title: PBMC_NK_donor4

city: New York

first: Sjoukje

middle: van der

last: Stegen

state: NY

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequencing data were trimmed using Trim Galore! 0.6.0 to remove Illumina adapters.
Resulting reads were mapped to the human reference genome (assembly GRCh38.86) using Salmon 0.13.1 in quasi-mapping-based mode, with GC bias correction, selective alignment, and range factorization.
The data was analysed using the statistical software R. The aggregated read counts were normalized for sequencing depth and RNA composition with DESeq2. Pseudogenes identified by the GENCODE project and lowly expressed genes were filtered out prior to downstream analysis. Principal Component Analysis (PCA) was performed with normalized read counts in R. Hierarchical Clustering Analysis was carried out with UPGMA method on Euclidean distance matrix. Correlation matrix was generated using Pearson’s statistics.
Assembly: Human reference genome (assembly GRCh38.86)
Supplementary files format and content: TRAC_1XX_iT_processed_data.csv: Matrix table with raw gene counts for every gene and every sample.

source_name: PBMC cells

extract_protocol:
Total RNA was isolated from 0.3-0.5x10^6 cells using the RNeasy 96 Kit (Qiagen, 74181) according to the manufacturer’s protocol. RNA quality was measured by High Sensitivity RNA ScreenTape (Agilent) on the Agilent 42000 TapeStation System. RNA quantity was measured using the Thermo Scientific Qubit Flex Fluorometer (Invitrogen).
200ng of total RNA was used per sample to generate mRNA library using NEBNext Ultra II Directional RNA Library Kit for Illumina (New England BioLabs) per sample. Final libraries were quantified using the Qubit 1X dsDNA HS Assay kit on the Qubit Flex Fluorometer. Library quality and size were measured using Agilent High Sensitivity D1000 ScreenTape.

value: human healthy-donor peripheral blood-derived NK cells

tag: genetic engineering

value: retroviral CAR expression


title: PBMC_NK_donor3

status: Public on Aug 23 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: PBMC_gdT_donor4

value: human healthy-donor peripheral blood-derived gd T cells


title: LAL-0020-B (MethylationEPIC)

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

address: Ctra. de Can Ruti, Cami de les Escoles s/n

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Minfi R package standard protocol
Minfi preprocessNoob (single-sample) normalized Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Saliva

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: look-alike couple

tag: tissue

value: Normal human saliva sample


title: PBMC_gdT_donor3


title: 3112102-PrefrontalCortex

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

library_source: genomic

data_processing:
The CpG_Me pipeline (https://github.com/ben-laufer/CpG_Me) was used to perform all data processing steps.
Trim Galore was used to trim adapters and methylation bias.
FastQ Screen was used to screen for sample contamination.
Bismark was used align to the reference genome, remove PCR duplicates, calculate coverage, extract CpG methylation, and generate genome-wide cytosine reports (CpG count matrices).
Picard Tools was used to calculate insert size metrics.
MultiQC was used for quality control.
Genome_build: rheMac10
Supplementary_files_format_and_content: Bismark genome-wide cytosine reports (CpG count matrices)

organism: Macaca mulatta

extract_protocol:
Automated. Promega Maxwell RSC ccfDNA Plasma Kit for cffDNA and Tecan workflow for Zymo Quick-DNA Miniprep Plus Kit for brain.
Swift BioSciences Accel-NGS Methyl-Seq DNA Library Kit

tag: group

value: Obese

tag: timepoint

tag: infantid

tag: birthgd

value: No

tag: foster

tag: cohort

tag: sample type

value: PrefrontalCortex


title: LAL-0029-A (MethylationEPIC)


title: LAL-0015-B (MethylationEPIC)


title: PBMC_CD8ab_donor3

value: human healthy-donor peripheral blood-derived CD8ab T cells

value: TRAC-targeted CAR expression


title: LAL-0016-B (MethylationEPIC)


title: PBMC_gdT_donor2


title: 3131106-Hippocampus

source_name: Hippocampus

value: Pravastatin

value: Hippocampus


title: LAL-0025-B (MethylationEPIC)


title: PBMC_gdT_donor1


title: 3112102-Hippocampus


title: 100230972-cffDNA

source_name: cffDNA

value: Control

value: Yes

value: cffDNA


title: LAL-0016-A (MethylationEPIC)


title: LAL-0020-A (MethylationEPIC)


title: 3122106-PrefrontalCortex

value: Restriction


title: PBMC_NK_donor1


title: LAL-0025-A (MethylationEPIC)


title: PBMC_CD8ab_donor2


title: 100230846-cffDNA


title: 3121105-Hippocampus


title: Col-0 wildtype_rep1

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

country: China

institute: Peiking University

description: polyA RNA isolated

data_processing:
Sequenced reads were preprocessed using Trimmomatic to remove reads in low quality and adaptor contamination (Bolger et al., 2014). The high-quality reads were aligned to Arabidopsis genome (TAIR 10) using Hisat2 (version 2.05; Kim et al., 2015) software using default parameters. Then, raw reads for each gene were calculated by HTseq (Anders et al., 2015) before calculating differential gene expression. Genes with a fold change >1.5 (FDR < 0.01) were defined as differentially expressed genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Col, csu5-1 and csu5-3 seedlings grown in constant W (14.59 μmol·m-2·s-1) light conditions for 5 days

extract_protocol:
Total RNA was isolated from the whole Arabidopsis seedlings using RNeasy plant mini kits (Qiagen). mRNA was extracted from total RNA using Dynabeads oligo (dT) (Invitrogen Dynal).
Quality control of DNase I treated mRNA was performed with an Agilent 2100 Bioanalyzer. cDNA libraries were generated, and sequencing was performed using the Illumina HiSeq 2500 platform according to the manufacturer's instruction (HiSequation 2500 user guide) by Novogene.

tag: ecotype

tag: genotype/variation

value: wildtype

value: seedlings


title: PBMC_CD4_donor3

value: human healthy-donor peripheral blood-derived CD4 T cells


title: 100230525-cffDNA


title: 3131106-Hypothalamus

source_name: Hypothalamus

value: Hypothalamus


title: PBMC_CD8ab_donor4


title: PBMC_NK_donor2

value: human healthy-donor peripheral blood-derived NK cells

value: retroviral CAR expression


title: LAL-0013-A (MethylationEPIC)

value: Normal human saliva sample


title: CD8ab_iT_rep4

source_name: T-iPSC-derived T cells

value: human T-iPSC-derived CD8ab T cells


title: LAL-0015-A (MethylationEPIC)


title: LAL-0008-B (MethylationEPIC)


title: CD8ab_iT_rep1


title: PBMC_CD4_donor2


title: PBMC_CD8ab_donor1


title: LAL-0008-A (MethylationEPIC)


title: PBMC_CD4_donor1


title: irCLIP CPEB4 PAR-CLIP, control, rep2

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

country: Germany

institute: Heidelberg University

data_processing:
Adapters were removed with cutadapt. Three prime adapter sequence : TGGAATTCTCGGGTGCCAAGG. Five prime adapter sequence for irCLIP: GTTCAGAGTTCTACAGTCCGACGATCCTGATC.
UMIs were removed with umi-tools. Parameter –bc-pattern is '(?P<umi_1>.{{4}}).*(?P<umi_2>.{{4}})$' for p32-CLIP and '(?P<umi_1>.{{7}}).*(?P<umi_2>.{{4}})$' for irCLIP.
The reads were mapped with STAR and segemehl aligners.
Peak calling was done with omniCLIP using unique reads and RNA-seq as background.
Raw peaks were processed in R. Scripts available at https://github.com/slebedeva/CPEB4_public.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files for plus(for) and minus (rev) strand for coverage, TC conversions and T deletions; bed files for peaks (control and RMD conditions)

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% (v/v) FBS (Sigma), 2 mM L-glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin (all PAN Biotech) and incubated at 37 °C in a 5% CO2 incubator.

extract_protocol:
The PAR-CLIP protocol was adapted from (Porter et al., 2021; Wessels et al., 2019). At least ~60x106 HeLa cells were used per experiment. After treating with RMD or solvent (DMSO) and 200 μM 4sU, cells were washed with PBS, crosslinked at 365 nm and 150 mJ/cm2, and the pellets were flash frozen. Pellets were lysed in iCLIP lysis buffer, cleared by centrifugation and digested with 0.1 U/μl RNAse I at 37 °C for 3 min. Immunoprecipitation was carried out with 20 μg of FLAG M2 antibody for 2 h at 4 °C. For 32P-CLIP, immunoprecipitated complexes were radioactively labeled, resolved on 3-8% NuPAGE gel and transferred to a nitrocellulose membrane. RNA was extracted by proteinase K digestion and used for library preparation with NEXTFLEX small RNA kit v3 (Perkin Elmer). For irCLIP, on-bead ligation of infrared dye labeled adapters was carried out prior to running a 4-12% NuPAGE gel, transfer to a membrane and proteinase K extraction.
Ligated RNA was isolated with oligo-dT beads and cDNA was produced, which is compatible with the small RNA Illumina adapters.

treatment_protocol: Cell were treated with 20 nM RMD or an equal volume of solvent (DMSO) for 14 h followed by subsequent labeling with 200 μM 4sU (Sigma-Aldrich) for 2 h.

tag: cell line

value: HeLa

tag: treatment

value: 16h DMSO, 2h 200uM 4SU

tag: clip antibody

value: anti-FLAG M2

tag: protocol

value: irCLIP

tag: fraction

value: immunoprecipitated RNA


title: 3121105-Hypothalamus

value: No


title: irCLIP CPEB4 PAR-CLIP, RMD, rep2

value: 16h RMD, 2h 200uM 4SU


title: CD8ab_iT_rep2

tag: cell type

tag: genetic engineering

value: TRAC-targeted CAR expression


title: LAL-0013-B (MethylationEPIC)

tag: look-alike couple

tag: tissue


title: 10023165500-cffDNA

tag: group

value: Pravastatin

tag: timepoint

value: cffDNA


title: p32 CPEB4 PAR-CLIP, RMD


title: From_SID_226_PostTreat_Blood_TMb

city: Miami

first: Maria

middle: T

last: Abreu

state: Florida

address: 1475 NW 12th Ave floor 1

department: Gastroenterology

institute: University of Miami

data_processing:
75-base single reads average 20M reads per sample (3.5B reads total).
Raw counts were generated based on Ensembl genes (Ensembl release 91) with HTSeq (ver.0.11)
Reads from T cell RNA-seq were mapped to the human genome (GRCh38) using STAR (ver.2.5.0) aligner
Fold changes of differential expression were estimated through DESeq2(1.22.2)
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: RawGeneCounts.xlsx

source_name: Blood (PBMC)

extract_protocol:
Total RNA was extracted via miRNAeasy Micro Kit (Qiagen, Germantown, MD)
Libraries were individually indexed and pooled in groups of 20. Each pool was run on a NextSeq500 flow cell (9 flow cells total)

treatment_protocol: Mucosal biopsies from UC and CD were digested for single cells and FAC sorted for Treg and Tmem subset  sorted from PBMCs and biopsies

value: Vedolizumab (VDZ)

tag: time

value: Post-treatment

tag: disease state

value: CD

value: Blood (PBMC)

value: Tmen

tag: location collected


title: CD8ab_iT_rep3


title: 10023130200-cffDNA

tag: infantid

tag: birthgd

value: Yes

tag: foster

tag: cohort

tag: sample type


title: irCLIP CPEB4 PAR-CLIP, RMD, rep1

tag: cell line

tag: treatment

tag: clip antibody


title: 100230625-cffDNA


title: p32 CPEB4 PAR-CLIP, control

tag: protocol

tag: fraction


title: irCLIP CPEB4 PAR-CLIP, control, rep1


title: LAL-0007-B (MethylationEPIC)

tag: look-alike couple

value: Normal human saliva sample


title: 10023120800-cffDNA


title: 10023185700-cffDNA

value: Obese


title: From_SID_224_PostTreat_Blood_TMb

tag: cell type


title: From_SID_225_PostTreat_Blood_TRb

value: Treg


title: LAL-0007-A (MethylationEPIC)

tag: tissue


title: LAL-0004-A (MethylationEPIC)


title: From_SID_222_PostTreat_Blood_TMb

value: UC


title: 100230524-cffDNA

tag: group

value: Restriction

tag: timepoint


title: LAL-0004-B (MethylationEPIC)


title: LAL-0003-A (MethylationEPIC)


title: From_SID_221_PostTreat_Blood_TRb

tag: time

tag: disease state


title: 10023120900-cffDNA

tag: infantid


title: From_SID_219_PostTreat_Blood_TRb

tag: location collected


title: From_SID_223_PostTreat_Blood_TRb


title: 100230829-cffDNA

tag: birthgd

tag: foster


title: From_SID_216_PostTreat_Blood_TMb

tag: sample type


title: From_SID_214_PostTreat_Blood_TMb


title: From_SID_218_PostTreat_Blood_TMb


title: From_SID_220_PostTreat_Blood_TMb


title: LAL-0003-B (MethylationEPIC)


title: From_SID_213_PostTreat_Blood_TRb


title: 100230675-cffDNA

tag: cohort


title: From_SID_215_PostTreat_Blood_TRb

tag: treatment


title: 100230277-cffDNA


title: From_SID_209_PostTreat_Blood_TRb


title: From_SID_208_PostTreat_Blood_TMb


title: 100226497-cffDNA

value: Control


title: 100228186-cffDNA

value: No


title: From_SID_212_PostTreat_Blood_TMb


title: From_SID_211_PostTreat_Blood_TRb


title: From_SID_206_PostTreat_Blood_TMb


title: From_SID_205_PostTreat_Blood_TRb


title: From_SID_210_PostTreat_Blood_TMb


title: From_SID_204_PostTreat_Blood_TMb


title: 100226365-cffDNA


title: DpteF strain stationary phase Replicate 3

type: mixed

city: Toulouse

first: Cláudia

last: Vicente

address: 135 avenue de Rangueil

country: France

institute: Toulouse Biotechnology Institute

description:
MUF_t2_r3
Streptomyces avermitilis MUF (ΔpteF::aac(3)IV-oriT)

hyb_protocol: Hybridization was carried out as previously described [Rodriguez-Garcia, A, et al. (2007) Proteomics 7(14)].

scan_protocol: Microarray chips were scanned in Agilent G2565BA and using the software Feature Extraction v8.1.

data_processing: Processed signal was obtained using the subtract method. Normalization was carried out combining a within-array normalization (median) with an inter-array normalization (cyclic loess).

organism: Streptomyces avermitilis

source_name: mycelium, stationary phase, MUF

label_protocol: cDNA and genomic DNA were labeled with Cy3 and Cy5 as previously described [Rodriguez-Garcia, A, et al. (2007) Proteomics 7(14)].

growth_protocol: Baffled flasks; YEME without sucrose medium; 30 ºC; 250 rpm.

extract_protocol: Total RNA was extracted using the commercial kit RNeasy Mini Kit (Qiagen). cDNA was synthesized using SuperScript™ III reverse transcriptase (Invitrogen).

tag: strain

value: NRRL 8165

value: mycelium

tag: growth phase

value: stationary phase

tag: genotype

source_name: mycelium, stationary phase, WT

extract_protocol: Genomic DNA was extracted using the Kirby mix procedure [Kieser, T, et al. (2000) John Innes Center, Norwich, United Kingdom].

value: wild-type


title: 100226366-cffDNA

value: Pravastatin

value: cffDNA


title: DpteF strain stationary phase Replicate 1

description:
MUF_t2_r1
Streptomyces avermitilis MUF (ΔpteF::aac(3)IV-oriT)


title: From_SID_203_PostTreat_Blood_TRb

value: Vedolizumab (VDZ)

value: Post-treatment


title: 100226250-cffDNA


title: DpteF strain stationary phase Replicate 2

description:
MUF_t2_r2
Streptomyces avermitilis MUF (ΔpteF::aac(3)IV-oriT)


title: DpteF strain exponential phase Replicate 3

description:
MUF_t1_r3
Streptomyces avermitilis MUF (ΔpteF::aac(3)IV-oriT)

source_name: mycelium, exponential phase, MUF

value: exponential phase


title: From_SID_201_PostTreat_Blood_TRb

value: CD

value: Blood (PBMC)


title: From_SID_202_PostTreat_Blood_TMb

value: Tmen


title: DpteF strain exponential phase Replicate 2

description:
MUF_t1_r2
Streptomyces avermitilis MUF (ΔpteF::aac(3)IV-oriT)


title: DpteF strain exponential phase Replicate 1

description:
MUF_t1_r1
Streptomyces avermitilis MUF (ΔpteF::aac(3)IV-oriT)


title: 100226821-cffDNA


title: From_SID_200_PostTreat_Blood_TMb


title: LAL-0010-B (HumanOmni5)

hyb_protocol: Genomic DNA was amplified, fragmented and hybridised to Illumina Infinium HumanOmni5-Quad BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting.

data_processing:
Genomic DNA extracted from saliva samples was genotyped using Illumina Infinium HumanOmni5-Quad BeadChips (Illumina).
Image data was analyzed using GenomeStudio 2.0.4 with GT module 2.0.4 (Illumina).

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Total DNA was isolated from saliva samples by standard procedures.

tag: look-alike couple

value: Normal human saliva sample


title: Wild-type strain stationary phase Replicate 3

description:
WT_t2_r3
Streptomyces avermitilis NRRL 8165


title: 100225914-cffDNA


title: 100226283-cffDNA


title: 100225693-cffDNA


title: From_SID_199_PostTreat_Blood_TRb

tag: cell type

value: Treg


title: Wild-type strain stationary phase Replicate 2

description:
WT_t2_r2
Streptomyces avermitilis NRRL 8165

tag: tissue


title: 100225678-cffDNA

tag: group

value: Restriction


title: From_SID_197_PostTreat_Blood_TRb


title: LAL-0006-B (HumanOmni5)


title: LAL-0006-A (HumanOmni5)


title: Wild-type strain stationary phase Replicate 1

description:
WT_t2_r1
Streptomyces avermitilis NRRL 8165


title: 100226630-cffDNA

value: Obese

tag: timepoint


title: Wild-type strain exponential phase Replicate 3

description:
WT_t1_r3
Streptomyces avermitilis NRRL 8165

source_name: mycelium, exponential phase, WT


title: From_SID_196_PostTreat_Blood_TMb

tag: time


title: LAL-0005-B (HumanOmni5)


title: Wild-type strain exponential phase Replicate 2

description:
WT_t1_r2
Streptomyces avermitilis NRRL 8165


title: 100225692-cffDNA

value: No


title: 100230639-cffDNA

value: Control

value: Yes


title: LAL-0005-A (HumanOmni5)


title: Healthy donor-8, bulkseq

city: San Francisco

first: Bridget

middle: P

last: Keenan

state: CA

address: 505 PARNASSUS AVE

institute: University of California San Francisco

data_processing:
RNAseq data were aligned to human genome build 38 with STAR (Dobin et al., 2013).
Low quality reads and ends of reads were trimmed using Trim Galore (Krueger, 2019).
Identification of single nucleotide polymorphisms (SNP) was performed using the Genome Analysis Toolkit (McKenna et al., 2010) and a final vcf file contains the SNP information for each sample.
Assembly: Genome Build: GRCh38 3.0.0

source_name: Peripheral blood mononuclear cells

extract_protocol:
The RNeasy Mini Kit (Qiagen) was used to extract RNA from minimum 2.5 x 105 cells per sample.
cDNA was prepared with the Smart-seq2 protocol (Picelli et al., 2014), and libraries were prepared using Nextera XT DNA Sample Preparation Kit.

value: Peripheral blood mononuclear cells

tag: disease state

value: Healthy


title: LAL-0010-A (HumanOmni5)


title: From_SID_195_PostTreat_Blood_TRb


title: LAL-0058-B (HumanOmni5)

hyb_protocol: Genomic DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

data_processing:
Genomic DNA extracted from saliva samples was genotyped using  Illumina Infinium HumanOmni5-Quad BeadChips (Illumina).
Image data was analyzed using GenomeStudio 2.0.4 with GT module 2.0.4 (Illumina).

extract_protocol: Total DNA was isolated from saliva samples by standard procedures


title: From_SID_198_PostTreat_Blood_TMb


title: 100230144-cffDNA

tag: infantid


title: Healthy donor-6, bulkseq


title: Healthy donor-5, bulkseq


title: Wild-type strain exponential phase Replicate 1

description:
WT_t1_r1
Streptomyces avermitilis NRRL 8165

value: NRRL 8165

value: mycelium

value: wild-type


title: LAL-0058-A (HumanOmni5)


title: From_SID_193_PostTreat_Blood_TMb

value: Vedolizumab (VDZ)

value: Post-treatment

value: UC

tag: location collected


title: 10023120600-cffDNA

value: Pravastatin

tag: birthgd

value: cffDNA


title: LAL-0049-B (HumanOmni5)

value: Normal human saliva sample


title: 100229622-cffDNA

tag: foster


title: Healthy donor-4, bulkseq


title: From_SID_192_PostTreat_Blood_TRb

tag: sample type

value: Blood (PBMC)

value: Treg


title: LAL-0049-A (HumanOmni5)


title: From_SID_191_PostTreat_Blood_TMb

value: Tmen


title: Healthy donor-3, bulkseq


title: From_SID_194_PostTreat_Blood_TMb


title: Healthy donor-2, bulkseq


title: LAL-0047-B (HumanOmni5)


title: 100230922-cffDNA

tag: cohort


title: Healthy donor-7, bulkseq


title: From_SID_190_PostTreat_Blood_TRb

tag: treatment


title: 100230830-cffDNA

value: No


title: LAL-0047-A (HumanOmni5)


title: From_SID_189_PostTreat_Blood_TMb


title: 100229607-cffDNA

value: Restriction


title: From_SID_188_PostTreat_Blood_TRb


title: 100229623-cffDNA


title: Biliary tract cancer patient-9, bulkseq

value: Biliary tract cancer


title: Healthy donor-1, bulkseq

value: Peripheral blood mononuclear cells


title: LAL-0046-B (HumanOmni5)


title: From_SID_187_PostTreat_Blood_TMb


title: LAL-0046-A (HumanOmni5)


title: From_SID_186_PostTreat_Blood_TRb


title: Biliary tract cancer patient-8, bulkseq


title: Biliary tract cancer patient-7, bulkseq


title: LAL-0045-B (HumanOmni5)


title: 100230885-cffDNA

value: Obese

value: Yes


title: 10023162200-cffDNA


title: Biliary tract cancer patient-6, bulkseq


title: LAL-0033-B (HumanOmni5)


title: From_SID_185_PostTreat_Blood_TMb

value: CD


title: 100230143-cffDNA


title: Biliary tract cancer patient-4, bulkseq


title: From_SID_184_PostTreat_Blood_TMb


title: Biliary tract cancer patient-5, bulkseq


title: From_SID_183_PostTreat_Blood_TRb


title: 100229976-cffDNA


title: 100229609-cffDNA


title: 100227295-cffDNA

value: Control


title: LAL-0033-A (HumanOmni5)


title: 100225959-cffDNA


title: From_SID_181_PostTreat_Blood_TRb

value: Vedolizumab (VDZ)


title: From_SID_182_PostTreat_Blood_TMb

value: Post-treatment


title: LAL-0045-A (HumanOmni5)


title: Biliary tract cancer patient-1, bulkseq


title: Biliary tract cancer patient-2, bulkseq


title: LAL-0025-B (HumanOmni5)


title: From_SID_180_PostTreat_Blood_TMb

value: UC


title: LAL-0029-B (HumanOmni5)


title: 100225935-cffDNA

value: Pravastatin


title: LAL-0025-A (HumanOmni5)


title: LAL-0029-A (HumanOmni5)


title: From_SID_178_PostTreat_Blood_TMb


title: 27_CD34mCD38p_3m

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

data_processing:
Sequencing was aligned using STAR 2.5.2b 45 against GRCh38 and transcript sequences downloaded from Ensembl build 90. Default parameters were used except for the following: “--chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax parameter 3 --alignSJstitchMismatchNmax 5 -1 5 5”. Counts were obtained using HTSeq v0.7.2. Variance stabilized normalized counts were generated. The variance stabilized normalized counts was generated by DESeq2 v1.22.2.
Assembly: GRCh38
Supplementary files format and content: VST_forCD34_DF_grch38_ForGEO_submission.txt
Supplementary files format and content: tab-delimited text data frame that includes VST values for each Sample

molecule: polyA RNA

extract_protocol:
RNA was harvested using mirVana™miRNA Isolation Kit with phenol (Invitrogen). Samples that passed quality control according to integrity (RIN>8) and concentration as verified on a Bioanalyzer pico chip (Agilent Technologies) were subjected to further processing by the Center for Applied Genomics, Sick Kids Hospital. The SMART-Seq v4 Kit (SSv4) (Takera) followed by Illumina Nextera XT library prep was used as recommended by the manufacturer.
Briefly, the same amount of RNA was used for library preparation. After cDNA conversion, cDNA was run on a bioanalyzer. 1ng of cDNA was used for the Nextera library preparation, then subjected to QC on a bioanalyzer and qPCR for the final library concentration.

value: patient derived AML model

tag: cell line

value: cultured for 3m


title: 28_CD34mCD38m_3m


title: LAL-0020-B (HumanOmni5)

value: Normal human saliva sample


title: From_SID_177_PostTreat_Blood_TRb

value: Blood (PBMC)

value: Treg


title: 26_CD34pCD38p_3m


title: 100225441-cffDNA

value: No

value: cffDNA


title: 100225840-cffDNA


title: Biliary tract cancer patient-3, bulkseq

value: Biliary tract cancer


title: From_SID_176_PostTreat_Blood_TMb

value: Tmen


title: LAL-0020-A (HumanOmni5)


title: LAL-0016-B (HumanOmni5)


title: From_SID_174_PostTreat_Blood_TMb


title: From_SID_173_PostTreat_Blood_TRb


title: 24_CD34mCD38m_3m


title: 100225915-cffDNA

value: Restriction


title: 100225567-cffDNA


title: 23_CD34mCD38p_3m


title: LAL-0016-A (HumanOmni5)


title: From_SID_170_PostTreat_Blood_TMb


title: LAL-0015-B (HumanOmni5)


title: LAL-0015-A (HumanOmni5)


title: 100225170-cffDNA


title: From_SID_172_PostTreat_Blood_TMb


title: 21_CD34pCD38m_3m


title: 100226198-cffDNA

value: Obese


title: From_SID_169_PostTreat_Blood_TRb

value: CD


title: 25_CD34pCD38m_3m


title: LAL-0013-A (HumanOmni5)


title: LAL-0013-B (HumanOmni5)


title: 100225465-cffDNA


title: 19_CD34mCD38p_2m

value: cultured for 2m


title: 100226285-cffDNA


title: 100229974-cffDNA

value: Control

value: Yes


title: LAL-0008-B (HumanOmni5)


title: LAL-0008-A (HumanOmni5)


title: 18_CD34pCD38p_2m


title: From_SID_166_PreTreat_Biopsy_TMb

source_name: Biopsy

value: control

value: Pre-treatment

value: Biopsy

value: Colon


title: 100229606-cffDNA


title: From_SID_165_PreTreat_Biopsy_TRb


title: 100229100-cffDNA


title: 20_CD34mCD38m_2m

value: patient derived AML model


title: From_SID_168_PostTreat_Blood_TMb

value: Vedolizumab (VDZ)

value: Post-treatment

value: UC

value: Blood (PBMC)


title: 17_CD34pCD38m_2m


title: 22_CD34pCD38p_3m

value: cultured for 3m


title: From_SID_164_PreTreat_Biopsy_TMb

value: Tmen


title: From_SID_167_PostTreat_Blood_TRb

value: Treg


title: LAL-0007-B (HumanOmni5)

value: Normal human saliva sample


title: LAL-0007-A (HumanOmni5)


title: LAL-0004-B (HumanOmni5)


title: 13_CD34pCD38m_12d

value: cultured for 12d


title: 14_CD34pCD38p_12d


title: LAL-0003-B (HumanOmni5)


title: 100230845-cffDNA

value: Pravastatin

value: No

value: cffDNA


title: 15_CD34mCD38p_12d


title: 100229076-cffDNA

value: Restriction


title: 12_CD34mCD38m_12d


title: 100230971-cffDNA

value: Obese


title: From_SID_160_PreTreat_Blood_TMb

value: control

value: Pre-treatment

value: CD


title: LAL-0003-A (HumanOmni5)


title: 16_CD34mCD38m_12d

value: patient derived AML model


title: From_SID_157_PreTreat_Biopsy_TRb

value: Biopsy

value: Colon


title: 100229101-cffDNA


title: 100230272-cffDNA


title: From_SID_156_PreTreat_Biopsy_TMb

value: Ileum


title: From_SID_162_PreTreat_Biopsy_TMb


title: 9_CD34pCD38m_12d


title: From_SID_163_PreTreat_Biopsy_TRb


title: From_SID_155_PreTreat_Biopsy_TRb


title: LAL-0004-A (HumanOmni5)


title: 100229605-cffDNA

value: Yes


title: 100229075-cffDNA


title: 11_CD34mCD38p_12d


title: 100230626-cffDNA


title: 6_CD34pCD38p_12d


title: From_SID_161_PreTreat_Biopsy_TRb


title: From_SID_153_PreTreat_Blood_TRb

value: Blood (PBMC)


title: 100225627-cffDNA


title: 10_CD34pCD38p_12d


title: 100229269-cffDNA


title: 100230276-cffDNA


title: From_SID_147_PreTreat_Blood_TMb

value: UC

value: Tmen


title: 100225568-cffDNA


title: 8_CD34mCD38m_12d

value: cultured for 12d


title: 100226655-cffDNA

value: Control


title: From_SID_154_PreTreat_Blood_TMb


title: From_SID_159_PreTreat_Blood_TRb

value: Treg


title: Fresh hCP1, patient 1

type: RNA

city: Sacramento

first: Thomas

middle: H

last: Ambrosi

address: 2700 Stockton Blvd

institute: UC Davis

description: Fresh CP1

hyb_protocol: Amplified cRNA was streptavidin-labeled, fragmented, and hybridized to Affymetrix HG-U133_Plus_2 arrays (Affymetrix).

scan_protocol: Arrays were scanned with a Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.

data_processing: Raw microarray data were submitted to Gene Expression Commons (http://gexc.riken.jp) where data normalization was computed against the Common Reference, a large collection of publicly available microarray data from the National Center for Biotechnology Information Gene Expression Omnibus. Meta-analysis of the Common Reference also provides the dynamic range of each probe set on the array.

label: biotin

source_name: Gene expression data from hCPs isolated from long bone fracture callus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Direct sort from freshly harvested human fracture tissue or one-week of expansion culture of purified hSSCs.

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

treatment_protocol: No treatment

value: Long bone fracture callus

value: hCP

tag: condition

value: Fresh

tag: age

value: 49 years


title: From_SID_145_PreTreat_Blood_TMb

value: control

value: Pre-treatment


title: 2_CD34pCD38p_12d

value: patient derived AML model


title: Fresh hCP3, patient 3

description: Fresh CP3


title: From_SID_149_PreTreat_Biopsy_TMb

value: Biopsy


title: Fresh hCP2, patient 2

description: Fresh CP2


title: Cultured hSSC2, patient 2

description: Cultured hSSC2

source_name: Gene expression data from SSCs isolated from long bone fracture callus and cultured for one week

value: hSSC

value: Cultured for one week


title: Cultured hSSC3, patient 3

description: Cultured hSSC3

value: 90 years


title: 3_CD34mCD38m_12d


title: 7_CD34mCD38p_12d


title: 100225599-cffDNA

value: Restriction

value: No

value: cffDNA


title: 1_CD34pCD38m_12d

value: cultured for 12d


title: From_SID_152_PreTreat_Biopsy_TMb

value: UC

value: Tmen

value: Colon


title: 100225936-cffDNA


title: A_CD34pCD38m_Donor

value: n/a (Donor)


title: 4_CD34mCD38p_12d


title: 100225020-cffDNA


title: Fresh hOP1, patient 1

description: Fresh hOP1

source_name: Gene expression data from hOPs isolated from long bone fracture callus

value: Long bone fracture callus

value: hOPs

value: Fresh

value: 46 years


title: Fresh hOP2, patient 2

description: Fresh hOP2

value: 66 years


title: 5_CD34pCD38m_12d

value: patient derived AML model


title: Etoposide treated OVCAR3 cells (Biological Replicate 2)

city: Kolkata

first: Kaushik

last: Sengupta

state: West Bengal

address: 1/AF Bidhannagar

department: Biophysics and Structural Genomics

country: India

institute: Saha Institute of Nuclear Physics

data_processing:
Hisat2 was used to align the fastqc checked fastq files with the reference.
Samtools was used to generate sorted BAM files.
Transcript assembly was carried out using StringTie
DESeq2 was used to generate differentially expressed genes and transcripts
Assembly: GRCh38
Supplementary files format and content: GTF file containing FPKM values generated from StringTie version 2.1.7

source_name: Etoposide treated OVCAR3 cells

growth_protocol:
NIH-OVCAR3 (Epithelial cells from the malignant ascites of patient with progressive adenocarcinoma of ovary)
NIH-OVCAR3 cell line was maintained in ATCC formulated RPMI 1640 supplemented with Penicillin-streptomycin to a final concentration of 1% and Fetal Bovine Serum (FBS) to a final concentration of 20%.

extract_protocol:
mRNA library preparation was performed using Kapa Hyperprep stranded library preparation kit (Roche,Switzerland) followed by sequencing on Novaseq 6000 (Illumina,Inc.,USA) using 2X100bp read length targeting 50 million paired-end reads.
2X100bp read length targeting 50 million paired-end reads

treatment_protocol: OVCAR3 cells were treated with 100ng/ml nocodazole for 16 hours and washed with PBS thrice and incubated in the fresh media for 3 hours before treatment with etoposide (Final Concentration :1.7µM) for 24 hours. DMSO was used as vehicle.

value: ovarian adenocarcinoma cell

value: ETOPOSIDE


title: 100224690-cffDNA

value: Pravastatin


title: Fresh hSSC3, patient 3

description: Fresh hSSC3

source_name: Gene expression data from hSSCs isolated from long bone fracture callus

value: hSSC

value: 72 years


title: From_SID_144_PreTreat_Blood_TRb

value: control

value: Pre-treatment

value: CD

value: Blood (PBMC)

value: Treg


title: Fresh hSSC1, patient 1

description: Fresh hSSC1


title: HDF (human dermal fibroblasts)

city: Okayama

first: Kiyofumi

last: Takabakake

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Oral Pathology and Medicine Graduate school of Medicine, Dentistry and Pharmaceutical Science

country: Japan

institute: Okayama University

description: gene expression in human dermal fibroblasts

hyb_protocol: 100 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SureScan Microarray Scanner G4900DA (Agilent Technologies) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner G4900DA (Agilent Technologies) using one color scan setting for 8x60k array slides. (Scan Area 71x21.6 mm, Scan resolution 10 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 (Read Only) and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA. Dye incorporation and cRNA yield were checked with the BioanalyzerRNA6000 Nano.

growth_protocol: HDF, G-SCs and P-SCs were maintained in α-MEM (Life Technologies, Thermo Fisher Scientific Inc) supplemented with 10% FBS and 1% antimycotic-antibiotic (Life Technologies, Thermo Fisher Scientific Inc., KK, Tokyo, Japan) at 37 ℃ in a humidified atmosphere of 5% CO2 and 95% air.

extract_protocol: RNA was prepared using the miRNeasy micro kit following the manufacturer's recommendations.  And the concentration of RNA were tested by Nanodrop One (Thermo Fisher Scientific).

value: HDF

value: fibroblasts


title: 100229077-cffDNA

source_name: cffDNA

value: Control

value: Yes

value: cffDNA


title: Fresh hSSC2, patient 2

description: Fresh hSSC2

value: Long bone fracture callus

value: Fresh

value: 66 years


title: From_SID_134_PreTreat_Blood_TMb

value: Tmen


title: From_SID_143_PreTreat_Blood_TMb

value: UC


title: 100224665-cffDNA

value: Restriction

value: No


title: P-SCs (Periodontal derived stromal cells)

description: gene expression in periodontal derived stromal cells

source_name: periodontal derived stromal cells

value: stromal cells


title: 100225730-cffDNA

value: Obese


title: DMSO treated OVCAR3 cells (Biological Replicate 1)

source_name: DMSO treated OVCAR3 cells

value: ovarian adenocarcinoma cell

value: DMSO


title: G-SCs (Gingival derived stromal cells)

description: gene expression in gingival derived stromal cells

source_name: gingival derived stromal cells


title: EYFP- pancreatic cells (post-pancreatitis)

city: Amsterdam

first: Leandro

last: Moreno

address: Meibergdreef 9

country: Netherlands

institute: AmsterdamUMC

data_processing:
Single cell sequencing data were aligned to the human reference genome (GRCh38) and processed using the CellRanger 2.1.0 software from 10x Genomics to generate unique molecular identifier (UMI) counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: CellRanger output

organism: Mus musculus

source_name: Pancreatic cells

extract_protocol: Single-cell libraries were generated using the Chromium Single Cell 5′ Library and Gel Bead Kit v1.1 according to the manufacturer’s instructions. Libraries were sequenced using HiSeq4000, and each position of the 10X chip was sequenced on an individual HiSeq4000 lane

tag: genotype/variation

tag: strain background


title: DMSO treated OVCAR3 cells (Biological Replicate 2)

tag: cell type


title: EYFP+ pancreatic cells (post-pancreatitis)


title: 100224688-cffDNA

tag: group


title: Patient2 TCR Treatment2 6 weeks

city: St. Louis

first: Michelle

last: Brennan

state: MO

address: 1100 South Grand Blvd

department: Biochemistry & Molecular Biology

institute: Saint Louis University School of Medicine

data_processing:
The read alignment, barcode processing, and gene counting was performed using the 10X Genomics Cell Ranger 5.0.1 software.
Assembly: GRCh38
Supplementary files format and content: For scRNA-seq samples, barcodes.tsv, features.tsv, matrix.mtx.
Supplementary files format and content: For scTCR-seq samples, clonotypes and filtered_contig_annotations .csv files
Library strategy: scTCR-seq

source_name: whole blood

extract_protocol:
Whole blood was collected in a Beckton Dickenson Vacutainer with 158 USP units sodium heparin. Blood was centrifuged at 1500 G for 10 minutes to separate cells from plasma. Plasma was collected and stored at -80 degrees Celsius. The cellular fraction was resuspended in 3-times the original blood volume and overlaid onto Ficoll-Paque PLUS (GE Healthcare Life Sciences). PBMC were separated from red blood cells by centrifugation at 2000 RPM for 30 minutes. The PBMC fraction was removed, washed 2-times in phosphate buffered saline (PBS), resuspended in freezing media consisting of 10% DMSO, 40% fetal bovine serum, 50% RPMI 1640 media (Gibco), frozen gradually at -80°C and then stored in liquid nitrogen prior to analysis. PBMCs were sorted to at least 99% purity based on CD8+ and CD4+ staining using a BD FACSAria III (BD Biosciences).
Library was performed according to the manufacter’s instructions (single cell 5’ protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reverse transcribed to cDNA. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads and amplified by PCR. One fraction of the amplified cDNA was used for gene expression library construction and another fraction of the amplified cDNA was further amplified to enrich T cell receptor sequences and used for TCR library construction.
scRNAseq (Gene expression + TCR)

tag: individual

value: melanoma

tag: tissue

value: whole blood

value: PBMC

tag: cell subset

value: CD8+/CD4+ T cells

value: 6 weeks

value: nivolumab+ipilimumab


title: Etoposide treated OVCAR3 cells (Biological Replicate 1)

value: ETOPOSIDE


title: From_SID_131_PreTreat_Biopsy_TMb

value: control

tag: time

value: Pre-treatment

tag: disease state

value: CD

value: Biopsy

value: Ileum


title: From_SID_133_PreTreat_Biopsy_TMb

value: Tmen

tag: location collected

value: Colon


title: 100229066-cffDNA

value: Control

tag: timepoint

tag: infantid

tag: birthgd

value: No

tag: foster

value: Yes

value: cffDNA


title: From_SID_129_PreTreat_Blood_TMb

source_name: Blood (PBMC)

tag: treatment

tag: sample type

value: Blood (PBMC)


title: 100228969-cffDNA

tag: cohort


title: Patient2 TCR Treatment1 3 weeks

value: melanoma

value: whole blood

value: PBMC

value: 3 weeks


title: SAM24386527

first: Mitchell

last: Rezzonico

data_processing:
Single-cell RNA sequencing data were processed with an in-house analysis pipeline as described (https://www.sciencedirect.com/science/article/pii/S2211124719317656). Reads were demultiplexed based on perfect matches to expected cell barcodes. Transcript reads were aligned to the mouse reference genome (GRCm38) using GSNAP (2013-10-10) (Wu and Nacu, 2010). Only uniquely mapping reads were considered for downstream analysis. Transcript counts for a given gene were based on the number of unique UMIs (up to one mismatch) for reads overlapping exons in sense orientation. Cell barcodes from empty droplets were filtered by requiring a minimum number of detected transcripts. Sample quality was further assessed based on the distribution of per-cell statistics, such as total number of reads, percentage of reads mapping uniquely to the reference genome, percentage of mapped reads overlapping exons, number of detected transcripts (UMIs), number of detected genes, and percentage of mitochondrial transcripts.
For samples SAM24376861, SAM24376862, SAM24381111, and SAM24381112 the R1 file provides the barcode representing the cell (positions 1-16) and the UMI (positions 17-24). The R2 file provides the insert sequence. For all other samples, L001 and L002 denote the sequencing lane. I1 refers to the index. R1 and R2 indicate read 1 and 2, respectively.
Genome_build: mm10

source_name: Corpus Callosum

extract_protocol: Single cell suspensions were processed using Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10X Genomics, PN-1000121) and Chromium Next GEM Chip G Single Cell Kit (10X GEnomics, PN-1000120) following manufacturer’s user guide. Cell-RT mix was prepared to aim 1,000 cells per sample and applied to Chromium™ Controller for GEM generation and barcoding. Then samples were subjected to post GEM-RT cleanup, cDNA amplification (11 cycles), and library construction according to the user guide. Sample index PCR was done with 12 cycles. Libraries were then quantified by Qubit dsDNA HS Assay Kit (Thermo Fisher Q33230) and profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies 5067-4626). Libraries were sequenced following 10X Genomics sequencing specification.


title: From_SID_132_PreTreat_Biopsy_TMb


title: SAM24386525


title: 100229624-cffDNA

value: Pravastatin


title: From_SID_128_PreTreat_Blood_TRb

value: control

value: Treg


title: Patient2 TCR Pre-treatment Baseline

value: CD8+/CD4+ T cells

value: 0 weeks

value: nivolumab+ipilimumab


title: 100229604-cffDNA


title: 100229268-cffDNA


title: Patient2 GEX Treatment2 6 weeks

library_source: transcriptomic single cell

data_processing:
The read alignment, barcode processing, and gene counting was performed using the 10X Genomics Cell Ranger 5.0.1 software.
Assembly: GRCh38
Supplementary files format and content: For scRNA-seq samples, barcodes.tsv, features.tsv, matrix.mtx.
Supplementary files format and content: For scTCR-seq samples, clonotypes and filtered_contig_annotations .csv files

value: 6 weeks


title: SAM24386523


title: Patient2 GEX Treatment1 3 weeks


title: Patient1 TCR Treatment2 6 weeks

value: nivolumab


title: 100228979-cffDNA


title: From_SID_127_PreTreat_Biopsy_TMb

value: Pre-treatment

value: CD

value: Biopsy

value: Tmen

value: Colon


title: From_SID_124_PreTreat_Blood_TRb

value: Blood (PBMC)


title: SAM24381114


title: 100228936-cffDNA

value: Restriction

value: No

value: cffDNA


title: SAM24386526


title: SAM24386522


title: From_SID_140_PreTreat_Blood_TMb


title: From_SID_126_PreTreat_Biopsy_TMb

value: Ileum


title: SAM24381113


title: From_SID_123_PreTreat_Biopsy_TMb

value: control


title: Patient2 GEX Pre-treatment Baseline

value: melanoma

value: whole blood

value: PBMC


title: 100230274-cffDNA

value: Obese


title: 100229275-cffDNA

value: Yes


title: Patient1 TCR Treatment1 3 weeks

value: CD8+/CD4+ T cells

value: 3 weeks

value: nivolumab


title: From_SID_121_PreTreat_Biopsy_TMb

value: Pre-treatment

value: CD

value: Biopsy


title: SAM24386524

description: NL

value: NL


title: SAM24381112


title: 100229067-cffDNA


title: From_SID_125_PreTreat_Blood_TMb

value: Blood (PBMC)

value: Tmen


title: From_SID_120_PreTreat_Biopsy_TRb

value: Treg


title: Patient1 TCR Pre-treatment Baseline

value: 0 weeks


title: Patient1 GEX Treatment2 6 weeks

value: 6 weeks


title: SAM24381111

description: NL


title: From_SID_118_PreTreat_Blood_TRb

value: control


title: SAM24376862


title: From_SID_117_PreTreat_Biopsy_TMb

value: Colon


title: Patient1 GEX Pre-treatment Baseline

value: melanoma

value: whole blood

value: PBMC


title: From_SID_119_PreTreat_Blood_TMb


title: SAM24376861

description: NL


title: OCIAML22, graft, CD34minus, WGS

data_processing:
We used HMMcopy (https://bioconductor.org/packages/release/bioc/html/HMMcopy.html) to detect copy number abnormalities. The whole genome sequencing data was aligned to hg38 using bwa v0.7.12 with default settings. Reads were sorted and duplicates were marked with picard v2.21.4. Copy number calls were made using both HMMcopy v0.1.1 and celluloid v0.11.7 with 1kb windows. Telomeric and centromeric regions were removed from further analysis. We considered anything with a copy number below 1.5 as a loss and greater than 2.5 as a gain.
Assembly: hg38
Supplementary files format and content: txt files for each sample sequenced that indicates chr, start and end. The last column indicates gain (1), neutral (0), loss (-1) based on the thresholds (2.5 and 1.5).
Library strategy: WGS

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Micro kit (Qiagen, ref 56304) following recommendations
Whole Genome Libraries, one hundred nanogram of sorted cell DNA from each sample was fragmented using a Covaris M220 Focused-ultrasonicator. Libraries were then generated using KAPA HyperPrep Kit (Roche, Cat# 07962363001) according to manufacturer’s instruction.

value: patient derived AML model

tag: cell line

value: graft, CD34minus


title: OCI-AML3 GDYO-rep1 [Bisulfite-Seq]

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Adaptors and poor quality bases were filtered with Trim Galore (v0.6.0) with default parameters.
Clean data were aligned to human reference genome GRCh37 with bismark (v0.21.0)
The CpG coverage reports were generated by the bismark_methylation_extractor function.
The CpG regions with coverage > 10 in all samples were retained and used for further analysis.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include CpG coverage reports for each Sample .

extract_protocol:
Genomic DNA was isolated using the QIAamp DNA blood mini kit (QIAGEN).
Libraries were constructed using the Pico Methyl-Seq library prep kit (Zymo Research), and each library was subjected to 150 bp pair-end sequencing on HiSeq 2500 device (Illumina).

treatment_protocol: 1 × 106 of OCI-AML3 were pre-treated with GDYO (20 μg/mL) for 24 h and then harvested.

tag: agent

value: GDYO


title: OCIAML22, graft, CD34positive, WGS

tag: cell type

value: graft, CD34positive


title: 100224913-cffDNA

data_processing:
The CpG_Me pipeline (https://github.com/ben-laufer/CpG_Me) was used to perform all data processing steps.
Trim Galore was used to trim adapters and methylation bias.
FastQ Screen was used to screen for sample contamination.
Bismark was used align to the reference genome, remove PCR duplicates, calculate coverage, extract CpG methylation, and generate genome-wide cytosine reports (CpG count matrices).
Picard Tools was used to calculate insert size metrics.
MultiQC was used for quality control.
Genome_build: rheMac10
Supplementary_files_format_and_content: Bismark genome-wide cytosine reports (CpG count matrices)

extract_protocol:
Automated. Promega Maxwell RSC ccfDNA Plasma Kit for cffDNA and Tecan workflow for Zymo Quick-DNA Miniprep Plus Kit for brain.
Swift BioSciences Accel-NGS Methyl-Seq DNA Library Kit

tag: group

value: Pravastatin

value: No

value: cffDNA


title: From_SID_116_PreTreat_Biopsy_TRb

value: Pre-treatment

value: CD

value: Biopsy


title: 100224945-cffDNA


title: From_SID_115_PreTreat_Biopsy_TMb

value: Tmen

value: Ileum


title: 100224527-cffDNA


title: From_SID_114_PreTreat_Biopsy_TRb

value: control

value: Treg


title: Donor, OCIAML22, bulk, WGS

value: bulk


title: OCI-AML3 control-rep2 [Bisulfite-Seq]


title: OCIAML22, bulk, 1month, inVitro, WGS

value: bulk, 1month, in vitro


title: CD34negative, OCIAML22, ATAC

library_source: other

data_processing:
Unaligned reads were mapped against the hg19 human reference genome using BWA 48 with default parameters. All duplicate reads, and reads mapped to mitochondria, chrY, an ENCODE blacklisted region or an unspecified contig were removed 49. MACS 2.0.10 50 callpeak was used to call peaks from aligned reads
Assembly: hg19
Supplementary files format and content: MACS2 Derived Called Peaks in narrowPeak format

molecule: other

extract_protocol: Library preparation for ATAC-Seq was performed by the  the “Princess Margaret Genomics Centre, Toronto, Canada (www.pmgenomics.ca) on 100,000 sorted CD34+CD38- OCI-AML22 cells that have been cultured for about 4 months (n=1 per population), with Nextera DNA Sample Preparation kit (FC-121-1030, Illumina), according to previously reported protocol 47.


title: OCI-AML3 GDYO-rep2 [Bisulfite-Seq]


title: 100225466-cffDNA

value: Restriction


title: 100226143-cffDNA

value: Control


title: OCI-AML3 control-rep1 [Bisulfite-Seq]


title: Patient1 GEX Treatment1 3 weeks

tag: individual

value: melanoma

value: whole blood

value: PBMC

value: CD8+/CD4+ T cells

value: 3 weeks

value: nivolumab


title: From_SID_113_PreTreat_Blood_TMb

data_processing:
75-base single reads average 20M reads per sample (3.5B reads total).
Raw counts were generated based on Ensembl genes (Ensembl release 91) with HTSeq (ver.0.11)
Reads from T cell RNA-seq were mapped to the human genome (GRCh38) using STAR (ver.2.5.0) aligner
Fold changes of differential expression were estimated through DESeq2(1.22.2)
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: RawGeneCounts.xlsx

extract_protocol:
Total RNA was extracted via miRNAeasy Micro Kit (Qiagen, Germantown, MD)
Libraries were individually indexed and pooled in groups of 20. Each pool was run on a NextSeq500 flow cell (9 flow cells total)

value: Pre-treatment

value: Blood (PBMC)


title: 100228981-cffDNA

value: Obese

value: No

value: cffDNA


title: 100228935-cffDNA


title: HeLa, R3

data_processing:
Reads were mapped with Bowtie v1.0.0 (Langmead et al., 2009) to the human transcriptome (Gencode V19 transcriptome as downloaded from the UCSC Genome Browser wgEncodeGencodeBasicV19 table), allowing a maximum of two mismatches and reporting all alignments in the best stratum. The sequences of the rabbit β-globin, firefly and renilla luciferase IVTs were included into the index.
Read counts were summarized at the gene level with an in-house-developed perl script discarding all reads that map to transcript isoforms of more than one gene (as defined by a common gene symbol).
To identify individually regulated mRNAs with DESeq2 v1.16.1, human read counts were normalized with the median ratio method before calculating mean fold changes. p-values for changes in mRNA expression were obtained from a likelihood ratio test (Love et al., 2014).
Genome_build: Gencode V19
Supplementary_files_format_and_content: csv file containing raw read counts per gene, expression values after normalization with DESeq2, fold changes, fold-changes determined with DESeq2 and p-values.

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS, Sigma), 2 mM L-Glutamine, 100 U/ml penicillin and 0.1 mg/ml streptomycin (all PAN Biotech) at 37°C in a humidified atmosphere with 5% CO2. Every two to three days, cells were carefully detached by scraping in warm 1x PBS and diluted 1:10.

extract_protocol:
RNA was extracted with the GeneMatrix universal RNA purification kit (Roboklon). 2 μg of total RNA was mixed with 0.83 fmol each of rabbit β-globin, firefly and renilla luciferase in vitro transcripts (IVTs).
After depletion of rRNA using the Ribo-Zero Gold Kit (Illumina), sequencing libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on a HiSeq 2500 device (Illumina) with 50 bases single end.

treatment_protocol: Cells were seeded at a density of 0.16 x 10^5 cells/cm2. On the following day, cells were treated with 20 nM Romidepsin (Abcam, ab143287) or an equal volume of solvent (DMSO) for 16 hours.

value: HeLa

value: RMD, 16h


title: 100224915-cffDNA


title: Cultured hSSC1, patient 1

description: Cultured hSSC1

tag: tissue

value: Long bone fracture callus

value: hSSC

tag: condition

value: Cultured for one week

tag: age

value: 26 years


title: 100224555-cffDNA

value: Restriction


title: From_SID_107_PreTreat_Blood_TMb

value: control

tag: time

tag: disease state

value: CD

value: Tmen


title: Bulk, OCIAML22, ATAC

value: patient derived AML model

value: bulk


title: HeLa, R2


title: single-cell RNA seq data of biopsy material from PCNSL patient 2

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

description:
annotation_cluster.csv
annotation_sample.csv
annotation_cluster_bc.csv

data_processing:
Raw bcl files were de-multiplexed using the cellranger or spaceranger mkfastq pipeline (cellranger v6.1, spaceranger v1.3)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count or spaceranger count pipeline with default parameters.
Assembly: GRCh38
Supplementary files format and content: Standard cellranger/spaceranger output format

source_name: biopsy

extract_protocol:
Biopsy samples were obtained using a frame-based (Leksell Stereotactic System, Elekta Instrument AB, Stockholm, Sweden) or a frameless image-guided (VarioGuide, Brainlab AG, Munich, Germany) stereotactic system. In all cases, the target point was defined within the contrast-enhancing, non-necrotic lymphoma-suspicious lesion.
The samples were loaded onto the 10x Genomics Chromium Single Cell Controller, using the Chromium Single Cell 3' Library & Gel Bead Kit v2-3. B cells were positively selected from blood-derived cells, using CD20-microbeads according to the manufacturer's protocol (Miltenyi). Biopsy-derived cells and B cell enriched blood cells in patient 1 were processed using CITE-seq supported scRNA-seq, all other samples were processed with standard scRNA-seq.  5µm FFPE sections of human PCNSL samples were placed on a Visium Gene Expression (GEX) slide (10x Genomics), which incorporates about 5000 molecularly barcoded and spatially encoded capture spots. Deparaffinization, hematoxylin and eosin (H&E) staining, and decrosslinking were performed according to the protocol of Visium Spatial Gene Expression for FFPE (10x Genomics).

value: biopsy-derived cells

tag: diagnosis

value: PCNSL

tag: type of library

value: RNA

tag: subject id


title: single-cell RNA seq data of blood from PCNSL patient 2

source_name: blood

value: B cell-enriched blood cells


title: 100224528-cffDNA

value: Obese

tag: timepoint

tag: infantid

tag: birthgd

value: No

tag: foster

value: cffDNA


title: From_SID_99_PreTreat_Biopsy_TMb

source_name: Biopsy

tag: treatment

value: Pre-treatment

value: UC

tag: sample type

value: Biopsy

tag: location collected

value: Colon


title: IR_Thr6_LL_BW_yiaU_R2

city: San Diego

first: Bernhard

middle: O.

last: Palsson

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

data_processing: Raw RNA-Seq reads were mapped to the original reference genome using Bowtie2 and transcript abundance was analyzed using summarizeOverlaps (Lawrence et al., 2013). Calculation of transcripts per million (TPM) and prediction of differentially expressed genes were conducted using DESeq2 (Love et al., 2014).

organism: Escherichia coli BW25113

source_name: Lexp_ycaN_BW25113 E. coli, M9 medium, L-Thr added_2

growth_protocol: RNA sequencing data were generated under aerobic exponential growth conditions in M9 medium  supplemented with 6mM L-threonine. The wild type BW25113 strain was grown as a control for the isogenic mutant strain. Pre-cultures for the RNA sequencing experiments were taken by scraping frozen stocks and growing the cells in LB medium. Cells were washed twice with M9 medium and inoculated at an OD600 of 0.05. The cells were collected at an OD600 of 0.9 (only ycaN, yiaU, ybhD mutants and WT control collected at OD600 of 2.2 for late-exponential phase)

extract_protocol:
Pelleted cells were stored at -80oC, and after cell resuspension and partial lysis, they were ruptured with a beat beater; the total RNA was extracted using a Qiagen RNA purification kit.
Paired-end RNA-Seq libraries were constructed using a KAPA RNA HyperPrep kit from Kapa Biosystems (Wilmington, MA, USA).

treatment_protocol: Cells were treated with the Qiagen RNA-protect bacterial reagent according to the manufacturer’s specifications.

tag: genotype

value: yiaU mutant


title: From_SID_96_PreTreat_Biopsy_TRb

value: control

tag: cell type

value: Treg


title: IR_Thr6_LL_BW_yiaU_R1

source_name: Lexp_ycaN_BW25113 E. coli, M9 medium, L-Thr added_1


title: IR_Thr6_LL_BW_ygfI_R2

source_name: Exp_ygfI_BW25113 E. coli, M9 medium, L-Thr added_2

value: ygfI mutant


title: single-cell RNA seq data of blood from PCNSL patient 1 part 3

tag: tissue


title: From_SID_97_PreTreat_Biopsy_TMb

value: Tmen


title: HeLa, R1

tag: cell line

value: HeLa

value: RMD, 16h


title: single-cell BCR seq data of CSF from PCNSL patient 1

source_name: CSF

value: CSF-derived leukocytes

value: PCNSL

value: BCR


title: single-cell BCR seq data of blood from PCNSL patient 1 part 3

value: B cell-enriched blood cells


title: C. elegans smRNA sequencing prg-1 replicate 1

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

data_processing:
Base calling and fastq file was done using Illumina Software.
Reads were trimmed of adapters and filtered of poorly sequenced reads was doen with TrimGalore.
Reads passing adapter trimming and quality control were collapsed using custrom shell scripts.
Processed reads were aligned using Bowtie1 Software.
Alignments were further processed using custom python scripts
Assembly: WS279
Supplementary files format and content: fasta file. Header is the sequence and count separated by a colon.

organism: Caenorhabditis elegans

source_name: Whole Animal

growth_protocol: Synchronised L1 plated on 135 mm NGM plates seeded with OP50 and at 20°C.

extract_protocol:
Approximately 100,000 synchronized L1 animals were plated on 135 mm NGM plates seeded with OP50 and grown at 20 °C until the animals reached gravid adult stage. Gravid adult populations were harvested using M9, and subsequently suspended in Trizol. Worms were lysed using the Fisherbrand Bead Mill 24 homogenizer, bromochloropropane was added to the lysis to perform RNA extraction. Isopropanol was then used to precipitate RNA from the aqueous phase. Small RNAs were isolated from total RNAs using the miRVana miRNA isolation kit (Thermo Fisher Scientific) according to the manufacturers protocol.
Small RNA samples from wild-type and mutants were first incubated with a recombinant 5’ polyphosphatase PIR-1 which removes the γ and β phosphates from 5´-triphosphorylated RNAs (Li et al. 2020; Pastore et al. 2021). The resulting monophosphorylated RNAs were ligated to the 3’ adaptor (5’rAppAGATCGGAAGAGCACACGTCTGAACTCCAGTCA/3ddC/3’, IDT) using T4 RNA ligase 2 in the presence of 25% PEG8000 (NEB) at 15 °C overnight. The 5’ adaptor (rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU, IDT) was then ligated to the product using T4 RNA ligase 1 (NEB) at 15 °C for 4 hours. The ligated products were converted to cDNA using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific). The cDNAs were amplified by PCR using Q5 High-Fidelity DNA polymerase (NEB), and the libraries were sequenced on an Illumina Novaseq platform (SP 2 X 50 bp) at the OSU Comprehensive Cancer Center genomics core.

value: Whole Animal

value: prg-1 mutant


title: From_SID_95_PreTreat_Biopsy_TMb

value: Pre-treatment


title: C. elegans smRNA sequencing wild type replicate 2

value: wild type


title: 100225142-cffDNA

first: Benjamin

last: Laufer

source_name: cffDNA

tag: group

value: Obese

value: No

tag: cohort

value: cffDNA


title: HeLa, C3

value: DMSO, 16h


title: From_SID_101_PreTreat_Blood_TMb

value: control

tag: time

tag: disease state

value: CD

value: Blood (PBMC)


title: HeLa, C2

value: HeLa


title: From_SID_100_PreTreat_Blood_TRb

value: Treg


title: From_SID_112_PreTreat_Blood_TRb


title: C. elegans smRNA sequencing prg-1 replicate 2


title: From_SID_94_PreTreat_Biopsy_TRb

value: UC

value: Biopsy

value: Ileum


title: C. elegans smRNA sequencing wild type replicate 1


title: HeLa, C1


title: IR_Thr6_LL_BW_ygfI_R1

source_name: Exp_ygfI_BW25113 E. coli, M9 medium, L-Thr added_1

value: ygfI mutant


title: From_SID_91_PreTreat_Biopsy_TMb

value: Tmen

value: Colon


title: single-cell RNA seq data of blood from PCNSL patient 1 part 1

value: B cell-enriched blood cells

tag: diagnosis

value: PCNSL

tag: type of library

value: RNA


title: CD34positive, OCIAML22, ATAC

value: patient derived AML model


title: single-cell BCR seq data of blood from PCNSL patient 1 part 1

value: BCR

tag: subject id


title: Mutant Embryo - rep16

city: Barcelona

first: Sean

middle: Akira

last: Montgomery

address: C/ del Dr. Aiguader 88

institute: Centre for Genomic Regulation

data_processing:
Reads were mapped using STAR v2.7.1a and further processed using Samtools v1.9.
Counts and Transcripts per Million per gene were calculated with RSEM v1.3.2.
Genome_build: Takv6; SRA:PRJDB11173; Download: https://marchantia.info/download/MpTak_v6.1/
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: Matrix table with TPM for every gene and every sample

organism: Marchantia polymorpha

source_name: Embryo

extract_protocol:
One single embryo was cleanly dissected by hand, and RNA was harvested using Tri-reagent. SmartSeq II protocol was used for the construction of cDNA libraries.
SmartSeq II

value: Cam-2 e(z)2/e(z)3 x Tak-1

value: Embryo


title: Mutant Embryo - rep15


title: IR_Thr6_LL_BW_ycaN_R1

source_name: Lexp_ycaN_BW25113 E. coli, M9 medium, L-Thr added_3

value: ycaN mutant


title: From_SID_89_PreTreat_Biopsy_TMb

value: control

value: Pre-treatment


title: Mutant Embryo - rep17


title: IR_Thr6_LL_BW_ycaN_R2

source_name: Lexp_ycaN_BW25113 E. coli, M9 medium, L-Thr added_4


title: single-cell RNA seq data of blood from PCNSL patient 1 part 2


title: From_SID_88_PreTreat_Biopsy_TRb

value: Treg


title: single-cell BCR seq data of biopsy material from PCNSL patient 1 part 3

value: biopsy-derived cells


title: IR_BW25113ybeF_M9_Glc_Thr6_R2

source_name: Exp_ybeF_BW25113 E. coli, M9 medium, L-Thr added_2

value: ybeF mutant


title: From_SID_93_PreTreat_Blood_TMb

source_name: Blood (PBMC)

value: UC

value: Blood (PBMC)


title: single-cell BCR seq data of blood from PCNSL patient 1 part 2


title: IR_BW25113ybeF_M9_Glc_Thr6_R1

source_name: Exp_ybeF_BW25113 E. coli, M9 medium, L-Thr added_1


title: single-cell RNA seq data of biopsy material from PCNSL patient 1 part 2


title: Mutant Embryo - rep12


title: IR_Thr6_LL_BW_ybhD_R2

source_name: Lexp_ybhD_BW25113 E. coli, M9 medium, L-Thr added_2

value: ybhD mutant


title: single-cell BCR seq data of biopsy material from PCNSL patient 1 part 2

source_name: biopsy


title: IR_Thr6_LL_BW_ybhD_R1

source_name: Lexp_ybhD_BW25113 E. coli, M9 medium, L-Thr added_1


title: From_SID_86_PreTreat_Biopsy_TRb

source_name: Biopsy

value: Biopsy

value: Ileum


title: Mutant Embryo - rep11


title: From_SID_90_PreTreat_Biopsy_TRb

value: Colon


title: IR_Thr6_LL_BW_WT_R2

source_name: Lexp_BW25113 E. coli, M9 medium, L-Thr added_2

value: WT


title: single-cell RNA seq data of biopsy material from PCNSL patient 1 part 3

value: PCNSL

value: RNA


title: From_SID_84_PreTreat_Blood_TRb


title: single-cell RNA seq data of CSF from PCNSL patient 1

value: CSF-derived leukocytes


title: IR_Thr6_LL_BW_WT_R1

source_name: Lexp_BW25113 E. coli, M9 medium, L-Thr added_1


title: Mutant Embryo - rep9

value: Cam-2 e(z)2/e(z)3 x Tak-1

value: Embryo


title: Mutant Embryo - rep14


title: IR_BW25113_M9_Glc_Thr6_R2

source_name: Exp_BW25113 E. coli, M9 medium, L-Thr added_2


title: From_SID_80_PreTreat_Blood_TMb

value: control

value: CD

value: Tmen


title: Mutant Embryo - rep8


title: Mutant Embryo - rep13


title: IR_BW25113_M9_Glc_Thr6_R1

source_name: Exp_BW25113 E. coli, M9 medium, L-Thr added_1


title: Mutant Embryo - rep7


title: From_SID_79_PreTreat_Blood_TRb

value: Pre-treatment

value: Treg


title: OCI-AML3 GDYO-rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data were trimmed by Trimmomatic (v0.38).
Clean data were aligned to the human reference genome GRCh37 by HISAT2 (v2.1.0) with default setting.
HTSeq (v0.11.2) was used to calculate genes counts with parameter “--mode intersection-strict --stranded no --minaqual 1”.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample .
Supplementary_files_format_and_content: Comma separated text files with FPKM values for each sample

extract_protocol:
Total RNA was extracted from OCI-AML3 cells in control and treatment groups with Trizol according to the manufacturer’s protocol.
First-strand cDNA synthesis and cDNA libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit (New England Biolads). cDNA quality was determined on Agilent 2100 BioAnalyzer (Agilent Technologies), and then sequenced on Illumina novaseq 6000 to obtain pair-end 150 bp reads.

tag: agent

value: GDYO


title: From_SID_87_PreTreat_Biopsy_TMb

value: UC


title: OCI-AML3 control-rep3


title: From_SID_85_PreTreat_Blood_TMb

value: Blood (PBMC)


title: Mutant Embryo - rep5


title: IR_BW25113ybdO_M9_Glc_Thr6_R2

source_name: Exp_ybdO_BW25113 E. coli, M9 medium, L-Thr added_2

value: ybdO mutant


title: single-cell RNA seq data of biopsy material from PCNSL patient 1 part 1

value: biopsy-derived cells


title: Mutant Embryo - rep10


title: single-cell BCR seq data of biopsy material from PCNSL patient 1 part 1

value: BCR


title: Tfh cells in the spleen of Mst1∆CD4 mice, biological replicate 2

first: Lin

last: Dong

address: No. 19, Xinjiekouwai Street, Haidian District

institute: Beijing Normal University

description: not collected

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: spleen

growth_protocol: Sorted Tfh cells were collected in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: spleen

value: not collected

value: sorted Tfh cells

value: Mst1 knockout

value: Intraperitoneal OVA sensitization of mice


title: Tfh cells in the spleen of Mst1∆CD4 mice, biological replicate 1

description: not collected


title: IR_BW25113ybdO_M9_Glc_Thr6_R1

source_name: Exp_ybdO_BW25113 E. coli, M9 medium, L-Thr added_1


title: Tfh cells in the spleen of WT mice, biological replicate 3

description: not collected

value: WT


title: From_SID_75_PreTreat_Blood_TRb

first: Maria

last: Abreu

value: control


title: Tfh cells in the spleen of Mst1∆CD4 mice, biological replicate 4

description: not collected


title: OCI-AML3 GDYO-rep3


title: Tfh cells in the spleen of WT mice, biological replicate 2

description: not collected


title: hSIO - IL22-

city: Utrecht

first: Jeff

last: DeMartino

address: Heidelberglaan 25

institute: Princess Maxima Center

data_processing:
Illumina output demultiplexed (bcl files) converted to fastq files using mkfastq (CellRanger v5.0.1)
Alignment, filtering, barcode and UMI counting done using cellranger count (CellRanger v5.0.1)
Genome_build: Genome Reference Consortium Human Build 38 + transgene constructs (MUC2-mNeonGreen; DEFA5-IRES-dsRed)
Supplementary_files_format_and_content: Per sample filtered_feature_bc_matrix output from CellRanger (v5.0.1); includes gene-barcode matrices, genes, barcodes

source_name: human small intenstinal organoids

extract_protocol:
Organoids were removed from the Cultrex Basement Membrane Extract (BME, Growth Factor Reduced, Type 2, R&D Systems), digested with TryplE (Thermo Fisher) for 10~15 mins into single cells, washed with ice-cold AdDMEM/F12 (GIBCO) and filtered into FACS tubes through cell strainer (Falcon) with Rho kinase inhibitor Y-27632 dihydrochloride (10 µM, Abmole Bioscience). Cells were co-stained with DAPI (Sigma) and DRAQ5 (Biostatus) and subjected for FACS sorting of live cells. FACS was performed on BD Influx™ cell sorter (BD Bioscience). 4,000 live cells per condition were subjected to droplet-based scRNA-seq using the 10x Genomics platform.
Libraries were prepared using the 10x Genomics Chromium 3’ Gene Expression solution v3.1

tag: condition


title: Mutant Embryo - rep6

source_name: Embryo

value: Cam-2 e(z)2/e(z)3 x Tak-1

value: Embryo


title: OCI-AML3 GDYO-rep1


title: Tfh cells in the spleen of Mst1∆CD4 mice, biological replicate 3

city: Beijing

description: not collected


title: From_SID_77_PreTreat_Biopsy_TMb

value: Pre-treatment

value: CD

value: Biopsy

value: Tmen

value: Ileum


title: Mutant Embryo - rep4


title: P33_UC_Uninflamed_ileum_1

data_processing:
4.18 billion paired-end reads (2.09 billion clusters) were generated, and 472 million paired-end reads (236 million clusters) were unindexed.
Reads were mapped to the GRCh38 reference sequence using STAR (ver 2.5.0,  Durbin et al, 2013) aligner.
Raw counts were generated based on Ensembl genes (GENCODE version 26) with featureCounts (version 1.5.0).
Fold changes of differential expression were estimated through DESeq2 (ver.3.11, Love et al. 2014)
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: csv format

source_name: Ileum

extract_protocol:
Cells were lysed with RLT buffer and RNA was extracted via RNeasy Mini Kit (Qiagen, Germantown, MD)
Libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (HMR; Roche Life Science, Wilmington, MA) and then using standard Illumina protocols

treatment_protocol: Mucosal biopsies were digested for single cells and sorted for CD11b+ cells via magnetic column cell sorting.

value: UC

tag: biologics


title: OCI-AML3 control-rep1


title: From_SID_71_PreTreat_Biopsy_TRb

tag: treatment

value: Treg


title: Mutant Embryo - rep3


title: From_SID_74_PreTreat_Biopsy_TMb

tag: sample type

value: Colon


title: OCI-AML3 control-rep2


title: From_SID_76_PreTreat_Blood_TMb

value: Blood (PBMC)

tag: location collected


title: From_SID_73_PreTreat_Biopsy_TRb


title: hSIO - IL22+

tag: genotype


title: From_SID_69_PreTreat_Blood_TRb

tag: cell type


title: Tfh cells in the spleen of WT mice, biological replicate 1

description: not collected

tag: tissue

value: spleen

value: not collected


title: From_SID_72_PreTreat_Biopsy_TMb


title: MC3T3-E1, mechanical loading

city: Guilin City

first: Cao

last: Zhen

address: 1 Zhiyuan Road, Lingui, Guilin, Guangxi 541004, P.R. China

institute: Guilin medical university

data_processing:
Paired-end sequencing was performed with Illumina HiSeq 3000
HISAT2 alignment program was used for mapping sequencing reads
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Assembly: mm9
Supplementary files format and content: Matrix with raw gene counts and RPKM for every gene and every sample

source_name: skull

growth_protocol: MC3T3 pre-osteoblastic cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA extraction procedures were performed using the Trizol method
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ Directional RNA LNEBNext® Ultra™ Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: MC3T3 cells grow at confluence he medium was replaced with conditioned medium of PC-3 cells, the MC3T3-E1 cells were subjected to mechanical tensile strain of 2,500 µε at 0.5 Hz for 1h/day.

value: skull

tag: cell line

value: pre-osteoblastic

value: MC3T3-E1 cells are treated with  the physiological mechanical tensile strain


title: Mutant Embryo - rep1


title: P32_CD_Uninflamed_colon_2

city: Miami

address: 1475 NW 12th Ave floor 1

institute: University of Miami

source_name: Colon

value: anti-TNF


title: From_SID_78_PreTreat_Biopsy_TMb

value: control


title: WT Embryo - rep10

value: Cam-2 x Tak-1

value: Embryo


title: WT Embryo - rep11


title: WT Embryo - rep7


title: From_SID_67_PreTreat_Biopsy_TRb

value: Pre-treatment


title: WT Embryo - rep9


title: From_SID_68_PreTreat_Biopsy_TMb

value: Biopsy


title: MC3T3-E1, conditioned medium of PC-3 cells

value: WT

value: MC3T3-E1 cells are treated with conditioned medium of PC-3 cells


title: WT Embryo - rep6


title: From_SID_66_PreTreat_Biopsy_TMb

value: UC

value: Tmen


title: P30_CD_Uninflamed_ileum_2

value: Ileum

value: CD


title: P30_CD_Inflamed_ileum_1


title: P29_CD_Uninflamed_ileum_1


title: WT Embryo - rep8


title: From_SID_65_PreTreat_Biopsy_TRb

value: Treg

value: Colon


title: P28_UC_Uninflamed_ileum_1


title: MC3T3-E1, control

value: skull


title: MC3T3-E1, conditioned medium of PC-3 cells and mechanical loading

value: pre-osteoblastic

value: MC3T3-E1 cells are treated with conditioned medium of PC-3 cells and the physiological mechanical tensile strain


title: WT Embryo - rep5


title: KLB_Hipp_FGF21_3day_lane2

city: Iowa City

first: Kyle

middle: Harrington

last: Flippo

state: IA

address: 169 Newton Road, 3320 PBDB

department: Neuroscience and Pharmacology

institute: University of Iowa

description: BD Rhapsody single cell WTA kit

data_processing:
Sequencing data was then quality filtered and annotated using the BD Rhapsody analysis pipeline while also correcting for artifacts which arise during library construction. Filtered and annotated data from vehicle and FGF21 treated mice were then combined and normalized in the R package Seurat using SCTransform. Imputation was performed using the Seurat Wrapper ALRA on the  dataset before final clustering (clustering resolution was set at 0.5 based on the number of cells sequenced) (Table S2) and gene expression analysis to account for dropout associated with 3'-barcoding-based approaches (Ziegenhain et al., 2017). ‘‘Cell type’’ classification of the clusters was determined based on expression of previously identified marker genes for neuronal and non-neuronal cell types.
Assembly: mm9
Supplementary files format and content: .csv, matrix of gene counts for individual cells

source_name: Hippocampus

extract_protocol:
The method used here for generating single cell suspensions was modified from a previously published protocol32. Individual mice were quickly decapitated, the brain was immediately extracted and placed in fresh ice-cold artificial cerebrospinal fluid (aCSF) containing 124 mM NaCl, 2.5 mM KCl, 1.2 mM NaH2PO4, 24 mM NaHCO3, 5 mM HEPES, 13 mM glucose, 2 mM MgSO4, and 2 mM CaCl2, bubbled with a carbogen gas (95% O2 and 5% CO2) and with a pH of 7.3 - 7.4. Brains were then sectioned on a vibratome and sections containing the dorsal hippocampus were placed in ice cold aCSF w/ actinomycin D (93 mM N-methyl-D-glucamine, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 10 mM MgSO4, 0.5 mM CaCl2, 5 mM sodium ascorbate, 2 mM thiourea, and 3 mM sodium pyruvate, 45 µM actinomycin D, pH of 7.3-7.4, bubbled with carbogen gas (95% O2 and 5% CO2) on ice for at least 15 minutes prior to dissection). The dorsal hippocampus was then dissected from each section, and tissue derived from three mice were pooled for each experimental condition. The tissue was then minced and placed in 2mg/ml Pronase in aCSF w/ actinomycin D and incubated at 37°C for 30 minutes. Following digestion, the Pronase solution was exchanged with ice-cold, carbogen-bubbled ACSF containing 1% fetal bovine serum and .01% BSA. The tissue was then titrurated using fire polished Pasteur pipets and strained through a 70 µM cell strainer. FACs sorting for tdTomato positive cells was performed as previously described21. Hoechst cell viability dye (Hoechst 33258) was added to the cell suspension at a final dilution of 4ug/ml just prior to sorting to allow for selection of living cells during FACs sorting. Cells were then FACs sorted for tdTomato fluorescence and viability via Hoechst staining. Sorting was performed on a BD FACS Aria II using a 130 mM nozzle, a sheath pressure of 10 p.s.i., and in the single cell sorting mode at the University of Iowa Flow Cytometry Facility.
FACS isolated cells were then loaded on the BD Rhapsody where capture of the single cells was performed per manufacturer instructions. Following lysis of the cells and capture of mRNA on oligonucleotide barcoded beads the cDNA synthesis was performed and cDNA libraries with Illumina sequencing adapters were generated per manufacturer instructions using the BD Rhapsody whole transcriptome analysis amplification kit. cDNA libraries were then sequenced on Illumina NovaSeq 6000 sequencers at the University of Iowa Genomics Core. Sequencing data was then quality filtered and annotated using the BD Rhapsody analysis pipeline while also correcting for artifacts which arise during library construction. Filtered and annotated data from vehicle and FGF21 treated mice were then normalized in the R package Seurat. Imputation was performed using the Seurat Wrapper ALRA on the normalized data set before final clustering (clustering resolution was set at 0.5 based on the number of cells sequenced) and gene expression analysis to account for dropout associated with 3’-barcoding-based approaches. “Cell type” classification of the clusters was determined based on expression of previously identified marker genes (mousebrain.org) for neuronal and non-neuronal cell types.

value: Hippocampus

tag: strain

value: 3 day FGF21 treatment


title: P27_CD_Inflamed_ileum_1

value: anti-TNF


title: KLB_Hipp_FGF21_3day_lane1

description: BD Rhapsody single cell WTA kit


title: From_SID_64_PreTreat_Biopsy_TMb

value: control


title: From_SID_63_PreTreat_Blood_TMb

source_name: Blood (PBMC)

value: Pre-treatment

value: Blood (PBMC)


title: KLB_Hipp_FGF21_1day_lane2

description: BD Rhapsody single cell WTA kit

value: 1 day FGF21 treatment


title: Mutant Embryo - rep2

value: Cam-2 e(z)2/e(z)3 x Tak-1

value: Embryo


title: WT Embryo - rep4

value: Cam-2 x Tak-1


title: P26_UC_Uninflamed_colon_2

value: UC


title: From_SID_62_PreTreat_Blood_TRb


title: KLB_Hipp_FGF21_1day_lane1

description: BD Rhapsody single cell WTA kit


title: WT Embryo - rep3


title: WT Embryo - rep2


title: P25_CD_Uninflamed_colon_1

value: Ileum

value: CD


title: P24_CD_Inflamed_colon_1

value: Colon


title: KLB_Hipp_Vehicle_lane1

description: BD Rhapsody single cell WTA kit

value: Vehicle


title: From_SID_61_PreTreat_Biopsy_TMb

value: Biopsy

value: Tmen


title: P22_UC_Uninflamed_colon_1


title: Mutant Embryo - H3K27me3_rep2

data_processing:
Library strategy: CUT&RUN
Reads were mapped using Bowtie2 v2.1.0 and further processed using Samtools v1.3 and Bedtools v2.17.0. Reads with MAPQ less than ten were removed with Samtools v1.3 and duplicates were removed with Picard v1.141. Inserts less than 150 bp were removed.
Bigwig files were made using deepTools v2.2.4
Genome_build: Takv6; SRA:PRJDB11173; Download: https://marchantia.info/download/MpTak_v6.1/
Supplementary_files_format_and_content: 1x genome coverage normalized bigWig files

extract_protocol:
DNA fragments were isolated from sorted nuclei treated with primary antibody and pAG-MNase
NEBNext Ultra II

tag: antibody

value: H3K27me3 (Millipore #07-449)


title: Littermate control, wild type Klf4 allele, SMC lineage negative

city: Stanford

first: Albert

last: Pedroza

state: CALIFORNIA

address: 870 Quarry Rd, Falk CVRB

department: Cardiothoracic Surgery

institute: Stanford University

data_processing:
The sequenced data were processed into expression matrices with the ‘Cell Ranger Single cell software suite 3.1.0’. Raw base-call files from NovaSeq 6000 sequencer were demultiplexed to first generate FASTQ files using the cellranger mkfastq pipeline.
Reads were aligned to a custom-built mouse genome (mm10-3.0.0 edited to include tdTomato gene insertion), cell barcodes and unique molecular identifiers were filtered and corrected using the cellranger count pipeline
The final output filtered expression matrices (matrix.mtx.gz), barcodes (barcodes.tsv.gz), and genes/features (features.tsv.gz) files are included as processed files with this submission.
Assembly: mm10-3.0.0
Supplementary files format and content: Three output files from the cellranger pipeline are included for each sample, which reflect the cell x gene expression matrix (matrix.mtx.gz), unique cell barcodes (barcodes.tsv.gz) and gene lists (features.tsv.gz) for each input library.

source_name: Aortic root

extract_protocol:
The aortic root was dissected completely and divided below the aortic valve. The ascending aorta was divided midway between the aortic valve and the takeoff of the brachiocephalic artery . Aortas were transferred to a separate dish and rinsed in HBSS. Specimens were combined into groups with age and genotype-matched animals as biologic replicates (n=4 per group). The aortas were then digested in enzymatic solution containing 2U/mL Liberase TM (Roche #05401127001) and 2U/mL elastase (Worthington #LS002279) in Hanks buffered saline solution (HBSS) for one hour. The cell suspension was filtered through a 70uM strainer, centrifuged and resuspended in cold HBSS. Suspensions were processed with FACS to seperate fluorescent (tdTomato+) SMC lineage-traced cells and lineage negative cells.. Samples were then processed using a 10x Genomics microfluidics chip to generate barcoded Gel Bead-In Emulsions (GEMs) according to manufacturer protocols.
Individual sample libraries were generate from single cell GEM captures using the Chromium 3' version 3 library prep protocol (10X Genomics). QC was performed following cDNA generation and final library construction.

value: Aortic root

tag: fbn1 genotype

value: Control

tag: klf4 genotype

tag: lineage

value: Non-SMC

tag: age

value: 24 Weeks

tag: Sex

value: Male


title: KLB_Hipp_Vehicle_lane2

description: BD Rhapsody single cell WTA kit

value: Hippocampus


title: WT Embryo - rep1


title: From_SID_60_PreTreat_Biopsy_TMb

value: control

tag: time

value: Pre-treatment

tag: disease state


title: P21_UC_Uninflamed_ileum_1

tag: biologics

value: anti-integrin


title: P23_CD_Uninflamed_colon_1


title: P20_UC_Uninflamed_ileum_1

value: UC


title: Littermate control, wild type Klf4 allele, SMC lineage positive

value: SMC


title: From_SID_59_PreTreat_Blood_TMb

tag: treatment

value: Blood (PBMC)


title: From_SID_57_PreTreat_Biopsy_TMb

tag: sample type

value: Colon


title: Marfan, wild type Klf4 allele, SMC lineage positive

value: Marfan syndrome


title: Marfan, floxed Klf4 allele, SMC lineage positive

value: floxed


title: From_SID_58_PreTreat_Blood_TRb

value: Treg

tag: location collected


title: Mutant Embryo - H3K27me3_rep1

tag: genotype

value: Cam-2 e(z)2/e(z)3 x Tak-1

value: H3K27me3 (Millipore #07-449)

value: Embryo


title: Marfan, wild type Klf4 allele, SMC lineage negative

value: Aortic root

value: Control

value: Non-SMC


title: WT Embryo - H3_rep2

value: Cam-2 x Tak-1

value: H3 (Abcam ab1791)


title: WT Embryo - H3_rep1


title: Marfan, floxed Klf4 allele, SMC lineage negative

value: 24 Weeks

value: Male


title: WT Embryo - H3K36me3_rep2

value: H3K36me3 (Abcam  ab9050)


title: From_SID_54_PreTreat_Biopsy_TRb

value: control

value: Pre-treatment

value: UC

value: Biopsy

tag: cell type


title: WT Embryo - H3K36me3_rep1

tag: tissue


title: From_SID_55_PreTreat_Biopsy_TMb

value: Tmen

value: Colon


title: P19_CD_Uninflamed_colon_1

value: CD

value: anti-TNF


title: MC38cells, Cryo, Day5 rep8

city: Guangzhou

first: YING

last: WU

state: CHINA

address: 651 Dongfeng East Rd

department: Department of Minimally Invasive Interventional Therapy

institute: Sun Yat-sen University Cancer Center

growth_protocol: MC38 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
C57BL/6J mice  xenografts were generated in 6-8-week-old C57BL/6J mice by subcutaneous implantation of 0.5 × 106 cells (one injection site per mouse/ both side). Animals were randomized in two groups (control VS cryoablation) for collection and analysis.
On the 7th day, the subcutaneous tumor of the mice grew to about 5-6mm in diameter. After anesthesia, one side of the tumor was subjected to cryoablation . The cryoprobes were inserted into the targeted lesions, and two 20-sec freezing cycles, separated by a passive 20-sec and an active 20-sec thawing session, were performed.In order to further study the molecular mechanism of the enhancement of anti-tumor immunity by cryoablation, the mice were sacrificed on the D5 day after freezing and then the contralateral tumors were immediately frozen in liquid nitrogen for 15 min and stored at -80 °C, parallel Bulk RNA sequencing.

tag: cell line

value: Mouse Colon Cancer Cells

value: WT

value: Cryoablation

value: Day 5


title: MC38cells, Cryo, Day5 rep6


title: From_SID_51_PreTreat_Biopsy_TMb


title: From_SID_50_PreTreat_Biopsy_TMb


title: From_SID_48_PreTreat_Blood_TMb

value: Blood (PBMC)


title: LAL-0061-B (HumanOmni5)

city: Badalona

first: Manel

last: Esteller

address: Ctra. de Can Ruti, Cami de les Escoles s/n

institute: Josep Carreras Leukaemia Research Institute (IJC)

data_processing:
Genomic DNA extracted from saliva samples was genotyped using Illumina Infinium HumanOmni5-Quad BeadChips (Illumina).
Image data was analyzed using GenomeStudio 2.0.4 with GT module 2.0.4 (Illumina).

source_name: Saliva

extract_protocol: Total DNA was isolated from saliva samples by standard procedures.

tag: look-alike couple

value: Normal human saliva sample


title: MC38cells, Cryo, Day5 rep3


title: From_SID_53_PreTreat_Blood_TMb


title: P19_CD_Uninflamed_ileum_1

value: Ileum


title: From_SID_52_PreTreat_Blood_TRb

value: Treg


title: WT Embryo - H3K9me1_rep2

value: Cam-2 x Tak-1

tag: antibody

value: H3K9me1 (Abcam ab9045)

value: Embryo


title: MC38cells, Cryo, Day5 rep4


title: From_SID_45_PreTreat_Blood_TMb

value: control

value: Pre-treatment


title: MC38cells, Cryo, Day5 rep7


title: P18_UC_Inflamed_colon_1

value: UC


title: P18_UC_Uninflamed_ileum_1


title: P17_UC_Inflamed_colon_2

value: Colon


title: WT Embryo - H3K9me1_rep1


title: WT Embryo - H3K27me3_rep2

value: H3K27me3 (Millipore #07-449)


title: MC38cells, Cryo, Day5 rep5


title: From_SID_44_PreTreat_Biopsy_TMb

source_name: Biopsy

value: Biopsy

value: Tmen


title: From_SID_47_PreTreat_Blood_TRb


title: WT Embryo - H3K27me3_rep1


title: MC38cells, Con, Day5 rep9

value: Mouse Colon Cancer Cells

value: WT

value: Control


title: From_SID_42_PreTreat_Biopsy_TMb


title: P17_UC_Uninflamed_ileum_1


title: LAL-0061-A (HumanOmni5)


title: MC38cells, Con, Day5 rep8

value: Day 5


title: P16_UC_Uninflamed_colon_2

value: anti-TNF


title: P15_UC_Uninflamed_colon_1


title: MC38cells, Cryo, Day5 rep2

value: Cryoablation


title: LAL-0051-A (HumanOmni5)

value: Normal human saliva sample


title: P15_UC_Uninflamed_ileum_1

value: Ileum


title: LAL-0044-B (HumanOmni5)


title: From_SID_39_PreTreat_Blood_TMb

value: CD

value: Blood (PBMC)


title: MC38cells, Con, Day5 rep6


title: From_SID_36_PreTreat_Biopsy_TMb

value: control


title: P16_UC_Inflamed_colon_1


title: LAL-0044-A (HumanOmni5)


title: MC38cells, Cryo, Day5 rep1


title: P17_UC_Inflamed_colon_1


title: P16_UC_Uninflamed_ileum_1


title: MC38cells, Con, Day5 rep4


title: LAL-0043-A (HumanOmni5)


title: LAL-0055-A (HumanOmni5)


title: From_SID_33_PreTreat_Biopsy_TMb

value: Pre-treatment


title: P13_UC_Inflamed_colon_2

value: UC


title: P15_UC_Inflamed_colon_2

value: Colon


title: LAL-0051-B (HumanOmni5)


title: MC38cells, Con, Day5 rep2


title: From_SID_32_PreTreat_Biopsy_TMb


title: From_SID_40_PreTreat_Biopsy_TMb


title: MC38cells, Con, Day5 rep5


title: LAL-0055-B (HumanOmni5)


title: MC38cells, Con, Day5 rep7


title: LAL-0036-B (HumanOmni5)


title: From_SID_34_PreTreat_Blood_TRb

value: Treg


title: From_SID_35_PreTreat_Blood_TMb


title: From_SID_29_PreTreat_Biopsy_TMb

value: Biopsy


title: P14_UC_Uninflamed_colon_1

value: anti-integrin


title: LAL-0032-B (HumanOmni5)


title: From_SID_27_PreTreat_Biopsy_TMb

value: Tmen


title: P14_UC_Uninflamed_ileum_1


title: LAL-0039-B (HumanOmni5)


title: FIP1, Proximal colon, rep1

city: Nashville

first: Izumi

last: Kaji

state: TN

address: Rm 10465H, MRB IV

department: Surgery

institute: Vanderbilt University Medical Center

description:
Read length 150
RCP_pC_1

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP).
Alignments were parsed using Tophat program.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene (Mortazavi et al. 2008).
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: tab-delimited text files include readcount for each Sample

source_name: Proximal colon

extract_protocol:
Epithelial cells were mechanically isolated from colon using micro forceps in ice-cold PBS containing 30 mM EDTA and immersed in TRIzol Reagent (Invitrogen 15596018).
Libraries were prepared by Novogene Corporation Inc. (Sacramento, CA). mRNA is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented  randomly by addition of fragmentation buffer. Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse  Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and  RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified doublestranded  cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA  fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select  cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system  (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR  products by AMPure XP beads.

value: Proximal colon

tag: tissue preparation

value: fresh tissue

value: epithelial cells

value: Rab11-FIP1 KO


title: FIP1, Distal colon, rep3

description:
Read length 150
RCP_dC_3

source_name: Distal colon

value: Distal colon


title: MC38cells, Con, Day5 rep3

value: Mouse Colon Cancer Cells

value: WT

value: Control

value: Day 5


title: P31_CD_Uninflamed_ileum_1

value: Ileum

value: CD

value: anti-TNF


title: From_SID_24_PreTreat_Blood_TRb

extract_protocol:
Total RNA was extracted via miRNAeasy Micro Kit (Qiagen, Germantown, MD)
Libraries were individually indexed and pooled in groups of 20. Each pool was run on a NextSeq500 flow cell (9 flow cells total)

value: control

value: Pre-treatment

value: UC

value: Blood (PBMC)


title: P14_UC_Inflamed_colon_2

value: Colon

value: anti-integrin


title: P12_UC_Uninflamed_ileum_1


title: LAL-0039-A (HumanOmni5)

value: Normal human saliva sample


title: MC38cells, Con, Day5 rep1


title: From_SID_23_PreTreat_Biopsy_TMb

value: Biopsy

value: Tmen


title: P9_UC_Inflamed_colon_1


title: From_SID_31_PreTreat_Blood_TMb


title: P12_UC_Inflamed_colon_1


title: P12_UC_Inflamed_colon_2


title: LAL-0028-B (HumanOmni5)


title: LAL-0043-B (HumanOmni5)


title: LAL-0036-A (HumanOmni5)


title: FIP2, Proximal colon, rep2

description:
Read length 150
FIP2_pC_2

value: Proximal colon

value: fresh tissue

value: epithelial cells

value: Rab11-FIP2 KO


title: FIP1, Proximal colon, rep3

description:
Read length 150
RCP_pC_3

value: Rab11-FIP1 KO


title: LAL-0030-A (HumanOmni5)


title: LAL-0022-B (HumanOmni5)


title: P7_UC_Uninflamed_colon_2


title: P7_UC_Inflamed_colon_1


title: P11_CD_Inflamed_ileum_1

value: Ileum


title: From_SID_25_PreTreat_Blood_TMb


title: P10_CD_Uninflamed_colon_1

value: CD


title: LAL-0032-A (HumanOmni5)


title: FIP1, Proximal colon, rep2

description:
Read length 150
RCP_pC_2


title: P10_CD_Inflamed_ileum_1

value: anti-TNF


title: LAL-0022-A (HumanOmni5)


title: FIP1, Distal colon, rep1

description:
Read length 150
RCP_dC_1

value: Distal colon


title: LAL-0030-B (HumanOmni5)


title: FIP1, Distal colon, rep2

description:
Read length 150
RCP_dC_2


title: From_SID_19_PreTreat_Blood_TMb

value: control

value: Pre-treatment


title: From_SID_10_PreTreat_Blood_TRb

value: Blood (PBMC)

value: Treg


title: FIP2, Proximal colon, rep3

description:
Read length 150
FIP2_pC_3


title: From_SID_15_PreTreat_Biopsy_TMb


title: From_SID_14_PreTreat_Biopsy_TRb


title: P9_UC_Uninflamed_ileum_1

value: UC

value: anti-integrin


title: From_SID_12_PreTreat_Biopsy_TRb

value: Biopsy


title: P8_CD_Inflamed_colon_2

value: Colon


title: P6_UC_Uninflamed_colon_1


title: P5_CD_Uninflamed_colon_1


title: FIP2, Distal colon, rep3

description:
Read length 150
FIP2_dC_3


title: BL6, Proximal colon, rep2

description:
Read length 150
BL6_pC_2

value: Proximal colon

value: wild type


title: LAL-0018-B (HumanOmni5)

value: Normal human saliva sample


title: From_SID_11_PreTreat_Blood_TMb

value: Tmen


title: P7_UC_Uninflamed_ileum_1


title: LAL-0028-A (HumanOmni5)


title: LAL-0018-A (HumanOmni5)


title: FIP2, Distal colon, rep2

description:
Read length 150
FIP2_dC_2

value: fresh tissue

value: epithelial cells

value: Rab11-FIP2 KO


title: P6_UC_Uninflamed_colon_2


title: FIP2, Proximal colon, rep1

description:
Read length 150
FIP2_pC_1


title: From_SID_6_PreTreat_Blood_TMb


title: BL6, Proximal colon, rep3

description:
Read length 150
BL6_pC_3


title: From_SID_9_PreTreat_Blood_TMb


title: LAL-0012-B (HumanOmni5)


title: From_SID_7_PreTreat_Biopsy_TMb


title: WT_1

city: Buenos Aires

first: Sieira

last: Rodrigo

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

data_processing:
Low-quality reads were removed using Trimmomatic v0.39
Reads were aligned witth Burrows Wheeler Alignment software (BWA)
RNA-seq counts were determined using FeatureCounts
RNA-seq differential expression analysis was performed using DESeq2
RNA-seq reads were aligned to sequences of the contigs of Bizionia argentinensis JUB59 genome sequencing project (https://www.ncbi.nlm.nih.gov/genome/?term=Bizionia+argentinensis+JUB59).
Genome_build: BizArg_1.0
Supplementary_files_format_and_content: tsv file generated by DESeq2 provides gene ID, base mean reads, log2 fold-change, log2 fold-change standard error, Wald statistic, Wald test p-value, and Bonferroni Hochberg corrected p-value for the expression of each gene.

organism: Bizionia argentinensis JUB59

source_name: WT cells

growth_protocol: B. argentinensis JUB59 strains were cultured in marine broth at 22 °C until the optical density at 600 nm (OD600) reached 1.4 (exponential phase).

extract_protocol:
Total RNA was isolated using Trizol Max Bacterial RNA Isolation Kit  (Ambion – Life Technologies) and then treated with TURBO DNAse (Ambion – Life Technologies)
RNA samples were submitted to NEB Microbe rRNA depletion kit, TruSeq stranded mRNA library preparation and 100-bp paired-end Illumina NovaSeq6000 sequencing.

value: Wild-type

tag: biological replicate


title: LAL-0012-A (HumanOmni5)


title: WT_3