produced by Illumina pipeline version 1.13.48
Base calls were extracted using illumina2bam tool release 0.03 from Wellcome Trust Sanger Institute. Standard Phred Scale
Reads were pre-processed with Cutadapt 1.2.1, to remove TruSeq adaptor sequences.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build NCBIM37.v65) And quantified using RSEM v1.17
Only genes with at least 2 counts per million in at least 3 samples were considered for statistical analysis.
Data were normalized and differential expression tested using the Bioconductor package EdgeR. Note that the number of somites in each sample was used as blocking variable in the mixed linear model. We considered as differentially expressed those genes with a Benjamini-Hochberg adjusted p-value <0.05.
Genome_build: NCBIM37.v65
Supplementary_files_format_and_content: normalized_matrix_table.xlsx file contains ENSEMBL gene Ids, MGI gene names and normalized counts per million obtained using edgeR

source_name: distal limb bud tips

growth_protocol: Pregant mice were generated crossing  HoxB6CreER/+;R26RMeis2a-IRES-EYFP/Meis2a-IRES-EYFP with R26RMeis2a-IRES-EYFP/Meis2a-IRES-EYFP.

extract_protocol:
The distal limb bud tips of somite-staged HoxB6CreER; R26Meis2a/Meis2a (experimental) or R26Meis2a/Meis2a (control) embryos were dissected and flash-frozen on liquid nitrogen (1 tube per embryo). For RNA extraction, we used the miRNAeasy kit from Qiagen, pooling the limb bud tips from 2 embryos per stage and genotype in order to obtain enough RNA.
Libraries were made using the standard TruSeq RNA Sample Preparation v2 Kit from Illumina

treatment_protocol: Pregnant mice were given 0.8mg of intraperioneal 4-hydroxy-tamoxifen at E8.3 days of gestation

value: distal limb bud tips

tag: Stage

value: 39 somites