title: Nascent RNA, chromatin-associated, pulse-chase time point 5 min

description:
chromatin fractionation at 0.5 M urea; fragmentation (0.1 M NaOH on ice) prior to 4-SU-label based purification of nascent RNA
CHR5

value: chromatin-associated, 4-SU-labeled RNA


title: MUC21585 CM-OXT-101-18-N

status: Public on Sep 21 2023

type: SRA

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

country: Germany

institute: Helmholtz Zentrum München

library_source: transcriptomic single cell

data_processing:
Technical replicates of the samples were merged, and reads were then mapped to rRNA (from Ensembl, GRCm38 release 102) using Bowtie2 (version 2.3.4.3114) and subsequently, unmapped reads were mapped to the mm10 genome (from Ensembl, GRCm38 release 102) using STAR (2.7.0115). Count matrices were generated by counting reads corresponding to gene exons using featureCounts (version 1.6.3116). Counts were transformed to FPKM and TPM using the actual feature length. The single-nuclei transcriptomics analysis of raw count matrix loaded into python and stored as AnnData object was performed using Scanpy version 1.7.1. Filtering of the cells was based on a minimum count number of 250. Filtering was applied to the matrix of 1536 single nuclei and 55579 genes. Nuclei that had >1000 and <4500 detected genes were kept. Genes detected in fewer than 25 cells and with read count below 250 were filtered out. Hence, only the nuclei having less than 4500 genes detected and a library size between 10000 and 200000 reads were kept. Applying this filtering strategy, the final matrix comprises 1202 single nuclei and 13867 genes. Batch effect corrections were performed employing combat using plates as a covariate.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
The single-nucleus RNA-seq2 methodology was used to capture a high number of transcripts from frozen tissues. the reaction volumes were miniaturized with the aid of the Mosquito HV robot. Per well, 2190 nL of Lysis Buffer 2 (LB2) were dispensed. The final volume of the mixture of Lysis Buffer (LB1 and LB2) was 3.125 μL, containing NP40 2%, Triton-X100 1%, 1/300,000 diluted ERCC RNA spike-in, 3′ SMART-seq CDS Primer II A and RNAse-free water. ERCC spike-ins (Thermo Fischer Scientific, Ref. 4456740; Lot no. 00892098) were diluted 1 in 10, with RNAse-free water with 0.4 U/μL Recombinant RNase Inhibitor (Takara Clontech, Ref. 2313A) and a fresh dilution of 1 in 300,000 was prepared before the first strand synthesis. Reverse transcription and Pre-PCR amplification steps were followed as described by the manufacturer with four-times reduced volumes for all steps.
Sequencing libraries were prepared using the Illumina Nextera XT DNA Sample Preparation kit (Illumina, Ref. FC-131-1096) and the combination of 384 Combinatorial Dual Indexes (Illumina- Set A to D, Ref. FC-131-2001 to FC-131-2004). In brief, 500 nL of the undiluted cDNA were transferred to a new 384 well-plate containing 1500 nL of Tagmentation Mix (TD and ATM reagents). Accordingly, all Nextera XT reagents (NT, NPM and i5/i7 indexes) were added stepwise to a final library volume of 5 μL per well. The final PCR amplification was performed through 12 cycles. Once the libraries were prepared, 500 nL from each well were pooled together into a tube (total volume of ~192 μL) to perform a final AMPure XP bead (Beckman Coulter, Ref. A63882) clean-up step. For our single nuclei libraries, two consecutive clean-ups with a ratio of sample to bead 0,9X led to library sizes between 200 and 1000 bp. Each plate, counting with a total of 384 libraries, was pooled together into one final library. A total of 4 final libraries were sequenced using an Illumina NovaSeq 6000 NGS sequencer in an SP XP flowcell, in a paired-end 150 bases length.

tag: cell type

value: Oxytocin neurons

tag: tissue

value: Brain

tag: strain

value: C57BL/6JRj -OXT-sun1-sfGFP

tag: age

value: 6 months

tag: Sex

value: Male

tag: treatment/diet

value: HFHS diet


title: Nascent RNA, chromatin-associated, pulse-chase time point 15 min

city: Heraklion

first: Evgenia

last: Ntini

address: Nik. Plastira 100

country: Greece

institute: IMBB-FORTH

description:
chromatin fractionation at 0.5 M urea; fragmentation (0.1 M NaOH on ice) prior to 4-SU-label based purification of nascent RNA
CHR15

library_source: transcriptomic

data_processing:
Reads were aligned to GRCh38/hg38 and to ERCC92 sequences using STAR version 2.5.4a.
Only uniquely aligned reads were kept
bigWig files were generated with WigToBigWig from UCSC utilities
Spike-in normalized strand-specific read counts over genomic features were extracted with bedtools coverage -s and normalized to feature length.
Code available under https://github.com/evgnt/chrTT-seq
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig

molecule: total RNA

organism: Homo sapiens

growth_protocol: MCF-7 cells were maintained in DMEM supplemented with 5 % fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Chromatin fractionation was done at 0.5 M urea and RNA was extracted from the chromatin-associated and nucleoplasmic fraction with acidic phenol (pH 4.5) and acidic phenol/chloroform.
RNA libraries for RNA-seq from 4-SU-labeled purified RNA were prepared using the TrueSeq Stranded mRNA Library Preparation Kit (without RiboZero).

treatment_protocol:
Cells were seeded to ~ 80 % confluency and labeled with 1 mM 4-thio-uridine for 8 min.
Cells were washed with PBS and chase was applied with 10 mM uridine for 5, 10, 15, 20 min.

tag: cell line

value: breast cancer cells

tag: genotype

value: WT

tag: treatment

value: 1mM 4-thiouridine for 8 min, followed by chase with 10 mM uridine

tag: time

value: 15 min chase

tag: molecule subtype


title: Nascent RNA, chromatin-associated, pulse-chase time point 10 min

description:
chromatin fractionation at 0.5 M urea; fragmentation (0.1 M NaOH on ice) prior to 4-SU-label based purification of nascent RNA
CHR10

value: 10 min chase


title: FOXP3 KO MT-2 biol rep 2

city: Chapel Hill

first: Jason

middle: Robert

last: Mock

state: NC

address: 125 Mason Farm Road

country: USA

institute: University of North Carolina

data_processing:
Illumina bcl2fastq v2.19 used for basecalling.
Sequence reads in FASTQ files were mapped to GRCh38 reference genome with GENCODE 37 gene annotation by STAR, and gene expression estimates were derived from StringTie using default parameters.
Assembly: GRCh38
Assembly: GENCODE human v37
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

source_name: cell line

growth_protocol: MT-2 cell line was obtained through the NIH AIDS Reagent Program. MT-2 cells were maintained in culture using RPMI 1640 supplemented with 10% fetal bovine serum, 2mM L-glutamine, and 100U/mL penicillin-streptomycin.

extract_protocol:
Total RNA was isolated using Zymo Direct-zol RNA MiniPrep with TRI Reagent miRNeasy kits from Zymo Research (Irvine, CA, USA) according to the manufacturer's instruction with the following modifications: 1) snap-frozen cells were lysed in at least 200 mL of TRI reagent without thawing cells; 2) cells were not centrifuged to collect debris before applying to column. ALl samples were eluted in 25 mL of DNase/RNase-Free water.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The wild type MT-2 cell line and the FOXP3 null MT-2 cell line were seeded at equal densities and grown in vitro at 37 C 5% CO2 for 3 days before cells were centrifuged at 400 x g for 5 minutes. Supernatant was removed and cell pellets were snap frozen in liquind nitrogen before being stored in liquid nitrogen.  Cell pellets were then prepared for mRNA after 4 separate experiments.

value: cell line

value: regulatory T cell

value: FOXP3 knockout

value: 3 days of in vitro culture


title: Liver 4 AOOs [AFIQ_FF]

city: New Haven

first: Mario

last: Strazzabosco

state: CT

address: 300 Cedar street

department: Internal Medicine

institute: Yale School of Medicine

data_processing:
CLC Genomics Workbench v 11.0.1
Low quality reads were trimmed and adapter conta,ination removed using Trim Galore(v0.5.0)
Trimmed sequence reads were mapped tohuman reference genome (hg38) using HISAT2(V2.1.0)
Gene expression levels were quantified using StringTie (v1.3.3b) with gene models(v27) from GENCODE project.
Assembly: hg38
Supplementary files format and content: Tab-separated values files include normalized values for each Sample

source_name: Biliary organoids

growth_protocol: Organoids were maintained in the media as described in Broutier et.al  NATURE PROTOCOLS, 2016.

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.

value: Biliary organoids

value: AOOs


title: Liver 2 AOOs [AFIM_FF]


title: Liver 1 AOOs [AFHW_FF]


title: MUC21582 CM-OXT-101-18-K

value: Oxytocin neurons


title: Liver 4 EMB [AFIQ_EMB]

value: EMB


title: Liver 3 EMB [1TPX_EMB]


title: Liver 2 EMB [AFIM_EMB]


title: Liver 3 AOOs [1TPX_FF]


title: MUC21581 CM-OXT-101-18-J

value: Brain

value: C57BL/6JRj -OXT-sun1-sfGFP


title: Nascent RNA, chromatin-associated, pulse-chase time point 20 min

description:
chromatin fractionation at 0.5 M urea; fragmentation (0.1 M NaOH on ice) prior to 4-SU-label based purification of nascent RNA
CHR20

value: 20 min chase

value: chromatin-associated, 4-SU-labeled RNA


title: Liver 1 EMB [AFHW_EMB]


title: Liver 4 10%BME [AFIQ_10M]

value: 10% BME


title: MUC21579 CM-OXT-101-18-H

value: 6 months

value: Male

value: SC diet


title: Liver 2 10%BME [AFIM_10M]


title: U2932 cells, miR-28+ ibrutinib,20h, rep2

city: Madrid

first: Carmen

middle: Gómez-Escolar

last: Arias

state: Madrid

address: Calle Melchor Fernández Almagro 3

country: Spain

institute: CNIC

data_processing:
bcl2fastq 2.20 Software (Illumina)
Trimmed sequence reads were mapped to GRCh38.p10 using Salmon v1.9
Read count extraction and normalization were performed using tximport with flags: tx2gene = tx2gene and countsFromAbundance = "lengthScaledTPM"
Assembly: GRCh38.p10
Supplementary files format and content: tab-delimited table of counts

source_name: U2932 ABC DLBCL cell line

extract_protocol:
RNA was harvested using miRneasy mini  kit (Qiagen).
Total RNA was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification
Libraries were sequenced on a HiSeq4000 (Illumina) to generate 60 bases single reads

treatment_protocol: control, miR-28, ibrutinib, or ibrutinib plus miR-28

value: U2932 ABC DLBCL cell line

tag: time of treatment


title: Nascent RNA, chromatin-associated, pulse-chase time point 0 min

description:
chromatin fractionation at 0.5 M urea; fragmentation (0.1 M NaOH on ice) prior to 4-SU-label based purification of nascent RNA
CHR0

value: breast cancer cells

value: WT

value: 1mM 4-thiouridine for 8 min, followed by chase with 10 mM uridine

value: 0 min chase


title: U2932 cells,miR-28+ ibrutinib,20h, rep1


title: U2932 cells, ibrutinib,20h, rep2

value: ibrutinib


title: U2932 cells, miR-28,20h, rep2


title: MUC21584 CM-OXT-101-18-M

value: HFHS diet


title: MUC21577 CM-OXT-101-18-F

value: Oxytocin neurons


title: U2932 cells, control,20h, rep3

source_name: U2932  ABC DLBCL cell line

value: U2932  ABC DLBCL cell line

value: control


title: U2932 cells, miR-28,20h, rep1


title: U2932 cells, control,20h, rep2


title: MUC21576 CM-OXT-101-18-E

value: Brain

value: C57BL/6JRj -OXT-sun1-sfGFP


title: U2932 cells, control,20h, rep1


title: MUC21575 CM-OXT-101-18-D


title: MUC21583 CM-OXT-101-18-L


title: Liver 1 10%BME [AFHW_10M]

value: Biliary organoids


title: Liver 3 10%BME [1TPX_10M]

value: 10% BME


title: MUC21578 CM-OXT-101-18-G

value: 6 months


title: MUC21572 CM-OXT-101-18-A

value: Male


title: MCF-7_DMSO  control_H3K9me2

city: Chennai

first: Arumugam

last: Rajavelu

state: Tamil Nadu

address: Adayar

department: Biotechnology

country: India

institute: IITM

library_source: genomic

data_processing:
FastQC for quality analysis and Cutadapt for adaptor trimming
ChIP seq reads were aligned to hg19/GRCh37 human genome built using Bowtie2
Peak calling was performed using MACS2 tool
ChIP-seq signals were background subtracted using MACS2 bdgcmp tool
Integrative Genomics Viewer (IGV) was used for visualization. Graphpad Prim (version 8) was used for generating the bar graph representing the number of genes bound by H3K9me2. R script (http://r-project.org/)was used to visualize the H3K9me2 peaks chromosome-wide at three different stages of P. falciparum
Assembly: hg19/GRCh37 human genome built
Supplementary files format and content: MACS peak files

molecule: genomic DNA

growth_protocol: The MCF-7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) with 10% Fetal Bovine Serum (FBS) (Invitrogen) and 1% penicillin and streptomycin  at 37 °C with 5% CO2.

extract_protocol:
Crosslinked chromatin was prepared by adding 1% formaldehyde to the culture for 5 min followed by the addition of glycine to 0.125 M final concentration for 5 minutes to stop the cross-linking. Chromatin was sheared by sonication in a Bioruptor UCD-200 (Diagenode) for 10 min at 30 s intervals, power setting high, to a size of 300–800 bp. ChIP was performed by adding 1.8 µg of H3K9me2 antibody to ChIP buffer (100 mM NaCl, 20 mM Tris pH-7.5, 6 mM EDTA, 1% Triton X- 100). The DMSO control and 27-HC treated samples  were added to the mixture and incubated at 4 °C for overnight, followed by the addition of 15 μl protein A Dynabeads and further incubated for 4 h. After washing with buffers containing 180 mM NaCl, immuno-precipitated DNA was eluted and purified using PCR purification columns.
Libraries for ChIP sequencing were prepared using NEB Next Ultra II DNA Library preparation kit. In brief, ChIP DNA and the Input DNA are subjected to various enzymatic steps for repair the ends and tailing with dA-tail followed by ligation of adapter sequences. These adapter ligated fragments are then size selected using SPRI beads. Next, the size selected fragments are indexed during limited cycle PCR to generate final libraries for paired-end sequencing. The resulting libraries are quantified before getting sequenced on Illumina HiSeq 2500/4000 system to generate 2X50 bp sequence reads.

treatment_protocol: The cells were maintained in phenol-red free DMEM (Sigma Cat#D1152) supplemented with 10% charcoal-stripped serum 72 h prior to treatment . Further the cells were either treated with DMSO or 27-HC  (1 µM) for 72 h.

value: ER +ve breast cancer

tag: chip antibody

value: H3K9me2  (Diagenode, C15410060)

value: DMSO


title: MCF-7_27-HC_H3K9me2

value: 27-hydroxycholesterol (1 µM)


title: S8_SUD_MIR_IB_2

description: SUDHL4 cells, miR-28+ ibrutinib,20h, rep2

source_name: SUDHL4 GCB-DLBCL cell line

value: SUDHL4 GCB-DLBCL cell line


title: S7_SUD_MIR_IB_1

description: SUDHL4 cells,miR-28+ ibrutinib,20h, rep1


title: MUC21580 CM-OXT-101-18-I


title: MUC21573 CM-OXT-101-18-B

value: SC diet


title: S6_SUD_SCR_IB_2

description: SUDHL4 cells, ibrutinib,20h, rep2

value: ibrutinib


title: S5_SUD_SCR_IB_1

description: SUDHL4 cells, ibrutinib,20h, rep1


title: S4_SUD_MIR_2

description: SUDHL4 cells, miR-28,20h, rep2


title: MCF-7_Input_H3K9me2

value: Untreated


title: MUC21574 CM-OXT-101-18-C

value: Oxytocin neurons


title: MUC21570 CM-OXT-101-17-O

value: HFHS diet


title: MUC21571 CM-OXT-101-17-P


title: S3_SUD_MIR_1

description: SUDHL4 cells, miR-28,20h, rep1


title: S2_SUD_SCR_2

description: SUDHL4 cells, control,20h, rep2

value: control


title: S1_SUD_SCR_1

description: SUDHL4 cells, control,20h, rep1


title: MUC21569 CM-OXT-101-17-N

value: Brain


title: MUC21568 CM-OXT-101-17-M

value: C57BL/6JRj -OXT-sun1-sfGFP


title: SCR_ib_4h_2

description: MD-901 cells, ibrutinib,4h, rep2

extract_protocol:
RNA was harvested using Rneasy mini  kit (Qiagen).
Total RNA was used to generate barcoded RNA-seq libraries using the NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions. First, poly A+ RNA was purified using poly-T oligo- attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. Next, cDNA ends were repaired and adenylated. The NEBNext adaptor was then ligated followed by second strand removal, uracile excision from the adaptor and PCR amplification
Libraries were sequenced on a HiSeq4000 (Illumina) to generate 60 bases single reads

value: MD-901 ABC-DLBCL cell line

tag: time of ibrutinib treatment


title: SCR_ib_20h_2

description: MD-901 cells, ibrutinib,20h, rep2


title: SCR_ib_20h_1

description: MD-901 cells, ibrutinib,20h, rep1


title: SCR_ib_4h_1

description: MD-901 cells, ibrutinib,4h, rep1


title: SCR_4h_1

description: MD-901 cells, control,4h, rep1


title: MUC21566 CM-OXT-101-17-K


title: MUC21565 CM-OXT-101-17-J


title: SCR_20h_2

description: MD-901 cells, control,20h, rep2


title: MUC21564 CM-OXT-101-17-I


title: MIR_ib_4h_1

description: MD-901 cells, miR-28+ ibrutinib,4h, rep1

value: miR-28+ ibrutinib


title: SCR_0h_2

description: MD-901 cells, control,0h, rep2


title: MIR_ib_4h_2

description: MD-901 cells, miR-28+ ibrutinib,4h, rep2


title: MUC21562 CM-OXT-101-17-G

value: 6 months


title: MIR_4h_2

description: MD-901 cells, miR-28,4h, rep2


title: SCR_0h_1

description: MD-901 cells, control,0h, rep1


title: MIR_ib_20h_2

description: MD-901 cells, miR-28+ ibrutinib,20h, rep2


title: U2932 cells, ibrutinib,20h, rep1

value: U2932 ABC DLBCL cell line


title: MUC21561 CM-OXT-101-17-F

value: Male


title: SCR_20h_1

description: MD-901 cells, control,20h, rep1


title: MIR_4h_1

description: MD-901 cells, miR-28,4h, rep1


title: MUC21563 CM-OXT-101-17-H


title: MIR_ib_20h_1

description: MD-901 cells,miR-28+ ibrutinib,20h, rep1


title: MUC21560 CM-OXT-101-17-E


title: MIR_20h_2

description: MD-901 cells, miR-28,20h, rep2


title: MIR_20h_1

description: MD-901 cells, miR-28,20h, rep1


title: MIR_0h_2

description: MD-901 cells, miR-28,0h, rep2


title: MUC21559 CM-OXT-101-17-D


title: MIR_0h_1

description: MD-901 cells, miR-28,0h, rep1


title: MUC21567 CM-OXT-101-17-L


title: SCR_4h_2

description: MD-901 cells, control,4h, rep2


title: S11B_NS4196_I_18

description: MD-901 tumor, miR-28+ibrutinib treated

source_name: Subcutaneous MD-901 tumor

growth_protocol: MD-901 tumors were grown subcutaneously in NSG mice

treatment_protocol: Doxycycline  was administered twice per week at 0.04% in the drinking water, and mice received daily 40 mg/kg intraperitoneal (IP) injections of ibrutinib (PCI-32765) from day 10 after the subcutaneous xenograft

value: DLBCL tumor tissue


title: MUC21558 CM-OXT-101-17-C


title: S10B_NS4195_I_16

description: MD-901 tumor, miR-28+ibrutinib treated


title: S9B_NS4174_I_15

description: MD-901 tumor, miR-28 treated


title: S8B_NS4173_D_14

description: MD-901 tumor, miR-28 treated


title: S7B_NS4171D_13

description: MD-901 tumor, miR-28 treated


title: MUC21557 CM-OXT-101-17-B


title: MUC21556 CM-OXT-101-17-A


title: MUC21555 CM-OXT-101-16-P


title: S6B_NS4187_D_8

description: MD-901 tumor, ibrutinib treated


title: FW_gill_sample5,replicate2,scRNA-seq

city: shenzhen

first: CNSA

last: CNGB

address: BGI

country: China

institute: BGI

description: DNBelab

data_processing:
Cell Ranger v3.0.2 was used for processing raw sequencing data generated using the Chromium Single Cell 3’ v2 kit, while DNBelab C Series scRNA analysis software (MGI,https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software)  was used to process the other data.
Assembly: CNGB (CNA0019297,https://db.cngb.org/search/project/CNP0001614/)
Supplementary files format and content: sparse matrix for count value
Supplementary files format and content: barcode list of count matrix cell name
Supplementary files format and content: gene list of count matrix rowname

molecule: polyA RNA

organism: Protopterus annectens

source_name: gill

extract_protocol:
The “AE_” samples were collected from terrestrialized lungfish for 33 days. Fresh collected tissues disaggregation and enzymatic dissociation were performed independently. Following dissociation, the resulting suspension was passed through a 40 μm filter (BD # 352340), and the filter was washed with 2 ml cold PBS to ensure efficient digestion and sufficient collection. The filter suspension was transferred to a 15 ml centrifuge tube and centrifuge at 4 ℃ with 300x g for 5 minutes. Then the supernatant was removed, and the centrifugation sediment was washed with 5 ml PBS+0.04%BSA and centrifuged again (4 ℃ at 300x g for 5 minutes), and the centrifugation sediment was rewashed with 5 ml PBS+0.04%BSA. After the centrifugation, the cell pellets were re-suspended in 300 μl PBS+0.04%BSA. All samples were stained, and cell viability was measured using Trypan Blue (Invitrogen) and manually counted using a hemocytometer (INCYTO). The cell suspension concentration was reconstituted to 1000 cells per µL in DPBS for DNBelab C4 system library preparation.
Except for two freshwater gill samples, all single-cell RNA-seq libraries were prepared using a DNBelab C Series Single Cell Library Prep Set (MGI, 1000021082) as previously described 122. These included 21 libraries from the lung (eleven libraries of the freshwater group and ten libraries of terrestrialized group) and 27 libraries from the gill (seventeen libraries of the freshwater group and ten libraries of terrestrialized group, libraries) were obtained. Briefly, single-cell suspensions were used for droplet generation, emulsion breakage, bead collection, reverse transcription, and cDNA amplification to generate barcoded libraries. Indexed libraries were constructed according to the manufacturer’s protocol. Libraries were constructed and the DNA nanoballs (DNBs) were loaded into the patterned nanoarrays and sequenced on a DNBSEQ-T1 sequencer at the China National GeneBank (Shenzhen, China) with the following sequencing strategy: 41-bp read length for read 1 and 100-bp read length for read 2.Two freshwater gill libraries (FW-gill9 and FW-gill10) were generated with a 10x Genomics Chromium 3′Reagent Kit instructions (v2) and sequenced on a MGISEQ 2000 sequencer. Gill cells were resuspended in PBS with 0.04% BSA and loaded into a 10x Genomics Chromium cell controller to generate a library for sequencing (28 base pairs for read 1 and 98 for read 2).

value: gill


title: S4B_NS4185_D_6

description: MD-901 tumor, ibrutinib treated


title: S5B_NS4186_D_7

description: MD-901 tumor, ibrutinib treated


title: FW_gill_sample5,replicate1,scRNA-seq

description: DNBelab


title: MUC21553 CM-OXT-101-16-N


title: Bill skin Replicate 6

first: Viktor

last: Feketa

state: Connecticut

address: 333 Cedar St SHM BE58

department: Cellular & Molecular Physiology

institute: Yale University School of Medicine

description: library kit used: Kapa mRNA Hyper Prep kit

data_processing:
Primary analysis performed using Illumina's CASAVA 1.8.2 software suite.
Raw sequencing reads were filtered and trimmed to retain high-quality reads using Trimmomatic v0.39 (Bolger et al., 2014) with default parameters.
Filtered high-quality reads from all samples were aligned to duck reference genome using STAR aligner v2.7.7a with default parameters (Dobin et al., 2013).
Aligned reads were counted by the featureCounts module within the Subread package v2.0.1 with default parameters (Liao et al., 2014).
Processing, normalization, and statistical analysis of read counts was performed using the EdgeR v3.38.4 package in R v4.2.1 (Robinson et al., 2010)
Normalized read counts were further normalized to gene length and expressed as “fragments per kilobase gene length per million mapped reads” (FPKM).
Statistical analysis of differential expression of genes between groups was performed using the GLM approach and the quasi-likelihood F-test, as implemented in the EdgeR package.
Assembly: The duck reference genome and the gene annotation were obtained from the National Center for Biotechnology Information (Anas platyrhynchos; assembly ZJU1.0; NCBI Annotation Release: 104; all files accessed on 4/30/2021).  Reference genome: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/GCF_015476345.1_ZJU1.0_genomic.fna.gz; Gene annotation: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/015/476/345/GCF_015476345.1_ZJU1.0/GCF_015476345.1_ZJU1.0_genomic.gff.gz; the gene annotation was filtered to include only protein-coding genes.
Supplementary files format and content: Processed data file in Excel format (.xlsx) contains raw read counts, normalized read counts, and FPKM values for 5/6 replicates/samples of Meissner corpuscles and bill skin for all protein-coding genes in duck genome annotation. It also includes mean normalized counts and FPKM values for both groups, P-values, adjusted FDR values, and fold change (log2) for statistical comparison of expression values between 2 groups.

organism: Anas platyrhynchos

source_name: Bill skin

growth_protocol: Meissner corpuscles were manually collected and pooled for subsequent transcriptomic analysis. These experiments were conducted in RNAse-free conditions. An aspiration pipette was pulled from capillary glass tubing (G150F-3, Warner Instruments, Hamden, CT) using a micropipette puller (P-1000, Sutter, Novato, CA) with a tip diameter of ~40–60 µM, filled with 3 µl of the RNA Lysis Buffer (Quick-RNA Microprep Kit, Zymo, Irvine, Ca). The tip was loaded into micromanipulator and used to aspirate 2–10 corpuscles per pipette (per sample) by applying negative pressure using a high-speed pressure clamp system (HSPC-1, ALA Scientific Instruments). Collected corpuscles were then deposited into a 0.5 ml tube containing 10 µl of the RNA Lysis Buffer. Nearby skin cells absent of any corpuscles were also collected for comparison. Samples were then stored at −80°C until RNA isolation. 5-6 total replicates were collected from 3 independent skin isolations.

extract_protocol:
Total RNA was extracted using Quick-RNA Microprep Kit (Zymo) according to manufacturer’s instructions. RNA concentration and integrity number (RIN) were assessed by Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA). RNA concentrations for corpuscles were in the range of 63–323 pg/µl and RIN values were in the range of 6.1–8.0.
Sequencing libraries were prepared using the Kapa mRNA Hyper Prep kit (KAPA Biosystems, Wilmington, MA) (skin samples) or the NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs, Ipswich, MA) (Meissner corpuscles samples).

value: Bill skin


title: MUC21552 CM-OXT-101-16-M


title: MUC21551 CM-OXT-101-16-L


title: S2B_NS4184_D_4

description: MD-901 tumor, control treated


title: S12B_NS4199_D_20

description: MD-901 tumor, miR-28+ibrutinib treated


title: MUC21550 CM-OXT-101-16-K


title: S3B_NS4184_I_5

description: MD-901 tumor, control treated


title: Bill skin Replicate 4


title: control heart, cryoinjured

city: Berlin

first: Suphansa

last: Sawamiphak

address: Robert Rossle strasse, 10

institute: Max Delbruck Centrum

description: 10x Genomics

data_processing:
the steps until acquiring the fastq files (demultiplexing, conversion to fastq) were done by the Genomics technology platform in Max Delbruck Centrum. Then Cell Ranger software v6.0.1 was used for counting, alignment with the fastq files. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) then Seu
Assembly: GRCz11 (release 104)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: heart

extract_protocol:
zebrafish with TgBAC(csf1ra:GAL4-VP16)i186; Tg(UAS:NTR-mCherry)c264  transgenes subjected to cryoinjury and hearts were collected at 7 dpi and transferred into dissociation solution containing 0.26 U/ml LiberaseTM enzyme mixture (Sigma) and 1X Pluronic F-68 (ThermoFisher) in HBSS. Hearts were incubated in dissociation solution for 30 minutes with shaking at 750 rpm at 37°C with intermittent pipetting (every 5 minutes). Live cells were sorted by FACS.
Library was constructed according to the manufacterer’s instructions of Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry). (library preparation was done by Genomics technology platform in Max Delbruck Centrum)

value: AB/TU

value: 7 days post injury

value: heart

value: cryoinjury


title: S1B_NS4182_I_3

description: MD-901 tumor, control treated


title: Bill skin Replicate 5


title: Bill skin Replicate 1


title: MUC21548 CM-OXT-101-16-I

value: Oxytocin neurons


title: heart, cryoinjured

description: 10x Genomics

extract_protocol:
zebrafish with TgBAC(csf1ra:GAL4-VP16)i186; Tg(UAS:NTR-mCherry)c264; Tg(UAS:adra1-3i-T2A-CFP) transgenes subjected to cryoinjury and hearts were collected at 7 dpi and transferred into dissociation solution containing 0.26 U/ml LiberaseTM enzyme mixture (Sigma) and 1X Pluronic F-68 (ThermoFisher) in HBSS. Hearts were incubated in dissociation solution for 30 minutes with shaking at 750 rpm at 37°C with intermittent pipetting (every 5 minutes). Live cells were sorted by FACS.
Library was constructed according to the manufacterer’s instructions of Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry). (library preparation was done by Genomics technology platform in Max Delbruck Centrum)


title: Bill skin Replicate 2


title: H101_S52

city: Fayetteville

first: Stavroula

last: Tsitkanou

state: AR

address: 155 North Stadium Drive

institute: University of Arkansas

description: HU female_total.xlsx

data_processing:
Sequenced reads were mapped to mm10 mouse genome assembly using STAR 2.7.8a with default parameters.
Aligned reads were quantified for gene counts, filtered to exclude genes  with high noise or a maximum count of less than or equal to 50.
The filtered counts were median ratio normalized and tested for statistical significance using DESeq2.
All steps were performed using the Partek® Flow® Software.
Supplementary files format and content: mm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Skeletal muscle Gastrocnemius

extract_protocol:
Gastrocnemius muscles were flash frozen in liquid nitrogen and RNA was isolated using TRIzol and the Zymo MicroPrep Kit and prepared for RNA-sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skeletal muscle Gastrocnemius

value: Hindlimb Unloading

value: Female

tag: time point


title: MUC21554 CM-OXT-101-16-O

value: Brain

value: C57BL/6JRj -OXT-sun1-sfGFP

value: HFHS diet


title: MUC21547 CM-OXT-101-16-H

value: 6 months

value: SC diet


title: H105_S58

description: HU female_total.xlsx


title: Meissner corpuscles Replicate 5

description: library kit used: NEBNext Single Cell/Low Input RNA Library Prep Kit

source_name: Meissner Corpuscle

value: Meissner Corpuscle


title: Meissner corpuscles Replicate 4


title: MUC21549 CM-OXT-101-16-J

value: Male


title: MUC21546 CM-OXT-101-16-G


title: Meissner corpuscles Replicate 3


title: Meissner corpuscles Replicate 1


title: H100_S50

description: HU female_total.xlsx


title: MUC21545 CM-OXT-101-16-F


title: H102_S54

description: HU female_total.xlsx


title: Bill skin Replicate 3


title: H109_S62

description: HU female_total.xlsx


title: primary CD4sp

city: Richmond

first: Simona

last: Zompi

state: California

address: 501 Canal Blvd

institute: Sangamo Therapeutics

description:
Tconv_Donor_2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using Cell Ranger software v7.0.0
Samples were integrated with Harmony v0.1.1 (https://portals.broadinstitute.org/harmony/articles/quickstart.html)
Analysis done with Seurat v4.3.0 (https://satijalab.org/seurat/)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: primary CD4sp

extract_protocol:
RNA from iPSC-Tregs, iPSC-CD4sp, primary Tregs, induced Tregs and primary Tconv was extracted using an RNA extraction kit (Qiagen) following differentiation (iPSC-Tregs and induced Tregs) or isolation and culture (primary Tregs and Tconv).  Primary cells were isolated from leukapheresis.
Library was performed according to the manufacturer's instructions (10x Genomics). Single cell RNA-sequencing libraries were sequenced on a NextSeq 500.

value: primary CD4sp


title: H108_S60

description: HU female_total.xlsx


title: MUC21543 CM-OXT-101-16-D


title: Meissner corpuscles Replicate 2


title: H88_S24

description: HU female_total.xlsx


title: H104_S56

description: HU female_total.xlsx


title: MUC21540 CM-OXT-101-16-A


title: H80_S3

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), irreversible, H3K27ac, CUT&RUN, rep2

city: Stanford

first: Taihei

last: Fujimori

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

data_processing:
Make genome file with synthetic reporter integration
Align reads to genome with Bowtie 2 version 2.3.4.1 with command 'bowtie2 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x {reference genome} -p 16 -1 {first mate of pair} -2 {second mate of pair} -S {output SAM file name}'
Convert SAM files to BAM files and subsequently sort and index BAM files with Samtools version 1.7
Quantify and mark duplicates with Picard version 11.0.7 with command 'java -jar {picard tool} MarkDuplicates -I {input sorted BAM file} -O {output deduplicated BAM file} -M {output metrics file} --REMOVE_DUPLICATES true'
Normalize by reads per million with bamCoverage version 3.3.1 with command 'bamCoverage --bam {input deduplicated BAM file} -o {output bedgraph file}  --outFileFormat bedgraph --extendReads --centerReads -p 12 --binSize 10 --normalizeUsing CPM'
Assembly: hg38
Supplementary files format and content: bedgraph files

growth_protocol: DMEM-GlutaMAX media (10566024, Gibco) supplemented with 1x Penicillin-Streptomycin-Glutamine (10378016, Gibco) and 10 % FBS (FB-15, Omega Scientific)

extract_protocol:
Cells were permeabilized by 0.025% digitonin followed by incubation with antibody and Mnase excision using CUTANA ChIC/CUT&RUN Kit (14-1048, EpiCypher)
Library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S, New England Biolabs) for H3K9me3, H3K4me3 (positive control), IgG (negative control) or CUTANA™ CUT&RUN Library Prep Kit with Primer Set 1 (14-1001, EpiCypher) for other modifications. Library fragment sizes were checked with Agilent 2100 Bioanalyzer.

value: Human embryonic kidney


title: HEK293T (B9 clone + KRAB), reactivated, H3K27ac, CUT&RUN, rep2


title: MUC21539 CM-OXT-101-15-P


title: MUC21541 CM-OXT-101-16-B


title: H84_S15

description: HU female_total.xlsx


title: MUC21538 CM-OXT-101-15-O


title: MUC21544 CM-OXT-101-16-E


title: HEK293T (B9 clone + KRAB), nodox, H3K27ac, CUT&RUN, rep2


title: H83_S12

description: HU female_total.xlsx


title: H87_S21

description: HU female_total.xlsx


title: H81_S6

description: HU female_total.xlsx


title: H82_S9

description: HU female_total.xlsx


title: MUC21542 CM-OXT-101-16-C


title: MUC21535 CM-OXT-101-15-L


title: MUC21534 CM-OXT-101-15-K


title: MUC21537 CM-OXT-101-15-N


title: HEK293T (B9 clone + KRAB), dox5days, H3K27ac, CUT&RUN, rep2


title: H85_S18

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), dox5days, H3K27ac, CUT&RUN, rep1


title: HEK293T (B9 clone + KRAB), nodox, H3K27ac, CUT&RUN, rep1


title: MUC21532 CM-OXT-101-15-I


title: HEK293T (B9 clone + KRAB), reactivated, H3K27ac, CUT&RUN, rep1


title: HEK293T (B9 clone + KRAB), reactivated, H3K9ac, CUT&RUN, rep2


title: MUC21533 CM-OXT-101-15-J


title: HEK293T (B9 clone + KRAB), irreversible, H3K9ac, CUT&RUN, rep2


title: HEK293T (B9 clone + KRAB), irreversible, H3K27ac, CUT&RUN, rep1


title: iPSC-CD4sp

description:
D50SP
10x Genomics


title: H78_S8

description: HU female_total.xlsx


title: MUC21531 CM-OXT-101-15-H


title: H74_S6

description: HU female_total.xlsx


title: MUC21530 CM-OXT-101-15-G


title: H70_S1

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), nodox, H3K9ac, CUT&RUN, rep2


title: HEK293T (B9 clone + KRAB), reactivated, H3K9ac, CUT&RUN, rep1


title: MUC21536 CM-OXT-101-15-M


title: MUC21529 CM-OXT-101-15-F


title: H79r_S5

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), dox5days, H3K9ac, CUT&RUN, rep2


title: MUC21528 CM-OXT-101-15-E


title: H73_S4

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), irreversible, H3K9ac, CUT&RUN, rep1


title: MUC21527 CM-OXT-101-15-D


title: MUC21526 CM-OXT-101-15-C


title: H72_S3

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), dox5days, H3K9ac, CUT&RUN, rep1


title: H71_S2

description: HU female_total.xlsx


title: H63_S33

description: HU female_total.xlsx


title: H76_S7

description: HU female_total.xlsx


title: MUC21523 CM-OXT-101-14-P


title: H60_S27

description: HU female_total.xlsx


title: MUC21525 CM-OXT-101-15-B


title: H66_S39

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), irreversible, H3K27me3, CUT&RUN, rep2


title: MUC21524 CM-OXT-101-15-A


title: HEK293T (B9 clone + KRAB), nodox, H3K9ac, CUT&RUN, rep1


title: MUC21522 CM-OXT-101-14-O


title: H68_S45

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), nodox, H3K27me3, CUT&RUN, rep2


title: HEK293T (B9 clone + KRAB), dox5days, H3K27me3, CUT&RUN, rep2


title: MUC21521 CM-OXT-101-14-N


title: H67_S42

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), reactivated, H3K27me3, CUT&RUN, rep1


title: HEK293T (B9 clone + KRAB), irreversible, H3K27me3, CUT&RUN, rep1


title: MUC21519 CM-OXT-101-14-L


title: H61_S30

description: HU female_total.xlsx


title: MUC21520 CM-OXT-101-14-M


title: HEK293T (B9 clone + KRAB), dox5days, H3K27me3, CUT&RUN, rep1


title: H65_S36

description: HU female_total.xlsx


title: H69_S48

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), reactivated, H3K27me3, CUT&RUN, rep2


title: MUC21517 CM-OXT-101-14-J


title: H97_S16

description: HU female_total.xlsx

value: Control


title: HEK293T (B9 clone + KRAB), nodox, H3K27me3, CUT&RUN, rep1


title: H94_S13

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), reactivated, H3K9me2, CUT&RUN, rep2


title: HEK293T (B9 clone + KRAB), dox5days, H3K9me2, CUT&RUN, rep2


title: MUC21514 CM-OXT-101-14-G


title: MUC21515 CM-OXT-101-14-H


title: MUC21516 CM-OXT-101-14-I


title: H90_S9

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), irreversible, H3K9me2, CUT&RUN, rep2


title: H99r_S14

description: HU female_total.xlsx


title: MUC21512 CM-OXT-101-14-E


title: H91_S10

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), reactivated, H3K9me2, CUT&RUN, rep1


title: MUC21513 CM-OXT-101-14-F


title: H92_S11

description: HU female_total.xlsx


title: MUC21511 CM-OXT-101-14-D


title: HEK293T (B9 clone + KRAB), nodox, H3K9me2, CUT&RUN, rep2


title: HEK293T (B9 clone + KRAB), irreversible, H3K9me2, CUT&RUN, rep1


title: H95_S15

description: HU female_total.xlsx


title: H93_S12

description: HU female_total.xlsx


title: HEK293T (B9 clone + KRAB), dox5days, H3K9me2, CUT&RUN, rep1


title: MUC21518 CM-OXT-101-14-K


title: MUC21509 CM-OXT-101-14-B


title: MUC21510 CM-OXT-101-14-C


title: 50_S33

description: HU male_total.xlsx


title: HEK293T (B9 clone + KRABY46A), dox5days, H3K9me3, CUT&RUN, rep2


title: HEK293T (B9 clone + KRAB), nodox, H3K9me2, CUT&RUN, rep1


title: MUC21508 CM-OXT-101-14-A


title: HEK293T (B9 clone + KRABY46A), nodox, H3K9me3, CUT&RUN, rep2


title: 54_S41

description: HU male_total.xlsx


title: 51_S35

description: HU male_total.xlsx


title: MUC21505 CM-OXT-101-13-N


title: MUC21506 CM-OXT-101-13-O


title: HEK293T (B9 clone + KRABY46A), nodox, H3K9me3, CUT&RUN, rep1


title: HEK293T (B9 clone + KRABY46A), dox5days, H3K9me3, CUT&RUN, rep1


title: MUC21507 CM-OXT-101-13-P


title: HEK293T (B9 clone + KRAB), reactivated, H3K9me3, CUT&RUN, rep2


title: MUC21504 CM-OXT-101-13-M


title: 49_S31

description: HU male_total.xlsx


title: MUC21502 CM-OXT-101-13-K


title: HEK293T (B9 clone + KRAB), irreversible, H3K9me3, CUT&RUN, rep2


title: HEK293T (B9 clone + KRAB), dox5days, H3K9me3, CUT&RUN, rep2


title: HEK293T (B9 clone + KRAB), nodox, H3K9me3, CUT&RUN, rep2


title: 53_S39

description: HU male_total.xlsx


title: MUC21501 CM-OXT-101-13-J


title: MUC21500 CM-OXT-101-13-I


title: HEK293T (B9 clone + KRAB), reactivated, H3K9me3, CUT&RUN, rep1


title: 30_S5

description: HU male_total.xlsx


title: 29_S4

description: HU male_total.xlsx


title: HEK293T (B9 clone + KRAB), irreversible, H3K9me3, CUT&RUN, rep1


title: MUC21499 CM-OXT-101-13-H


title: 55_S27

description: HU male_total.xlsx


title: HEK293T (B9 clone + KRAB), dox5days, H3K9me3, CUT&RUN, rep1


title: 33_S8

description: HU male_total.xlsx


title: 48_S29

description: HU male_total.xlsx


title: HEK293T (B9 clone + KRAB), nodox, H3K9me3, CUT&RUN, rep1


title: 28_S3

description: HU male_total.xlsx


title: 31_S6

description: HU male_total.xlsx


title: MUC21498 CM-OXT-101-13-G


title: 52_S37

description: HU male_total.xlsx


title: 32_S7

description: HU male_total.xlsx


title: MUC21497 CM-OXT-101-13-F


title: MUC21503 CM-OXT-101-13-L


title: HEK293T (B9 clone + KRAB), nodox, IgG, CUT&RUN


title: HEK293T (B9 clone + KRAB), nodox, H3K4me3, CUT&RUN


title: MUC21495 CM-OXT-101-13-D


title: MUC21496 CM-OXT-101-13-E


title: islet cells, S961

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were performed using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: P_filtered_gene_bc_matrix.mtx, S_filtered_gene_bc_matrix.mtx
Supplementary files format and content: matrix files containing gene expression values ( raw counts). Rows are genes presented with gene names identifiers (hgnc_symbol annotation) and columns are cells.

source_name: Pancreatic islets of langerhans

extract_protocol:
Islets were isolated from the pancreata of mock (P) and S961 (S)-treated mice , dissociated, stained with Propidium Iodide to exclude dead cells, and PI-negative cells were FACS sorted.
Libraries were generated as per  manufacturer’s instructions (Chromium 10x Genomics, single cell 3’ kit v2 ).

treatment_protocol: Mice were treated for 6 days with PBS (P) or  12nM S961 (S), a potent insulin receptor antagonist. S961-treated mice became hyperglycemic 48h after the beginning of the treatment and remained so till the end of the experiment.

value: Pancreatic islets of langerhans

value: islet cells


title: 35_S28

description: HU male_total.xlsx


title: MUC21494 CM-OXT-101-13-C


title: MUC21493 CM-OXT-101-13-B


title: 34_S25

description: HU male_total.xlsx


title: MUC21492 CM-OXT-101-13-A


title: MUC21491 CM-OXT-101-12-P


title: Thoracic spinal cord, WT, rep2

city: Taipei

first: Jun-An

last: Chen

address: 128 Academia Road, Section 2

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
CLC Genomics Workbench 12.0.3
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.01, discard short reads (<25))
Trimmed sequence reads were mapped to mm10 using CLC genomic benchwork (parameters- mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.9 similarity fraction: 0.9)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: excel files which include the TPM and RPKM values for each Sample

source_name: Thoracic spinal cord

extract_protocol:
Spinal cord tissues at thoracic and lumbar segments are dissected and RNA is harvested using Direct-zol RNA Miniprep Plus RNA kit (R2072).
Libraries were prepared using TruSeq Stranded mRNA library preparation kit (Cat# 20020594) following Illumina's protocol

value: Thoracic spinal cord

value: C57BL/6J WT


title: 18_S3

description: HU male_total.xlsx

value: Skeletal muscle Gastrocnemius


title: MUC21490 CM-OXT-101-12-O

value: Oxytocin neurons


title: Thoracic spinal cord, TKO, rep2


title: Thoracic spinal cord, WT, rep1


title: Thoracic spinal cord, TKO, rep1


title: 25_S16

description: HU male_total.xlsx

value: Hindlimb Unloading


title: Lumbar spinal cord, WT, rep1

source_name: Lumbar spinal cord

value: Lumbar spinal cord


title: MUC21488 CM-OXT-101-12-M

value: Brain

value: C57BL/6JRj -OXT-sun1-sfGFP


title: 27_S2

description: HU male_total.xlsx


title: 26_S1

description: HU male_total.xlsx


title: 20_S7

description: HU male_total.xlsx


title: MUC21489 CM-OXT-101-12-N

value: 6 months

value: HFHS diet


title: 21_S9

description: HU male_total.xlsx


title: 22_S11

description: HU male_total.xlsx


title: Lumbar spinal cord, WT, rep2


title: Lumbar spinal cord, TKO, rep2


title: MUC21487 CM-OXT-101-12-L


title: islet cells, PBS

description: 10x Genomics

value: PBS


title: MUC21486 CM-OXT-101-12-K

value: Male


title: 17_S2

description: HU male_total.xlsx


title: 753_Aire_WT

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

institute: Weizmann Institute of Science

data_processing:
Data was processed using UTAP pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).  R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded over genes annotated in RefSeq release using htseq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with the betaPrior set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Assembly: mm10
Supplementary files format and content: Tab delimited files include raw counts values for each sample

source_name: medullary thymic epithelial cells (mTEChi)

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. mTEChi were sorted and RNA was extracted using Dynabeads. MARSseq protocol was used construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et. Al. 2014)

value: NOD

value: 4.5 weeks

value: Aire +/+


title: MUC21484 CM-OXT-101-12-I

source_name: Brain

extract_protocol:
The single-nucleus RNA-seq2 methodology was used to capture a high number of transcripts from frozen tissues. the reaction volumes were miniaturized with the aid of the Mosquito HV robot. Per well, 2190 nL of Lysis Buffer 2 (LB2) were dispensed. The final volume of the mixture of Lysis Buffer (LB1 and LB2) was 3.125 μL, containing NP40 2%, Triton-X100 1%, 1/300,000 diluted ERCC RNA spike-in, 3′ SMART-seq CDS Primer II A and RNAse-free water. ERCC spike-ins (Thermo Fischer Scientific, Ref. 4456740; Lot no. 00892098) were diluted 1 in 10, with RNAse-free water with 0.4 U/μL Recombinant RNase Inhibitor (Takara Clontech, Ref. 2313A) and a fresh dilution of 1 in 300,000 was prepared before the first strand synthesis. Reverse transcription and Pre-PCR amplification steps were followed as described by the manufacturer with four-times reduced volumes for all steps.
Sequencing libraries were prepared using the Illumina Nextera XT DNA Sample Preparation kit (Illumina, Ref. FC-131-1096) and the combination of 384 Combinatorial Dual Indexes (Illumina- Set A to D, Ref. FC-131-2001 to FC-131-2004). In brief, 500 nL of the undiluted cDNA were transferred to a new 384 well-plate containing 1500 nL of Tagmentation Mix (TD and ATM reagents). Accordingly, all Nextera XT reagents (NT, NPM and i5/i7 indexes) were added stepwise to a final library volume of 5 μL per well. The final PCR amplification was performed through 12 cycles. Once the libraries were prepared, 500 nL from each well were pooled together into a tube (total volume of ~192 μL) to perform a final AMPure XP bead (Beckman Coulter, Ref. A63882) clean-up step. For our single nuclei libraries, two consecutive clean-ups with a ratio of sample to bead 0,9X led to library sizes between 200 and 1000 bp. Each plate, counting with a total of 384 libraries, was pooled together into one final library. A total of 4 final libraries were sequenced using an Illumina NovaSeq 6000 NGS sequencer in an SP XP flowcell, in a paired-end 150 bases length.


title: 23_S13

description: HU male_total.xlsx


title: 750_Aire_WT

value: medullary thymic epithelial cells (mTEChi)


title: MUC21483 CM-OXT-101-12-H

value: SC diet


title: 16_S15

description: HU male_total.xlsx


title: 749_Aire_KO

value: Aire -/-


title: MUC21481 CM-OXT-101-12-F


title: 748_Aire_KO


title: MUC21482 CM-OXT-101-12-G


title: 10_S4

description: HU male_total.xlsx


title: 15_S12

description: HU male_total.xlsx


title: 746_Aire_KO


title: MUC21480 CM-OXT-101-12-E


title: MUC21479 CM-OXT-101-12-D


title: 745_Aire_WT


title: 7_S1

description: HU male_total.xlsx


title: MUC21485 CM-OXT-101-12-J


title: 12_S8

description: HU male_total.xlsx


title: mouse lung cDC1 scRNA-seq

city: Chicago

first: Gye Young

last: Park

state: IL

address: 840 S. Wood St

department: Medicine, Pulmonary

institute: University of Illinois at Chicago

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Single cell transcriptomes were analyzed further using Seurat. We filltered cells with following creteria :nFeature_RNA (the number of genes detected) >500 & nCount_RNA (the total number of molecules detected within a cell)  > 2000 & percent.MT  < 10 . We performed feature selection to retain the 6000 genes with the most variable expression, controlling for mean expression level, as these are likely to be most informative in differentiating cell sub-populations.
Normalized gene expression was computed in units of CPM (counts per million) and log-scaled. Dimensionality reduction was performed using PCA (principle component analysis), retaining the top 50  principle components based on statistical significance (PCA Heatmap)
Assembly: mm10
Supplementary files format and content: Excel, matrix files, Seurat Object

source_name: Lung

extract_protocol:
Single cells were isolated from mouse lung tissue using dispase and either lung cDC1 (XCR1+) or cDC2(CD172a+) were seperatly isolated by flow sorter.
Library preparation was performed using the 10X Chromium v3.1 kit, according to the manufacturer’s protocol (#CG000183)
Library was multiplexed in one S4 lane in Novaseq 6000 and sequenced with 2x150nt cycles.

value: Lung

value: conventional DC1

value: 8-10 weeks


title: mouse lung cDC2 scRNA-seq

description: 10x Genomics

value: conventional DC2


title: 9_S14

description: HU male_total.xlsx

value: Skeletal muscle Gastrocnemius

value: Hindlimb Unloading


title: Lumbar spinal cord, TKO, rep1

value: Lumbar spinal cord


title: MUC21477 CM-OXT-101-12-B

value: Oxytocin neurons

value: Brain

value: C57BL/6JRj -OXT-sun1-sfGFP

value: 6 months


title: MUC21476 CM-OXT-101-12-A

value: Male


title: KO2 [1883,1884,1887,1888,1889]

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

institute: Fox Chase Cancer Center

data_processing:
Raw sequence reads were aligned to the mouse genome (GRCm38) using the STAR algorithm
The number of raw counts in each known gene  was enumerated using htseq-count from the HTSeq package.
Differential expression between samples and across different conditions was assessed for statistical significance using the R/ Bioconductor package DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimiited text file include raw count values for each sample

source_name: Egfr mKO

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer's instructions.
RNA libraries were prepared using the NEBNext ® Ultra TM II Directional RNA Library Prep Kit

value: Heart

value: Cardiac Cd11b+ non-myocyte

value: EGFR -/- (myeloid-specific)


title: KO3 [2037,2038,1945,1946,1947,1948]


title: MUC21478 CM-OXT-101-12-C

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

data_processing:
Technical replicates of the samples were merged, and reads were then mapped to rRNA (from Ensembl, GRCm38 release 102) using Bowtie2 (version 2.3.4.3114) and subsequently, unmapped reads were mapped to the mm10 genome (from Ensembl, GRCm38 release 102) using STAR (2.7.0115). Count matrices were generated by counting reads corresponding to gene exons using featureCounts (version 1.6.3116). Counts were transformed to FPKM and TPM using the actual feature length. The single-nuclei transcriptomics analysis of raw count matrix loaded into python and stored as AnnData object was performed using Scanpy version 1.7.1. Filtering of the cells was based on a minimum count number of 250. Filtering was applied to the matrix of 1536 single nuclei and 55579 genes. Nuclei that had >1000 and <4500 detected genes were kept. Genes detected in fewer than 25 cells and with read count below 250 were filtered out. Hence, only the nuclei having less than 4500 genes detected and a library size between 10000 and 200000 reads were kept. Applying this filtering strategy, the final matrix comprises 1202 single nuclei and 13867 genes. Batch effect corrections were performed employing combat using plates as a covariate.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

value: SC diet


title: 39_S34

description: HU male_total.xlsx

value: Control


title: MUC21474 CM-OXT-101-11-O

value: HFHS diet


title: 43_S40

description: HU male_total.xlsx


title: 42_S38

description: HU male_total.xlsx


title: WT2 [1789,1790,1791,1792,1899]

source_name: Egfr f/f

value: WT


title: 37_S30

description: HU male_total.xlsx


title: MUC21473 CM-OXT-101-11-N


title: MUC21472 CM-OXT-101-11-M


title: 19_S5

description: HU male_total.xlsx


title: 14_S10

description: HU male_total.xlsx


title: MUC21471 CM-OXT-101-11-L


title: 38_S32

description: HU male_total.xlsx


title: TCM_rep-3

city: Philadelphia

first: daniel

last: beiting

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

data_processing:
The adaptor-trimmed reads were aligned to the mouse genome mm10 by STAR v. 2.7.2d with default parameters.
Expression levels for each gene were counted by VERSE v. 0.1.4.
Normalization and differential expression (DE) analysis was conducted by DESeq2 v. 1.28.1 using Vehicle-treated group as the control.

source_name: splenocytes

extract_protocol: RNA was extracted using mini RNA isolation kit and concentration was measured using nanodrop2000.

value: cytotoxic T lymphocytes (CTLs)

value: TCM


title: MUC21470 CM-OXT-101-11-K

city: Neuherberg


title: 11_S6

description: HU male_total.xlsx

value: Skeletal muscle Gastrocnemius


title: MUC21475 CM-OXT-101-11-P


title: 46_S26

description: HU male_total.xlsx


title: Vehicle_rep-3

value: FCM


title: KO1 [1878,1879,1880,1881,1882]


title: MUC21469 CM-OXT-101-11-J


title: 41_S36

description: HU male_total.xlsx


title: Vehicle_rep-2


title: MUC21468 CM-OXT-101-11-I


title: Vehicle_rep-1


title: WT3 [1897,2040,2041,2042,2043]


title: E0771-17AAG2_S1

city: Augusta

first: Ahmed

last: Chadli

state: GA

address: 1410 Laney Walker BLVD

department: Cancer Center

institute: Augusta University

data_processing:
Illumina BCL2.0 fastq software used for basecalling.
Sequenced reads were  mapped to mm9 whole genome using STAR aligner
Normalized FPKM counts were calculated using Cufflinks and Cuffdiff tools for outputting differntially expressed genes with log2 fold changes and q values.
Genome_build: mm9
Supplementary_files_format_and_content: excel file, log2 fold change

growth_protocol: E0771 murine cells were allowed to grow in 6-well tissue culture plates for 48 hrs supplemented with complete RPMI-1640 media (Corning, # 10-040-CV) and 10% FBS.

extract_protocol:
Total RNA was extracted using Purelink RNA Mini kit with On-column PureLink Dnase Treatment
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with EnnA (7.4 µM) or 17-AAG (0.5 µM) for 24 hrs.

tag: strain background

value: Murine breast cancer cells


title: MUC21466 CM-OXT-101-11-G

value: Oxytocin neurons


title: MUC21465 CM-OXT-101-11-F

value: Brain


title: MUC21467 CM-OXT-101-11-H

value: C57BL/6JRj -OXT-sun1-sfGFP


title: MUC21464 CM-OXT-101-11-E

value: 6 months


title: E0771-EnnA2_S5

value: EnnA


title: E0771-EnnA1_S3


title: WT1 [1785,1786,1787,1788,1896]

value: Heart


title: MUC21463 CM-OXT-101-11-D

value: Male


title: E0771-17AAG1_S2


title: MUC21461 CM-OXT-101-11-B


title: MUC21462 CM-OXT-101-11-C


title: TCM_rep-2


title: MUC21460 CM-OXT-101-11-A


title: TCM_rep-1


title: E0771-DMSO1_S6

value: DMSO


title: E0771-DMSO2_S4


title: MUC21458 CM-OXT-101-10-O


title: MUC21457 CM-OXT-101-10-N


title: MUC21456 CM-OXT-101-10-M


title: MUC21459 CM-OXT-101-10-P


title: Induced Treg

description:
SC-21-03_induced_Treg_manuf_protocol
10x Genomics

source_name: Induced Treg

value: Induced Treg


title: MUC21455 CM-OXT-101-10-L


title: MUC21453 CM-OXT-101-10-J


title: MUC21454 CM-OXT-101-10-K


title: iPSC-Treg

description:
SC-21-03_D57_CD25high_sorted_iPSC-Treg
10x Genomics

source_name: iPSC-Treg

value: iPSC-Treg


title: MUC21451 CM-OXT-101-10-H

value: SC diet


title: primary Treg

description:
SC-21_6_Treg_donor2_cultured
10x Genomics

source_name: primary Treg

value: primary Treg


title: MUC21452 CM-OXT-101-10-I

value: HFHS diet


title: MUC21448 CM-OXT-101-10-E


title: CRISPR screen - M2- ALAS2(8)

city: Boston

first: Stephen

last: Elledge

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

library_source: other

data_processing:
Data from four lanes of Illumina sequencing instrument are merged.
Constant sequences of the GPS6.0 vector were trimmed away via Cutadapt
For each bin, the number of reads perfectly mapped to each peptide was counted via Bowtie2
After normalizing the differences in sequencing depth for each bin, the PSI of each peptide was calculated as a weighted average of its distribution across the 6 bins, leading to a PSI score in between 1 (most unstable) and 6 (most stable).
For CRISPR screens, MAGeCK was used to determine enrichment.
Assembly: custom peptidome library
Supplementary files format and content: Read counts are provided as a tab-delimited txt file containing aligned sequence id and the number of occurances
Supplementary files format and content: PSI data is provided in supplementary table 1 in Microsoft Excel format. The three sheets are GPS peptidome replicate1, GPS peptidome replicate2, and GPS peptidome with MLN4924 respectively.
Supplementary files format and content: mageck scores are provided in tab delimited files with the suffix _mageck.txt containing the output of gene_summary.txt

molecule: other

growth_protocol: We cultured HEK293T (ATCC CRL-3216) cells at 37C and 5% CO2 in DMEM, high glucose, GlutaMAX™ Supplement, pyruvate (ThermoFisher Scientific) added with 10% fetal bovine serum (HyClone), 1% of 10,000 U/mL Penicillin-Streptomycin (ThermoFisher Scientific)

extract_protocol:
For each bin, we performed genomic DNA extraction (QIAGEN Gentra Puregene Cell Kit).
We amplified the peptide sequences cloned into GFP by PCR with Q5 Hot Start Polymerase (NEB) using PCR primers annealing to constant sequences shared across the library. We then purified the amplicons (QIAGEN PCR purification kit).

treatment_protocol: We packaged GPS-peptidome lentiviral libraries and transduced HEK293T at low multiplicity of infection (MOI). Two days after transduction, hygromycin was added to eliminate untransduced cells and 7-9 days after transduction, cells were sorted into 6 bins in approximately 1:1 ratio according to the GFP/DsRed ratio.

value: cell line

value: library of Ub knockout

value: lentiviral transduction


title: CRISPR screen - M2-34 DLST (7)


title: MUC21449 CM-OXT-101-10-F


title: CRISPR screen - M2-40 MDN1 (196)


title: MUC21445 CM-OXT-101-10-B


title: MUC21450 CM-OXT-101-10-G


title: CRISPR screen - M2-35 CDC6 (1)


title: MUC21446 CM-OXT-101-10-C


title: CRISPR screen - M2-9 ADCY2 (37)


title: MUC21443 CM-OXT-101-9-P


title: MUC21442 CM-OXT-101-9-O


title: CRISPR screen - M2-14 ATP2B2 (34)


title: CRISPR screen - M2-19 CCDC3 (10)


title: MUC21444 CM-OXT-101-10-A


title: Liver, GALP treated (less weight loss group)

type: RNA

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

source_name: Control liver Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Experimental protocols were reviewed and approved by the Animal Care Committee of Hoshi University School of Pharmacy and Pharmaceutical Sciences. Male C57BL/6 mice (8 weeks-old) purchased from Tokyo Laboratory Animals Science Co., Ltd. (Tokyo, Japan). The animals were housed at the Animal Institution in Hoshi University. They were maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light : 12 h dark cycle with free access to water and rodent chow.

extract_protocol: kit: QIAGEN, RNeasy Plus Micro

treatment_protocol: To observe changes in the body weight induced by intranasal GALP administration, DIO mice were created by ad libitum feeding of a high-fat diet to C57BL/6 mice for 14 weeks. The DIO mice used for intranasal GALP administration weighed 40 g or more. Sixteen DIO mice were divided into two groups, the GALP intranasal administration group and the control group (n = 8 per group), and acclimatized for 2 weeks. Porcine GALP (1-60) purchased from Bachem AG (Bubendorf, Switzerland) was dissolved in saline containing 5% α-cyclodextrin to a concentration of 1 nmol. Saline was used for the control group. After acclimatization, mice in both groups were intranasally administered 2 μL of vehicle alone were intranasal injected by pushing a plastic 10 μL gel-loading pipette tip attached to a 10 μL micropipette through the naris, once daily for 11 consecutive days, and changes in body weight were observed. Body weights were measured at the time of each intranasal administration. Livers were sampled, post-decapitation of the C57BL/6J mice, immediately frozen in liquid nitrogen and transferred to a -80°C deep freezer. Control and GALP intranasal administration mouse livers (n=8) were each powdered in liquid nitrogen and stored at -80°C until total RNA extraction and metabolome analyses.

tag: disease state

value: diet-induced obesity (DIO)

value: liver

value: saline

tag: group

value: less weight loss group

source_name: GALP treated liver Cy5

value: GALP


title: MUC21440 CM-OXT-101-9-M

tag: cell type

value: Oxytocin neurons

tag: tissue

value: Brain

value: C57BL/6JRj -OXT-sun1-sfGFP

value: 6 months


title: MUC21439 CM-OXT-101-9-L

tag: strain

tag: age

value: Male


title: CRISPR screen - M1-19 UNC13D (26)


title: CRISPR screen - M1-14 VRK3 (15)


title: Liver, GALP treated (greater weight loss group)

value: greater weight loss group


title: CRISPR screen - M1-25 MMP2 (13)


title: CRISPR screen - M2-47 ZNF19 (8)


title: Liver, GALP treated (less weight loss group), dye-swap

source_name: GALP treated liver Cy3

source_name: Control liver Cy5


title: Liver, GALP treated (greater weight loss group), dye-swap


title: MUC21441 CM-OXT-101-9-N

tag: Sex

tag: treatment/diet


title: CRISPR screen - M1-23 GLB1L (2)

tag: cell line

tag: genotype


title: CRISPR screen - M2-12 CCDC17 (9)

tag: treatment


title: CRISPR screen - M1-15 IFNA8 (5)


title: MUC21437 CM-OXT-101-9-J


title: CRISPR screen - M1-7 CEP152 (52)


title: MUC21447 CM-OXT-101-10-D

value: SC diet


title: MUC21438 CM-OXT-101-9-K


title: MUC21436 CM-OXT-101-9-I


title: CRISPR screen - M1-4 COL11A2 (20)


title: CRISPR screen - M1-3 SH3BP2 (2)


title: CRISPR screen - CDHR4 (23)


title: MUC21434 CM-OXT-101-9-G


title: MUC21433 CM-OXT-101-9-F


title: CRISPR screen - CD68 (8)


title: MUC21432 CM-OXT-101-9-E


title: MUC21431 CM-OXT-101-9-D


title: CRISPR screen - ANKRD27 (23)


title: CRISPR screen - CFB (17)


title: B6_F1_GS_Control_C44

city: Kyoto

first: Takashi

last: Shinohara

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo

department: Graduate School of Medicine

institute: Kyoto University

description: Germline stem cells of natural mating derived mice.

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome using STAR (version 2.6.0c), with the GENCODE M21 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-1.16.
The gene expression levels were caluculated using HTSeq (version 0.11.2) and DESeq2 (v1.22.2) with GENCODE M21 annotation gtf file (protein-coding genes).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Germline stem cell

growth_protocol: Germline stem cells were maintained in IMDM supplemented with 10 ng/ml human FGF2, 15 ng/ml rat GDNF, 25 mg/ml insulin, 100 mg/ml transferrin, 200 mg/ml pyruvic acid, 60 mM putrecine, 30 nM Sodium selenite, 6 mg/ml D-(+)-glucose, 0.1 % DL-lactic acid, 5 mg/ml AlubMAX, 2 mM L-glutamine, 5x10-5 M 2-mercaptoethanol, MEM vitamin solution, non-essential amino acids, 10-4 M ascorbic acid, 10 mg/ml d-biotin, 30 ng/ml b-estradiol, 60 ng/ml progesterone, 1 mg/ml Fetuin, 1 % CD lipid concentrate, 0.2% cholesterol solution, and 5 % knockout serum replacement.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Germline stem cell

value: WT

value: no


title: B6_F1_GS_ICSI_M1_21

description: Germline stem cells of ICSI-derived mice.

value: ICSI


title: MUC21430 CM-OXT-101-9-C


title: GPS peptidome with MLN4924 Bin6

description: Supplementary Table 1_Raw data of GPS peptidome screens (Control + MLN4924).xlsx

value: cell line


title: GPS peptidome with MLN4924 Bin4


title: B6_F1_GS_ICSI_M1_20


title: GPS peptidome with MLN4924 Bin3


title: B6-F1-GS-ICSI-M1-17

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome using STAR (version 2.7.9a), with the GENCODE M25 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-3.4.
The gene expression levels were caluculated using HTSeq (version 0.13.5) and DESeq2 (v1.30.1) with GENCODE M25 annotation gtf file.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: Germline stem cells of ICSI-derived mice


title: GPS peptidome with MLN4924 Bin5


title: B6-F1-GS-ICSI-M1-11


title: MUC21429 CM-OXT-101-9-B


title: MUC21435 CM-OXT-101-9-H


title: MUC21427 CM-OXT-101-8-P

value: HFHS diet


title: GPS peptidome with MLN4924 Bin2


title: B6-F1-GS-Control-C29

source_name: Germline stem cells of natural mating derived mice


title: MUC21428 CM-OXT-101-9-A


title: MUC21426 CM-OXT-101-8-O


title: MUC21425 CM-OXT-101-8-N


title: GPS peptidome with MLN4924 Bin1


title: sRNAseq_C_Col_Ctr//AGe//rMf_Rep3

city: Kearneysville

first: Zongrang

last: Liu

state: WV

address: 2217 Wiltshire Road

department: Appalachian Fruit Research Station

institute: USDA-ARS

data_processing:
The obtained reads were trimmed and aligned to the reference Arabidopsis genome (TAIR10) using Bowtie software
Those reads mapped to the AGe, AGp, M2 regions within a 17.3-kb genomic region were retrieved and counted using htseq-count (version 0.13.5; Anders et al., 2015) for calculation of the value of Normalized Read Per Million mapped reads (NRPM) in each region
Supplementary files format and content: xls file includes the value of NRPM in the AGe and AGp/M2 regions  within the 17.3-kb genomic region for each sample

organism: Arabidopsis thaliana

source_name: Young flower

extract_protocol:
Arabidopisis plants were transformed with various transgene cassetts for evaluation of silencing efficiency and mutant flower frequncy.
Total RNA was extracted from young flowers pooled from five to ten lines with the same phenotype for each replicate using Tri-Reagent (Sigma, MO) followed by two rounds of phenol–chloroform extraction (50:50).
About 200 -500 ng of total RNA was used for construction of sRNA-seq libraries with different kits. sRNA-seq libraries for the Group A samples were made using the NEXTflex™ Small RNA-Seq Kit v3 (BIOO Scientific, Austin, Texas) accoding to intrusction provided whle the libraries for the Group B and C samples were biult using Illumina TruSeq Small RNA Library Prep Kit.
sRNA-seq

treatment_protocol: Arabidopsis plants were grown under a 16/8h light:dark photoperiod at 20-22˚C for approximately 4-5 weeks prior to transformation.

value: Young flower

tag: flower phenotype

value: rMf

value: Floral structure change


title: B6_F1_GS_Control_C45


title: sRNAseq_C_Col_Ctr//AGe//rMf_Rep2


title: MUC21424 CM-OXT-101-8-M


title: MUC21423 CM-OXT-101-8-L


title: GPS peptidome replicate2 Bin4

value: control


title: GPS peptidome replicate2 Bin5


title: MUC21422 CM-OXT-101-8-K

value: Oxytocin neurons


title: sRNAseq_C_Col_Ctr//AGe//rMf_Rep1


title: B6-F1-GS-Control-C37


title: sRNAseq_C_kan1-11_Ctr//AGe//rMf_Rep3


title: MUC21420 CM-OXT-101-8-I

value: Brain


title: sRNAseq_C_kan1-11_Ctr//AGe//rMf_Rep2


title: sRNAseq_C_kan1-11_Ctr//AGe//rMf_Rep1


title: MUC21419 CM-OXT-101-8-H

value: C57BL/6JRj -OXT-sun1-sfGFP


title: MUC21421 CM-OXT-101-8-J

value: 6 months


title: GPS peptidome replicate1 Bin5


title: GPS peptidome replicate1 Bin6


title: GPS peptidome replicate2 Bin1


title: MUC21418 CM-OXT-101-8-G

value: Male


title: sRNAseq_C_hdp2-1_ARE//AGe//sMf_Rep3

value: sMf


title: GPS peptidome replicate2 Bin2


title: sRNAseq_C_hdp2-1_ARE//AGe//sMf_Rep1


title: GPS peptidome replicate1 Bin4


title: sRNAseq_C_hdp2-1_ARE//AGe//rMf_Rep3


title: GPS peptidome replicate2 Bin6


title: MUC21416 CM-OXT-101-8-E

value: SC diet


title: GPS peptidome replicate1 Bin3


title: MUC21415 CM-OXT-101-8-D


title: sRNAseq_C_hdp2-1_ARE//AGe//rMf_Rep2


title: GPS peptidome replicate1 Bin2


title: sRNAseq_C_hdp2-1_ARE//AGe//rMf_Rep1


title: MUC21414 CM-OXT-101-8-C


title: GPS peptidome replicate2 Bin3


title: GPS peptidome replicate1 Bin1


title: sRNAseq_C_hdp2-1_Wt flower_Rep3

value: Wt


title: sRNAseq_C_hdp2-1_ARE//AGe//sMf_Rep2


title: MUC21412 CM-OXT-101-8-A


title: MUC21413 CM-OXT-101-8-B


title: sRNAseq_C_hdp2-1_Wt flower_Rep1


title: control7_kidney

city: São Paulo

first: Fabiano

last: Pinheiro Da Silva

state: São Paulo

address: Av Dr Arnaldo, 455 sala 3189

country: Brazil

institute: Faculdade de Medicina da Universidade de São Paulo

data_processing:
The libraries were quantified by Qubit dsDNA High Sensitivity Assay Kit (Life Technologies Corporation, Carlsbad, CA, United States) and the median sizes were determined by TapeStation 4200 (Agilent Technologies, USA), using the High Sensitivity D1000 ScreenTape assay, to form an equimolar pool.
Sequencing was performed as a 75-bp single-read, single-index run on a NextSeq 500 next-generation sequencer (Illumina, San Diego, CA, United States) with High Output kit.
Quality control analysis was performed using FastQC software, showing a Phred value superior to 30
Trimmomatic software was used to trim low-quality reads and adapters. Raw reads were aligned to the hg38 reference through HISAT2 software. Quantification of the gene expression data was performed through the function featureCounts of the R package Rsubread and the counts were normalized according to log2CPM.
Differential expression analysis was performed by the R package edgeR (FDR < 0.1 was considered significant), comparing each male patient with sepsis with all male uninfected controls and the female patients with sepsis with all female uninfected controls.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains results of differential expression analysis in edgeR
Supplementary files format and content: columns indicate gene ID, logFc, p-value and FDR

source_name: kidney

extract_protocol:
Total RNA was extracted from the tissue samples using RNeasy and AllPrep Micro Kit (Qiagen, Germantown, MD, United States), in accordance with the manufacturer’s protocol.
cDNA libraries were prepared for the 84 samples, starting with 500 pg of total RNA, using the QUANTSeq 3’mRNA-Seq Library Prep Kit FWD HT for Illumina (Lexogen, Wien, Austria), in accordance with the manufacturer’s protocol.

value: kidney


title: control7_colon

source_name: colon

value: colon


title: MUC21410 CM-OXT-101-7-O

source_name: Brain


title: MUC21417 CM-OXT-101-8-F


title: MUC21409 CM-OXT-101-7-N


title: MUC21411 CM-OXT-101-7-P


title: control7_lungs

source_name: lung

value: lung


title: control7_hippocampus

source_name: hippocampus

value: hippocampus


title: sRNAseq_C_hdp2-1_Wt flower_Rep2


title: sRNAseq_C_hdp1-1_ARE//AGE_sMf_Rep3


title: MUC21407 CM-OXT-101-7-L

value: HFHS diet


title: sRNAseq_C_hdp1-1_ARE//AGE_sMf_Rep2

value: Young flower


title: MUC21408 CM-OXT-101-7-M


title: sRNAseq_C_hdp1-1_ARE//AGE_sMf_Rep1


title: control7_heart

source_name: heart

value: heart


title: control7_cortex

source_name: brain prefrontal cortex

value: brain prefrontal cortex


title: sRNAseq_C_hdp1-1_ARE//AGE_rMf_Rep3

value: rMf

value: Floral structure change


title: sRNAseq_C_hdp1-1_ARE//AGE_rMf_Rep2


title: control6_kidney


title: MUC21406 CM-OXT-101-7-K

value: Oxytocin neurons

value: Brain


title: MUC21405 CM-OXT-101-7-J

value: C57BL/6JRj -OXT-sun1-sfGFP

value: 6 months


title: sRNAseq_C_hdp1-1_ARE//AGE_rMf_Rep1


title: control6_lungs


title: MUC21404 CM-OXT-101-7-I

value: Male


title: control6_heart


title: control6_colon


title: sRNAseq_C_hdp1-1_Wt flower_Rep2


title: control6_hippocampus


title: sRNAseq_C_hdp1-1_Wt flower_Rep1


title: MUC21402 CM-OXT-101-7-G

value: SC diet


title: sRNAseq_C_suvh1-2_ARE//AGE_sMf_Rep3

value: sMf


title: MUC21400 CM-OXT-101-7-E


title: control6_cortex


title: control5_colon


title: MUC21401 CM-OXT-101-7-F


title: sRNAseq_C_suvh1-2_ARE//AGE_sMf_Rep1


title: control5_kidney

value: kidney


title: sRNAseq_C_suvh1-2_ARE//AGE_sMf_Rep2


title: sRNAseq_C_suvh1-2_Wt flower_Rep3

value: Wt


title: MUC21399 CM-OXT-101-7-D


title: sRNAseq_C_suvh1-2_Wt flower_Rep2


title: MUC21398 CM-OXT-101-7-C


title: MUC21397 CM-OXT-101-7-B


title: control5_lungs

value: lung


title: control5_heart


title: control5_hippocampus

value: hippocampus


title: control5_cortex


title: sRNAseq_C_kan1-11_Wt flower_Rep3


title: sRNAseq_C_hdp1-1_Wt flower_Rep3


title: MUC21403 CM-OXT-101-7-H


title: MUC21396 CM-OXT-101-7-A


title: sRNAseq_C_suvh1-2_Wt flower_Rep1


title: MUC21395 CM-OXT-101-6-P

value: HFHS diet


title: control4_colon

value: colon


title: MUC21394 CM-OXT-101-6-O


title: MUC21393 CM-OXT-101-6-N


title: sRNAseq_C_kan1-11_Wt flower_Rep2

value: Young flower


title: control4_kidney


title: sRNAseq_C_kan1-11_Wt flower_Rep1


title: control4_lungs


title: sRNAseq_C_Col_Wt flower_Rep3

value: Col


title: MUC21391 CM-OXT-101-6-L


title: control4_heart

value: heart


title: MUC21392 CM-OXT-101-6-M


title: MUC21390 CM-OXT-101-6-K


title: sRNAseq_C_Col_Wt flower_Rep1

value: Floral structure change


title: MUC21389 CM-OXT-101-6-J

value: Oxytocin neurons


title: control4_hippocampus


title: sRNAseq_C_Col_Wt flower_Rep2


title: sRNAseq_B_kan1-11_ARE//AGe//Wt flower_A


title: control3_kidney


title: control4_cortex

value: brain prefrontal cortex


title: MUC21387 CM-OXT-101-6-H

value: Brain

value: C57BL/6JRj -OXT-sun1-sfGFP


title: sRNAseq_B_ddm1-1_Ctr//AGe_rMf_Rep3

value: rMf


title: sRNAseq_B_kan1-11_ARE//AGe//Wt flower_B


title: sRNAseq_B_ddm1-1_Ctr//AGe_rMf_Rep2


title: control3_colon


title: MUC21385 CM-OXT-101-6-F

value: 6 months

value: Male

value: SC diet


title: MUC21386 CM-OXT-101-6-G


title: sRNAseq_B_ddm1-1_Ctr//AGe_rMf_Rep1


title: control3_lungs


title: control3_hippocampus


title: MUC21384 CM-OXT-101-6-E


title: control3_cortex


title: sRNAseq_B_ddm1-1_ARE//AGe_rMf_Rep3


title: MUC21388 CM-OXT-101-6-I


title: control2_colon


title: sRNAseq_B_ddm1-1_ARE//AGe_rMf_Rep2


title: MUC21382 CM-OXT-101-6-C


title: MUC21383 CM-OXT-101-6-D


title: sRNAseq_B_ddm1-1_ARE//AGe_rMf_Rep1


title: control2_lungs


title: MUC21381 CM-OXT-101-6-B


title: control2_kidney

value: kidney


title: control3_heart


title: sRNAseq_B_ddm1-1_ARE//AGe_sMf_Rep3

value: sMf


title: control2_heart


title: sRNAseq_B_ddm1-1_ARE//AGe_sMf_Rep2


title: control2_hippocampus

value: hippocampus


title: sRNAseq_B_ddm1-1_ARE//AGe_sMf_Rep1


title: MUC21377 CM-OXT-101-5-N

value: HFHS diet


title: MUC21380 CM-OXT-101-6-A


title: control1_colon

value: colon


title: MUC21378 CM-OXT-101-5-O


title: sRNAseq_B_ddm1-1_Wt flower_Rep3

value: Young flower

value: Wt


title: control2_cortex


title: sRNAseq_B_ddm1-1_Wt flower_Rep2


title: MUC21376 CM-OXT-101-5-M


title: sRNAseq_B_ddm1-1_Wt flower_Rep1


title: MUC21375 CM-OXT-101-5-L


title: sRNAseq_B_met1-1_Ctr//AGe_rMf_Rep3


title: control1_kidney


title: control1_lungs

value: lung


title: sRNAseq_B_met1-1_Ctr//AGe_rMf_Rep2

value: Floral structure change


title: control1_heart

value: heart


title: control1_hippocampus


title: MUC21372 CM-OXT-101-5-I

value: Oxytocin neurons


title: MUC21373 CM-OXT-101-5-J

value: Brain


title: control1_cortex

value: brain prefrontal cortex


title: MUC21379 CM-OXT-101-5-P

value: C57BL/6JRj -OXT-sun1-sfGFP


title: sRNAseq_B_met1-1_ARE//AGe_rMf_Rep2

value: rMf


title: sRNAseq_B_met1-1_ARE//AGe_rMf_Rep1


title: sepsis7_colon


title: sepsis7_kidney


title: MUC21370 CM-OXT-101-5-G

value: 6 months

value: Male


title: MUC21369 CM-OXT-101-5-F

value: SC diet


title: sepsis7_lungs


title: MUC21368 CM-OXT-101-5-E


title: sRNAseq_B_met1-1_ARE//AGe_sMf_Rep3

value: sMf


title: sepsis7_heart


title: sRNAseq_B_met1-1_ARE//AGe_sMf_Rep2


title: MUC21374 CM-OXT-101-5-K


title: sRNAseq_B_met1-1_ARE//AGe_sMf_Rep1


title: MUC21367 CM-OXT-101-5-D


title: sepsis7_hippocampus

value: hippocampus


title: MUC21366 CM-OXT-101-5-C


title: sRNAseq_B_met1-1_Ctr//AGe_rMf_Rep1


title: sepsis7_cortex


title: sRNAseq_B_met1-1_ARE//AGe_rMf_Rep3


title: MUC21365 CM-OXT-101-5-B


title: sRNAseq_B_met1-1_Wt flower_Rep2


title: MUC21371 CM-OXT-101-5-H


title: sepsis6_colon


title: sRNAseq_B_met1-1_Wt flower_Rep1


title: sepsis6_lungs


title: sepsis6_heart


title: MUC21363 CM-OXT-101-4-P

value: HFHS diet


title: sRNAseq_B_Col_Wt flower_Rep3

value: Col


title: sepsis6_hippocampus


title: MUC21362 CM-OXT-101-4-O


title: sRNAseq_B_Col_Wt flower_Rep2

value: Young flower


title: sepsis6_cortex


title: sRNAseq_B_Col_Wt flower_Rep1

value: Wt


title: sRNAseq_B_met1-1_Wt flower_Rep3


title: MUC21361 CM-OXT-101-4-N


title: MUC21360 CM-OXT-101-4-M


title: sepsis5_kidney

value: kidney


title: sepsis5_lungs

value: lung


title: MUC21359 CM-OXT-101-4-L


title: sepsis5_colon

value: colon


title: sRNAseq_B_Col_ARE//AGe_Wt flower_Rep3

value: Floral structure change


title: MUC21357 CM-OXT-101-4-J

value: Oxytocin neurons

value: Brain


title: sepsis5_heart

value: heart


title: sRNAseq_B_Col_ARE//AGe_Wt flower_Rep1


title: sRNAseq_A_M317_AGe_rMf_Rep3

value: rMf


title: MUC21356 CM-OXT-101-4-I

value: C57BL/6JRj -OXT-sun1-sfGFP

value: 6 months


title: MUC21355 CM-OXT-101-4-H

value: Male

value: SC diet


title: MUC21364 CM-OXT-101-5-A


title: MUC21358 CM-OXT-101-4-K


title: sepsis5_hippocampus

value: hippocampus


title: sepsis5_cortex

value: brain prefrontal cortex


title: sRNAseq_A_M317_AGe_rMf_Rep2


title: sepsis4_kidney


title: MUC21353 CM-OXT-101-4-F


title: sepsis4_colon


title: sRNAseq_A_M317_AGe_rMf_Rep1


title: sRNAseq_B_Col_ARE//AGe_Wt flower_Rep2


title: sRNAseq_A_M317_AGe_sMf_Rep2

value: sMf


title: sepsis4_lungs


title: MUC21352 CM-OXT-101-4-E


title: MUC21351 CM-OXT-101-4-D


title: sRNAseq_A_M317_AGe_sMf_Rep1

value: Young flower


title: sRNAseq_A_M318_AGe_rMf_Rep3


title: sRNAseq_A_Col_AGp_Sterile flower

value: Sterile


title: sepsis4_heart


title: MUC21349 CM-OXT-101-4-B


title: sRNAseq_A_M318_AGe_rMf_Rep2


title: MUC21348 CM-OXT-101-4-A


title: MUC21350 CM-OXT-101-4-C


title: MUC21347 CM-OXT-101-3-P

value: HFHS diet


title: MUC21354 CM-OXT-101-4-G


title: sepsis3_kidney

value: kidney


title: sepsis3_colon

value: colon


title: sRNAseq_A_M317_AGe_sMf_Rep3

value: Floral structure change


title: sRNAseq_A_M318_AGe_sMf_Rep3


title: sRNAseq_A_M318_AGe_sMf_Rep2


title: sepsis3_heart


title: sRNAseq_A_M318_AGe_sMf_Rep1


title: MUC21345 CM-OXT-101-3-N

value: Oxytocin neurons


title: MUC21344 CM-OXT-101-3-M

value: Brain


title: sRNAseq_A_Col_Ctr//AGe_Wt flower_Rep3

value: Wt


title: sepsis4_hippocampus


title: sRNAseq_A_Col_Ctr//AGe_Wt flower_Rep1


title: sepsis3_cortex


title: sRNAseq_A_Col_Ctr//AGe_Wt flower_Rep2


title: MUC21342 CM-OXT-101-3-K


title: MUC21343 CM-OXT-101-3-L


title: sRNAseq_A_M318_AGe_rMf_Rep1

value: rMf


title: sRNAseq_A_Col_AGP//AGe_rMf_Rep3


title: sepsis4_cortex


title: MUC21341 CM-OXT-101-3-J

value: C57BL/6JRj -OXT-sun1-sfGFP


title: sepsis2_lungs

value: lung


title: sepsis3_hippocampus


title: sepsis2_kidney


title: sepsis2_heart

value: heart


title: MUC21339 CM-OXT-101-3-H

value: 6 months

value: Male

value: SC diet


title: sepsis2_hippocampus

value: hippocampus


title: sRNAseq_A_Col_AGP//AGe_rMf_Rep2

value: Young flower


title: MUC21340 CM-OXT-101-3-I


title: MUC21346 CM-OXT-101-3-O


title: sepsis3_lungs


title: sRNAseq_A_Col_AGP//AGe_rMf_Rep1


title: sepsis2_cortex

value: brain prefrontal cortex


title: sRNAseq_A_Col_AGP//AGe_sMf_Rep3

value: sMf


title: MUC21337 CM-OXT-101-3-F


title: MUC21338 CM-OXT-101-3-G


title: sepsis1_colon


title: sRNAseq_A_Col_AGP//AGe_sMf_Rep2


title: MUC21336 CM-OXT-101-3-E


title: sepsis1_kidney

value: kidney


title: sepsis1_lungs


title: sRNAseq_A_Col_AGP//AGe_sMf_Rep1


title: MUC21334 CM-OXT-101-3-C


title: MUC21335 CM-OXT-101-3-D


title: sRNAseq_A_M317_Wt flower_Rep2


title: MUC21333 CM-OXT-101-3-B


title: sepsis1_hippocampus


title: sRNAseq_A_M318_Wt flower_Rep3


title: sepsis1_cortex

source_name: prefrontal brain cortex

value: prefrontal brain cortex


title: MUC21332 CM-OXT-101-3-A


title: sRNAseq_A_M318_Wt flower_Rep2

value: Floral structure change


title: sRNAseq_A_M318_Wt flower_Rep1


title: Patient_1438_Post_Treatment_CNV

city: Calgary

first: Nizar

last: Bahlis

state: Alberta

address: 3330 Hospital Dr NW HMRB328

department: Divisions of Hematology and Oncology

country: Canada

institute: University of Calgary

data_processing:
library strategy: CNV-seq
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters.
Assembly: Human referene genome GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from cellranger-dna pipeline

source_name: Primary CD138+ MM cells

growth_protocol: Primary CD138+ MM cells were obtained from the BM aspirates of MM patients at the time of diagnostic procedure, using positive selection with CD138 microbeads (Miltenyi Biotech, Auburn, CA) and accordingly to manufacturer’s instructions.  CD138+ fractions were subsequently analyzed by flow cytometry in order to confirm the sample’s purity. HEK293T cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% FBS, 100 U/mL penicillin and 100 g/mL streptomycin. All of the listed cells above were cultured at 37°C and 5% CO2.

extract_protocol: For single-cell DNA library generation for CNV single-cell suspensions of primary MM cells were processed according to 10X Genomics Reagent Kits User Guide (CG000153). Single cells were partitioned in a hydrogel matrix by combining with a CB polymer to form Cell beads (CBs) using a microfluidic chip. Post a first encapsulation, CBs were treated to lyse the encapsulated cells and denature the genomic DNA (gDNA). The denatured gDNAs in the CB were then accessible to amplification and barcoding. A second microfluidic encapsulation step was then required to partition the CB with 10x barcode Gel Beads (GBs) to generate GEMs. Immediately after barcoding and amplification, 10x barcoded fragments were pooled and attached to standard Illumina adaptors. For all the single cell methods, quality control and quantification was performed using a Kapa Library Quantification qPCR kit (Kapa Biosystems) on a BioRad qPCR instrument prior to preparing a single pool containing equal amounts of each library. This pool was then subjected to on-board cluster formation and sequencing on an Illumina NextSeq 500 sequencer with a high-output v2.5 150 sequencing kit for RNA-seq and ATAC-seq and 300 cycle sequencing kit for CNV-seq as per the standard Illumina protocols. After sequencing, the bcl data was converted to fastq data files using the Illumina BCL2FASTQ utility. Samples were processed with CellRanger suite v3.0 and downstream analyses were realized with Seurat, Monocle, Signac, and Cicero R packages.

tag: patient number

value: post

value: Primary CD138+ MM cells

tag: library preparation

value: 10X Genomics Single Cell Copy Number Variation


title: sRNAseq_A_SALK_137982_rMf

data_processing:
The obtained reads were trimmed and aligned to the reference Arabidopsis genome (TAIR10) using Bowtie software
Those reads mapped to the AGe, AGp, M2 regions within a 17.3-kb genomic region were retrieved and counted using htseq-count (version 0.13.5; Anders et al., 2015) for calculation of the value of Normalized Read Per Million mapped reads (NRPM) in each region
Supplementary files format and content: xls files include the value of NRPM in the AGe and AGp/M2 regions  within the 17.3-kb genomic region for each sample

extract_protocol:
Arabidopisis plants were transformed with various transgene cassetts for evaluation of silencing efficiency and mutant flower frequncy.
Total RNA was extracted from young flowers pooled from five to ten lines with the same phenotype for each replicate using Tri-Reagent (Sigma, MO) followed by two rounds of phenol–chloroform extraction (50:50).
About 200 -500 ng of total RNA was used for construction of sRNA-seq libraries with different kits. sRNA-seq libraries for the Group A samples were made using the NEXTflex™ Small RNA-Seq Kit v3 (BIOO Scientific, Austin, Texas) accoding to instructions provided while the libraries for the Group B and C samples were built using Illumina TruSeq Small RNA Library Prep Kit.
sRNA-seq with HiSEq 4000

value: rMf


title: MUC21330 CM-OXT-101-2-O

department: Institute for Diabetes and Obesity

value: Oxytocin neurons

value: Brain

value: C57BL/6JRj -OXT-sun1-sfGFP

value: HFHS diet


title: MUC21331 CM-OXT-101-2-P

value: 6 months

value: Male


title: MUC21328 CM-OXT-101-2-M


title: Patient_P1606_Post_Treatment_scRNA-seq

data_processing:
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters.
Assembly: Human referene genome GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

extract_protocol: Single-cell library preparation for RNA-sequencing primary MM cells were processed according to 10X Genomics reagent Kits User Guide (CG00052 v2 Chemistry). Cells were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) using 10X GemCode Technology. Primers containing (i) an Illumina R1 sequence, (ii) a 16 bp 10x barcode, (iii) a 10 bp Unique Molecular Identifier (UMI) and (iv) a poly-dT primer sequence were incubated with partitioned cells resulting in barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents/primers, then cDNA was amplified by PCR. Enzymatic Fragmentation and Size Selection was used to optimize cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added during GEM incubation, whereas P5, P7, a sample index (i7), and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation and PCR.

value: Post

value: 10X Genomics Single Cell RNAseq v2 Chemistry


title: MUC21327 CM-OXT-101-2-L


title: MUC21329 CM-OXT-101-2-N


title: Patient_P1722_Pre_Treatment_scRNA-seq

value: Pre


title: sRNAseq_A_Col_35Se//AGe_rMf_Rep3

value: Young flower


title: sRNAseq_A_SALK_049844_rMf


title: Patient_P1395_Pre_Treatment_scRNA-seq


title: sRNAseq_A_Col_35Se//AGe_rMf_Rep1


title: sRNAseq_A_M317_Wt flower_Rep1

value: Wt


title: sRNAseq_A_Col_35Se//AGe_rMf_Rep2


title: sepsis1_heart

value: heart


title: MUC21326 CM-OXT-101-2-K


title: Patient_P1396_Pre_Treatment_scRNA-seq


title: MUC21324 CM-OXT-101-2-I


title: Patient_P1809_Post_Treatment_scRNA-seq


title: sRNAseq_A_Col_Ctr//AGe_rMf_Rep3

value: Floral structure change


title: MUC21325 CM-OXT-101-2-J


title: sRNAseq_A_M317_Wt flower_Rep3


title: Patient_P1751_Pre_Treatment_scRNA-seq


title: MUC21323 CM-OXT-101-2-H

value: SC diet


title: sRNAseq_A_Col_Ctr//AGe_rMf_Rep2


title: Patient_P1388_Pre_Treatment_scRNA-seq

value: Primary CD138+ MM cells


title: Patient_P1680_Pre_Treatment_scRNA-seq


title: MUC21321 CM-OXT-101-2-F


title: sRNAseq_A_Col_Ctr//AGe_rMf_Rep1


title: MUC21322 CM-OXT-101-2-G


title: sRNAseq_A_Col_Wt flower_Rep2

value: Col


title: Patient_P1752_Pre_Treatment_scRNA-seq


title: Patient_P1461_Post_Treatment_scRNA-seq


title: MUC21320 CM-OXT-101-2-E


title: MUC21319 CM-OXT-101-2-D


title: sRNAseq_A_Col_Wt flower_Rep1


title: MUC21318 CM-OXT-101-2-C


title: Patient_P1643_Pre_Treatment_scRNA-seq


title: Patient_P1345_Post_Treatment_scRNA-seq


title: Patient_P1675_Post_Treatment_scRNA-seq


title: sows liver (low bile acid group) input

city: Wuhan

first: Tongxin

last: Wang

address: Hongshan Huazhong Agricultural University

institute: Huazhong Agricultural University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: http://ftp.ensembl.org/pub/release-104/fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa11.1.dna_sm.toplevel.fa.gz
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Sus scrofa

source_name: liver

extract_protocol:
One hundred million cells  were fixed with 1% formaldehyde and sonicated for 8 min (10s on and 15s off) on ice  with a 2-mm microtip with a 40% output control and 90% duty cycle setting.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter.

value: liver

value: hepatocytes

value: female

tag: chip-antibody


title: sows liver (high bile acid group) IP

value: Anti-H4K12la (PTM1411)


title: MUC21317 CM-OXT-101-2-B

value: Oxytocin neurons

value: Brain

value: C57BL/6JRj -OXT-sun1-sfGFP


title: MUC21316 CM-OXT-101-2-A

value: 6 months

value: Male


title: Patient_P1299_Pre_Treatment_scRNA-seq

tag: time point

value: Pre

value: 10X Genomics Single Cell RNAseq v2 Chemistry


title: Patient_P1608_Pre_Treatment_scRNA-seq


title: MUC21314 CM-OXT-101-1-O

value: HFHS diet


title: ssRNAseq_B_Col_ARE//AGe_Wt flower_Rep2

data_processing:
The obtained reads were trimmed and aligned to the reference Arabidopsis genome (TAIR10) using using HISAT2 with default parameters.
Those reads mapped to the sense and antisense starnds of AGe, AGp/M2 regions within a 17.3-kb genomic region were retrieved and counted using htseq-count (version 0.13.5; Anders et al., 2015) for calculation of the value of Normalized Read Per Million mapped reads (NRPM) in each region
Supplementary files format and content: xls file includes the value of NRPM in the AGe and AGp/M2 regions  within the 17.3-kb genomic region for each sample

growth_protocol: Arabidopsis plants were grown under a 16/8h light:dark photoperiod at 20-22˚C for approximately 4-5 weeks prior to transformation.

extract_protocol:
Total RNA was extracted from young flowers pooled from five to ten lines with the same phenotype for each replicate using Tri-Reagent (Sigma, MO) followed by two rounds of phenol–chloroform extraction (50:50).
Approximately one µg of total RNA was used for construction of strand-specific RNA-seq (ssRNA-seq) library using the Illumina TruSeq® Stranded Total RNA Library Preparation Kit with Ribo-Zero™ Plant kit and different barcode Index primers. ssRNA-seq libraries for the Group A samples were made using TruSeq RNA CD barcode Index primers, while the Group B samples  using TruSeq Unique Dual Index (UDI) primers.  The total RNA was first treated with Turbo DNA-free (Fisher Scientific) to remove residual genomic DNA followed by Ribosomal RNA depletion, first- and second-strand cDNA synthesis, 3’ end adenylation, adapter ligation, and DNA fragment enrichment (12 cycles) according to the TruSeq stranded total RNA protocol provided. RNA fragmentation (3 minutes) was performed.  Libraries were pooled and sequenced using HiSeq X-Ten platform.

treatment_protocol: Arabidopisis plants were transformed with various transgene cassetts for evaluation of silencing efficiency and mutant flower frequncy.

value: Young flower

value: Wt


title: MUC21315 CM-OXT-101-1-P


title: ssRNAseq_B_Col_ARE//AGe_Wt flower_Rep3

value: Floral structure change


title: MUC21313 CM-OXT-101-1-N


title: Patient_P1722_Pre_Treatment_ATAC-seq

data_processing:
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters using cellranger-atac count.
Assembly: Pre-generated human reference GRCh38
Supplementary files format and content: Filtered peak barcode matrix in hdf5 format and a BED-like tabular file where each line represents a unique ATAC-seq fragment captured by the assay from CellRanger-atac count.

extract_protocol: For single-cell library preparation for ATAC-seq the desired number of nuclei were targeted and processed according to 10X Genomics Reagent Kits User Guide (CG000168). The Nuclei Isolation was performed ad indicated in the nuclei Isolation protocol for Single Cell ATAC Sequencing (10x Genomics). Based on the starting number of cells and desired final nuclei concentration primary MM cells were washed, lysed and re-suspended in appropriate volume of chilled Diluted Nuclei Buffer. The resulting nuclei were then immediately used to generate scATAC-seq libraries. ScATAC-seq libraries were prepared according to 10X Genomics Reagent Kits User Guide. Briefly, the desired number of nuclei were combined with ATAC Buffer and master mix to form transposed Nuclei. Single-cell GEMs were then generated, amplified and subjected to bead clean-ups. Indexed sequencing libraries were constructed using Chromium i7 Sample Index and the barcode sequencing libraries subjected to a final bead clean-up prior to quantification.

value: Primary CD138+ MM cells

value: 10X Genomics Single Cell ATACseq v1 Chemistry


title: Patient_P1606_Post_Treatment_ATAC-seq

value: Post


title: ssRNAseq_B_Col_ARE//AGe_Wt flower_Rep1


title: MUC21312 CM-OXT-101-1-M


title: sows liver (high bile acid group) input

value: liver

value: hepatocytes


title: ssRNAseq_B_hdp2-1_ARE//AGe_sMf_Rep2

value: sMf


title: MUC21311 CM-OXT-101-1-L

value: Oxytocin neurons


title: Patient_P1395_Pre_Treatment_ATAC-seq


title: Patient_P1461_Post_Treatment_ATAC-seq