title: SAM1712

city: BENGALURU

first: KARABA

middle: N

last: NATARAJA

state: KARNATAKA

address: BELLARY ROAD

department: CROP PHYSIOLOGY

institute: UNIVERSITY OF AGRICULTURAL SCIENCES BENGALURU

data_processing:
bcl2fastq v2.20 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, using Trimmomatic0.36
The reads are then mapped to Morus notabilis genome using HISAT2
Transcript level abundance was calculated using featurecounts
Genome_build: Morus notabilis(ASM41409v2)
Supplementary_files_format_and_content: tab-delimited text files include Normalized Data values for each Sample

organism: Morus alba

source_name: Drought stressed_leaf

growth_protocol: Plants were raised in pots of about 30kg  capacity and plants were maintained for three months in the form of bush and two different levels of irrigations were given during the experimental period.

extract_protocol:
Leaf tissue was collected and total RNA was isolated and processed for sequencing after quality check
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One set of plants were maintained at 100% soil field capacity whole other set was maintained at 40% soil field capacity for 14 days and leaf tissue was collected for RNA seq analysis

value: Dudia white

value: Drought stressed (treatment)

value: Mature leaf tissue (mesophyll tissue)


title: CB03_DL1_ILC2_CD5p

status: Public on Aug 25 2021

type: SRA

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description: in vitro generated

library_source: transcriptomic

data_processing:
The unstranded sequence reads were mapped to human GRCh37/hg19 genome with TopHat2 in very-sensitive settings for Bowtie2 and Genecode release 19, SNPs removed.
Gene expression was quantified by featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

molecule: total RNA

organism: Homo sapiens

source_name: Derived from CD34+ progenitors from CB

extract_protocol:
CD34+ hematopoetic progenitors were sorted and plated on OP9 or OP9-DL1. Media was supplemented with 10% human AB serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and cytokine mix. Cytokine mix consisted of SCF, Flt3L, IL-7, and IL-15 when stated (all 20 ng/ml) and IL-3 (all cultures: 5 ng/ml). After one week IL-3 supplementation was dropped. After two weeks Flt3L was reduced to 5 ng/ml. Medium and cytokines were refreshed every 3-4 days by replacing half of the media containing 1x concentration of cytokines. At day 7, 14 and 21 cells were replated onto fresh OP9 or OP9-DL1 onto flat bottom plates. To replate, cells were collected by forceful pipetting and passed through a 50µm filter to remove OP9/OP9-DL1 cells, wells and filter were washed 2x with PBS, cells were counted and up to 50000 cells/well were replated. Cells were harvested at day 30 and RNA was isolated.
RNA was isolated using RNeasy Plus Micro Kit (QIAGEN) when cell numbers were < 5x105 and Nucleospin RNAII kit (Macherey-Nagel) when cell numbers were > 5x105. RNA quality was determined on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent).
Illumina libraries were prepared using Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) and Nextera XT DNA Sample Preparation Kit (Illumina), with 10 ng of purified cDNA, according to the manufacturer’s instructions

tag: donor

tag: cell type

tag: condition


title: SAM1710

country: India

tag: genotype

tag: treatment

value: Well irrigated (control)

tag: tissue


title: CB03_OP9_IL-15_NK/ILC1_CD94p

description: in vitro generated


title: Alb-Cre 48h oil rep2

city: Zurich

first: Sabine

last: Werner

address: Otto-Stern-Weg 7

department: Department of Biology

country: Switzerland

institute: ETH Zurich

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Alignment of reads was performed using Kallisto software, version 0.44.0 using the following parameters: quant -t 8 --bias --bootstrap-samples 10 --seed 42 --single --rf-stranded --fragment-length 150 --sd 70, and reference genome version GRCm38.p6 from GENCODE project with gene model annotation version M23
For differential expression analysis, the edgeR software, version v3.28.0 was used with the following parameters: Normalization  method - TMM (trimmed mean of m-values), data modelling -  glm (generalised linear model), statistical test - QL (quasi likelihood), Benjamini Hochberg (BH) multiple testing correction. Prior to differential expression analysis, data were filtered by estimated counts with the threshold of 20 to avoid inclusion of genes that are expressed at extremely low levels.
Genome_build: GRCm38.p6, gene model annotation version M23
Supplementary_files_format_and_content: Matrix file with normailzed counts and FPKM

organism: Mus musculus

source_name: Primary hepatocytes

extract_protocol:
Hepatocytes were isolated after perfusion with Liberase  following differential centrifugation and Percoll gradient purification. RNA was isolated using the Total RNA Mini Kit (IBI Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eight- to ten-week-old male mice were injected intraperitoneally (i.p.) with a single dose of CCl4 (0.4 mg/g body weight diluted in olive oil) between 8 a.m. and 12 p.m. Vehicle-injected (oil) served as controls.

value: Primary hepatocytes

tag: strain

value: Alb-Cre

value: 48h oil


title: Specific pathogen-free mice [mRNA]

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Colonic lamina propria mononuclear cells

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

value: Balb/c

tag: Sex

value: Male

value: Colon


title: Cortex_AD_REPLICATE7

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray hybridization intensity data were filtered to remove undetected and array control probes, before computing log z-score for each sample to identify and exclude possible outlying samples via clustering, scatter plots, and principal components analysis. After removal of the outlying samples, a sample-specific quantile normalization of the filtered raw average signal was employed to yield quantile normalized log scale z-scores. These quantile z-scores were used to ensure a standard normal distribution in further statistical analysis, including ANOVA, t- and z-testing. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a combination of thresholds, including p<value 0.05, 30% false discovery rate (FDR), and average signal intensity of comparison >0. The gene expression change z-ratio values were then used as input to perform Parametric Analysis of Gene Set Enrichment (PAGE) testing. For each gene set change, an aggregate z-score, and p-value with false discovery change was calculated and reported for statistical significance.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

extract_protocol: RNA was purified with Nucleospin RNA isolation kit following manufacturer’s protocol (Macherey-Nagel, #740955.250).

treatment_protocol: All animal experiments were performed and approved by NIA Animal Care and Use Committee. All the animals were maintained at the National Institute on Aging under standard conditions and fed standard animal chow. The APP/PS1 mouse strain (#stock number 004462 in Jackson’s laboratory) was from Prof. Mark Mattson’s laboratory. APP/PS1 mice and their WT littermates were used for experiments. The APP/PS1 mice were treated with NR (12 mM) in drinking water starting from 7 months (the age at which Aβ plaques appear) to 12 months. The NR treatment was performed as previously reported. From 9-month-old, the mice were subsequently evaluated for behavioral endpoints.

tag: genotype/variation

value: APP/PS1 AD

value: Brain

tag: brain region

value: Cortex

value: CTR

tag: treatment duration

tag: age

value: 12 months


title: Alb-Cre 48h oil rep1


title: CB01_DL1_CD161n_CD5p

description: in vitro generated


title: Germ-free mice [mRNA]


title: SAM1709


title: CB01_DL1_ILC2_CD5p

description: in vitro generated


title: Hub_22_7_knockout_HiC

city: LA

first: Zhiheng

last: Liu

state: CA

address: 610 Charles E Young Dr S

institute: UCLA

library_source: genomic

data_processing:
FASTQ files were aligned by BWA to hg19 genome
Hi-C contact counts and normalized counts were idenfited with Juicer pipeline with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C contact counts in .hic format

molecule: genomic DNA

source_name: genomic modified cell line

growth_protocol: K562 cells stably expressing Cas9 were infected with pgRNA for selected Hub loci. The cells were collected for EGFP+ population at Day 9 and sorted cells were allowed to recover for 2hr before proceeding to Hi-C library.

extract_protocol: Hi-C sample preparation was performed according to Arima-HiC kit (Arima Genomics Inc) as described by the manufacturer.

treatment_protocol: 1 million cells were fixed with 2% Formaldehyde for 10 minutes at room temperature, followed by adding Stop Solution 1 (Arima-HiC kit) for 5 minutes. The fixed cells were wash with PBS before snap freezing for Hi-C library preparation

tag: cell line

value: Lymphoblast

tag: genomic locus deleted

tag: restriction enzyme

value: Arima (multi-enzyme)


title: Z2_RNA-seq

city: Shanghai

first: Qian

last: Bian

state: Shanghai

address: Pudong New District, Jinzun Rd, No.115

department: Ninth People’s Hospital

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
All RNA-seq raw data were trimmed to remove low-quality reads and adapters with Trim Galore (Version 0.6.5).
The clean reads were then mapped to the mouse reference genome (mm10) using the STAR aligner(Dobin et al., 2013) with default parameters and the annotated genes were counted by HTSeq (Anders, Pyl, & Huber, 2015).
The raw counts files were normalized using the DESeq2 package and heatmaps was generated using the ggplot2 and pheatmap packages in R.
Genome_build: mm10

source_name: spermatocytes

extract_protocol:
Murine spermatocytes were isolated by FACS as described previously (Gaysinskaya, Soh, van der Heijden, & Bortvin, 2014; Getun, Torres, & Bois, 2011) with modification. Wild-type or mutant mice of different ages were used for isolation of spermatocytes at different stages: 7-11 days old mice were used for isolating Sertoli, spermatogonia, and preleptotene cells, 2-week old mice for zygotene cells, 3- to 5-week-old mice for pachytene, diplotene, and Metaphase II cells, and 1-2 months old SUN1 W151R mutant mice for zygotene-like spermatocytes
Total RNA was extracted from ~50k purified pre-leptotene, leptotene and zygotene spermatocytes by RNeasy Micro Kit (Qiagen, 74004) according to the manufacturer’s instructions. The cDNA was synthesized and amplified using the Single Cell Full Length mRNA-Amplification Kit (Vazyme, N712). The RNA-seq libraries were constructed from the amplified cDNA using the TruePrep DNA Library Prep Kit V2 for Illumina® (Vazyme, TD503). The PCR and size-selection of RNA-seq libraries were conducted as described in Hi-C library construction. The RNA-Seq libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode.

value: Zygotene


title: Cortex_AD_NR_REPLICATE1

value: NR

value: 5 months


title: Cortex_AD_REPLICATE6


title: CB01_DL1_ILC2_CD5n

description: in vitro generated


title: Cortex_AD_REPLICATE5


title: L2_RNA-seq

value: Leptotene


title: Z1_RNA-seq


title: CB01_DL1_IL-15_NK/ILC1_CD94p

description: in vitro generated


title: L1_RNA-seq


title: SAM1711

value: Dudia white

value: Drought stressed (treatment)

value: Mature leaf tissue (mesophyll tissue)


title: Cortex_AD_REPLICATE3


title: Cortex_AD_REPLICATE4


title: CB01_DL1_IL-15_NK/ILC1_CD94n

description: in vitro generated


title: gdT_IL2_IPP_GSI_rep3

city: Greater Noida

first: Sanjeev

last: Galande

state: Uttar Pradesh

address: Center of Excellence in Epigenetics  Department of Life Sciences  School of Natural Sciences  Shiv Nadar Institute of Eminence  NH91, Tehsil Dadri

department: Biology

institute: Shiv Nadar University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38
HISATv2.0.1 was used to map the paired reads
Count matrix were generated using feature counts of the SubRead package v1.0.1
DE was performed using Deseq2 in R v3.1.5
Genome_build: hg38
Supplementary_files_format_and_content: Raw count -matrices for all the treatments

source_name: Blood

growth_protocol: gdT cells were magnetically isolated and cultured for 72 hrs

extract_protocol:
Total RNA was extracted from each sample using TriZol method
1 ug of RNA was used to prepare library using TruSeq Stranded mRNA Sample Prep Kit (Illumina #20020594) by standard Illumina protocol

treatment_protocol: 3 replicates of 1 million gdT cells each were treated with IL2, IL2+HDMAPP, IL2+IPP, IL2+anti-CD3, IL2+HDMAPP+GSI, IL2+IPP+GSI, IL2+anti-CD3+GSI

value: hIL2 + IPP + GSI

value: PBMCs


title: gdT_IL2_HDMAPP_GSI_rep3

value: hIL2 + HDMAPP + GSI


title: CB01_OP9_IL-15_ILC3

description: in vitro generated


title: gdT_IL2_antiCD3_rep3

value: hIL2 + anti-CD3


title: PreL2_RNA-seq

value: Preleptotene


title: PreL1_RNA-seq


title: gdT_IL2_IPP_rep3

value: hIL2 + IPP


title: CB01_OP9_IL-15_NK/ILC1_CD94p

description: in vitro generated


title: gdT_IL2_HDMAPP_rep3

value: hIL2 + HDMAPP


title: gdT_IL2_rep3


title: C57_Male_rep4

city: Chapel Hill

first: Wei

last: Shi

state: NC

address: 221 Fordham Hall

institute: UNC-Chapel Hill

data_processing:
Libraries were run on a HiSeq2500 (Illumina) with 2×150 bp paired end reads.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_ID feature in the annotation file. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: comma-separated values file includes Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: comma-separated values file includes Matrix table with normalized gene counts for every gene and every sample

extract_protocol:
Hearts were dissected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

value: Male


title: C57_Male_rep2


title: PD_CTCF_Cut&Tag

data_processing:
Library strategy: CuT&Tag
The CTCF CUT&Tag data processing and analysis were conducted as described before (Zheng Y et al (2020). Protocol.io) with minimal changes. Low-quality reads and adapters were trimmed by Trim Galore (Version 0.6.5).
The clean reads were mapped to the mm10 genome with bowtie2 (v2.4.2)(Langmead & Salzberg, 2012; Langmead, Wilks, Antonescu, & Charles, 2019) and duplicates were removed with Picard (“Picard Toolkit.” 2019. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/; Broad Institute).
Genome_build: mm10

extract_protocol:
Murine spermatocytes were isolated by FACS as described previously (Gaysinskaya, Soh, van der Heijden, & Bortvin, 2014; Getun, Torres, & Bois, 2011) with modification. Wild-type or mutant mice of different ages were used for isolation of spermatocytes at different stages: 7-11 days old mice were used for isolating Sertoli, spermatogonia, and preleptotene cells, 2-week old mice for zygotene cells, 3- to 5-week-old mice for pachytene, diplotene, and Metaphase II cells, and 1-2 months old SUN1 W151R mutant mice for zygotene-like spermatocytes
CUT&Tag libraries for Sertoli, pre-leptotene, leptotene/zygotene and pachytene/diplotene cells were generated as previously described(Kaya-Okur et al., 2019) with Hyperactive In-Situ ChIP Library Prep Kit for Illumina kit (Vazyme Biotech, TD901). Briefly, 50k cells for each CUT&Tag library were incubated with 10μl balanced concanavalin A–coated magnetic beads at room temperature for 10 min. The bead-bound cells were resuspended with 50μl of antibody buffer. 1 microgram anti-CTCF(Rabbit monoclonal to CTCF,  Abcam, ab128873) antibody  and Rabbit IgG(Yeasen, 36113ES10) was then added to the bead-bound cells. After 2-hour incubation at room temperature, the primary antibody was discarded carefully and 0.5μl secondary antibody diluted with 50μl Dig-wash Buffer was added to the cells. The cells were then incubated at room temperature for 1 hour. Afterwards, samples were washed gently with 800μl Dig-wash Buffer, and 0.58μl pG–Tn5 together with 100μl Dig-300 buffer was added to the samples. After 1-hour incubate at room temperature, samples were washed gently with 800μl Dig-300 Buffer. 300μl Tagmentation Buffer was then added to each sample and the samples were incubated at 37 °C for 1 h. The interactions were quenched by adding 10μl 0.5M EDTA,3μl 10% SDS and 2.5μl 20 mg/ml Proteinase K and incubating the samples at 50 °C for 1 hour. Phenol-chloroform and ethanol precipitation, as well as PCR and size-selection were performed as described in Hi-C library construction. All CUT&Tag libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode subsequently.

value: Pachytene/Diplotene

tag: cut&tag antibody


title: LZ_CTCF_Cut&Tag

value: Leptotene/Zygotene

value: anti-CTCF(Rabbit monoclonal to CTCF,  Abcam, ab128873)


title: untreated_gdT_rep3

value: untreated


title: PD_IgG_Cut&Tag

value: Rabbit IgG(Yeasen, 36113ES10)


title: Cortex_AD_REPLICATE1

value: APP/PS1 AD

value: Brain

value: Cortex

value: CTR

value: 12 months


title: gdT_IL2_antiCD3_GSI_rep2

value: hIL2 + anti-CD3 + GSI

value: PBMCs


title: C57_Male_rep1


title: Cortex_WT_NR_REPLICATE6

value: WT

value: NR

value: 5 months


title: gdT_IL2_IPP_GSI_rep2

value: hIL2 + IPP + GSI


title: Derived from CD34+ progenitors from CB

data_processing:
The Cell Ranger Single Cell Software Suite 3.0.2 was used to perform sample demultiplexing, barcode processing, and single cell 3’ v3 gene counting with GRCh38 as reference and expected cell number of 10000; polymorphisms removed.
Antibody- and hashtag-reads were pseudoaligned with kallisto v0.46.0 to a mismatch matrix generated with kite and counted with bustools v0.39.2.
A stringent filtering strategy was performed to remove low quality cells and doublets. Only cells which were found in ADT, HTO and transcriptome libraries, uniquely marked by a hashtag, with counts (5000 < x < 12,500) and percent mitochondrial reads (x < 10 %) were retained for analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcode information for each read, stored as TAG fields; h5: aggregated gene count matrix in hdf5 format. ADT.txt: tab-delimited text file including antibody UMI counts with cellular barcodes corresponding to the transcriptome sequencing. HTO.txt: tab-delimited text file including hashtag UMI counts with cellular barcodes corresponding to the transcriptome sequencing. cells_filtered.txt: list of barcodes after filtering out doublets and low quality cells.

growth_protocol: CD34+ hematopoetic progenitors were sorted and plated on OP9 or OP9-DL1. Media was supplemented with 10% human AB serum, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and cytokine mix. Cytokine mix consisted of SCF, Flt3L, IL-7, and IL-15 when stated (all 20 ng/ml) and IL-3 (all cultures: 5 ng/ml). After one week IL-3 supplementation was dropped. After two weeks Flt3L was reduced to 5 ng/ml. Medium and cytokines were refreshed every 3-4 days by replacing half of the media containing 1x concentration of cytokines. At day 7, 14 and 21 cells were replated onto fresh OP9 or OP9-DL1 onto flat bottom plates. To replate, cells were collected by forceful pipetting and passed through a 50µm filter to remove OP9/OP9-DL1 cells, wells and filter were washed 2x with PBS, cells were counted and up to 50000 cells/well were replated. Cells were harvested at day 30 and RNA was isolated.

extract_protocol:
Cells were loaded in the ChromiumTM Controller for partitioning single cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs) aiming at a recovery of 12000 cells. Single Cell 3′ reagent kit v3.1 was used for reverse transcription, cDNA amplification and library construction of gene expression libraries (10x Genomics) according to the manufacturer’s instructions. TotalSeqTM-A libraries were prepared following the protocol for 10x Single Cell 3′ Reagent Kit v3.1 provided by BioLegend, including primer sequences and reagent specifications. All libraries were quantified using a QubitTM 2.0 Fluorometer (ThermoFisher) and quality was tested on a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). Libraries were sequenced on a NovaSeq 6000 S1 Flow cell (CeGaT GmbH Tübingen), read configurations were set to 28 (R1), 9 (i7), 91 (R2). Antibody and hashtag libraries were amplified using the KAPA HiFi ready mix with primers containing Illumina Small RNA RPIx sequences and Truseq D70x_s, respectively.
Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1

treatment_protocol: FACS sort and CITE-Seq staining: Cells were FACS-sorted as CD45p cells which were Lineage (CD14, CD123, FcERa, Viability dye) negative, combined with the following CITE-Seq 34 anitbodies: CD117, CD304(Neuropilin-1), CD254 (RANKL), CD336 (NKp44), CD196(CCR6), CD34, CD7, CD127(IL-7Rα), CD1a, CD5, CD3(SK7), CD4, CD8a, TCRα/β, TCRγ/δ, CD183(CXCR3), CD94, NKp80, CD335(NKp46), CD294(CRTH2), CD278(ICOS), HLA-DR, integrinβ7, CD49d (a4), CD19, CD161, CD2, KLRG1, CD56, CD16, Siglec-7, KIR2DL1, KIR2DL2, KIR3DL1. Cells were individually hashtaged per donor and per condition.

value: Umbillical cordblood

tag: sorting strategy


title: C57_Female_rep4

value: heart

value: Female


title: gdT_IL2_HDMAPP_GSI_rep2

value: hIL2 + HDMAPP + GSI


title: PreL_CTCF_Cut&Tag

value: Preleptotene

value: anti-CTCF(Rabbit monoclonal to CTCF,  Abcam, ab128873)


title: PreL_IgG_Cut&Tag

value: Rabbit IgG(Yeasen, 36113ES10)


title: C57_Male_rep3

value: Male


title: Cortex_AD_REPLICATE2

value: APP/PS1 AD

value: Brain

value: Cortex


title: gdT_IL2_antiCD3_rep2

value: hIL2 + anti-CD3


title: Sertoli_CTCF_Cut&Tag

value: Sertoli


title: Cortex_WT_NR_REPLICATE4

value: WT

value: 12 months


title: LZ_IgG_Cut&Tag

value: Leptotene/Zygotene


title: gdT_IL2_IPP_rep2

value: hIL2 + IPP

value: PBMCs


title: Sertoli_IgG_Cut&Tag


title: C57_Female_rep1

value: heart


title: gdT_IL2_HDMAPP_rep2

value: hIL2 + HDMAPP


title: MII_2_Hi-C

data_processing:
Hi-C reads were mapped to the mm10 genome and filtered using the hiclib pipeline (https://bitbucket.org/mirnylab/hiclib) as described previously (Crane et al.).
The mapped Hi-C fragments of replicates were combined and converted into cooler format using the cooler package (https://github.com/mirnylab/cooler, Abdennur & Mirny, 2020).
Genome_build: mm10
Supplementary_files_format_and_content: cool

extract_protocol:
Murine spermatocytes were isolated by FACS as described previously (Gaysinskaya, Soh, van der Heijden, & Bortvin, 2014; Getun, Torres, & Bois, 2011) with modification. Wild-type or mutant mice of different ages were used for isolation of spermatocytes at different stages: 7-11 days old mice were used for isolating Sertoli, spermatogonia, and pre-leptotene cells,  2-week old mice for zygotene cells, 5-week old mice for pachytene, diplotene, and Metaphase II cells, and 1-2 months old SUN1 W151R mutant mice for zygotene-like spermatocytes
Hi-C libraries of different cell types were prepared using a previously described in situ Hi-C protocol (Rao et al., 2014) with minor modifications. 0.1 to 1 million cells were fixed with 920 ul 1% v/v formaldehyde in 1x HBSS at room temperature for 10 minutes with mixing. 2.5M Glycine was added to the cells to make the final concentration of Glycine 0.2 M. Cells were incubated at RT for 5 min with mixing and on ice for at least 15 min to quench crosslinking. The fixed cells were centrifuged at 3000xg for 10 min at 4°C. The supernatant was discarded and cell pellets were resuspended with 100 ul ice-cold Hi-C lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630) with protease inhibitors. Samples were incubated on ice for 15 minutes and centrifuged for 5 minutes at 3,000xg at 4°C to isolate nuclei. The nuclei pellets were washed once with 100 ul 1x NEB Buffer 3.1, resuspended in 2 ul 10x NEB Buffer 3.1, 14 ul ddH2O, and 4 ul of 0.5% SDS and then incubated at 65°C for 5 min to open up chromatin. 2.2 μl of 10% Triton X-100 (Sigma, 93443) was added to the samples, and samples were incubated at 37°C for 15 minutes to quench SDS. To digest chromatin, 0.5 μl of 10X NEB 3.1 Buffer, 1.5 ul ddH2O, and 1 ul (50U) of DpnII restriction were added into the samples to bring total reaction volume to ~25 ul.  Digestion was performed overnight at 37°C on a thermomixer with interval shaking (shake at 950rpm for 10 sec with 5 min intervals). Following digestion, samples were incubated at 65°C for 20 min to inactivate the restriction enzyme, then cool to RT on ice. To fill the restriction overhangs, 6μl of fill-in master mix (3.75μl of 0.4mM biotin-14-dATP (Life Technologies, 19524-016), 0.15μl of 10mM dCTP/dGTP/dTTP, 1μl of 5U/μl Klenow fragment (3’ → 5’ exo-), 0.6μl 10X NEB 3.1, 0.2μl Milli-Q water) was added to the reaction and samples were incubated at 37°C for 1 hr in thermomixer (shake at 950rpm for 10 sec with 5 min intervals). 90 ul of ligation master mix (49.8μl of water, 24μl of 5X T4 DNA ligase buffer (Invitrogen), 10μl of 10% Triton X-100, 1.2μl of 10mg/ml Bovine Serum Albumin (100X BSA), 5μl of 1 U/ μl T4 DNA Ligase (Invitrogen)) was then added and samples were mixed by inverting and incubated at 16 °C for 4 hours. After ligation, samples were centrifuged for 5 min at 3,000g. The pellets were washed with 100 ul 1X NEB buffer 3 and resuspended with 50 ul 1X NEB buffer. To reverse crosslinking, 3ul 20mg/ml proteinase K (NEB, P8102) and 5μl of 10% SDS were added into the samples and then incubated at 65°C for 2hrs. Phenol-chloroform extraction and ethanol precipitation were performed. The purified DNA was dissolved in 130ul 1x Tris Buffer and sheared by Covaris M220(Peak Incident Power: 50W; Duty factor: 20%; Cycles per Burst: 200; Treatment Time: 65s). To minimize sample loss, size selection was not performed after shearing. End repair of DNA fragments and ligation with Illumina Truseq adapters was performed using End Repair/dA-Tailing Module (NEB, E7442L) and Ligation Module (NEB, E7445L) according to product manuals. Following adaptor ligation, the total volume of DNA samples was brought to 300 ul with Milli-Q H2O. To purify biotinylated DNA fragments, 50μl Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602) were washed twice with 100μl 1X Tween Washing Buffer (TWB, 5mM Tris-HCl (pH 7.5); 0.5mM EDTA; 1M NaCl; 0.05% Tween 20), and then resuspended in 300μl 2X Binding Buffer (10mM Tris-HCl (pH 7.5); 1mM EDTA; 2M NaCl) before being added to DNA samples. The samples were incubated at RT for 15 minutes with rotation to bind biotinylated DNA to the streptavidin beads. Beads were washed twice with 100μl 1X TWB on a Thermomixer at 55°C for 2 min with mixing and resuspended in 50ul Milli-Q water. Samples were amplified with Phusion High-Fidelity DNA Polymerase (Thermo, F-530L) for 4-7 cycles. For size selection, 0.5X volumes of AMPure XP beads (Beckman Coulter, A63881) prewarmed to RT was added to the PCR products and samples were incubated at RT for 5 minutes. Samples were then separated on a magnet. The clear solution was mixed with another 0.5X volumes of AMPure XP beads by pipetting and incubated at RT for 5 minutes.  Samples were again separated on a magnet and the clear solution was discarded. Beads were washed once with 700μl freshly made 70% ethanol without mixing. After removing ethanol, tubes containing beads were left on the magnet for 5 minutes with lids open to allow the remaining ethanol to evaporate completely. DNA was eluted from beads with 25-50μl of 1X Tris buffer. All Hi-C libraries were sequenced on Illumina Nova Seq 6000 platform at PE150 mode.

value: Wild Type

value: meiosis II


title: C57_Female_rep3

value: Female


title: E95_Male_rep3

data_processing:
Libraries were run on a HiSeq2500 (Illumina) with 2×150 bp paired end reads.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_ID feature in the annotation file. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: comma-separated values file includes Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: comma-separated values file includes Matrix table with normalized gene counts for every gene and every sample

extract_protocol:
Embryonic hearts were dissected from E9.5 embryos, and sex were determined by genotyping the Sry gene with non-heart tissues of the embryos, and cardiac RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: MII_1_Hi-C


title: E95_Male_rep2


title: untreated_gdT_rep2

value: untreated


title: C57_Female_rep2


title: PreL_2_Hi-C

value: pre-leptotene stage


title: Auto_Zanoni_LP2_070821_Trx_HUMAN_s5-torrent-server-vm_230_IonCode_0116.gene.chp Signal

city: Boston

first: Achille

last: Broggi

state: MA

address: 300 Longwood Ave

department: Pediatrics/Immunology

institute: Boston Children's Hospital

data_processing:
Raw sequences were aligned and processed by Torrent Suite 5.12.1 according to standard analysis procedures. Output normalized counts (in read per milion) were generated. (see *.chp files )
Supplementary_files_format_and_content: Processed data files (.chp) contain normalized counts (read per million) .

source_name: BAL Positive 25

extract_protocol:
mRNA was extracted with Purelink mRNA extraction kit according to manufacturer's instructons.
cDNA was prepared with SUPERSCRIPT VILO cDNA synthesis kit (Thermo), Library was prepared with IonChef using: Ion AmpliSeq™ Transcriptome Human Gene Expression Panel, Chef-Ready Kit

value: bronchoalveolar lavage fluid

tag: age group


title: Auto_Zanoni_LP2_070821_Trx_HUMAN_s5-torrent-server-vm_230_IonCode_0114.gene.chp Signal

source_name: BAL Positive 23


title: E95_Male_rep1

value: Male


title: E95_Male_rep4


title: E95_Female_rep4


title: PreL_1_Hi-C

tag: cell type


title: gdT_IL2_IPP_GSI_rep1

value: hIL2 + IPP + GSI


title: Auto_Zanoni_LP2_070821_Trx_HUMAN_s5-torrent-server-vm_230_IonCode_0113.gene.chp Signal

source_name: BAL Positive 22


title: gdT_IL2_antiCD3_GSI_rep1

value: hIL2 + anti-CD3 + GSI


title: Spg_2_Hi-C

value: spermatogonia


title: Auto_Zanoni_LP2_070821_Trx_HUMAN_s5-torrent-server-vm_230_IonCode_0112.gene.chp Signal

source_name: BAL Negative 46


title: gdT_IL2_rep2


title: Cortex_WT_REPLICATE6

value: WT

value: Brain

value: Cortex

value: CTR


title: Cortex_WT_NR_REPLICATE5

value: NR

value: 5 months

value: 12 months


title: Spg_1_Hi-C

value: Wild Type


title: Cortex_WT_NR_REPLICATE2


title: E95_Female_rep3

value: heart


title: E95_Female_rep2

value: Female


title: Cortex_WT_NR_REPLICATE1


title: gdT_IL2_HDMAPP_GSI_rep1

value: hIL2 + HDMAPP + GSI

value: PBMCs


title: Cortex_WT_NR_REPLICATE3


title: Sertoli_2_Hi-C

value: Sertoli


title: Cortex_WT_REPLICATE5


title: Cortex_WT_REPLICATE3


title: gdT_IL2_antiCD3_rep1

value: hIL2 + anti-CD3


title: Auto_Zanoni_LP2_070821_Trx_HUMAN_s5-torrent-server-vm_230_IonCode_0110.gene.chp Signal

source_name: BAL Negative 35

value: bronchoalveolar lavage fluid


title: E95_Female_rep1


title: Sertoli_1_Hi-C


title: gdT_IL2_IPP_rep1

value: hIL2 + IPP


title: gdT_IL2_HDMAPP_rep1

value: hIL2 + HDMAPP


title: F1-3

first: Kexin

last: Zou

address: 131 Dongan Rd.

department: School of Medicine

institute: Fudan University

data_processing:
bcl2fastq version 2.1 software used for basecalling with default parameters
Raw reads were filtered by skewer v0.2.2
Reads were aligned to the mm10 genome assembly using Bismark v0.16.3
Differential Methylation was indentied by DSS v2.30.0, with parameters, delta=0.05, p.threshold=0.05,minlen=50, minCG=3 , dis.merge=50, pct.sig=0.5
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include chromesome, position,  mC reads, non-mC reads and regions of differentially methylated genes.

source_name: sperm

extract_protocol:
Sperm were obtained from the caudal epididymis of 16-week-old F1 male mice. Then, the sperm were washed in phosphate-buffered saline and centrifuged to pellet, frozen in liquid nitrogen.
DNA libraries were prepared for sequencing using standard Illumina protocols.

value: ICR

value: sperm

tag: sample type

value: GDM


title: Auto_Zanoni_LP1_070721_Trx_HUMAN_s5-torrent-server-vm_228_IonCode_0108.gene.chp Signal

source_name: BAL Negative 25


title: Cortex_WT_REPLICATE4

value: WT

value: Brain

value: Cortex

value: CTR


title: Auto_Zanoni_LP2_070821_Trx_HUMAN_s5-torrent-server-vm_230_IonCode_0109.gene.chp Signal

source_name: BAL Negative 34


title: Cortex_WT_REPLICATE1

value: 12 months


title: gdT_IL2_rep1


title: Auto_Zanoni_LP2_070821_Trx_HUMAN_s5-torrent-server-vm_230_IonCode_0111.gene.chp Signal

source_name: BAL Negative 44


title: untreated_gdT_rep1

value: untreated


title: F1-2


title: Auto_Zanoni_LP1_070721_Trx_HUMAN_s5-torrent-server-vm_228_IonCode_0106.gene.chp Signal

source_name: Swab > 30 CT 48

value: naso-pharingeal SWAB

tag: viral load tertile

tag: severity grade


title: Auto_Zanoni_LP1_070721_Trx_HUMAN_s5-torrent-server-vm_228_IonCode_0107.gene.chp Signal

source_name: Swab > 30 CT 46

tag: tissue


title: Dendritic cells - D1690_uninf

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

country: France

institute: Institut Curie

data_processing:
Demultiplexing was done with cellranger’s mkfastq (v 4.0)
Reads were aligned using cellranger (v 2.1) with the human hg38 genome and MVA genome (NC_006998.1)
Cell calling was done with cellranger (v 4.0) in conjonction with EmptyDrops from DropletUtils package (v 1.6.1)
Dimensionality reduction and donor effect removal were done using the MNN method from Seurat R package (v 3.2.2)
Clustering was done using Louvain algorithm implementation in Seurat
Differential expression was done using the MAST package (v 1.12) with a log2FC threshold of 0.5 and a FDR of 0.05, aswell as min.pct of 0.3
Genome_build: hg38
Genome_build: NC_006998.1
Supplementary_files_format_and_content: Tab-delimited table of filtered barcodes produced by cellranger
Supplementary_files_format_and_content: Tab-delimited table of filtered ENSEMBL and Symbol of genes
Supplementary_files_format_and_content: Filtered count matrix produced by cellranger
Supplementary_files_format_and_content: Count matrix for all samples produced with Seurat, after EmptyDrop’s cell calling
Supplementary_files_format_and_content: Normalized count matrix for all samples produced with Seurat, after EmptyDrop’s cell calling
Supplementary_files_format_and_content: Tab-delimited table of cells metadata
Supplementary_files_format_and_content: Tab-delimited table of raw barcodes from cellranger
Supplementary_files_format_and_content: Tab-delimited table of all ENSEMBL and Symbol of genes

source_name: monocyte-derived dendritic cell

growth_protocol: Blood was received the day of donation and obtained from LRSC plus tubing. Subsequently, PBMCs were isolated the same day and stored in DC medium at 4°C over night. After CD14+ isolation, monocytes were seeded in 10 cm perti dishes at 1 million per ml in DC medium supplemented with human GM-CSF (Miltenyi) at 10 ng/ml, and IL-4 (Miltenyi) at 50 ng/ml for 5 days to obtain MDDCs.

extract_protocol:
24 hpi infection with MVA MOI 0.5 MDDCs were sorted according to FSC/SSC characteristics and DAPI staining, and subsequently was loaded on a 10× Chromium instrument (10× Genomics) according to manufacturer’s protocol based on the 10× GEMCode proprietary technology. Single-cell RNA-Seq libraries were prepared using Chromium Single Cell 3′ v2 Reagent Kit (10× Genomics) according to manufacturer’s protocol.
Indexed sequencing libraries were constructed using the reagents from the Chromium Single Cell 3′ v2 Reagent Kit, following these steps: (1) fragmentation, end repair, and A-tailing; (2) size selection with SPRI select; (3) adaptor ligation; (4) post ligation cleanup with SPRI select; (5) sample index PCR and cleanup with SPRI select beads.

treatment_protocol: At day 5 of MDDC differentiation, cells were harvested, counted and resuspended in fresh DC medium supplemented with GM-CSF (20 ng/ml) and IL-4 (100 ng/ml) at a concentration of 1 million per ml. 1 ml of MDDCs were seeded in round-bottom 96-well plates and stimulated/infected with 1 ml of MVA dilutions.

tag: infection

value: Uninfected

tag: disease state

value: healthy donor

value: immature monocyte-derived dendritic cell

tag: donor


title: D_2

tag: strain

tag: genotype

value: Wild Type

value: diplotene stage


title: Auto_Zanoni_LP1_070721_Trx_HUMAN_s5-torrent-server-vm_228_IonCode_0105.gene.chp Signal

source_name: Swab > 30 CT 47


title: C3

tag: age

value: control


title: F1-1


title: C2


title: Auto_Zanoni_LP1_070721_Trx_HUMAN_s5-torrent-server-vm_228_IonCode_0104.gene.chp Signal

source_name: TF Negative 25


title: P_1

value: pachytene stage


title: Z_1

value: zygotene stage


title: P_2


title: Dendritic cells - D1690_MVA_05

value: Infected (50 percent infection)


title: D_1


title: Ly49H+ NK_retrogenic spleen

city: München

first: Sophie

last: Flommersfeld

address: Trogerstr. 30

department: Institute for Medical Microbiology, Immunology and Hygiene

institute: Technical University of Munich

description: scRNAseq

data_processing:
Cell Ranger (version 2.1.0; 10x Genomics) was used for demultiplexing and alignment using default parameters.
velocyto 27 (version 0.17.17) performed counting of spliced and unspliced RNA molecules to create loom file.
Python software package SCANPY (version 1.4.4) was used for downstream analysis.
Cells filtered out that express < 1200 and >3000 genes, > 6000 counts, > 0.03% mitochondrial genes.
Gene counts were per-cell normalized and (log+1)-transformed.
Cell cycle, percent mito and n_counts were regressed out.
Genome_build: Mouse reference genome GRCm38 release 84
Supplementary_files_format_and_content: Output of the Cell Ranger Analysis Pipeline (mtx and tsv files; unfiltered and unnormalized).
Supplementary_files_format_and_content: Unnormalized and unfiltered loom-file, containing information about spliced and unspliced mRNA counts.

source_name: splenic NK cells

extract_protocol:
Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics).
Chromium Single Cell 3′ Library Construction Kit (10x Genomics).
Paired-end, single indexing.

value: spleen

value: Ly49H+ NK cells


title: Cortex_WT_REPLICATE2

tag: genotype/variation

value: WT

value: Brain

tag: brain region

tag: treatment

tag: treatment duration


title: L_2

source_name: spermatocytes

value: leptotene stage


title: Dendritic cells - D1689_uninf


title: L_1


title: Auto_Zanoni_LP1_070721_Trx_HUMAN_s5-torrent-server-vm_228_IonCode_0102.gene.chp Signal

source_name: TF Negative 23


title: C1

value: ICR

value: sperm


title: Dendritic cells - D1689_MVA_05

data_processing:
Demultiplexing was done with cellranger’s mkfastq (v 2.1)
Reads were aligned using cellranger (v 4.0) with the human hg38 genome and MVA genome (NC_006998.1)
Cell calling was done with cellranger (v 4.0) in conjonction with EmptyDrops from DropletUtils package (v 1.6.1)
Dimensionality reduction and donor effect removal were done using the MNN method from Seurat R package (v 3.2.2)
Clustering was done using Louvain algorithm implementation in Seurat
Differential expression was done using the MAST package (v 1.12) with a log2FC threshold of 0.5 and a FDR of 0.05, aswell as min.pct of 0.3
Genome_build: hg38
Genome_build: NC_006998.1
Supplementary_files_format_and_content: Tab-delimited table of filtered barcodes produced by cellranger
Supplementary_files_format_and_content: Tab-delimited table of filtered ENSEMBL and Symbol of genes
Supplementary_files_format_and_content: Filtered count matrix produced by cellranger
Supplementary_files_format_and_content: Count matrix for all samples produced with Seurat, after EmptyDrop’s cell calling
Supplementary_files_format_and_content: Normalized count matrix for all samples produced with Seurat, after EmptyDrop’s cell calling
Supplementary_files_format_and_content: Tab-delimited table of cells metadata
Supplementary_files_format_and_content: Tab-delimited table of raw barcodes from cellranger
Supplementary_files_format_and_content: Tab-delimited table of all ENSEMBL and Symbol of genes


title: Auto_Zanoni_LP1_070721_Trx_HUMAN_s5-torrent-server-vm_228_IonCode_0103.gene.chp Signal

source_name: TF Negative 24

value: naso-pharingeal SWAB


title: Z_2


title: Y2_Replicate2 [X2y2]

status: Public on Aug 24 2021

first: Guoping

address: 138 Yi Xue Yuan Road

data_processing:
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:mm10）using Hisat2（version:2.0.4).
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized the counts using TMM (Trimmed mean of M values)
edgeR was used to find the differential expression genes
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Cat#74106, QIAGEN) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ovary tissue from E13, E15, E17, P0, P3, P5, P7, P14, P21, P60, Year2  WT mice, which were dissected in ice-cold HBSS.These tissues were flash frozen in the nitrogen and then stored into -80 oC

value: ovary


title: Y2_Replicate1 [X2y1]


title: Y1_Replicate1 [X12m1]


title: P60_Replicate2 [P602]

value: Postnatal day60


title: Y1_Replicate2 [X12m2]


title: P60_Replicate1 [P601]


title: Grape berry 45 days after flower sequencing sample

city: Nanjing

first: Chen

last: Wang

address: Weigang 1 Hao

institute: Nanjing Agricultural University

data_processing:
HCS1.5 + RTA1.13.48 + BclConverter-1.9.0-11-03-08 HCS为HiSeq Sequencing Control Software，RTA is Real-time analysis software，the sequencing profiles were performed basecalling，and turned into binary file bcl，then the bcl file was tranferred into the readable sequence file by the BclConverter-1.9.0-11-03-08 software,  the quality value of the fasta produced by this version is phred+64.
We use software developed by BGI (unpublished)to deal with the data from HiSeq sequencing  adaptor sequence,  or low-quality sequence
Map the small RNA tags to genome by SOAP to analyze their expression and distribution on the genome with paremeter -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap
If there is miRNA information of the species in miRBase , we use NCBI BLAST softare analysis the known miRNA, the main paremeter is -p blastn -F F -e 0.01, the other parameter is deault.  If there is no miRNA information of the species in miRBase ,We use software developed by BGI tag2miRNA with deault paremeter
Map to GeneBank databse, Rfam database to identify all small RNA contain rRNA、sRNA、snRNA、tRNA with Blast software with paremeter -p blastn -F F -e 0.01
Genome_build: We developed a prediction software Mireap to predict novel miRNA by exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the unannotated small RNA tags which could be mapped to genome. Mireap can be accessed from the following link: http://sourceforge.net/projects/mireap/
Supplementary_files_format_and_content: We use plant targets prediction pipeline for indentify target prediction are based on those suggested by Allen et al. (microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell, 2005, 121:207-221) - Supplemental document S1 and by Schwab et al. (Specific effects of microRNAs on the plant transcriptome. Dev. Cell, 2005, 8: 517 - 527)

organism: Vitis vinifera

extract_protocol:
The modified CTAB method
RNA libraries were prepared for sequencing using standard Illumina protocols
small RNA Solexa sequencing and mRNA Degradome sequencing

tag: time point

value: Grape berry with 45 days


title: Grape berry 90 days after flower sequencing sample

value: Grape berry with 90 days


title: Grape berry 5 days after flower sequencing sample

value: Grape berry with 5 days


title: P21_Replicate2 [P212]

value: Postnatal day21


title: P14_Replicate1 [P141]

value: Postnatal day14


title: P14_Replicate2 [P142]


title: P21_Replicate1 [P211]


title: P7_Replicate1 [P71]

value: Postnatal day7


title: P3_Replicate1 [P31]

value: Postnatal day3


title: P7_Replicate2 [P72]


title: E17_Replicate2 [E17-2]

value: Embryonic day17


title: P0_Replicate1 [P01]

value: Postnatal day0


title: P3_Replicate2 [P32]


title: E17_Replicate1 [E17-1]


title: P0_Replicate2 [P02]


title: E15_Replicate1 [E15-2]

value: Embryonic day15


title: E15_Replicate2 [E15-3]


title: E13_Replicate2 [E13-2]

value: Embryonic day13


title: E13_Replicate1 [E13-1]


title: WT_rep2

city: Saint Louis

first: Andrea

last: Santeford

state: MO

address: 660 S. Euclid Ave.

department: Opthalmology

institute: Washington University School of Medicine

description:
mRNA
counts.txt

data_processing:
For miRNA analysis from RNAseq of 3 to 30 months C57Bl/6 WT samples: Sequencing reads were analyzed using Cofactor Genomics EXP software and aligned to the mouse mm9 genome. Overlapping reads were clustered together to assemble expressed loci and provide respective counts and coverage levels for each loci. Coverage was calculated by $alignedBases/$coveredBases. 6x cutoff of cluster depth corresponding to Integer(sequencedBases/integer(genomeBases)). In order to allow cross sample comparative expression between small-RNAs, all counts and expression levels were normalized to the sample with the fewest reads. A pair-wise comparison was performed between samples and logs2 ratios were computed for each expressed small-RNA.
For RNAseq analysis of macrophages from miR-146b knockout and wildtype littermate controls: Second mate was used for sample demultiplexing. Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All. Gene expression was obtained via ht-seq and DESeq2 for differential expression. Gene expression was obtained using in-house scripts based on MACS and HTSeq (https://github.com/ctlab/quant3p).
For scRNA-seq: Data was analyzed first using Cellranger 3.1.0 and mapped to the mouse mm10 genome with default parameters. Expression matrices were reanalyzed using Monocle3 (v0.2.1) (44). Initial clustering identified minor contamination (<1%) of cells not expressing macrophage markers (Emr1, Mertk, Csf1r, and Cd68) that were removed from further analyses. tSNE-dimension reduction was performed on the top principal components learned from the 317 genes with the highest variance across the cells that passed quality filters (>5000 mRNA counts) and the Louvain method was used to define clusters. The Monocle3 fit_models() function with the following parameters (model_formula_str = "~library + 1") was used to asses differential gene expression.
Genome_build: For miRNA analysis of C57Bl/6 3-30 month macrophages: mmu9 (MGSCv37)
Genome_build: For RNAseq and single-cell RNAseq analyses of Lys2 Cre+/-; miR146b conditional knockout macrophages and littermate controls: mmu10 (GRCm38)
Supplementary_files_format_and_content: mirSeq_3-30months.txt
Supplementary_files_format_and_content: counts.txt
Supplementary_files_format_and_content: *.tar: Tar archives of barcodes.tsv, features.tsv, and matrix.mtx files.

source_name: peritoneal macrophage

growth_protocol: Macrophages were harvested by peritoneal lavage 4 days post-IP injection with 4% Thioglycollate and plated in DMEM containing 10% FBS, 1% L-glutamine, and 1% Penicillin/Streptomycin. Cells were allowed to adhere to the plate overnight, followed by 3-4 washes in DPBS to remove non-adherent cells. Complete DMEM was replaced and cells were rested for 24hours prior to harvest for RNA isolation.

extract_protocol:
Macrophage total mRNA was extracted using RNeasy RNA Isolation kit (Qiagen).
cDNA synthesis was carried out using custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded with consecutive acid-alkali treatment. Subsequently, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) clean-up. The mixture was enriched by PCR for 12 cycles and SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) purified to yield final strand-specific RNA-seq libraries.

value: Lyz2 Cre +/- X miR-146b flox/flox; C57Bl/6J

value: 3 months

value: Peritoneal macrophage


title: WT_rep4

description:
mRNA
counts.txt


title: WT_rep3

description:
mRNA
counts.txt


title: KO_rep1

description:
mRNA
counts.txt


title: KO_rep2

description:
mRNA
counts.txt


title: KO_rep4

description:
mRNA
counts.txt


title: KO_rep3

description:
mRNA
counts.txt


title: NAc scRNA-Seq Sample9

city: Doha

first: Mohamed Nadhir

last: Djekidel

state: Doha

address: Gharafa

department: Translational Medicine Department

country: Qatar

institute: Sidra Medicine

data_processing:
Raw sequencing data were processed with cellranger (v.13.1) (Zheng et al., 2017) for sample demultiplexing, cell barcode detection and single-cell expression matrices generation. In brief, the “cellranger  mkfastq” command was used to demultiplex the different samples, extract the UMI barcodes and generate the fastq files. The gene-cell expression matrices were then generated for each sample separately using the “cellranger count” command by aligning the reads to the mm9 genome. In total 11 single-cell gene expression matrices were generated, corresponding to the 11 biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: tab separated files

source_name: NAc

growth_protocol: Adult mice were housed in our animal facility with 12 h light/dark cycles and food ab libitum. Animals were used for analysis in accordance with protocols approved by the Institutional Animal Care and Use Committee

extract_protocol:
For single cell dissociation of nucleus accumbens (NAc), the mice were anesthetized and the entire brain was quickly removed and transferred into ice-cold Hibernate A/B27 medium (60 ml Hibernate A medium with 1 ml B27 and 0.15 ml Glutamax). The coronal sections containing NAc were cut with brain matrix and further sliced into 0.5 mm slices in ice-cold Hibernate A/B27 medium. Then the NAc tissue was dissected from each slice under dissection microscope and subjected to tissue dissociation (Figure S1A). The NAc tissues were further dissociated into single-cell suspension with a papain-based dissociation protocol (Brewer and Torricelli, 2007) with some modifications. Briefly, the tissues from two animals were cut into small pieces and incubated in dissociation medium (Hibernate A-Ca medium with 2 mg/ml papain and 2X Glutamax) at 300C for 35-40 min with constant agitation. After washing with 5 ml Hibernate A/B27 medium, the tissues were triturated with fire polished glass Pasteur pipettes for 10 times in 2 ml Hibernate A/B27 medium to generate single-cell suspension, which was repeated for three times. To remove debris, the 6 ml single-cell suspension was loaded on a 4-layer OptiPrep gradient (Brewer and Torricelli, 2007) and centrifuged at 800 g for 15 min at 40C. Fractions 2 – 4 were then collected and washed with 5 ml Hibernate A/B27 medium and 5 ml DPBS with 0.01% BSA. The cells were spun down at 200 g for 3 min and re-suspended in 0.2 ml DPBS with 0.01% BSA. A 10 μl cell suspension was stained with Trypan Blue and the live cells were counted. During the entire procedure, the tissues or cells were kept in ice-cold solutions except for the papain digestion.
The cells suspension was diluted with DPBS containing 0.01% BSA to 300 - 330 cells/μl for single cell capture. Single cells and barcoded beads were captured into droplets with 10X Chromium platform (10X Genomics) according to the protocol from the manufacturer (Zheng et al., 2017). After cell capture, reverse transcription, cDNA amplification and sequencing library preparation were perform as described in the same protocol (Zheng et al., 2017). The libraries were sequenced on Illumina Hiseq 2500 sequencer with pair-end sequencing (Read1: 26bp, Index: 8bp, Read2: 98bp).
10x

tag: line

value: NAc

tag: Sex

value: male

value: 8-10 weeks


title: NAc scRNA-Seq Sample10


title: NAc scRNA-Seq Sample11


title: NAc scRNA-Seq Sample3


title: NAc scRNA-Seq Sample6


title: NAc scRNA-Seq Sample7


title: MKN7_EB_H3K27ac_shCTRL

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie1.0.1.
Duplication reads were removed from aligned file by using picard-tools-1.119.
Alignments were filtered for ENCODE blacklisted regions (ENCODE Project Consortium, 2012, doi: 10.1038/nature11247).
The mapped sequence reads were extended to 100 bp and converted to the continuous signal data in bedGraph format using HOMER makeUCSCfile command.  BedGraph files were converted to bigwig files using UCSC BedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Gastric cancer cell line

growth_protocol: These cells were cultured in RPMI 1640 (Wako, Tokyo, Japan) with 10% fetal bovine serum (FBS) (HyClone SH30910.03, GE Healthcare, Chicago, IL) and Penicillin-Streptomycin (Sigma-Aldrich, St. Louis, MO) at 37 °C in 5% CO2 incubator.

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA Biosystems) following the manufacturer’s protocol.

tag: cell type

value: Gastric cancer cell line

tag: chip antibody


title: NAc scRNA-Seq Sample2


title: NAc scRNA-Seq Sample8


title: MKN7_WT_H3K27ac (MKN7_EB control)


title: NAc scRNA-Seq Sample1


title: NAc scRNA-Seq Sample4


title: NAc scRNA-Seq Sample5


title: MKN7_EB_H3K27ac_shEHF


title: MKN7_WT_H3K4me3 (MKN7_EB control)

value: H3K4me3_ChIP (Active Motif, 39159, lot 25817005)


title: MKN7_WT_H3K4me1 (MKN7_EB control)

value: H3K4me1_ChIP (CST, 5326S, lot 3)


title: MKN7_EB_H3K4me1_Bulk_cells


title: WT_rep1

description:
mRNA
counts.txt


title: Day 114 SFTPCI73T/tdT iAEC2s [C11_b]

first: Carlos

last: Villacorta-Martin

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
The sample was processed using the standard Cellranger v.2 pipeline
Reads were mapped to hg19 with TdTomato reporter
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: hg19 with TdTomato reporter
Supplementary_files_format_and_content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: SPC2-ST-C11 (SFTPCI73T/tdT) human iPSC line

growth_protocol: To generate iAEC2s, we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors using methods we have previously described (Hawkins et al., JCI 2017; Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019). In brief, cells maintained in mTeSR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) for 3 days (day 0-3) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent and passaged into 6-well dishes pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation media (cSFDM) base as previously described (Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019), supplemented with 2 µM Dorsomorphin (‘‘DS’’; Stemgent) and 10 µM SB431542 (‘‘SB’’; Tocris). For the first 24 hour after passaging, 10 µM Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (day 3-6), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media until day 16, as we have previously published (Jacob et al., Cell Stem Cell 2017). ‘‘CBRa’’ media consists of cSFDM base supplemented with 3 µM CHIR99021 (Tocris), 10 ng/ml recombinant human BMP4 (rhBMP4, R&D Systems), and 100 nM retinoic acid (RA, Sigma). On day 16 of differentiation, live cells were sorted on a high-speed cell sorter (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., JCI 2017). Sorted lung progenitors were resuspended in undiluted growth factor reduced 3D Matrigel (Corning) at a concentration of approximately 400 cells/µl and distal/alveolar differentiation of cells was performed in CK+DCI media, consisting of cSFDM base supplemented with 3 µM CHIR99021, 10 ng/mL rhKGF (CK), and 50 nM dexamethasone (Sigma), 0.1 mM 8-Bromoadenosine 30,50-cyclic monophosphate sodium salt (Sigma) and 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI). SFTPCtdTomato+ cells were sorted on day 51 of differentiation. iAEC2s were single-cell passaged in self-renewing 3D alveolosphere cultures approximately every 2 weeks (day 65, day 82, day 101) through day 114. On day 114, all live SFTPCtdTomato+ cells were sorted and encapsulated for scRNA-seq using the 10X Chromium System.

extract_protocol:
cells were lysed in Trizol; single cells were captured for sequencing library prepration using a 10X Chromium
Resulting cDNA libraries were sequenced on an Illumina NextSeq 500 instrument (Illumina, USA). Single cell capture was conducted at the Boston University Single Cell Sequencing Core using a 10X Genomics Chromium System.
3' RNA-seq single cells

tag: developmental stage

value: day 114 distal lung directed differentiation

tag: culture media

value: CK+DCI

tag: isolation method

value: FACS purification for live day 114 cells


title: Day 114 SFTPCI73T/tdT iAEC2s [C11]


title: Day 114 SFTPCtdT/WT iAEC2s [B2]

source_name: SPC2-ST-B2 (SFTPCtdT/WT)  human iPSC line


title: Day 113 SFTPCtdT/WT iAEC2s [B2]

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to hg19 with TdTomato reporter
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: hg19 with TdTomato reporter
Supplementary_files_format_and_content: standard output from the cellranger count pipeline: count matrices compressed in the HDF5 (Hierarchical Data Format) format

growth_protocol: To generate iAEC2s, we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors using methods we have previously described (Hawkins et al., JCI 2017; Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019). In brief, cells maintained in mTeSR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) for 3 days (day 0-3) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent and passaged into 6-well dishes pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation media (cSFDM) base as previously described (Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019), supplemented with 2 µM Dorsomorphin (‘‘DS’’; Stemgent) and 10 µM SB431542 (‘‘SB’’; Tocris). For the first 24 hour after passaging, 10 µM Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (day 3-6), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media until day 13, as we have previously published (Jacob et al., Cell Stem Cell 2017). ‘‘CBRa’’ media consists of cSFDM base supplemented with 3 µM CHIR99021 (Tocris), 10 ng/ml recombinant human BMP4 (rhBMP4, R&D Systems), and 100 nM retinoic acid (RA, Sigma). On day 13 of differentiation, live cells were sorted on a high-speed cell sorter (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., JCI 2017). Sorted lung progenitors were resuspended in undiluted growth factor reduced 3D Matrigel (Corning) at a concentration of approximately 400 cells/µl and distal/alveolar differentiation of cells was performed in CK+DCI media, consisting of cSFDM base supplemented with 3 µM CHIR99021, 10 ng/mL rhKGF (CK), and 50 nM dexamethasone (Sigma), 0.1 mM 8-Bromoadenosine 30,50-cyclic monophosphate sodium salt (Sigma) and 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI). SFTPCtdTomato+ cells were sorted on day 41 and again on day 79 of differentiation. iAEC2s were single-cell passaged in self-renewing 3D alveolosphere cultures approximately every 10-12 days (day 57, day 68, day 79, day 91, day 103) through day 113. On day 113, live SFTPCtdTomato+ cells were sorted and encapsulated for scRNA-seq using the 10X Chromium System.

value: day 113 distal lung directed differentiation

value: FACS purification for live day 113 SFTPCtdTomato+ cells


title: Day 30 SFTPCI73T/tdT iAEC2s [C11]

data_processing:
The sample was processed using the standard Cellranger v.2 pipeline
Reads were mapped to hg19 with TdTomato reporter
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: hg19 with TdTomato reporter
Supplementary_files_format_and_content: standard output from the cellranger count pipeline: count matrices compressed in the HDF5 (Hierarchical Data Format) format

growth_protocol: To generate iAEC2s, we performed PSC directed differentiation via definitive endoderm into NKX2-1 lung progenitors using methods we have previously described (Hawkins et al., JCI 2017; Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019). In brief, cells maintained in mTeSR1 media were differentiated into definitive endoderm using the STEMdiff Definitive Endoderm Kit (StemCell Technologies) for 3 days (day 0-3) and after the endoderm-induction stage, cells were dissociated with gentle cell dissociation reagent and passaged into 6-well dishes pre-coated with growth factor reduced Matrigel in ‘‘DS/SB’’ anteriorization media, consisting of complete serum-free differentiation media (cSFDM) base as previously described (Jacob et al., Cell Stem Cell 2017; Jacob et al., Nat Protoc 2019), supplemented with 2 µM Dorsomorphin (‘‘DS’’; Stemgent) and 10 µM SB431542 (‘‘SB’’; Tocris). For the first 24 hour after passaging, 10 µM Y-27632 was added to the media. After anteriorization in DS/SB media for 3 days (day 3-6), cells were cultured in ‘‘CBRa’’ lung progenitor-induction media until day 15, as we have previously published (Jacob et al., Cell Stem Cell 2017). ‘‘CBRa’’ media consists of cSFDM base supplemented with 3 µM CHIR99021 (Tocris), 10 ng/ml recombinant human BMP4 (rhBMP4, R&D Systems), and 100 nM retinoic acid (RA, Sigma). On day 15 of differentiation, live cells were sorted on a high-speed cell sorter (MoFlo Legacy or MoFlo Astrios EQ) to isolate NKX2-1+ lung progenitors based on CD47hi/CD26neg gating (Hawkins et al., JCI 2017). Sorted lung progenitors were resuspended in undiluted growth factor reduced 3D Matrigel (Corning) at a concentration of approximately 400 cells/µl and distal/alveolar differentiation of cells was performed in CK+DCI media, consisting of cSFDM base supplemented with 3 µM CHIR99021, 10 ng/mL rhKGF (CK), and 50 nM dexamethasone (Sigma), 0.1 mM 8-Bromoadenosine 30,50-cyclic monophosphate sodium salt (Sigma) and 0.1 mM 3-Isobutyl-1-methylxanthine (IBMX; Sigma) (DCI). On day 30, live SFTPCtdTomato+ positive cells were sorted and encapsulated for scRNA-seq using the 10X Chromium System.

value: day 30 distal lung directed differentiation

value: FACS purification for live day 30 SFTPCtdTomato+ cells


title: MKN7_EB_H3K27ac_Bulk_cells


title: MKN7_EB_H3K4me3_Bulk_cells


title: Day 113 SFTPCI73T/tdT iAEC2s [C11]


title: OE19-baseline-2

city: Farmington

first: Charles

last: Lee

state: Connecticut

address: 10 Discovery Dr

institute: The Jackson Laboratory

description:
sgRNA fragment library
Genomic DNA of GeCKO V2 library transducted OE19 cells was extracted and sgRNA framents were PCR amplified as sequencing library

data_processing:
Library strategy: CRISPR screen
sgRNA library sequences were assembled into a Burrows-Wheeler index using bowtie v2.3.2
fastq files were evaluated using fastqc v0.11.5
high-quality reads were mapped to the screening library with <2bp mismatches using Bowtie v2.3.2
read counts fro different samples were counted using MAGeCK v0.5.6
Genome_build: Human CRISPR Knockout Pooled Library (GeCKO v2)
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: gastric cancer cell line

growth_protocol: Human GC cell lines (N87, OE19) were obtained from the American Type Culture Collection (ATCC). All cell lines were cultured in RPMI1640 medium (Life Technologies) with 10% FBS (Life Technologies), penicillin (100 U/mL; Life Technologies), and streptomycin (100 U/mL; Life Technologies). The human GeCKO lentiviral pooled library lentiCRISPR v2 in one plasmid system was purchased from Addgene (Cat # 1000000048) as two half-libraries (library A and library B). Genome-wide loss of function screen using GeCKO library was carried out as described.  Briefly, the library plasmid DNA was transformed using electroporation method in Lucigen Endura electrocompetent cells (Lucigen). The grown colonies were recovered from the plates, followed by plasmid DNA extraction using the Endotoxin-Free NucleoBond Xtra Maxi Plus EF kit (Takara).

extract_protocol:
The genomic DNA of gastric cancer cell lines (N87 and OE19)  was extracted using the Zymo Research Quick-gDNA MidiPrep according to the manufacturer’s protocol for PCR amplification and deep sequencing of the genomic regions containing the sgRNAs was conducted.
To prepare the sgRNA library for NGS, set up a PCR  reaction for each of the 10 NGS-Lib-Fwd primers and 1 NGS-Lib-KO- Rev or NGS-Lib-SAM-Rev barcode primer. After the reaction is complete, pool the PCR reactions and purify the PCR product by using the QIAquick PCR purification kit according to the manufacturer’s directions.  Quantify the purified PCR product and run 2 µg of the product on a 2% (wt/vol) agarose gel. Successful reactions should yield a ~260-270bp product for the knockout library. Gel extract using the QIAquick gel extraction kit according to the manufacturer’s directions. Quantify the gel-extracted samples using the Qubit dsDNA HS Assay Kit according to the manufacturer’s instructions.
PCR amplify the integrated sgRNA fragment from pooled gastric cacner genomic DNA to generate sgRNA library for NGS sequencing.

treatment_protocol: Pooled lentiviral libraries are transduced to 1x10^8 GC cells with 3x10^6 cells plated per transduction well. The multiplicity of infection (MOI) is about 0.3 to ensure that most cells receive only one stably integrated RNA guide. Puromycin (1.5 μg/mL for OE19 cells and 0.75ug/ml for N87 cells) was added to the cells at 24h post transduction and maintained for 7 days. Baseline cells were harvested after puromycin selection. Then transduced GC cells were treated with lapatinib (1uM for OE19 cells and 0.5uM for N87 cells) or an equal volume DMSO for 14 days and the survived cells were harvested. For each cell line, two separate infection replicates were performed. The genomic DNA was extracted for PCR amplification and deep sequencing of the genomic regions containing the sgRNAs was conducted

tag: cell line

value: gastric cancer

tag: pooled crispr library conducted

value: GeCKO V2 library

tag: drug treatment

value: No treatment

tag: sgrna transduction

value: lentivirus


title: OE19-Lapatinib-Day14-2

description:
sgRNA fragment library
GeCKO V2 library transducted OE19 cells were treated by lapatinib for 14 days, genomic DNA was extracted and sgRNA framents were PCR amplified as sequencing library

value: 1uM lapatinib treatment for 14 days


title: OE19-baseline-1


title: Day 30 SFTPCtdT/WT iAEC2s [B2]


title: SCM rep 3

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description:
BL/6 SCM 4
MEH088_SCM

hyb_protocol: Hybridized according to the GeneChip Mouse 2.0 ST array protocol

scan_protocol: GeneChips were scanned using the affymetrix GCS3000 7G system

data_processing: The scanned images are then analyzed with Expression Console software (Affymetrix) to obtain raw data and metrics for Quality Controls. The distribution of raw data show no outlier experiment. Affymetrix probe-set data were normalized using the robust multi-array average (RMA) method.

label: Biotin

source_name: Bl/6 SCM

label_protocol: Biotinylated according to the GeneChip Mouse 2.0 ST array protocol

growth_protocol: Tumors harvested when mice reached humane endpoints as determined by SJCRH IACUC.

extract_protocol: Extracted with Qiagen's miRNeasy RNA extraction protocol according to manufacturer's protocol.

treatment_protocol: Four wild-type tumors and four Pten cKO tumors.

tag: tissue

value: sternocleidomastoid muscle

tag: genotype

value: muscle control


title: ASP cKO tumor rep 4

description:
SPA.161.3
MEH128_ASPcKO

source_name: Pten cKO tumor

value: tumor

value: aP2-Cre;SmoM2;Pten fl/fl


title: ASP cKO tumor rep 1

description:
SPA.190
MEH125_ASPcKO


title: OE19-Lapatinib-Day14-1


title: OE19-DMSO-Day14-2

description:
sgRNA fragment library
GeCKO V2 library transducted OE19 cells were treated by DMSO for 14 days, genomic DNA was extracted and sgRNA framents were PCR amplified as sequencing library

value: DMSO contorl treatment for 14days


title: ASP wt tumor rep 4

description:
SPA.84
MEH124_ASPWT

source_name: wild-type tumor


title: SCM rep 1

description:
BL/6 SCM 1
MEH086_SCM


title: ASP cKO tumor rep 3

description:
SPA.219
MEH127_ASPcKO


title: SCM rep 4

description:
BL/6 SCM 5
MEH089_SCM


title: ASP wt tumor rep 1

description:
SPA.184.2
MEH121_ASPWT


title: SCM rep 2

description:
BL/6 SCM 2
MEH087_SCM


title: OE19-DMSO-Day14-1


title: N87-baseline-2

description:
sgRNA fragment library
Genomic DNA of GeCKO V2 library transducted N87 cells was extracted and sgRNA framents were PCR amplified as sequencing library


title: 520258

city: San Francisco

first: Denise

middle: M

last: Wolf

address: 2340 Sutter st

institute: University of California, San Francisco

hyb_protocol: Performed by Agendia Inc (Irvine, CA)

scan_protocol: Performed by Agendia Inc (Irvine, CA)

data_processing:
gnormalized signal (log2) data, as provided in the raw files on each patient, was extracted and aligned to the 75th quantile across arrays by Agendia. All values indicated for non-conformity, as indicated by the 'gIsFeatNonUnifOL' column in the raw files, are NA'd out. Probeset level data per array were mean-collapsed to the gene level, and genes common to the two platforms identified.  Expression data from the first ~900 I-SPY 2 patients distributed over the two platforms were combined into a single gene-level dataset over the set of common genes after batch-adjusting using ComBat [PMID:16632515].  The data matrix for this study constitutes 233 samples from this larger COMBAT-combined expression set.  Linear adjustment factors were derived from the larger ComBat operation, per platform, and can be used against these 233 samples for batch correcting on raw files.  The linear adjustment factors and updated probe annotation files per platform are provided.
The data matrix provided contains platform corrected, normalized expression values from two different platforms.  Data is collapsed on the gene level as was used in the analysis.

source_name: Breast cancer biopsy (pre-treatment)

label_protocol: Performed by Agendia Inc (Irvine, CA)

extract_protocol: Extraction, labeling, hybridization, and scanning are performed by Agendia Inc (Irvine, CA).  This company is referenced by the platforms used: GPL20078 and GPL16233.

value: breast cancer

tag: hr

tag: mp

tag: pcr

tag: arm

value: Control Arm


title: 395076


title: ASP wt tumor rep 2

description:
SPA.181
MEH122_ASPWT


title: 515565


title: N87-DMSO-Day14-1

description:
sgRNA fragment library
GeCKO V2 library transducted N87 cells were treated by DMSO for 14 days, genomic DNA was extracted and sgRNA framents were PCR amplified as sequencing library


title: N87-Lapatinib-Day14-1

description:
sgRNA fragment library
GeCKO V2 library transducted N87 cells were treated by lapatinib for 14 days, genomic DNA was extracted and sgRNA framents were PCR amplified as sequencing library

value: 0.5uM lapatinib treatment for 14 days


title: N87-DMSO-Day14-2


title: N87-Lapatinib-Day14-2


title: N87-baseline-1


title: 629606

value: Ganitumab Arm


title: 775346


title: 549172


title: 942017


title: 771813


title: 698094


title: 809037


title: 357017


title: ASP cKO tumor rep 2

description:
SPA.193
MEH126_ASPcKO


title: QKI-5 control rep1

first: Xing

last: Fu

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

data_processing:
We trimmed the first nine nucleotides at 5’ ends of raw reads which included a four-nucleotide barcode and five random nucleotides (e.g. NNN[barcode]NN), and removed the 3’ adaptor sequences by cutadapt.
The clean reads were mapped against the human genome (version hg19/NCBI37) allowing one mismatch and single hits using Bowtie.
The unaligned reads were mapped to transcript sequences.
The crosslink sites were identified at one nucleotide upstream of the aligned reads by custom script.
Genome_build: hg19
Supplementary_files_format_and_content: The processed data is in BED format. Column1:chromosome, Column2:start, Column3:end, Column4:ID, Column5:number of reads, Column6: strand

source_name: BEAS2B cells

growth_protocol: BEAS2B cells were grown at 37 ˚C in Dulbecco’s Modified Eagle’s medium supplemented with 10% fetal bovine serum.

extract_protocol:
RNAs in the immunoprecipitated complex were subjected to PK treatment followed by phenolization, precipitation with ethanol, dry and dissolving.
For iCLIP cDNA library preparation, purified RNAs were reverse-transcribed with a primer containing barcodes. The resulting cDNAs were purified by PAGE, circularized by single-stranded DNA ligase (Epicentre), linearized by restriction enzyme cleavage, and amplified by PCR. The iCLIP cDNA library was processed on an Illumina HiSeq 2000 sequencer.

treatment_protocol: Five 10 cm dish of BEAS2B cells were irradiated with UV at 150 mJ/cm2. After cell lysis, RNAs were partially fragmented using 10 μl high (1:50) or low (1:5000) dilutions of 5 μg/μl RNase A (QIAGEN) followed by immunoprecipitation with 10 μg anti-QKI5 antibody immobilized on protein A Dynabeads (Life Technologies). RNAs were then ligated at 3’ ends to a DNA adapter and radioactively labeled by T4 polynucleotide kinase (Fermentas), and the protein–RNA complex was transferred to a nitrocellulose membrane.

value: bronchial epithelial

tag: clip antibody


title: QKI-5 control rep3


title: QKI-5 iCLIP rep2

value: QKI-5 (self-made)


title: QKI-5 iCLIP rep3


title: QKI-5 control rep2


title: QKI-5 iCLIP rep1


title: ASP wt tumor rep 3

description:
SPA.130
MEH123_ASPWT


title: plasma_DWM_24mo_HUMAN

type: protein

first: Jonathan

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

hyb_protocol: Hybridized by SomaLogic (http://somalogic.com/wp-content/uploads/2017/06/SSM-002-Technical-White-Paper_010916_LSM1.pdf)

scan_protocol: Scanned by SomaLogic (http://somalogic.com/wp-content/uploads/2017/06/SSM-002-Technical-White-Paper_010916_LSM1.pdf)

data_processing: Hybridization Control Normalization, Median Signal Normalization, and Calibration by SomaLogic.  The Relative fluorescence units provided in the sample data tables are the processed data provided by SomaLogic and these values were used to draw the conclusions for the study. Raw data were not provided by SomaLogic.

label: biotin

molecule: protein

source_name: plasma

label_protocol: Biotin labeled by SomaLogic (http://somalogic.com/wp-content/uploads/2017/06/SSM-002-Technical-White-Paper_010916_LSM1.pdf)

extract_protocol: Extracted from plasma by SomaLogic (http://somalogic.com/wp-content/uploads/2017/06/SSM-002-Technical-White-Paper_010916_LSM1.pdf)

value: plasma

tag: acrostic

value: HUMAN

tag: group

value: DWM

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: white blood count (10^6 / ml)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

tag: dmcure

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):0


title: plasma_DWM_24mo_POETS

tag: tissue

tag: acrostic

value: POETS

tag: group

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi


title: plasma_RYGB_12mo_QUART

value: QUART

value: RYGB

tag: basal metabolic rate

tag: body fat (%)

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: white blood count (10^6 / ml)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):100

value: meal tolerance test glucose time 15 min (mg/dl):193

value: meal tolerance test glucose time 30 min (mg/dl):184

value: meal tolerance test glucose time 60 min (mg/dl):155

value: meal tolerance test glucose time 120 min (mg/dl):110

value: meal tolerance test insulin time 0 min (mcU/ml):3.15000009536743

value: meal tolerance test insulin time 15 min (mcU/ml):49.1479988098145

value: meal tolerance test insulin time 30 min (mcU/ml):46.9259986877441

value: meal tolerance test insulin time 60 min (mcU/ml):18.2549991607666

value: meal tolerance test insulin time 120 min (mcU/ml):4.61199998855591

tag: homair

tag: homab

tag: matsuda

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):1

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):2776.515

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):2398.515

value: change in insulin from 0 to 30 min (mcU/ml):43.776

value: change in glucose from 0 to 30 min (mg/dl):84

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.5211428

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.1654422


title: plasma_RYGB_24mo_VISTA

tag: tissue

value: plasma

tag: acrostic

value: VISTA

tag: group

value: RYGB

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

tag: dmcure


title: plasma_DWM_0mo_INTRO

tag: tissue

tag: acrostic

value: INTRO

value: DWM

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: white blood count (10^6 / ml)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):64

value: meal tolerance test glucose time 15 min (mg/dl):79

value: meal tolerance test glucose time 30 min (mg/dl):121

value: meal tolerance test glucose time 60 min (mg/dl):137

value: meal tolerance test glucose time 120 min (mg/dl):144

value: meal tolerance test insulin time 0 min (mcU/ml):4.1710000038147

value: meal tolerance test insulin time 15 min (mcU/ml):3.97699999809265

value: meal tolerance test insulin time 30 min (mcU/ml):14.7489995956421

value: meal tolerance test insulin time 60 min (mcU/ml):14.5459995269775

value: meal tolerance test insulin time 120 min (mcU/ml):12.4940004348755

tag: homair

tag: matsuda

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):0

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):1452.18

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):951.66

value: change in insulin from 0 to 30 min (mcU/ml):10.578

value: change in glucose from 0 to 30 min (mg/dl):57

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.1855789

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.0444927


title: plasma_RYGB_0mo_REMIX

tag: tissue

value: plasma

value: REMIX

tag: group

value: RYGB

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):85

value: meal tolerance test glucose time 15 min (mg/dl):105

value: meal tolerance test glucose time 30 min (mg/dl):128

value: meal tolerance test glucose time 60 min (mg/dl):147

value: meal tolerance test glucose time 120 min (mg/dl):131

value: meal tolerance test insulin time 0 min (mcU/ml):16.6469993591309

value: meal tolerance test insulin time 15 min (mcU/ml):22.0890007019043

value: meal tolerance test insulin time 30 min (mcU/ml):51.3779983520508

value: meal tolerance test insulin time 60 min (mcU/ml):53.9650001525879

value: meal tolerance test insulin time 120 min (mcU/ml):46.5419998168945

tag: homab

tag: dmcure

value: insulin total area under curve (mcU/ml · 120 min):5436.877

value: insulin incremental area under curve (mcU/ml · 120 min):3439.238

value: change in insulin from 0 to 30 min (mcU/ml):34.731

value: change in glucose from 0 to 30 min (mg/dl):43

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.8076977

value: oral disposition index = dinsg030 / mttins0:0.0485191


title: plasma_RYGB_12mo_SCOPE

tag: tissue

value: plasma

tag: acrostic

value: SCOPE

tag: group

value: RYGB

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: white blood count (10^6 / ml)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):86

value: meal tolerance test glucose time 15 min (mg/dl):181

value: meal tolerance test glucose time 30 min (mg/dl):212

value: meal tolerance test glucose time 60 min (mg/dl):181

value: meal tolerance test glucose time 120 min (mg/dl):129

value: meal tolerance test insulin time 0 min (mcU/ml):3.15000009536743

value: meal tolerance test insulin time 15 min (mcU/ml):31.306999206543

value: meal tolerance test insulin time 30 min (mcU/ml):54.75

value: meal tolerance test insulin time 60 min (mcU/ml):15.2220001220703

value: meal tolerance test insulin time 120 min (mcU/ml):5.25

tag: homair

tag: matsuda

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):0

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):2567.595

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):2189.595

value: change in insulin from 0 to 30 min (mcU/ml):51.6

value: change in glucose from 0 to 30 min (mg/dl):126

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.4095238

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.1300076


title: plasma_RYGB_3mo_VISTA

tag: tissue

value: plasma

tag: acrostic

value: VISTA

value: RYGB

tag: height (cm)

tag: mo

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):82

value: meal tolerance test glucose time 15 min (mg/dl):128

value: meal tolerance test glucose time 30 min (mg/dl):121

value: meal tolerance test glucose time 60 min (mg/dl):121

value: meal tolerance test glucose time 120 min (mg/dl):106

value: meal tolerance test insulin time 0 min (mcU/ml):4.13800001144409

value: meal tolerance test insulin time 15 min (mcU/ml):23.1299991607666

value: meal tolerance test insulin time 30 min (mcU/ml):17.8209991455078

value: meal tolerance test insulin time 60 min (mcU/ml):20.4419994354248

value: meal tolerance test insulin time 120 min (mcU/ml):8.08199977874756

tag: homab

tag: dmcure

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):1

value: insulin total area under curve (mcU/ml · 120 min):1941.307

value: insulin incremental area under curve (mcU/ml · 120 min):1444.747

value: change in insulin from 0 to 30 min (mcU/ml):13.683

value: change in glucose from 0 to 30 min (mg/dl):39

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.3508461

value: oral disposition index = dinsg030 / mttins0:0.0847864


title: plasma_RYGB_24mo_LAKES

value: plasma

value: LAKES

tag: group

value: RYGB

tag: albumin/creatinine ratio

tag: serum creatinine (mg/dl)

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: white blood count (10^6 / ml)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):0


title: Pdgfc+/+ mouse with irradation, biological rep2

city: Guangzhou

first: Lekun

last: Fang

address: Yuancunerheng Road

institute: Sun Yat-sen University

description: Gene expression data from distal colorectal tissue of Pdgfc+/+ mouse with irradation

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA according to the manufacturer’s instructions of GeneChip® (Affymetrix, Santa Clara, CA, US).

growth_protocol: All mice were housed under temperature-controlled condition with a 12-hour light/dark cycle in an SPF environment.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were anesthetized by peritoneal injection with 5 % chloral hydrate and subjected to 25 Gy (2.14 Gy/min) local γ-irradiation. Eight weeks after radiation, the control and radiation groups were sacrificed and the colo-rectums about 1 cm above anus were separated for the following steps.

tag: tissue

value: distal colorectum

tag: strain

tag: genotype

value: Pdgfc+/+

tag: treatment

value: irradation


title: plasma_RYGB_12mo_LAKES

tag: acrostic

tag: group

tag: height (cm)

tag: mo

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: basal metabolic rate

tag: body fat (%)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):80

value: meal tolerance test glucose time 15 min (mg/dl):215

value: meal tolerance test glucose time 30 min (mg/dl):201

value: meal tolerance test glucose time 60 min (mg/dl):154

value: meal tolerance test glucose time 120 min (mg/dl):108

value: meal tolerance test insulin time 0 min (mcU/ml):3.15000009536743

value: meal tolerance test insulin time 15 min (mcU/ml):74.7239990234375

value: meal tolerance test insulin time 30 min (mcU/ml):76.9810028076172

value: meal tolerance test insulin time 60 min (mcU/ml):12.9289999008179

value: meal tolerance test insulin time 120 min (mcU/ml):3.15000009536743

tag: homair

tag: homab

tag: matsuda

tag: dmcure

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):3552.863

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):3174.863

value: change in insulin from 0 to 30 min (mcU/ml):73.831

value: change in glucose from 0 to 30 min (mg/dl):121

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.6101736

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.1937059


title: Pdgfc+/+ mouse with irradation, biological rep1

source_name: distal colorectal tissue of Pdgfc+/+ mouse with irradation

tag: tissue

value: distal colorectum

tag: strain

tag: genotype

value: Pdgfc+/+

tag: treatment

value: irradation


title: Pdgfc+/+ mouse with irradation, biological rep3


title: plasma_RYGB_0mo_FLAGS

value: plasma

tag: acrostic

value: FLAGS

tag: group

value: RYGB

tag: height (cm)

tag: mo

tag: albumin/creatinine ratio

tag: dbp (mmhg)

tag: sbp (mmhg)

tag: serum creatinine (mg/dl)

tag: waist (cm)

tag: weight (kg)

tag: bmi

tag: fat mass (lb)

tag: fat free mass (lb)

tag: 6 min walk test distance (m)

tag: 6 min walk test heart rate (beats/min)

tag: alt (iu/l)

tag: ast (iu/l)

tag: hematocrit (%)

tag: white blood count (10^6 / ml)

tag: fasting plasma glucose (mg/dl)

tag: total cholesterol (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):118

value: meal tolerance test glucose time 15 min (mg/dl):142

value: meal tolerance test glucose time 30 min (mg/dl):149

value: meal tolerance test glucose time 60 min (mg/dl):165

value: meal tolerance test glucose time 120 min (mg/dl):136

value: meal tolerance test insulin time 0 min (mcU/ml):14.7089996337891

value: meal tolerance test insulin time 15 min (mcU/ml):37.5449981689453

value: meal tolerance test insulin time 30 min (mcU/ml):51.2869987487793

value: meal tolerance test insulin time 60 min (mcU/ml):55.2550010681152

value: meal tolerance test insulin time 120 min (mcU/ml):40.6879997253418

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):0

value: insulin total area under curve (mcU/ml · 120 min):5534.565

value: insulin incremental area under curve (mcU/ml · 120 min):3769.485

value: change in insulin from 0 to 30 min (mcU/ml):36.578

value: change in glucose from 0 to 30 min (mg/dl):31

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):1.179935

value: oral disposition index = dinsg030 / mttins0:0.0802186


title: plasma_RYGB_3mo_KAYAK

tag: tissue

value: plasma

tag: acrostic

value: KAYAK

tag: group

value: RYGB

tag: height (cm)

tag: mo

tag: basal metabolic rate

tag: body fat (%)

tag: ldl cholesterol (mg/dl)

tag: hdl cholesterol (mg/dl)

tag: triglycerides (mg/dl)

value: meal tolerance test glucose time 0 min (mg/dl):88

value: meal tolerance test glucose time 15 min (mg/dl):175

value: meal tolerance test glucose time 30 min (mg/dl):219

value: meal tolerance test glucose time 60 min (mg/dl):198

value: meal tolerance test glucose time 120 min (mg/dl):149

value: meal tolerance test insulin time 0 min (mcU/ml):4.87799978256226

value: meal tolerance test insulin time 15 min (mcU/ml):44.3479995727539

value: meal tolerance test insulin time 30 min (mcU/ml):81.4609985351562

value: meal tolerance test insulin time 60 min (mcU/ml):53.5639991760254

value: meal tolerance test insulin time 120 min (mcU/ml):30.863000869751

tag: homair

tag: homab

tag: matsuda

tag: dmcure

value: FPG < 126 and HbA1c < 6.5 (0 = no; 1 = yes; 9 = missing):1

tag: instauc

value: insulin total area under curve (mcU/ml · 120 min):5870.947

tag: insiauc

value: insulin incremental area under curve (mcU/ml · 120 min):5285.587

value: change in insulin from 0 to 30 min (mcU/ml):76.583

value: change in glucose from 0 to 30 min (mg/dl):131

value: change in insulin from 0 to 30 min / change in glucose from 0 to 30 min (mcU/ml / mg/dl):0.5846031

tag: odi

value: oral disposition index = dinsg030 / mttins0:0.1198448