title: WBJPE161031-170

tag: developmental stage


title: WBJPE161031-169

status: Public on Dec 28 2020

type: SRA

city: Hangzhou

first: Zi

last: Yin

address: YuHangTang Road N0.866

country: China

institute: Zhejiang University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
alignment was conducted with Tophat
use the FindAllMarkers function in the Seurat(version 2.3.4)to find markers for every cluster compared to all remaining cells
Genome_build: mm9
Supplementary_files_format_and_content: Excel files include markers for every cluster compared to all remaining cells;p_val:p_val (unadjusted);avg_logFC : log fold-chage of the average expression between the two groups. Positive values indicate that the feature is more highly expressed in the first group;p_val_adj : Adjusted p-value, based on bonferroni correction using all features in the dataset.

molecule: total RNA

organism: Mus musculus

source_name: E12.5_hind limb

extract_protocol:
Single-cell capture, RNA extraction and cDNA preparation were performed following the methods described in the Fluidigm protocol (PN 100-9886, Using the C1 High-Throughput IFC to Generate Single-Cell cDNA Libraries for mRNA Sequencing).
3' end enrichment with Illumina Nextera XT

treatment_protocol: We collected single cell suspension from embryonic SCX-GFP mouse hindlimb at E10.5, E12.5 and E15.5.

tag: strain

value: C57BL/6 Transgenic Mouse

tag: genotype/variation

value: SCX-GFP mouse

tag: tissue

value: hind limb


title: WBJPE161031-167


title: Subject ID: IN.GBU.430_IgG

type: protein

city: Irvine

first: Joseph

middle: John

last: Campo

state: CA

address: 1 Technology Dr., STE E309

country: USA

institute: Antigen Discovery, Inc.

hyb_protocol: Milk samples were diluted 1:5 in a 1.5 mg/mL E. coli lysate solution (Antigen Discovery, Inc., Irvine, CA) in protein arraying buffer (GVS, Cat. 10485356, Sanford, ME) and incubated at room temperature for 30 min. For milk samples previously diluted in preservative solution, samples were diluted 1:2.5 in the lysate solution. Microarray slides were hydrated in arraying buffer and then probed with 250 µL of the preincubated milk samples using sealed, fitted slide chambers to avoid cross-contamination between arrays. Arrays were incubated overnight at 4°C with agitation, washed three times with Tris-buffered saline (TBS)-0.05% Tween 20 (Thermo Scientific, J77500K8, diluted 20x in molecular grade water), and incubated with Cy3-conjugated anti-human IgG diluted 1:200 in arraying buffer and biotin-conjugated anti-Human IgA diluted 1:1000 (Jackson ImmunoResearch, Cat. 709-165-098 and Cat. 109-065-011, West Grove, PA). Arrays were washed three times with TBS–0.05% Tween 20 and incubated with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Cat. D7-2212, Frederick, MD) at room temperature, protected from light. Arrays were washed 3x with TBS–0.05% Tween 20, 3x with TBS, and once with water and then air dried by being centrifuged at 1,000 x g for 4 min and left overnight in a desiccator before scanning.

scan_protocol: Probed microarrays were scanned using a GenePix 4300A high-resolution microarray scanner (Molecular Devices, Sunnyvale, CA), and an image file (.tiff) was saved for each array using GenePix pro 7 software. The signals in the scanned images were quantified using Mapix software (Innopsys).

data_processing: All further data processing was performed in R (http://www.R-project.org). Data were normalized by first transforming raw values using the base 2 logarithm. Next, the data set was normalized to remove systematic effects by subtracting the median signal intensity of the IVTT control spots from the IVTT antigen spots for each sample. Since the IVTT control spots carry not only the chip, sample, and batch-level systematic effects, but also antibody background reactivity to the E. coli cell-free IVTT system, this procedure normalizes the data and provides a relative measure of the specific antibody binding versus the nonspecific antibody binding to the IVTT controls. With the normalized data, a value of 0.0 means that the intensity is no different than that of the IVTT controls, a value of 1.0 indicates a doubling (2-fold) with respect to IVTT control spots, a value of 2.0 indicates 4-fold, 3.0 indicates 8-fold, etc. The normalized signal intensity of the purified protein spots is represented as the base 2 logarithm of the raw signal intensities.

label: Cy3-conjugated anti-human IgG

molecule: protein

organism: Homo sapiens

source_name: human breast milk

label_protocol: Cy3-conjugated anti-human IgG (Jackson ImmunoResearch, Cat. 709-165-098, West Grove, PA)

extract_protocol: Sampling protocol: In PE, SW, USC, and USW, milk was collected using an electric breast pump. In all other cohorts, milk was manually expressed. Except for those collected in ETR, samples were immediately placed on ice, aliquoted within 30 min, and frozen at −20°C. Milk collected in ETR was preserved in a 1:1 ratio with Milk Preservation Solution (Norgen Biotek, Cat. 44800, Thorold, Ontario) and frozen within 6 d. We have shown previously that this method can maintain bacterial DNA integrity in human milk held at 37°C for at least 2 wk (34). All samples were shipped on dry ice to the University of Idaho, where they were immediately frozen at −20°C.

tag: region

value: The Gambia, urban

tag: mother's age

tag: infant's sex

tag: time post-partum

tag: parity

tag: delivery

value: Vaginal

tag: bmi

tag: bmi code

value: OVERWEIGHT

tag: mother's height (cm)

tag: companion animals

value: YES

tag: agricultural animals

tag: adjusted household density

tag: molecule type

value: IgG


title: Subject ID: IN.GBU.429_IgG

value: NORMAL

value: NO


title: WBJPE161031-166

tag: developmental stage


title: Subject ID: IN.GBU.427_IgG


title: WBJPE161031-165

tag: strain


title: WBJPE161031-164

tag: genotype/variation


title: WBJPE161031-163

tag: tissue


title: WBJPE161031-162


title: Subject ID: IN.GBU.425_IgG

tag: region


title: Subject ID: IN.GBU.426_IgG

tag: mother's age


title: WBJPE161031-161


title: WBJPE161031-168


title: Subject ID: IN.GBU.424_IgG

tag: infant's sex


title: Subject ID: IN.GBU.439_IgG

tag: time post-partum


title: Subject ID: IN.GBU.432_IgG

tag: parity


title: Subject ID: IN.GBU.420_IgG

tag: delivery


title: WBJPE161031-160


title: Subject ID: IN.GBU.419_IgG

tag: bmi

value: UNDERWEIGHT


title: Subject ID: IN.GBU.422_IgG

tag: bmi code


title: WBJPE161031-159


title: WBJPE161031-158


title: WBJPE161031-171


title: Subject ID: IN.GBU.417_IgG

tag: mother's height (cm)


title: Subject ID: IN.GBU.418_IgG

tag: companion animals


title: Subject ID: IN.GBU.416_IgG

tag: agricultural animals


title: WBJPE161031-156


title: Subject ID: IN.GBU.415_IgG

tag: adjusted household density


title: WBJPE161031-155


title: Subject ID: IN.GBU.414_IgG

value: OBESE

tag: molecule type


title: Subject ID: IN.GBU.413_IgG


title: WBJPE161031-154

tag: developmental stage


title: WBJPE161031-153

tag: strain


title: WBJPE161031-157

tag: genotype/variation


title: Subject ID: IN.GBU.412_IgG


title: Subject ID: IN.GBU.421_IgG


title: WBJPE161031-150

tag: tissue


title: Subject ID: IN.GBU.411_IgG

tag: region


title: WBJPE161031-149


title: Subject ID: IN.GBU.410_IgG

tag: mother's age


title: WBJPE161031-148


title: WBJPE161031-145


title: Subject ID: IN.GBU.408_IgG

tag: infant's sex


title: WBJPE161031-151


title: WBJPE161031-146


title: WBJPE161031-147


title: Subject ID: IN.GBU.407_IgG

tag: time post-partum


title: Subject ID: IN.GBU.405_IgG

tag: parity


title: Subject ID: IN.GBU.404_IgG

tag: delivery


title: WBJPE161031-144


title: WBJPE161031-143


title: Subject ID: IN.GBU.403_IgG

tag: bmi


title: Subject ID: IN.GBU.402_IgG

tag: bmi code


title: WBJPE161031-152


title: Subject ID: IN.GBU.423_IgG

tag: mother's height (cm)


title: WBJPE161031-141


title: Subject ID: IN.GBU.401_IgG

tag: companion animals


title: Subject ID: IN.GBU.409_IgG

tag: agricultural animals


title: WBJPE161031-139


title: WBJPE161031-140


title: Subject ID: IN.GBR.339_IgG

value: The Gambia, rural

tag: adjusted household density


title: WBJPE161031-138


title: WBJPE161031-137


title: Subject ID: IN.GBU.406_IgG

tag: molecule type


title: Subject ID: IN.GBR.340_IgG


title: WBJPE161031-135

tag: developmental stage


title: Subject ID: IN.GBR.335_IgG


title: Subject ID: IN.GBR.336_IgG


title: WBJPE161031-133

tag: strain


title: WBJPE161031-134

tag: genotype/variation


title: WBJPE161031-132

tag: tissue


title: Subject ID: IN.GBR.332_IgG

tag: region


title: Subject ID: IN.GBR.331_IgG

tag: mother's age


title: Subject ID: IN.GBR.337_IgG

tag: infant's sex


title: WBJPE161031-142


title: WBJPE161031-131


title: Subject ID: IN.GBR.330_IgG

tag: time post-partum


title: WBJPE161031-129


title: WBJPE161031-130


title: Subject ID: IN.GBR.329_IgG

tag: parity


title: Subject ID: IN.GBR.333_IgG

tag: delivery


title: Subject ID: IN.GBR.338_IgG

tag: bmi


title: Subject ID: IN.GBR.328_IgG

tag: bmi code


title: WBJPE161031-136


title: Subject ID: IN.GBR.327_IgG

tag: mother's height (cm)


title: WBJPE161031-128


title: WBJPE161031-127


title: WBJPE161031-125


title: Subject ID: IN.GBR.334_IgG

tag: companion animals


title: Subject ID: IN.GBR.325_IgG

tag: agricultural animals


title: Subject ID: IN.GBR.326_IgG

tag: adjusted household density


title: WBJPE161031-124


title: Subject ID: IN.GBR.324_IgG

tag: molecule type


title: WBJPE161031-123

tag: developmental stage


title: WBJPE161031-122

tag: strain


title: WBJPE161031-121

tag: genotype/variation


title: Subject ID: IN.GBR.323_IgG


title: Subject ID: IN.GBR.321_IgG


title: WBJPE161031-120

source_name: E10.5_hind limb

tag: tissue


title: WBJPE161031-119


title: Subject ID: IN.GBR.320_IgG

tag: region


title: Subject ID: IN.GBR.319_IgG

tag: mother's age


title: WBJPE161031-118


title: Subject ID: IN.GBR.317_IgG

tag: infant's sex


title: Subject ID: IN.GBR.318_IgG

tag: time post-partum


title: WBJPE161031-117


title: WBJPE161031-115


title: WBJPE161031-116


title: WBJPE161031-126


title: Subject ID: IN.GBR.315_IgG

tag: parity


title: Subject ID: IN.GBR.316_IgG

tag: delivery


title: Subject ID: IN.GBR.314_IgG

tag: bmi


title: Subject ID: IN.GBR.313_IgG

tag: bmi code


title: WBJPE161031-114


title: Subject ID: IN.GBR.312_IgG

tag: mother's height (cm)


title: WBJPE161031-112


title: WBJPE161031-113


title: WBJPE161031-111


title: Subject ID: IN.GBR.311_IgG

tag: companion animals


title: Subject ID: IN.GBR.322_IgG

tag: agricultural animals


title: WBJPE161031-109


title: Subject ID: IN.GBR.310_IgG

tag: adjusted household density


title: WBJPE161031-110


title: Subject ID: IN.GBR.308_IgG

tag: molecule type


title: Subject ID: IN.GBR.309_IgG


title: WBJPE161031-108

tag: developmental stage


title: WBJPE161031-106

tag: strain


title: Subject ID: IN.GBR.307_IgG


title: Subject ID: IN.GBR.306_IgG


title: WBJPE161031-105

tag: genotype/variation


title: Subject ID: IN.GBR.305_IgG


title: Subject ID: IN.GBR.304_IgG


title: WBJPE161031-104

tag: tissue


title: WBJPE161031-103


title: Subject ID: IN.GBR.302_IgG

tag: region


title: Subject ID: IN.GBR.303_IgG

tag: mother's age


title: WBJPE161031-102


title: WBJPE161031-100


title: Subject ID: IN.GBR.301_IgG

tag: infant's sex


title: WBJPE161031-99


title: WBJPE161031-101


title: WBJPE161031-97


title: Subject ID: IN.ETU.044_IgG

value: Ethiopia, urban

tag: time post-partum


title: Subject ID: IN.ETU.043_IgG

tag: parity


title: Subject ID: IN.ETU.045_IgG

tag: delivery


title: Subject ID: IN.ETU.042_IgG

tag: bmi


title: WBJPE161031-94


title: Subject ID: IN.ETU.040_IgG

tag: bmi code


title: WBJPE161031-98


title: Subject ID: IN.ETU.037_IgG

tag: mother's height (cm)


title: Subject ID: IN.ETU.041_IgG

tag: companion animals


title: Subject ID: IN.ETU.039_IgG

tag: agricultural animals


title: WBJPE161031-92


title: WBJPE161031-107


title: WBJPE161031-91


title: Subject ID: IN.ETU.038_IgG

tag: adjusted household density


title: WBJPE161031-90


title: Subject ID: IN.ETU.035_IgG

tag: molecule type


title: Subject ID: IN.ETU.036_IgG


title: WBJPE161031-88

tag: developmental stage


title: WBJPE161031-89

tag: strain


title: Subject ID: IN.ETU.033_IgG


title: WBJPE161031-96

tag: genotype/variation


title: WBJPE161031-87

tag: tissue


title: WBJPE161031-86


title: WBJPE161031-95


title: Subject ID: IN.ETU.031_IgG

tag: region


title: WBJPE161031-85


title: Subject ID: IN.ETU.030_IgG

tag: mother's age


title: WBJPE161031-93


title: Subject ID: IN.ETU.025_IgG

tag: infant's sex


title: WBJPE161031-84


title: WBJPE161031-83


title: WBJPE161031-82


title: Subject ID: IN.ETU.024_IgG

tag: time post-partum


title: Subject ID: IN.ETU.034_IgG

tag: parity


title: Subject ID: IN.ETU.023_IgG

tag: delivery


title: WBJPE161031-79


title: Subject ID: IN.ETU.021_IgG

tag: bmi


title: Subject ID: IN.ETU.032_IgG

tag: bmi code


title: WBJPE161031-81


title: Subject ID: IN.ETU.022_IgG

tag: mother's height (cm)


title: WBJPE161031-77


title: Subject ID: IN.ETU.020_IgG

tag: companion animals


title: WBJPE161031-76


title: Subject ID: IN.ETU.019_IgG

tag: agricultural animals


title: Subject ID: IN.ETU.017_IgG

tag: adjusted household density


title: Subject ID: IN.ETU.018_IgG

tag: molecule type


title: WBJPE161031-78

tag: developmental stage


title: WBJPE161031-75

tag: strain


title: Subject ID: IN.ETU.016_IgG


title: Subject ID: IN.ETU.028_IgG


title: WBJPE161031-73

tag: genotype/variation


title: WBJPE161031-74

tag: tissue


title: WBJPE161031-72


title: Subject ID: IN.ETU.013_IgG

tag: region


title: Subject ID: IN.ETU.015_IgG

tag: mother's age


title: Subject ID: IN.ETU.014_IgG

tag: infant's sex


title: WBJPE161031-71


title: Subject ID: IN.ETU.012_IgG

tag: time post-partum


title: WBJPE161031-80


title: Subject ID: IN.ETU.011_IgG

tag: parity


title: WBJPE161031-68


title: WBJPE161031-69


title: Subject ID: IN.ETU.009_IgG

tag: delivery


title: WBJPE161031-67


title: Subject ID: IN.ETU.008_IgG

tag: bmi


title: WBJPE161031-66


title: WBJPE161031-65


title: WBJPE161031-64


title: Subject ID: IN.ETU.007_IgG

tag: bmi code


title: Subject ID: IN.ETU.004_IgG

tag: mother's height (cm)


title: WBJPE161031-61


title: Subject ID: IN.ETU.002_IgG

tag: companion animals


title: WBJPE161031-62


title: Subject ID: IN.ETU.006_IgG

tag: agricultural animals


title: WBJPE161031-63


title: WBJPE161031-59


title: Subject ID: IN.ETU.001_IgG

tag: adjusted household density


title: Subject ID: IN.ETR.142_IgG

value: Ethiopia, rural

tag: molecule type


title: Subject ID: IN.ETR.140_IgG


title: Subject ID: IN.ETR.141_IgG


title: WBJPE161031-57

tag: developmental stage


title: WBJPE161031-58

tag: strain


title: WBJPE161031-56

tag: genotype/variation


title: Subject ID: IN.ETU.010_IgG


title: Subject ID: IN.ETR.137_IgG


title: Subject ID: IN.ETR.139_IgG


title: Subject ID: IN.ETR.138_IgG


title: WBJPE161031-55

tag: tissue


title: Subject ID: IN.ETR.136_IgG

tag: region


title: WBJPE161031-52


title: WBJPE161031-54


title: Subject ID: IN.ETR.135_IgG

tag: mother's age


title: WBJPE161031-60


title: Subject ID: IN.ETR.132_IgG

tag: infant's sex


title: Subject ID: IN.ETR.134_IgG

tag: time post-partum


title: Subject ID: IN.ETR.133_IgG

tag: parity


title: WBJPE161031-51


title: WBJPE161031-50


title: WBJPE161031-47


title: WBJPE161031-49


title: Subject ID: IN.ETR.131_IgG

tag: delivery


title: Subject ID: IN.ETR.129_IgG

tag: bmi


title: WBJPE161031-46


title: WBJPE161031-44


title: Subject ID: IN.ETR.127_IgG

tag: bmi code


title: WBJPE161031-48


title: Subject ID: IN.ETR.125_IgG

tag: mother's height (cm)


title: WBJPE161031-43


title: WBJPE161031-42


title: Subject ID: IN.ETR.123_IgG

tag: companion animals


title: Subject ID: IN.ETR.124_IgG

tag: agricultural animals


title: WBJPE161031-53


title: WBJPE161031-41


title: WBJPE161031-40


title: Subject ID: IN.ETR.121_IgG

tag: adjusted household density


title: WBJPE161031-39


title: Subject ID: IN.ETR.119_IgG

tag: molecule type


title: WBJPE161031-37

tag: developmental stage


title: Subject ID: IN.ETR.118_IgG


title: WBJPE161031-70

tag: strain


title: WBJPE161031-45

tag: genotype/variation


title: Subject ID: IN.ETR.115_IgG


title: Subject ID: IN.ETR.130_IgG


title: Subject ID: IN.ETR.117_IgG


title: WBJPE161031-35

tag: tissue


title: WBJPE161031-33


title: Subject ID: IN.ETR.114_IgG

tag: region


title: Subject ID: IN.ETR.128_IgG

tag: mother's age


title: WBJPE161031-36


title: Subject ID: IN.ETR.112_IgG

tag: infant's sex


title: WBJPE161031-32


title: Subject ID: IN.ETR.111_IgG

tag: time post-partum


title: Subject ID: IN.ETR.113_IgG

tag: parity


title: Subject ID: IN.ETR.122_IgG

tag: delivery


title: WBJPE161031-34


title: Subject ID: IN.ETR.108_IgG

tag: bmi


title: WBJPE161031-31


title: WBJPE161031-30


title: Subject ID: IN.ETR.107_IgG

tag: bmi code


title: WBJPE161031-29


title: WBJPE161031-28


title: WBJPE161031-38


title: Subject ID: IN.ETR.105_IgG

tag: mother's height (cm)


title: Subject ID: IN.ETR.106_IgG

tag: companion animals


title: Subject ID: IN.ETR.104_IgG

tag: agricultural animals


title: WBJPE161031-26


title: Subject ID: IN.ETR.103_IgG

tag: adjusted household density


title: WBJPE161031-25


title: WBJPE161031-24


title: Subject ID: IN.ETR.102_IgG

tag: molecule type


title: Subject ID: IN.USW.1041_IgA

label: biotin-conjugated anti-Human IgA/streptavidin-conjugated SureLight P-3

label_protocol: biotin-conjugated anti-Human IgA (Jackson ImmunoResearch, Cat. 109-065-011, West Grove, PA) / streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Cat. D7-2212, Frederick, MD)

value: U.S. Washington

value: IgA


title: Subject ID: IN.ETR.101_IgG


title: WBJPE161031-23

value: C57BL/6 Transgenic Mouse

tag: developmental stage


title: WBJPE161031-22

tag: strain

value: SCX-GFP mouse


title: WBJPE161031-20

tag: genotype/variation

value: hind limb


title: Subject ID: IN.USW.1038_IgA


title: WBJPE161031-19

tag: tissue


title: Subject ID: IN.USW.1039_IgA

tag: region


title: Subject ID: IN.USW.1037_IgA

tag: mother's age


title: WBJPE161031-17


title: WBJPE161031-16


title: Subject ID: IN.USW.1036_IgA

tag: infant's sex


title: WBJPE161031-15


title: WBJPE161031-27


title: Subject ID: IN.USW.1034_IgA

tag: time post-partum

value: cSection


title: Subject ID: IN.USW.1035_IgA

tag: parity

value: Vaginal


title: WBJPE161031-14


title: WBJPE161031-13


title: Subject ID: IN.USW.1031_IgA

tag: delivery


title: Subject ID: IN.USW.1030_IgA

tag: bmi


title: WBJPE161031-12


title: WBJPE161031-11


title: Subject ID: IN.USW.1040_IgA

tag: bmi code


title: WBJPE161031-21


title: WBJPE161031-10


title: WBJPE161031-18


title: Subject ID: IN.USW.1027_IgA

value: OVERWEIGHT

tag: mother's height (cm)


title: WBJPE161031-9


title: Subject ID: IN.USW.1028_IgA

tag: companion animals


title: Subject ID: IN.USW.1026_IgA

tag: agricultural animals


title: Subject ID: IN.USW.1029_IgA

tag: adjusted household density


title: WBJPE161031-8


title: Subject ID: IN.USW.1022_IgA

value: YES

tag: molecule type


title: WBJPE161031-2

tag: developmental stage


title: WBJPE161031-6

tag: strain


title: Subject ID: IN.USW.1032_IgA


title: WBJPE161031-7

tag: genotype/variation


title: WBJPE161031-5

tag: tissue


title: Subject ID: IN.USW.1033_IgA

tag: region


title: WBJPE161031-4


title: Subject ID: IN.USW.1020_IgA

tag: mother's age


title: Subject ID: IN.USW.1024_IgA

tag: infant's sex


title: Subject ID: IN.USW.1025_IgA

tag: time post-partum


title: Subject ID: IN.USW.1021_IgA

tag: parity


title: Subject ID: IN.USW.1019_IgA

tag: delivery


title: WBJPE161031-1


title: Subject ID: IN.USW.1018_IgA

tag: bmi


title: Subject ID: IN.USW.1017_IgA

tag: bmi code


title: Ssu72 KO hepatocyte Pol II pSer2 ChIP

city: Suwon

first: Hyun-Soo

last: Kim

address: 2066, SEOBU-RO, JANGAN-GU, SUWON-SI, GYEONGGI-DO

department: School of medicine

country: South Korea

institute: SUNGKYUNKWAN UNIVERSITY

library_source: genomic

data_processing:
MACS 1.4.2 used for basecalling.
Raw reads were mapped to UCSC mouse genome browser (GRCm38/mm10 assembly) using ELAND algorithm integrated within Illumina sequencing analysis software.
All duplicate tags with identical sequences and possible sequencing artifacts were filtered out with PICRAD 1.76 pipeline.
Genome ChIP-seq data were generated using MACS 1.4.2 with unique mapped reads. Read counts of all ChIP-Seq peaks were normalized through comparison between library-size-normalized input and ChIP samples.
Genome_build: mm10
Supplementary_files_format_and_content: Each sample was generated by bigwig files

molecule: genomic DNA

source_name: hepatocyte

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-chromatin complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit and sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: hepatocyte

value: Purified hepatocytes of 6weeks mice

tag: virus infection

value: Cre recombinase adenovirus infection

tag: genotype

value: Ssu72 KO

tag: chip antibody

value: phospho CTD Ser2 (Millipore, 3E10, 04-1571)


title: Ssu72 KO hepatocyte Pol II pSer5 ChIP

value: phospho CTD Ser5 (Millipore, 3E8, 04-1572)


title: WBJPE161031-3


title: Subject ID: IN.USW.1016_IgA

value: OBESE

tag: mother's height (cm)

tag: companion animals

tag: agricultural animals

value: NO

tag: adjusted household density

tag: molecule type


title: Subject ID: IN.USW.1015_IgA

tag: region

value: U.S. Washington


title: Input hepatocyte DNA

tag: strain

tag: developmental stage

value: Luciferase adenovirus infection

value: WT

value: none (input)


title: Ssu72 WT hepatocyte Pol II pSer5 ChIP


title: Subject ID: IN.USW.1023_IgA

tag: mother's age

tag: infant's sex

tag: time post-partum

value: IgA


title: Ssu72 KO hepatocyte Pol II ChIP

value: Rpb1 (Santa Cruz Biotechnology, sc-899)


title: Subject ID: IN.USW.1014_IgA

tag: parity

tag: delivery

value: Vaginal

tag: bmi

value: NORMAL


title: Subject ID: IN.USW.1011_IgA

tag: bmi code

value: OVERWEIGHT


title: Subject ID: IN.USW.1012_IgA

value: YES


title: Ssu72 WT hepatocyte Pol II ChIP

tag: cell type

value: hepatocyte

value: Purified hepatocytes of 6weeks mice

tag: virus infection

tag: genotype


title: Sample_480

data_processing:
Single-cell RNA sequence reads were evaluated by AfterQC. Bad reads were detected automatically and removed. Bases at 3' end of the read were further timmed by NGSQCToolkit if their PHRED quality score were less than.
The reads were mapped to the mouse genome(mm10) using bowtie2.
The mapped reads for genes were counted via featureCounts. Gene expression was represented by CPM (tags per million).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: SCX-GFP transgenic hind limb_E15.5

extract_protocol:
Single-cell capture, RNA extraction and cDNA synthesis were performed following the methods described in the Fluidigm protocol(PN 100-9886)
The cDNA reaction products were quantified using the Qubit and were then diluted to a final concentration of 0.2 ng/ μl using C1 Harvest Reagent. The diluted cDNA reaction products were then converted into mRNA-seq libraries using the Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1096, -2001 and -2002) following the manufacturer’s instructions.

treatment_protocol: Single-cell experiments were performed on the embryonic SCX-GFP C57BL/6 Transgenic Mouse  hindlimb at E10.5, E12.5 and E15.5. In general, embryonic experiments were performed on pooled sibling limbs of one litter (three to five limbs per pool). For each time point, embryos were dissected and limbs were isolated. We  finely chopped the tissue with small scissors in a drop of DMEM, and then digested the tissues in type I Collagenase 0.1% / Trypsin 0.05% (Life Technologies) diluted in low-glucose Dulbecco’s modified Eagle’s (L-DMEM) medium (Gibco) solution at 37°C for 10 min. Then, we let tissues to settle down and collected the supernatant in a fresh 50 ml tube, before adding 10-20% of fetal bovine serum to quench trypsin (on ice to stop collagenase). We repeated digestion steps for twice or more till all tissues are digested. The supernatants were then pooled. We filtered the pooled supernatants through 40µ cell filters (Falcon BD), and centrifuge for 10 min at 1600 rpm, before re-suspending the pellet in DMEM containing 2% serum, and kept cell suspension on ice until load on chip.

tag: strain background

tag: genotype/variation

value: SCX-GFP transgenic

tag: tissue

value: hind limb


title: Ssu72 KO hepatocyte Ssu72 ChIP

value: Cre recombinase adenovirus infection

value: Ssu72 KO

tag: chip antibody

value: Ssu72 (Cell Signaling, #12816)


title: Sample_479


title: Subject ID: IN.USW.1008_IgA

tag: region

value: U.S. Washington

value: OBESE

tag: mother's height (cm)

tag: companion animals

tag: agricultural animals

value: NO

tag: adjusted household density

tag: molecule type


title: Subject ID: IN.USW.1010_IgA

tag: mother's age

tag: infant's sex

tag: time post-partum

tag: parity


title: Sample_477

tag: developmental stage


title: Subject ID: IN.USW.1009_IgA

tag: delivery

tag: bmi

tag: bmi code


title: Subject ID: IN.USW.1006_IgA

value: cSection


title: Subject ID: IN.USW.1013_IgA

value: IgA


title: Subject ID: IN.USW.1007_IgA


title: Sample_476

tag: strain background

tag: genotype/variation


title: Subject ID: IN.USW.1005_IgA


title: Subject ID: IN.USW.1004_IgA


title: Sample_473

tag: tissue


title: Sample_474


title: Subject ID: IN.USW.1002_IgA

tag: region


title: Subject ID: IN.USW.1003_IgA

tag: mother's height (cm)


title: Sample_471


title: Subject ID: IN.USW.1001_IgA

tag: companion animals


title: Subject ID: IN.USC.1126_IgA

value: U.S. California

tag: agricultural animals


title: Ssu72 WT hepatocyte Ssu72 ChIP

tag: strain

tag: cell type

tag: virus infection

value: Luciferase adenovirus infection

tag: genotype

tag: chip antibody


title: Subject ID: IN.USC.1125_IgA

tag: mother's age

tag: infant's sex

tag: time post-partum

tag: parity

value: Vaginal

tag: adjusted household density

tag: molecule type


title: Sample_470

tag: strain background

tag: genotype/variation

tag: developmental stage


title: Sample_478

tag: tissue


title: Sample_469


title: Subject ID: IN.USC.1124_IgA

tag: region

tag: delivery

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: companion animals


title: Sample_472


title: Subject ID: IN.USC.1122_IgA

value: NORMAL

tag: agricultural animals


title: Sample_467


title: Sample_466


title: Sample_464


title: Subject ID: IN.USC.1120_IgA

tag: mother's age

value: YES


title: Subject ID: IN.USC.1121_IgA

tag: infant's sex


title: Sample_475


title: Sample_465


title: Subject ID: IN.USC.1119_IgA

tag: time post-partum

value: OVERWEIGHT


title: Sample_463


title: Subject ID: IN.USC.1118_IgA

tag: parity


title: Subject ID: IN.USC.1116_IgA

tag: adjusted household density


title: Sample_462


title: Subject ID: IN.USC.1115_IgA

tag: molecule type


title: Sample_461

tag: strain background


title: Subject ID: IN.USC.1108_IgA


title: Sample_460

tag: genotype/variation


title: Sample_458

tag: developmental stage


title: Sample_457

tag: tissue


title: Sample_456


title: Sample_459


title: Subject ID: IN.USC.1101_IgA

tag: region


title: Sample_468


title: Subject ID: IN.USC.1102_IgA

tag: delivery


title: Subject ID: IN.USC.1109_IgA

tag: bmi


title: Subject ID: IN.SW.925_IgA

value: Sweden

tag: bmi code


title: Subject ID: IN.SW.924_IgA

tag: mother's height (cm)


title: Sample_455

value: SCX-GFP transgenic


title: Sample_454

value: hind limb


title: Sample_452


title: Sample_453


title: Subject ID: IN.SW.918_IgA

tag: companion animals


title: Sample_450


title: Subject ID: IN.SW.923_IgA

tag: agricultural animals


title: Sample_451


title: Subject ID: IN.SW.920_IgA

tag: mother's age


title: Subject ID: IN.SW.922_IgA

tag: infant's sex


title: Sample_448


title: Sample_449


title: Subject ID: IN.USC.1123_IgA

tag: time post-partum


title: Subject ID: IN.SW.916_IgA

tag: parity


title: Subject ID: IN.SW.917_IgA

tag: adjusted household density


title: Sample_447


title: Subject ID: IN.SW.915_IgA

tag: molecule type


title: Subject ID: IN.SW.913_IgA


title: Sample_446

tag: strain background


title: Sample_444

tag: genotype/variation


title: Subject ID: IN.SW.912_IgA


title: Sample_442

tag: developmental stage


title: Subject ID: IN.SW.911_IgA


title: Subject ID: IN.SW.910_IgA


title: Subject ID: IN.SW.908_IgA


title: Subject ID: IN.SW.921_IgA


title: Subject ID: IN.SW.907_IgA


title: Subject ID: IN.SW.909_IgA


title: Sample_440

tag: tissue


title: Sample_439


title: Sample_437


title: Subject ID: IN.SW.906_IgA

tag: region


title: Sample_436


title: Sample_438


title: Subject ID: IN.SW.905_IgA

tag: delivery


title: Subject ID: IN.SW.904_IgA

tag: bmi


title: Sample_435


title: Sample_443


title: Subject ID: IN.SW.902_IgA

tag: bmi code


title: Subject ID: IN.SP.843_IgA

value: Spain

tag: mother's height (cm)


title: Sample_433


title: Subject ID: IN.SW.901_IgA

tag: companion animals


title: Subject ID: IN.SP.842_IgA

tag: agricultural animals


title: Subject ID: IN.SP.841_IgA

tag: mother's age


title: Sample_432


title: Subject ID: IN.SP.840_IgA

tag: infant's sex


title: Sample_445


title: Sample_430


title: Sample_429


title: Subject ID: IN.SP.839_IgA

tag: time post-partum


title: Subject ID: IN.SP.838_IgA

tag: parity


title: Subject ID: IN.SP.837_IgA

tag: adjusted household density


title: Sample_428


title: Sample_441


title: Sample_425


title: Subject ID: IN.SP.836_IgA

tag: molecule type


title: Sample_424

tag: strain background


title: Subject ID: IN.SP.834_IgA


title: Sample_423

tag: genotype/variation


title: Sample_431

tag: developmental stage


title: Subject ID: IN.SP.833_IgA


title: Sample_434

tag: tissue


title: Sample_421


title: Subject ID: IN.SP.831_IgA

tag: region


title: Subject ID: IN.SP.829_IgA

tag: delivery


title: Sample_419


title: Sample_420


title: Subject ID: IN.SP.830_IgA

tag: bmi


title: Sample_426


title: Sample_418


title: Subject ID: IN.SP.828_IgA

tag: bmi code


title: Sample_417


title: Sample_416


title: Subject ID: IN.SP.827_IgA

tag: mother's height (cm)


title: Sample_422


title: Subject ID: IN.SP.835_IgA

tag: companion animals


title: Sample_415


title: Subject ID: IN.SP.826_IgA

tag: agricultural animals


title: Sample_427


title: Sample_414


title: Subject ID: IN.SP.832_IgA

tag: mother's age


title: Subject ID: IN.SP.823_IgA

tag: infant's sex


title: Subject ID: IN.SP.822_IgA

tag: time post-partum


title: Sample_412


title: Subject ID: IN.SP.824_IgA

tag: parity


title: Subject ID: IN.SP.821_IgA

tag: adjusted household density


title: Subject ID: IN.SP.820_IgA

tag: molecule type


title: Sample_413

tag: strain background


title: Sample_410

tag: genotype/variation


title: Subject ID: IN.SP.819_IgA


title: Sample_409

tag: developmental stage


title: Sample_407

tag: tissue


title: Sample_408


title: Subject ID: IN.SP.825_IgA

tag: region


title: Sample_406


title: Sample_405


title: Subject ID: IN.SP.817_IgA

tag: delivery


title: Subject ID: IN.SP.815_IgA

tag: bmi


title: Subject ID: IN.SP.812_IgA

tag: bmi code


title: Subject ID: IN.SP.813_IgA

tag: mother's height (cm)


title: Sample_404


title: Subject ID: IN.SW.903_IgA

tag: companion animals


title: Sample_402


title: Sample_403


title: Subject ID: IN.SP.810_IgA

tag: agricultural animals


title: Sample_411


title: Sample_401


title: Subject ID: IN.SP.809_IgA

tag: mother's age


title: Sample_400


title: Subject ID: IN.SP.807_IgA

tag: infant's sex


title: Sample_399


title: Sample_398


title: Subject ID: IN.SP.808_IgA

tag: time post-partum


title: Subject ID: IN.SP.805_IgA

tag: parity


title: Sample_396


title: Sample_397


title: Sample_395


title: Subject ID: IN.SP.804_IgA

tag: adjusted household density


title: Subject ID: IN.SP.803_IgA

tag: molecule type


title: Subject ID: IN.SP.811_IgA


title: Subject ID: IN.SP.801_IgA


title: Sample_394

tag: strain background


title: Sample_392

tag: genotype/variation


title: Sample_391

tag: developmental stage


title: Sample_393

tag: tissue


title: Sample_390


title: Subject ID: IN.PE.741_IgA

tag: region

value: Peru


title: Subject ID: IN.PE.742_IgA

tag: delivery


title: Subject ID: IN.PE.743_IgA

tag: bmi


title: Sample_389


title: Subject ID: IN.PE.739_IgA

tag: bmi code


title: Sample_388


title: Subject ID: IN.PE.738_IgA

tag: mother's height (cm)


title: Sample_386


title: Sample_387


title: Subject ID: IN.PE.737_IgA

tag: companion animals


title: Subject ID: IN.PE.735_IgA

tag: agricultural animals


title: Subject ID: IN.PE.736_IgA

tag: mother's age


title: Subject ID: IN.SP.818_IgA

tag: infant's sex


title: Sample_384


title: Sample_385


title: Subject ID: IN.PE.734_IgA

tag: time post-partum


title: Subject ID: IN.SP.802_IgA

tag: parity


title: Sample_383


title: Subject ID: IN.PE.733_IgA

tag: adjusted household density


title: Sample_382


title: Subject ID: IN.PE.732_IgA

tag: molecule type


title: Sample_380

tag: strain background


title: Subject ID: IN.PE.740_IgA


title: Sample_377

tag: genotype/variation


title: Subject ID: IN.PE.730_IgA


title: Sample_378

tag: developmental stage


title: Subject ID: IN.PE.727_IgA


title: Subject ID: IN.PE.729_IgA


title: Subject ID: IN.PE.731_IgA


title: Sample_379

tag: tissue


title: Subject ID: IN.PE.728_IgA

tag: region


title: Sample_375


title: Subject ID: IN.PE.726_IgA

tag: delivery


title: Sample_376


title: Sample_373


title: Subject ID: IN.PE.723_IgA

tag: bmi


title: Subject ID: IN.PE.725_IgA

tag: bmi code


title: Sample_370


title: Sample_369


title: Subject ID: IN.PE.722_IgA

tag: mother's height (cm)


title: Sample_381


title: Subject ID: IN.PE.720_IgA

tag: companion animals


title: Subject ID: IN.PE.719_IgA

tag: agricultural animals


title: Subject ID: IN.PE.718_IgA

tag: mother's age


title: Sample_368


title: Sample_371


title: Ssu72 WT hepatocyte Pol II pSer2 ChIP

tag: strain

tag: cell type

value: hepatocyte

value: Purified hepatocytes of 6weeks mice

tag: virus infection

tag: genotype

value: WT

tag: chip antibody

value: phospho CTD Ser2 (Millipore, 3E10, 04-1571)


title: Subject ID: IN.PE.716_IgA

tag: infant's sex

tag: time post-partum

tag: parity

value: NO

tag: adjusted household density

tag: molecule type


title: Subject ID: IN.PE.715_IgA

tag: region

tag: delivery

value: cSection

value: IgA


title: Sample_366

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Subject ID: IN.PE.724_IgA

tag: mother's age

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: companion animals

tag: agricultural animals


title: Sample_364


title: Sample_367


title: Subject ID: IN.PE.713_IgA

tag: infant's sex


title: Sample_365


title: Subject ID: IN.PE.717_IgA

tag: time post-partum


title: Subject ID: IN.PE.714_IgA

tag: parity

value: OBESE


title: Sample_362


title: Subject ID: IN.PE.711_IgA

tag: adjusted household density


title: Subject ID: IN.PE.721_IgA

value: Vaginal

tag: molecule type


title: Sample_359


title: Subject ID: IN.PE.710_IgA

tag: region

value: NORMAL


title: Sample_358


title: Sample_361


title: Sample_374


title: Sample_372


title: Subject ID: IN.PE.709_IgA

tag: delivery

value: YES


title: Sample_356

tag: strain background


title: Subject ID: IN.PE.707_IgA


title: Sample_363

tag: genotype/variation


title: Subject ID: IN.PE.708_IgA


title: Sample_355

tag: developmental stage


title: Sample_353

tag: tissue


title: Sample_352


title: Subject ID: IN.PE.705_IgA

tag: mother's age


title: Subject ID: IN.PE.706_IgA

tag: bmi


title: Subject ID: IN.PE.712_IgA

tag: bmi code


title: Subject ID: IN.PE.704_IgA

tag: mother's height (cm)


title: Subject ID: IN.PE.703_IgA

tag: companion animals


title: Subject ID: IN.PE.702_IgA

tag: agricultural animals


title: Sample_351


title: Subject ID: IN.PE.701_IgA

tag: infant's sex

value: OVERWEIGHT


title: Sample_360


title: Sample_350


title: Subject ID: IN.KE.643_IgA

value: Kenya

tag: time post-partum


title: Sample_349

value: SCX-GFP transgenic


title: Sample_345

value: hind limb


title: Subject ID: IN.KE.641_IgA

tag: parity


title: Sample_354


title: Subject ID: IN.KE.639_IgA

tag: adjusted household density


title: Subject ID: IN.SP.806_IgA

value: Spain

tag: molecule type


title: Subject ID: IN.KE.638_IgA

tag: region


title: Sample_344


title: Sample_343


title: Subject ID: IN.KE.637_IgA

tag: delivery


title: Subject ID: IN.KE.636_IgA


title: Sample_341

tag: strain background


title: Sample_347

tag: genotype/variation


title: Sample_342

tag: developmental stage


title: Subject ID: IN.KE.635_IgA


title: Subject ID: IN.KE.633_IgA


title: Sample_340

tag: tissue


title: Sample_339


title: Sample_338


title: Sample_337


title: Subject ID: IN.KE.634_IgA

tag: mother's age


title: Subject ID: IN.KE.644_IgA

tag: bmi


title: Subject ID: IN.KE.632_IgA

tag: bmi code


title: Sample_348


title: Sample_336


title: Subject ID: IN.KE.642_IgA

tag: mother's height (cm)


title: Subject ID: IN.KE.630_IgA

tag: companion animals


title: Subject ID: IN.KE.629_IgA

tag: agricultural animals


title: Subject ID: IN.KE.631_IgA

tag: infant's sex


title: Sample_346


title: Sample_335


title: Sample_334


title: Sample_333


title: Subject ID: IN.KE.626_IgA

tag: time post-partum


title: Subject ID: IN.KE.627_IgA

tag: parity


title: Sample_332


title: Sample_331


title: Sample_330


title: Subject ID: IN.KE.624_IgA

value: UNDERWEIGHT

tag: adjusted household density


title: Subject ID: IN.KE.625_IgA

tag: molecule type


title: Sample_329


title: Subject ID: IN.KE.622_IgA

tag: region


title: Subject ID: IN.KE.620_IgA

tag: delivery


title: Sample_327

tag: strain background


title: Sample_325

tag: genotype/variation


title: Sample_326

tag: developmental stage


title: Subject ID: IN.KE.621_IgA


title: Sample_324

tag: tissue


title: Subject ID: IN.KE.619_IgA

tag: mother's age


title: Sample_323


title: Subject ID: IN.KE.617_IgA

tag: bmi


title: Subject ID: IN.KE.628_IgA

tag: bmi code


title: Subject ID: IN.KE.616_IgA

tag: mother's height (cm)


title: Subject ID: IN.KE.613_IgA

tag: companion animals


title: Subject ID: IN.KE.615_IgA

tag: agricultural animals


title: Subject ID: IN.KE.614_IgA

tag: infant's sex


title: Sample_320


title: Sample_322


title: Sample_321


title: Subject ID: IN.KE.612_IgA

tag: time post-partum


title: Sample_319


title: Sample_318


title: Sample_328


title: Subject ID: IN.KE.623_IgA

tag: parity


title: Sample_317


title: Sample_316


title: RNA_Sis_transgene_suc_rep1

city: Kyoto

first: Naomichi

last: Takemata

address: Kyoto University, Katsura, Nishikyo-ku

department: Synthetic Chemistry and Biological Chemistry

country: Japan

institute: Kyoto University

data_processing:
3C-seq reads were mapped to the genome of S. acidocaldarius DSM639 (GenBank ID: CP000077.1) or S. islandicus REY15A (GenBank ID: CP002425.1) using HiC-Pro version 2.9.0 (Servant et al., 2015) with default parameters. The genomic coordinates of each Sulfolobus species were re-defined so that they started from the first base of the AluI site in the original definition. Valid read were used to generate raw contact matrices. The intra-bin ligations were discarded by setting the values on the corresponding diagonal to zero. The raw contact matrices were iteratively corrected with MAX_ITER = 500 (and FILTER_LOW_COUNT_PERC = 0.01 for S. islandicus) to generate normalized contact matrices.
To calculate Transcripts Per Million (TPM), RNA-seq reads from each biological replicate were mapped in a strand-specific manner using Salmon version 0.8.2 (Patro et al., 2017). When gene expression was quantified at the operon level, reads were mapped to operons predicted by Operon-mapper (Taboada et al., 2018).
Genome_build: CP000077.1, CP002425.1
Supplementary_files_format_and_content: 3C-seq: tab-delimited tables. The first and second columns show genomic bins. The third column shows interaction scores (raw number of reads or normalized value) between bins in the first and second columns. RNA-seq: tab-delimited tables showing Transcripts Per Million (TPM) values for each genes.

organism: Saccharolobus islandicus

source_name: Microorganism

extract_protocol: To prepare the material for RNA-seq library construction, RNA was extracted as described previously (Takemata et al., 2019). After treatment with DNase, the RNA was ethanol-precipitated and dissolved in DEPC-treated water. Libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

tag: genotype

value: DpyrEF DlacS DargD SiRe_0163::ParaS-lacS-argD

value: Log-phase cells supplied with sucrose and grown shaking

tag: strain


title: RNA_Sis_transgene_suc_rep2


title: RNA_Sis_transgene_ara_rep1

value: Log-phase cells supplied with arabinose and grown shaking


title: Sample_315


title: Subject ID: IN.KE.610_IgA

tag: region

tag: adjusted household density

tag: molecule type


title: Sample_314

tag: strain background

tag: genotype/variation


title: Sample_313

tag: developmental stage

tag: tissue


title: RNA_Sis_ara_rep2

value: DpyrEF DlacS


title: Sample_312


title: Subject ID: IN.KE.608_IgA

tag: mother's age

tag: delivery

tag: bmi

value: NO


title: RNA_Sis_transgene_ara_rep2


title: Sample_311


title: Sample_357


title: Sample_310


title: Sample_309


title: RNA_Sis_ara_rep1


title: Sample_307


title: Sample_308


title: RNA_Sis_slaAB_rep2

value: DpyrEF DlacS DargD DslaAB::argD

value: Log-phase cells supplied with sucrose and grown without shaking


title: Sample_305


title: Subject ID: IN.KE.607_IgA

tag: bmi code

tag: mother's height (cm)

tag: companion animals

value: IgA


title: Sample_306


title: Subject ID: IN.KE.605_IgA

tag: infant's sex

tag: time post-partum

value: Vaginal

tag: agricultural animals


title: Subject ID: IN.KE.611_IgA

tag: parity

value: NORMAL


title: Subject ID: IN.KE.606_IgA

tag: region


title: RNA_Sis_slaAB_rep1

tag: genotype

tag: strain


title: Sample_304

tag: strain background


title: Subject ID: IN.KE.604_IgA

tag: adjusted household density

tag: molecule type


title: Sample_301

tag: genotype/variation

tag: developmental stage

tag: tissue


title: RNA_Sis_slaAB_ctrl_rep1


title: Sample_303


title: Sample_300


title: Subject ID: IN.KE.603_IgA

tag: mother's age

tag: delivery

value: cSection

tag: bmi


title: Sample_302


title: Subject ID: IN.KE.602_IgA

tag: bmi code

tag: mother's height (cm)

tag: companion animals


title: Subject ID: IN.KE.609_IgA

tag: infant's sex

tag: time post-partum

value: OBESE

tag: agricultural animals


title: RNA_Sis_suc

tag: genotype


title: 3C_Sis_transgene_ara_rep2

extract_protocol: To prepare the material for 3C-seq library construction, cells were crosslinked, permeabilized, and treated with AluI. The DNA was then subjected to proximity ligation, crosslink reversal, and phenol extraction followed by isopropanol precipitation. Libraries were constructed using NEBNext Ultra DNA Library Prep Kit for Illumina.

tag: strain


title: Subject ID: IN.KE.601_IgA

tag: region

value: Kenya

tag: parity


title: Sample_299

tag: strain background

value: SCX-GFP transgenic


title: Sample_298

tag: genotype/variation

value: hind limb


title: Sample_296

tag: developmental stage


title: RNA_Sis_slaAB_ctrl_rep2


title: Sample_295

tag: tissue


title: 3C_Sis_transgene_ara_rep1


title: 3C_Sis_transgene_suc_rep2


title: Sample_293


title: Sample_292


title: Subject ID: IN.GN.544_IgA

value: Ghana

tag: mother's age

value: OVERWEIGHT

tag: adjusted household density

tag: molecule type


title: 3C_Sis_transgene_suc_rep1

value: DpyrEF DlacS DargD SiRe_0163::ParaS-lacS-argD


title: Sample_294


title: Subject ID: IN.GN.542_IgA

tag: delivery

tag: bmi

tag: bmi code


title: Subject ID: IN.GN.541_IgA

tag: infant's sex

tag: mother's height (cm)

tag: companion animals


title: Sample_290


title: 3C_Sis_ara_rep2

tag: genotype


title: Sample_288


title: Subject ID: IN.GN.540_IgA

tag: time post-partum

tag: agricultural animals


title: 3C_Sis_ara_rep1

tag: strain


title: Sample_287

tag: strain background


title: Sample_289

tag: genotype/variation


title: Sample_297

tag: developmental stage


title: Sample_286

tag: tissue


title: Subject ID: IN.GN.539_IgA

tag: region

tag: mother's age

tag: parity

value: YES


title: Sample_285


title: Subject ID: IN.GN.538_IgA

tag: delivery

tag: adjusted household density

tag: molecule type


title: Sample_284


title: Sample_283


title: 3C_Sis_slaAB_rep1


title: 3C_Sis_slaAB_rep2


title: Subject ID: IN.GN.536_IgA

tag: infant's sex

tag: bmi

tag: bmi code


title: 3C_Sis_slaAB_ctrl_rep2

tag: genotype


title: Sample_280

source_name: SCX-GFP transgenic hind limb_E12.5


title: Sample_291


title: Subject ID: IN.GN.537_IgA

tag: time post-partum

tag: mother's height (cm)

tag: companion animals


title: Sample_281

tag: strain background


title: Sample_282

tag: genotype/variation


title: 3C_Sis_suc_rep2

tag: developmental stage

value: Log-phase cells supplied with sucrose and grown shaking

tag: strain


title: Subject ID: IN.GN.534_IgA

tag: region

tag: agricultural animals


title: Subject ID: IN.GN.535_IgA

tag: mother's age

tag: parity


title: Sample_278

tag: tissue


title: Sample_279


title: Sample_277


title: 3C_Sis_slaAB_ctrl_rep1

value: DpyrEF DlacS


title: Sample_276


title: Subject ID: IN.GN.533_IgA

tag: delivery

value: NO

tag: adjusted household density

tag: molecule type


title: Sample_275


title: Sample_273


title: Subject ID: IN.GN.532_IgA

tag: infant's sex

tag: bmi

tag: bmi code


title: Sample_272


title: RiboSeq dMazEFpF rep2

city: Manchester

first: Fedor

last: Bezrukov

address: Brunswick Street, Schuster laboratory

department: Department of Physics and Astronomy

country: United Kingdom

institute: The University of Manchester

description: Library: Ribosome protected fragments

data_processing:
Library strategy: Ribo-seq
Results of Ribo-Seq were aligned to RefSeq assembly GCF_000013425.1 combined with pRAB11 sequence (accession JN635500.1) using STAR aligner , with the adaptor sequence removed using ‘--clip3pAdapterSeq CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC’ option
P-site location of a ribosome protected fagment (RPF) was defined as the 3’ end of the read minus 15. Only RPF with the length 25-31 were used. Wig files give the number of selected RPF with P-site in the given position.
The raw counts for translational signal were defined by the number of RPF with the P-site within gene CDS, excluding first 30 and last 6 nucleotides, to remove the effects of translational initiation and termination. CPM were obtained after normalization by the total number of reads aligned to genome, exluding plasmid and ribosomal RNA reads (ingenome-rRNA columns of riboseq_libsizes.csv)
Genome_build: GCF_000013425.1
Supplementary_files_format_and_content: RNA-seq bigWig files contain coverage of the plus and minus strand of the mRNA with RNA-Seq data, with assumption of the average fragment length equal to 200nt. Ribo-Seq bigWig files contain the numbers of ribosome protected fragments with the position of the P-site (position of the 3’end of the fragment -15 nucleotides) n the given position of genome. _rawcounts.csv files contains the raw counts of RNA or RPF for each gene for all samples. _cpm.csv files contain Counts Per Milion values for RNA and RPF for each sample. _libsizes.csv give number of reads aligned to genome, plasmid, and ribosomal RNA that are used for normalization of CPM.

organism: Staphylococcus aureus

source_name: Bacterial liquid culture

growth_protocol: Cultures were grown on Mueller Hinton Broth (MHB) media in the presence of 15 μg/ml of chloramphenicol (Cm) till OD600 of 0.5-0.7 at 37°C with shaking. To induce mazF expression in pRAB11-MazF samples, anhydrotetracycline (ATc) was added till final concentration 0.2 µM and cultures were incubated 10min at 37°C with shaking.

extract_protocol:
To obtain polysomes from S. aureus 1 ml of night culture was diluted in 250 ml of MHB media and grown till an OD600 of 0.5 at 37°C. ATc induction was done for 10 min. To block translation Cm was added till final concentration 100 μg/ml and culture was incubated for 2 min at 37°C and then quickly chilled with ice cubes. After centrifugation pellets were washed in 2 ml of cold Resuspension Buffer (RB) (20 mM Tris (pH 8.0), 10 mM MgCl2, 5 mM CaCl2, 100 mM NH4Cl, 1 mM Cm). After centrifugation pellets were resuspended in 0.8 ml of cold Lysis Buffer (RB plus 0.1% IGEPAL, 0.4% Triton X-100, 100 U/ml RNase-free DNase I (Roche), 0.5 U/μl SUPERaseIn (Ambion), Protease Inhibitors (Roche)). Suspension was incubated on ice for 5 min and frozen in drops in liquid nitrogen. Drops were milled 5 times with 1-min cycles at 30 Hz in CryoMill MM400 (Retsch) in 10 ml grinding jar with 15 mm grinding ball. For cell extract preparation cell powder was thawed in 50 ml tube and centrifugated at 4000 g, 4°C for 1 min. Supernatant (SN) was clarified at 16000 g, 4°C for 1 min and centrifugated in a new tube at 16000g, 4°C for 10 min.  To obtain ribosome footprints 1000 U of S7 Micrococcal Nuclease S7 (Roche) was added per 1 mg of nucleic acids. Samples were incubated for 1 h at 25°C with rotation at 190 rpm. Reaction was quenched by the addition of EGTA to a final concentration 6 mM. 0.5 mg of nucleic acids were loaded to the linear sucrose gradients 10-50% prepared on the Gradient Buffer (20 mM Tris (pH 8.0), 10 mM MgCl2, 100 mM NH4Cl. Tubes were centrifuged at 217000 g (35000 rpm, SW41 Ti rotor (Beckman Coulter)) for 3 h at 4°C. Fractions were collected using a UA/6 detector (ISCO). After centrifugation 750 μl of fractions were collected and incubated with 10 μl of proteinase K (NEB, 800 U/ml) and 10 μl of SDS 10% over night at 4°C. RNAs were isolated with phenol-chloroform
libraries were prepared as described (Ingolia et al., 2009; McGlincy and Ingolia, 2017)

value: HG003 delta-mazEF

tag: plasmid


title: Subject ID: IN.GN.531_IgA

tag: time post-partum

tag: mother's height (cm)

tag: companion animals


title: RiboSeq dMazEFpF rep1

description: Library: Ribosome protected fragments


title: Sample_271

tag: strain background

tag: genotype/variation

tag: developmental stage


title: Sample_270


title: Sample_269


title: Sample_267


title: Subject ID: IN.GN.530_IgA

tag: region

tag: agricultural animals


title: Sample_268


title: RiboSeq dMazEF rep1

description: Library: Ribosome protected fragments

tag: strain


title: Sample_266

tag: tissue


title: Subject ID: IN.GN.529_IgA

tag: mother's age

tag: parity

tag: delivery


title: Subject ID: IN.GN.528_IgA

tag: infant's sex

tag: adjusted household density

tag: molecule type


title: Sample_265


title: Sample_263


title: RiboSeq WT rep2

description: Library: Ribosome protected fragments

tag: plasmid


title: Sample_264


title: Subject ID: IN.GN.527_IgA

tag: time post-partum

tag: bmi

tag: bmi code


title: Sample_274

tag: strain background


title: RiboSeq WT rep1

description: Library: Ribosome protected fragments


title: Subject ID: IN.GN.525_IgA

tag: mother's height (cm)

tag: companion animals


title: Sample_260

tag: genotype/variation

tag: developmental stage


title: Subject ID: IN.GN.523_IgA

tag: region

tag: agricultural animals


title: 3C_Sis_suc_rep1

tag: genotype

tag: strain


title: RiboSeq dMazEF rep2

description: Library: Ribosome protected fragments


title: Sample_258

tag: tissue


title: Subject ID: IN.GN.522_IgA

tag: mother's age

tag: infant's sex

tag: parity

tag: delivery


title: NOD_mouse_IEC_TM3

type: RNA

city: Piscataway

first: Xue-Song

last: Zhang

state: NJ

address: 679 Hoes Lane West, Room 113

department: CABM

institute: Rutgers University

description: cecal material transfer

hyb_protocol: Hydridized according to the manufacturer's protocol. the hybridization mixture is allowed to bind to the magnetic beads by the Capture Probe. Wash steps are performed and excess Reporter Probes and non-target cellular transcripts are removed during wash steps. After washing, the Capture Probes and Target/Probe complexes are eluted off of the beads and are hybridized to magnetic beads complementary to the Reporter Probe. Wash steps are performed and excess Capture Probes are washed away. Finally, the purified Target/Probe complexes are eluted off and are immobilized in the cartridge for data collection. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

scan_protocol: Scanned according to the manufacturer's protocol. Data Collection is carried out in the nCounterÎ Digital Analyzer. At the highest standard data resolution, 555_1155 fields of view (FOV) are collected per flow cell using a microscope objective and a CCD camera yielding data of hundreds of thousands of target molecule counts. Digital images are processed on the nCounter Digital Analyzer and the barcode counts are tabulated in a comma separated value (CSV) format. (http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf)

data_processing: Probe set summarization was performed by Counts were first filtered away no detected genes based on internal negative controls, and normalized according to manufacturer’s instructions, and Spearman’s rank correlation Principal component analysis were performed based on 414 expression-detected genes using statistical software XLSTAT data analytics package (Addinsoft, New York, NY), and heatmap was generated based on the normalized counts of 65 significantly differentiated immune genes between each other groups (p<0.05) using statistical software Heatmapper.

label: Nanostring

source_name: T1D project

label_protocol: Labeled according to the manufacturer's protocol. The probe pair consists of a Reporter Probe, which carries the signal on its 5' end, and a Capture Probe which carries a biotin on the 3' end. The color codes carry six positions and each position can be one of four colors, thus allowing for a large diversity of tags that can be mixed together in a single well for direct hybridization to target and yet still be individually resolved and identified during data collection. http://www.nanostring.com/media/pdf/MAN_nCounter_Gene_Expression_Assay.pdf

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers protocols

value: NOD

tag: gender

value: male

tag: age

tag: cell type

value: ileal epithelial cells

tag: batch


title: NOD_mouse_IEC_TM2

description: cecal material transfer


title: Sample_256

tag: strain background


title: NOD_mouse_IEC_TM1

description: cecal material transfer


title: Subject ID: IN.GN.521_IgA

tag: time post-partum

value: Vaginal

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: companion animals

tag: adjusted household density

tag: molecule type

value: IgA


title: Sample_255

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Sample_262


title: Subject ID: IN.GN.520_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

tag: agricultural animals


title: NOD_mouse_IEC_TP3

description: 1PAT antibiotics

tag: strain

tag: gender

tag: age

tag: cell type

tag: batch


title: Sample_261

tag: strain background


title: Subject ID: IN.GN.519_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

value: NORMAL

tag: mother's height (cm)

tag: companion animals


title: Sample_254

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Sample_253


title: Sample_259


title: Sample_249


title: NOD_mouse_IEC_TP2

description: 1PAT antibiotics


title: Sample_250


title: Sample_251


title: Subject ID: IN.GN.518_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

tag: adjusted household density

tag: molecule type


title: Sample_257


title: NOD_mouse_IEC_TP1

description: 1PAT antibiotics

tag: strain

tag: gender

tag: age

tag: cell type

tag: batch


title: Sample_247

tag: strain background


title: NOD_mouse_IEC_CP3

description: control


title: Sample_248


title: Subject ID: IN.GN.517_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

value: OBESE

tag: mother's height (cm)

tag: agricultural animals


title: Sample_246

tag: genotype/variation

value: SCX-GFP transgenic

tag: developmental stage

tag: tissue


title: Subject ID: IN.GN.516_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

tag: companion animals

tag: adjusted household density


title: Sample_245

value: hind limb


title: Sample_244


title: RNA dMazEFpF rep2

data_processing:
Results of RNA-Seq were aligned to RefSeq assembly GCF_000013425.1 combined with pRAB11 sequence (accession JN635500.1) using STAR aligner
To construct coverage Wig files, aligned single end RNA-Seq read fragments were extended upstream to 200 nt length (note, that the strand of the aligned sequances should be inverted first). Then genome coverage was calculated from extended read fragments.
The raw read counts were associated with the RefSeq gene annotations (the tmRNA region was added to the annotations manually using the location from AureoWiki). CPM were obtained after obtained normalization by the total number of aligned reads, exluding ribosomal RNA reads (ingenome+plasmid-rRNA columns of rnaseq_libsizes.csv)
Genome_build: GCF_000013425.1
Supplementary_files_format_and_content: RNA-seq bigWig files contain coverage of the plus and minus strand of the mRNA with RNA-Seq data, with assumption of the average fragment length equal to 200nt. Ribo-Seq bigWig files contain the numbers of ribosome protected fragments with the position of the P-site (position of the 3’end of the fragment -15 nucleotides) n the given position of genome. _rawcounts.csv files contains the raw counts of RNA or RPF for each gene for all samples. _cpm.csv files contain Counts Per Milion values for RNA and RPF for each sample. _libsizes.csv give number of reads aligned to genome, plasmid, and ribosomal RNA that are used for normalization of CPM.

extract_protocol:
Cultures with either the empty vector or the vector containing MazF were grown till OD600 of 0.5 at 37°C with shaking. ATc induction was done for 10 min. For total RNA isolation 8 ml of culture were immediately mixed with 40 ml of -80°C cold ethanol-acetone mixture (1:1). Cells were collected by centrifugation for 10 min at 4000 g, 4°C. Pellets were washed with 1 ml of cold TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0), resuspended in 100 µl of TE with 1 mg/ml of lysostaphin and 2 µl of RNasinePlus (Promega, N2611), and incubated for 5 min at 37°C. Total RNAs were purified with the ReliaPrep RNA kit (Promega, Z6011) in biological duplicates.
Ribosomal RNAs were depleted with RiboZero rRNA Removal Kit for Bacteria (Illumina). Libraries were created using the Illumina TruSeq stranded mRNA kit. 1st strand cDNAs were synthesized with random hexamer primer.

tag: strain

tag: plasmid


title: Sample_243

tag: strain background


title: Subject ID: IN.GN.515_IgA

value: Ghana

tag: time post-partum

tag: delivery

tag: molecule type


title: Sample_242


title: Sample_241


title: Subject ID: IN.GN.514_IgA

tag: bmi

tag: bmi code

tag: mother's height (cm)


title: NOD_mouse_IEC_CP2

description: control

tag: gender

tag: age

tag: cell type

tag: batch


title: Sample_240

tag: genotype/variation

tag: developmental stage

tag: tissue


title: NOD_mouse_IEC_CP1

description: control


title: Sample_239


title: Subject ID: IN.GN.513_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

value: cSection

tag: companion animals

tag: agricultural animals

tag: adjusted household density


title: RNA dMazEF rep2

tag: strain

tag: plasmid


title: Sample_238

tag: strain background


title: Sample_237


title: RNA dMazEF rep1


title: Sample_236


title: Sample_235


title: Subject ID: IN.GN.512_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: molecule type


title: RNA WT rep1


title: Sample_233

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Sample_234


title: Subject ID: IN.GN.511_IgA

tag: region

tag: mother's age

tag: infant's sex


title: RNA WT rep2


title: Subject ID: IN.GN.510_IgA

tag: parity

value: UNDERWEIGHT

tag: companion animals

tag: agricultural animals


title: Sample_231


title: Sample_230


title: Subject ID: IN.GN.509_IgA

value: OVERWEIGHT

tag: adjusted household density


title: RNA dMazEFpF rep1

tag: strain

tag: plasmid


title: Sample_232

tag: strain background


title: Sample_229


title: Sample_228


title: Subject ID: IN.GN.508_IgA

tag: time post-partum

tag: delivery

tag: bmi


title: Sample_226


title: Sample_227


title: Subject ID: IN.GN.506_IgA

tag: bmi code

tag: mother's height (cm)

tag: molecule type


title: Sample_224

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Subject ID: IN.GN.505_IgA

tag: region

tag: mother's age

tag: infant's sex

value: YES


title: Sample_225


title: Sample_223


title: Sample_222


title: Sample_220


title: Sample_221


title: Subject ID: IN.GN.503_IgA

tag: parity

tag: companion animals

tag: agricultural animals


title: Subject ID: IN.GN.502_IgA

tag: adjusted household density


title: Sample_218

tag: strain background


title: Sample_219


title: Sample_217


title: Sample_216


title: Subject ID: IN.GN.501_IgA

tag: time post-partum


title: Sample_215


title: Sample_214


title: Subject ID: IN.GBU.444_IgA

value: The Gambia, urban

tag: delivery


title: Subject ID: IN.GN.504_IgA

tag: bmi

value: NO


title: Sample_213


title: Sample_212


title: Sample_252


title: Sample_211


title: Subject ID: IN.GBU.440_IgA

tag: bmi code


title: Subject ID: IN.GBU.439_IgA

tag: mother's height (cm)


title: Subject ID: IN.GBU.438_IgA

tag: molecule type


title: Sample_210

tag: genotype/variation


title: Sample_209

tag: developmental stage


title: Subject ID: IN.GBU.437_IgA


title: Sample_205

tag: tissue


title: Sample_204


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu12_C (baboon_oa)

type: genomic

city: Chicago

first: Genevieve

last: Housman

state: IL

address: 920 East 58th Street, CLSC 317

department: Genetic Medicine

institute: University of Chicago

description: medial condyle osteoarthritic adult distal femur articular cartilage from baboon

hyb_protocol: Infinium MethylationEPIC array

scan_protocol: standard illumina scanner

data_processing:
Raw fluorescent data were normalized using the Noob background correction    method with dye-bias normalization followed with a between-array    normalization method (functional normalization) as implemented in the R    package minfi. After normalization, methylation values (beta values) for    each site were calculated as the ratio of methylated probe signal intensity    to the sum of both methylated and unmethylated probe signal intensities.
Those probes with failed detection levels (p-value > 0.05) in greater than    10% of samples were removed. Cross-reactive probes, probes containing SNPs    at the CpG site, probes detecting SNP information, probes detecting    methylation at non-CpG sites, and probes targeting sites within the sex    chromosomes were also removed using the minfi package in R.
Lastly, probes that were determined to be non-specific to each nonhuman    primate genome were also removed. Filtering for these files was based    on Hernando-Herraez  et al. (2013). Briefly, all 485,512 probes were mapped to the appropriate    nonhuman primate genome, and only those probes that successfully mapped to    the genome, had only 1 unique hit, and targeted CpG sites were retained.    Additionally, probes were kept for subsequent analyses only if they had 0    mismatches in 5bp closest to and including the CpG site, and had 0-2    mismatches in 45bp not including the CpG site.
- Hernando-Herraez I, Prado-Martinez J, Garg P, Fernandez-Callejo M,       Heyn H, Hvilsom C, et al. Dynamics of DNA methylation in recent human and       great ape evolution. PLOS Genet 2013;9:e1003763.
Nonhuman Primate Genome: Papio anubis

label: Cy5 and Cy3

organism: Papio sp.

label_protocol: 400ng of DNA was bisulphite converted using the EZ DNA methylation kit (Zymo Research)

extract_protocol: genomic DNA was extracted from pulverized trabecular bone or homogenized cartilage using a phenol-cholorform protocol

tag: Sex

tag: age (years)

tag: steady state weight (kg)

value: cartilage

tag: age cohort

value: adult

tag: disease state

value: osteoarthrtic


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu31_C (baboon_oa)

source_name: osteoarthritic adult distal femur articular cartilage from baboon

value: male


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu14_C (baboon_oa)

value: female


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu52_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu23_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu20_C (baboon_oa)


title: Sample_202


title: Subject ID: IN.GBU.435_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

value: Vaginal

tag: companion animals

tag: agricultural animals

value: IgA


title: Subject ID: IN.GBU.436_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

value: NORMAL

tag: adjusted household density


title: Subject ID: IN.GBU.434_IgA

tag: mother's height (cm)

tag: molecule type


title: Sample_208

tag: strain background

tag: genotype/variation

value: SCX-GFP transgenic

tag: developmental stage

tag: tissue


title: Sample_200

value: hind limb


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu27_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Sample_203


title: Sample_206


title: Sample_201


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu22_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu11_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu04_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu25_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu54_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu51_C (baboon_oa)


title: Sample_198


title: Sample_197


title: Sample_194


title: Sample_191


title: Subject ID: IN.GBU.432_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

tag: companion animals

tag: agricultural animals


title: Subject ID: IN.GBU.433_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: adjusted household density


title: Sample_192

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Sample_193


title: Subject ID: IN.GBU.431_IgA

tag: molecule type


title: Sample_196


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu28_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Subject ID: IN.GBU.427_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

tag: companion animals

tag: agricultural animals


title: Subject ID: IN.GBU.430_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: adjusted household density


title: Subject ID: IN.GBU.429_IgA

tag: molecule type


title: Sample_195

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Sample_189


title: Sample_190


title: Sample_207


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu02_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Sample_188


title: Sample_199


title: Sample_187


title: Subject ID: IN.GBU.426_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

tag: companion animals

tag: agricultural animals


title: Sample_186


title: Sample_184


title: Subject ID: IN.GBU.425_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: adjusted household density


title: Sample_185

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu05_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Sample_181


title: Sample_180


title: Subject ID: IN.GBU.423_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

tag: companion animals

tag: molecule type


title: Subject ID: IN.GBU.424_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: agricultural animals


title: Sample_179

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Subject ID: IN.GBU.422_IgA

tag: adjusted household density


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu07_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Subject ID: IN.GBU.421_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

tag: companion animals

tag: molecule type


title: Sample_177


title: Sample_182


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu38_C (baboon_oa)


title: Sample_178


title: Sample_183


title: Subject ID: IN.GBU.420_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: agricultural animals


title: Sample_176

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu32_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Sample_175


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu15_C (baboon_oa)


title: Sample_173


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu17_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu16_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu26_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu24_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu30_C (baboon_oa)


title: Sample_174


title: Sample_170


title: Sample_167


title: Subject ID: IN.GBU.417_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

tag: companion animals

tag: adjusted household density


title: Sample_166


title: Sample_169


title: Sample_172


title: Subject ID: IN.GBU.419_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: molecule type


title: Subject ID: IN.GBU.416_IgA

tag: agricultural animals


title: Subject ID: IN.GBU.415_IgA


title: Sample_171

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Sample_168


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu09_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Sample_165


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu01_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur articular cartilage Panu35_C (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu32_B (baboon_oa)

description: medial condyle osteoarthritic adult distal femur trabecular bone from baboon

value: bone


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu28_B (baboon_oa)

source_name: osteoarthritic adult distal femur trabecular bone from baboon


title: Sample_164


title: Sample_163


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu11_B (baboon_oa)


title: Sample_162


title: Sample_161


title: Subject ID: IN.GBU.413_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: parity

tag: companion animals

tag: adjusted household density


title: Sample_160


title: Sample_159


title: Sample_157


title: Sample_156


title: Sample_155


title: Subject ID: IN.GBU.412_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: molecule type


title: Subject ID: IN.GBU.411_IgA

tag: agricultural animals


title: Sample_158

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Subject ID: IN.GBU.410_IgA

tag: region


title: Sample_154


title: Subject ID: IN.GBU.414_IgA

tag: mother's age

value: OBESE


title: Subject ID: IN.GBU.418_IgA

tag: infant's sex


title: Subject ID: IN.GBU.409_IgA

tag: parity


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu22_B (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu51_B (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu54_B (baboon_oa)


title: Subject ID: IN.GBU.408_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

tag: companion animals

tag: adjusted household density


title: Sample_152

tag: strain background

tag: genotype/variation

tag: developmental stage


title: Sample_151

tag: tissue


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu27_B (baboon_oa)


title: Sample_150


title: Sample_149


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu20_B (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu12_B (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu04_B (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu25_B (baboon_oa)


title: Sample_148


title: Sample_144


title: Sample_146


title: Sample_153


title: Subject ID: IN.GBU.406_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: mother's height (cm)

tag: agricultural animals

tag: molecule type


title: Subject ID: IN.GBU.407_IgA

tag: parity

value: UNDERWEIGHT


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu14_B (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Sample_141


title: Subject ID: IN.GBU.404_IgA

tag: time post-partum

tag: delivery

tag: bmi

tag: bmi code

tag: companion animals

tag: adjusted household density


title: Subject ID: IN.GBU.405_IgA

tag: region

tag: mother's age


title: Subject ID: IN.GBU.403_IgA

tag: infant's sex

tag: mother's height (cm)


title: Sample_145

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: Subject ID: IN.GBU.402_IgA

tag: parity

tag: agricultural animals

tag: molecule type


title: Sample_143


title: Sample_140


title: Sample_147


title: Sample_138


title: Sample_139


title: Subject ID: IN.GBU.401_IgA

tag: time post-partum

value: OVERWEIGHT


title: Subject ID: IN.GBR.340_IgA

value: The Gambia, rural

tag: delivery

value: YES


title: Sample_135


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu35_B (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu05_B (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu30_B (baboon_oa)


title: Sample_132


title: Sample_142


title: Sample_133


title: Sample_134


title: Sample_130


title: Sample_137


title: Sample_128


title: Subject ID: IN.GBR.337_IgA

tag: region

tag: mother's age

tag: bmi

tag: bmi code

tag: companion animals

value: NO

tag: adjusted household density


title: Sample_136

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu23_B (baboon_oa)


title: Subject ID: IN.GBR.339_IgA

tag: infant's sex

tag: time post-partum

tag: parity

tag: mother's height (cm)

tag: agricultural animals

tag: molecule type


title: Sample_131


title: Subject ID: IN.GBR.338_IgA

tag: delivery


title: Subject ID: IN.GBR.336_IgA

tag: region


title: Sample_129


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu31_B (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu24_B (baboon_oa)


title: Sample_125

tag: strain background


title: Sample_124

tag: genotype/variation


title: Subject ID: IN.GBR.334_IgA

tag: mother's age

tag: bmi

tag: bmi code

tag: companion animals

tag: adjusted household density


title: Sample_127

tag: developmental stage

tag: tissue


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu52_B (baboon_oa)


title: Sample_120

source_name: SCX-GFP transgenic hind limb_E10.5


title: Sample_122


title: Sample_121


title: Sample_123


title: Sample_118


title: Sample_119


title: Subject ID: IN.GBR.333_IgA

tag: infant's sex

tag: time post-partum

tag: parity

tag: mother's height (cm)

tag: agricultural animals

tag: molecule type


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu26_B (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort


title: Sample_117

tag: strain background

tag: genotype/variation


title: Subject ID: IN.GBR.332_IgA

tag: region

tag: mother's age

tag: delivery

tag: bmi

tag: bmi code


title: Subject ID: IN.GBR.331_IgA

tag: infant's sex

tag: companion animals

tag: adjusted household density


title: Subject ID: IN.GBR.335_IgA

tag: time post-partum

tag: parity

tag: mother's height (cm)


title: Sample_116

tag: developmental stage

tag: tissue


title: Subject ID: IN.GBR.330_IgA

tag: agricultural animals

tag: molecule type


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu15_B (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu38_B (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu01_B (baboon_oa)


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu16_B (baboon_oa)


title: Sample_126

tag: strain background

tag: genotype/variation


title: Sample_115


title: Subject ID: IN.GBR.329_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: delivery

tag: bmi

tag: bmi code


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu17_B (baboon_oa)


title: Sample_114

tag: developmental stage


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu07_B (baboon_oa)

tag: tissue


title: Sample_113


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu09_B (baboon_oa)


title: Sample_112


title: genomic DNA from healthy adult distal femur articular cartilage Panu03_C (baboon_oa)

description: medial condyle healthy adult distal femur articular cartilage from baboon

value: cartilage

value: healthy


title: genomic DNA from healthy adult distal femur articular cartilage Panu43_C (baboon_oa)

source_name: healthy adult distal femur articular cartilage from baboon

value: adult


title: genomic DNA from osteoarthritic adult distal femur trabecular bone Panu02_B (baboon_oa)

value: osteoarthrtic


title: Sample_110


title: Sample_111


title: Subject ID: IN.GBR.327_IgA

tag: time post-partum

tag: parity

tag: mother's height (cm)

tag: companion animals

tag: agricultural animals

tag: adjusted household density


title: Sample_108


title: Subject ID: IN.GBR.324_IgA

tag: molecule type


title: Sample_109

tag: strain background


title: Subject ID: IN.GBR.325_IgA


title: Subject ID: IN.GBR.326_IgA


title: Subject ID: IN.GBR.328_IgA


title: Subject ID: IN.GBR.323_IgA


title: genomic DNA from healthy adult distal femur articular cartilage Panu48_C (baboon_oa)

tag: Sex

value: female

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Sample_107

tag: genotype/variation


title: Sample_106


title: Subject ID: IN.GBR.322_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: delivery

value: Vaginal

tag: bmi

tag: bmi code


title: Sample_105

tag: developmental stage

tag: tissue


title: Subject ID: IN.GBR.321_IgA

tag: time post-partum

tag: parity

tag: mother's height (cm)

tag: companion animals

tag: agricultural animals

tag: adjusted household density

value: IgA


title: Subject ID: IN.GBR.320_IgA

tag: molecule type


title: genomic DNA from healthy adult distal femur articular cartilage Panu47_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Sample_104

tag: strain background

tag: genotype/variation


title: genomic DNA from healthy adult distal femur articular cartilage Panu44_C (baboon_oa)


title: Sample_103


title: Subject ID: IN.GBR.318_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: delivery

tag: bmi

tag: bmi code

value: NORMAL


title: Subject ID: IN.GBR.319_IgA

tag: time post-partum

tag: parity

tag: mother's height (cm)

tag: companion animals


title: Sample_101

value: SCX-GFP transgenic

tag: developmental stage

tag: tissue


title: Sample_100

value: hind limb


title: genomic DNA from healthy adult distal femur articular cartilage Panu34_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)


title: Subject ID: IN.GBR.317_IgA

tag: agricultural animals

tag: adjusted household density

tag: molecule type


title: genomic DNA from healthy adult distal femur articular cartilage Panu10_C (baboon_oa)

value: male

tag: age cohort

tag: disease state


title: genomic DNA from healthy adult distal femur articular cartilage Panu29_C (baboon_oa)


title: Subject ID: IN.GBR.316_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: delivery


title: Sample_99

tag: strain background

tag: genotype/variation


title: Sample_102


title: Subject ID: IN.GBR.314_IgA

tag: time post-partum

tag: parity

tag: bmi

tag: bmi code

tag: mother's height (cm)

tag: companion animals


title: Subject ID: IN.GBR.315_IgA

tag: agricultural animals


title: genomic DNA from healthy adult distal femur articular cartilage Panu36_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: tissue


title: Sample_98

tag: developmental stage


title: CF homozygous E528E_biological replicate 2

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

description: rectal organoid CF-patient homozygous GluE528

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 10
Genome read mapping using bowtie2 (0.12.9), parameters: -l 16 -n 1 -e 50 -m 1—strata—best y
Read counting using bedtools, version 2.17.0, parameter: -s
Genome_build: Homo sapiens Ensemble build GRCh37
Supplementary_files_format_and_content: Unique read counts per gene per kilobase and million mapped readsRPKM

source_name: rectal organoid

growth_protocol: Crypts were isolated from rectal biopsies collected from a cystic fibrosis ppatient homozygous from the CFTR variant c.1584G>A. The organoids were expanded in d DMEM/F12 (Invitrogen), supplemented with Glutamax (2 mmol/L; ThermoFisher), murine epidermal growth factor (50 µg/L), the cell culture supplements B27 and N2 (all from Invitrogen), [Leu-15]-Gastrin (10 nmol/L), N-acetylcysteine (1 mmol/L), nicotinamide (10 mmol/L), HEPES (10 mmol/L), CHIR99021 (10 µmol/L; only present during the first 2 days after (re-)seeding),  SB202190(3 µmol/L; all from Sigma-Aldrich), Y-27632 (10 µmol/L; only present during the first 2 days after (re-)seeding), prostaglandin E2 (10 nmol/L), A83-01 (0.5 µmol/L; all from Tocris), and an antibiotic formulation (Primocin; Invivogen). In addition, conditioned cell culture media containing the following growth factors were added: noggin (10% v/v), R-spondin 1 (20% v/v) and Wnt3a (50% v/v).

extract_protocol:
Total RNA from each sample was extracted in TRIzol reagent (Sigma Aldrich). Total RNA samples were DNaseI treated (5 U DNaseI / 5µg RNA, 30 min, 37°C), spiked-in and rRNA depleted using Ribo-Zero™ Magnetic Gold kit (Human/Mouse/Rat)
RNA-size selection and generation of the cDNA libraries was performed as described (Ingolia et al, 2009; doi: 10.1126/science.1168978)

tag: passenge

value: rectal organoid

tag: disease state

value: mild cystic fibrosis


title: Subject ID: IN.GBR.313_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: delivery

value: OVERWEIGHT

tag: adjusted household density

tag: molecule type


title: Subject ID: IN.GBR.312_IgA

value: The Gambia, rural

tag: time post-partum

tag: parity

tag: bmi

tag: bmi code


title: Sample_97

tag: strain background

tag: genotype/variation


title: genomic DNA from healthy adult distal femur articular cartilage Panu18_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

tag: age cohort


title: genomic DNA from healthy adult distal femur articular cartilage Panu13_C (baboon_oa)

tag: tissue

tag: disease state


title: Sample_96

tag: developmental stage


title: genomic DNA from healthy adult distal femur articular cartilage Panu40_C (baboon_oa)


title: CF homozygous E528E_biological replicate 1

tag: passenge


title: Subject ID: IN.GBR.311_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: delivery

tag: mother's height (cm)

tag: companion animals

tag: agricultural animals

value: YES


title: Sample_95

tag: strain background


title: Severe

city: London

first: Val

last: Yianni

address: Guy's Hospital, Great Maze Pond

department: Centre for Craniofacial & Regenerative Biology

institute: King's College London

data_processing:
Illumina Casava1.7 software used for basecalling.
CellRanger v3 pipeline used for alignment and count file generation
Clustering analysis performed using Seurat v3
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 (HDF5) files containing counts for each sample + bam files for each sample

molecule: polyA RNA

source_name: Gingiva Biopsy

extract_protocol:
Dissection followed by enzymatic dissociation
10x 3' RNAseq (V3)

value: Severe Periodontitis

tag: age

value: Adult


title: Sample_94

tag: genotype/variation


title: genomic DNA from healthy adult distal femur articular cartilage Panu06_C (baboon_oa)

tag: Sex

tag: age (years)

value: cartilage

value: healthy


title: Subject ID: IN.GBR.310_IgA

tag: time post-partum

tag: parity

tag: bmi

tag: bmi code

tag: adjusted household density

tag: molecule type


title: Sample_93

tag: developmental stage

tag: tissue


title: Mild

tag: disease state

value: Mild Periodontitis


title: genomic DNA from healthy adult distal femur articular cartilage Panu37_C (baboon_oa)

value: female

tag: steady state weight (kg)

tag: age cohort

value: adult


title: Subject ID: IN.GBR.309_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: delivery

value: Vaginal

tag: mother's height (cm)

tag: companion animals

tag: agricultural animals

value: IgA


title: genomic DNA from healthy adult distal femur articular cartilage Panu41_C (baboon_oa)

tag: Sex

tag: age (years)


title: genomic DNA from healthy adult distal femur articular cartilage Panu50_C (baboon_oa)


title: Healthy 2

value: Healthy

tag: age


title: Healthy 1


title: Subject ID: IN.GBR.308_IgA

tag: time post-partum

tag: parity

tag: bmi

tag: bmi code

value: NORMAL

tag: adjusted household density


title: Sample_92

tag: strain background

tag: genotype/variation

value: SCX-GFP transgenic

tag: developmental stage

tag: tissue

value: hind limb


title: genomic DNA from healthy adult distal femur articular cartilage Panu49_C (baboon_oa)

value: male

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Subject ID: IN.GBR.307_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: delivery

tag: mother's height (cm)

tag: companion animals

tag: molecule type


title: Subject ID: IN.GBR.306_IgA

tag: time post-partum

tag: parity

tag: bmi

tag: agricultural animals


title: Sample_90

tag: strain background

tag: genotype/variation


title: T47D_Day_14

city: Pearl River

first: Reeja

last: Maskey

state: NY

address: 401 N Middletown Rd

department: Oncology Research & Development

institute: PFIZER INC.

data_processing:
RNA -Seq profiling was conducted by Q2 solutions company. RNAs were pair-end sequenced with read length of 2 x 100bps. Raw reads were mapped to the human hg19 reference genome using Bowtie 2 (v2.2.5).
Expected counts and normalized expression levels of genes in transcripts per million (TPM) were generated by RSEM (v1.2.20).
Genome_build: hg19
Supplementary_files_format_and_content: The excel spreadsheet include the table that shows normalized expression levels of genes in TPM in all samples.

source_name: Luminal breast cancer_palbociclib Day_14

growth_protocol: Cell lines were maintained in RPMI-1640 with L-glutamine growth media supplemented with 10% heat-inactivated fetal bovine serum at 37 oC in a humidified incubator with 5% CO2.

extract_protocol:
Collected cells were lysed and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions for RNA-Sequencing analysis.
Illumina stranded mRNA seq kit

treatment_protocol: Cells were seeded at 100,000 cells per well into 6-well culture plates. After 24 h, cells were treated with 500 nM palbociclib for 2, 7, 10 and 14 days. At the indicated timepoints, cells were collected and pooled from 3 wells per cell line. For the vehicle treated control, cells were collected from log phase growing cultures alongside 2 days- palbociclib treated cells.

tag: cell line

tag: cell type

value: Luminal breast cancer

tag: breast cancer type

value: ER positive HER2 negative

tag: treatment/time point

value: palbociclib Day_14


title: Sample_89

tag: developmental stage

tag: tissue


title: Sample_91


title: Subject ID: IN.GBR.305_IgA

tag: region

value: The Gambia, rural

tag: mother's age

tag: infant's sex

tag: bmi code

value: OVERWEIGHT

value: YES

tag: adjusted household density


title: genomic DNA from healthy adult distal femur articular cartilage Panu46_C (baboon_oa)

tag: Sex

tag: age (years)

tag: steady state weight (kg)

value: cartilage

tag: age cohort

tag: disease state

value: healthy


title: genomic DNA from healthy adult distal femur articular cartilage Panu19_C (baboon_oa)

value: female


title: Sample_88

tag: strain background

tag: genotype/variation


title: genomic DNA from healthy adult distal femur articular cartilage Panu42_C (baboon_oa)

value: adult


title: T47D_Day_2

source_name: Luminal breast cancer_palbociclib Day_2

tag: cell line

tag: cell type

value: palbociclib Day_2


title: genomic DNA from healthy adult distal femur articular cartilage Panu39_C (baboon_oa)


title: genomic DNA from healthy adult distal femur articular cartilage Panu53_C (baboon_oa)


title: genomic DNA from healthy adult distal femur articular cartilage Panu45_C (baboon_oa)


title: Subject ID: IN.GBR.303_IgA

tag: time post-partum

tag: parity

tag: delivery

value: Vaginal

tag: bmi

value: UNDERWEIGHT

tag: mother's height (cm)

tag: companion animals

value: NO

tag: agricultural animals

tag: molecule type

value: IgA


title: Sample_87

value: SCX-GFP transgenic

tag: developmental stage

tag: tissue

value: hind limb


title: T47D_log phase_untreated

description: T47D_log phase_untreated_L1.D706

source_name: Luminal breast cancer_log phase_untreated

value: Luminal breast cancer

tag: breast cancer type

tag: treatment/time point

value: log phase_untreated


title: genomic DNA from healthy adult distal femur articular cartilage Panu55_C (baboon_oa)

tag: Sex

value: male

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

tag: disease state


title: Sample_86

tag: strain background

tag: genotype/variation


title: Subject ID: IN.GBR.302_IgA

source_name: human breast milk

tag: region

value: The Gambia, rural

tag: mother's age

tag: infant's sex

tag: time post-partum

tag: parity

tag: delivery

tag: bmi code

value: NORMAL

tag: adjusted household density


title: MCF7_Day_14

tag: cell line

tag: cell type

tag: breast cancer type

value: ER positive HER2 negative

value: palbociclib Day_14


title: MCF7_Day_10

source_name: Luminal breast cancer_palbociclib Day_10

tag: treatment/time point

value: palbociclib Day_10


title: Subject ID: IN.GBR.304_IgA

tag: bmi

tag: mother's height (cm)

tag: companion animals

tag: agricultural animals

value: YES

tag: molecule type


title: T47D_Day_10


title: Sample_85

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: tissue


title: T47D_Day_7

source_name: Luminal breast cancer_palbociclib Day_7

value: palbociclib Day_7


title: Sample_84


title: MCF7_Day_7


title: Sample_83


title: MCF7_Day_2

value: palbociclib Day_2


title: Subject ID: IN.GBR.301_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: time post-partum

tag: parity

value: Vaginal


title: Subject ID: IN.ETU.045_IgA

value: Ethiopia, urban

tag: delivery

tag: bmi code

tag: adjusted household density


title: Subject ID: IN.ETU.044_IgA

tag: bmi

value: NO


title: Subject ID: IN.ETU.043_IgA

tag: mother's height (cm)

value: IgA


title: genomic DNA from healthy adult distal femur articular cartilage Panu21_C (baboon_oa)

tag: Sex

value: female

tag: age (years)

tag: steady state weight (kg)

value: cartilage

tag: age cohort

value: adult

tag: disease state

value: healthy


title: Sample_82

tag: strain background

tag: genotype/variation

value: SCX-GFP transgenic

tag: developmental stage

value: hind limb


title: genomic DNA from healthy adult distal femur articular cartilage Panu33_C (baboon_oa)

tag: tissue


title: genomic DNA from healthy adult distal femur trabecular bone Panu49_B (baboon_oa)

description: medial condyle healthy adult distal femur trabecular bone from baboon

value: male

value: bone


title: genomic DNA from healthy adult distal femur articular cartilage Panu08_C (baboon_oa)


title: Subject ID: IN.ETU.042_IgA

tag: region

tag: mother's age

tag: infant's sex

value: NORMAL

tag: companion animals

tag: agricultural animals

tag: molecule type


title: MCF7_log phase_untreated

description: MCF7_log phase_untreated_L1.D711

tag: cell line

tag: cell type

value: Luminal breast cancer

tag: breast cancer type

value: ER positive HER2 negative

tag: treatment/time point

value: log phase_untreated


title: genomic DNA from healthy adult distal femur trabecular bone Panu50_B (baboon_oa)

source_name: healthy adult distal femur trabecular bone from baboon

tag: Sex

tag: age (years)

tag: steady state weight (kg)


title: CAMA1_Day_14

value: palbociclib Day_14


title: CAMA1_Day_10

value: palbociclib Day_10


title: Sample_80

tag: strain background


title: genomic DNA from healthy adult distal femur articular cartilage Panu56_C (baboon_oa)

tag: age cohort

tag: disease state


title: genomic DNA from healthy adult distal femur trabecular bone Panu06_B (baboon_oa)

tag: tissue


title: genomic DNA from healthy adult distal femur trabecular bone Panu36_B (baboon_oa)


title: CAMA1_Day_7

value: palbociclib Day_7


title: CAMA1_log phase_untreated

description: CAMA1_log phase_untreated_L1.D704


title: genomic DNA from healthy adult distal femur trabecular bone Panu18_B (baboon_oa)


title: Subject ID: IN.ETU.040_IgA

tag: region

value: Ethiopia, urban

tag: time post-partum

tag: parity

tag: delivery

value: Vaginal

tag: bmi

tag: bmi code

tag: mother's height (cm)

value: NO

tag: adjusted household density


title: Sample_77

tag: genotype/variation

tag: developmental stage


title: CAMA1_Day_2

tag: cell line

tag: cell type

tag: breast cancer type

tag: treatment/time point

value: palbociclib Day_2


title: Sample_76

tag: strain background


title: Sample_79


title: genomic DNA from healthy adult distal femur trabecular bone Panu29_B (baboon_oa)

tag: Sex

value: female

tag: age (years)

tag: steady state weight (kg)

tag: age cohort

value: adult

tag: disease state


title: Sample_81

value: SCX-GFP transgenic

tag: tissue


title: Subject ID: IN.ETU.037_IgA

tag: region

tag: mother's age

tag: infant's sex

tag: time post-partum

tag: parity

tag: delivery

tag: bmi

tag: companion animals

tag: agricultural animals

value: YES

tag: molecule type

value: IgA


title: Subject ID: IN.ETU.038_IgA

tag: bmi code

value: OVERWEIGHT

tag: mother's height (cm)

tag: adjusted household density


title: Subject ID: IN.ETU.039_IgA


title: Subject ID: IN.ETU.041_IgA

value: NORMAL


title: Subject ID: IN.ETU.036_IgA


title: genomic DNA from healthy adult distal femur trabecular bone Panu40_B (baboon_oa)

tag: Sex

value: male

tag: age (years)

tag: steady state weight (kg)

value: bone

value: healthy