title: DMS_pladB_Rep2

city: PALO ALTO

first: Rhiju

last: Das

state: CA

address: 279 Campus Dr, B419 Beckman Center

institute: Stanford University

description: d1_d2_combined_rfcount_rfnorm_processed.tar.gz

data_processing:
cutadapt was used remove adapter sequences including indexing primer sequences and the universal cloning linker.
Sequencing reads were aligned to various sequence sets of interest, including introns, complete pre-mRNA ORFs for genes containing introns, and coding mRNA sequences for genes containing introns, rRNA sequences, and structured control RNAs. Paired-end alignment was performed with Bowtie2 using the alignment parameters: --local --sensitive-local --maxins=800 --ignore-quals --no-unal --mp 3,1 --rdg 5,1 --rfg 5,1 --dpad 30. For analysis combining replicates, alignment files were merged with samtools. Alignments were sorted and indexed using samtools.
UMI-tools was used to extract UMI tags from reads prior to removing adapter sequences by matching to the expected pattern from our RT primers, and after alignment, reads with matching mapped positions and UMI tags were then deduplicated using the UMI-tools60 dedup function with default parameters for paired-end reads.
Mutational frequencies and coverage values were obtained by processing alignment files using RNAframework executables. For each library and reference sequence set, first rf-count was run with the flag -m to compute mutation counts, using all other default parameters. Coverage statistics were obtained for each sequence with rf-rctools stats, and per-position mutation counts and per-position coverage statistics were obtained with rf-rctools view.
Normalized reactivity values were obtained with rf-norm, using Rouskin scoring with 90% Winsorizing for normalization, reactive bases A and C, and dynamic resizing of the normalization window to account for A/C frequencies (flags: -sm 2 -nm 2 -ow -rb AC -dw).
Assembly: S. cerevisiae intron reference sequences were obtained from Talkish, et al. 2019 (doi: 10.1371/journal.pgen.1008249). Coding ORF annotations were obtained from the Saccharomyces Genome Database for the S288C reference genome. Pre-mRNA reference sequences were obtained using the sacCer3 UCSC genome assembly.
Supplementary files format and content: Coverage values, mutational frequencies, and reactivity values are provided for all introns. RNA count files (.rc) and index files (index.rci) from the rfcount module of RNAframework are included. Also provided are coverage values from from rf-rctools stats (files ending with stats.txt), and per-position coverage and mutational frequency statistics (files ending with view.txt). Normalized reactivity values are included from the rfnorm module of RNAframework (one file per intron in folder ending with _reactivity/).
Supplementary files format and content: For biological replicates, combined processed data files are provided which include mutational frequencies, coverage, and reactivity values when combining reads from both replicates.

organism: Saccharomyces cerevisiae

growth_protocol: Strains were grown at 30 oC on YPD plates and in YPD liquid medium. Single colonies of YOH001 were used to inoculate overnight cultures, diluted to OD600 0.1, and grown to OD600 0.5-0.6. Biological replicates were obtained from distinct single colonies.

extract_protocol:
RNA was extracted using the YeaStar RNA Kit (Zymo Research), using 7.5 μL of Zymolase for every 2.5 mL starting cell culture and shortening the Zymolase incubation to 15 minutes at 30 oC to reduce RNA fragmentation.
We first depleted the extracted RNA of rRNA using RNase H to deplete rRNA with complementary oligos. We used an RNA Clean and Concentrator-5 (Zymo) column with the size-selection protocol to exclude RNA below a size cutoff of 200 nucleotides. RNA was fragmented with Ambion fragmentation reagents, end-repaired with rSAP (NEB), and then ligated to an adenylated universal DNA cloning linker with T4 RNA ligase 2 truncated KQ (NEB). Excess DNA linker was degraded with 5’ Deadenylase (NEB) and RecJf (NEB). We reverse transcribed RNA with TGIRT enzyme (InGex), and we size-selected cDNA (200 - 400 nucleotide size range) using a denaturing PAGE gel extraction to remove excess RT primer. cDNA was circularized with CircLigase ssDNA Ligase (Lucigen), and index sequences and Illumina sequencing adapters were added via PCR to generate the final library.

treatment_protocol: We carried out splicing inhibition and DMS treatment for two biological replicates, splicing inhibition only for a no-modification control, and DMS treatment only for the control without splicing inhibition. For conditions with splicing inhibition, we treated cultures with 5 μM pladB using 50 μL of 1 mM pladB for every 10 mL of culture, and we incubated cultures at 30 oC for 1 hour with shaking. We treated cultures with 3% DMS or an equivalent volume of H2O for the no-modification control. Treated cells were incubated at 30 °C for 5 minutes, and the reaction was quenched with 20 mL stop solution (30% 2-mercaptoethanol, 50% isoamyl alcohol) for every 10 mL of culture.

value: +pladB, +DMS


title: Control6_snATACseq

status: Public on Jul 28 2022

type: SRA

city: SAINT LOUIS

first: Parker

middle: C

last: Wilson

state: MO

address: 660. S Euclid Ave., CB 8118

country: USA

institute: Washington University in St. Louis

library_source: transcriptomic

data_processing:
Fastq files was processed with cellranger-atac v2.0 count using refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Filtered barcode-peak matrix and fragment file
snRNA-seq: cellranger count v4.0
snATAC-seq: cellranger-atac count v2.0
Genome_build: snRNA-seq: GRCh38-2020-A.premrna
Genome_build: snATAC-seq: refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Supplementary_files_format_and_content: A total of 11 snRNA-seq libraries from this repository (1 control, 2 DKD), GSE13188213 (3 control, 3 DKD), and GSE151302 (2 control; samples 4 and 5) were counted with cellranger count v4.0 and a custom pre-mrna reference on GRCh38. A total of 13 snATAC-seq libraries from this repository (1 control, 7 dkd) and GSE151302 (5 control) were counted with cellranger-atac count v2.0 and refdata-cellranger-arc-GRCh38-2020-A-2.0.0.

molecule: total RNA

organism: Homo sapiens

source_name: Human Kidney Cortex - Control6

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in Nuclei Buffer (10× Genomics, PN-2000153), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
10xGenomics snATAC-seq library(v1 chemistry)
snATAC-seq
Nuclear isolation from bulk kidney cortex https://www.protocols.io/view/nuclei-isolation-from-human-kidney-for-single-nucl-nahdab6
10X genomics single cell gene expression OR single cell ATAC
snRNA-seq and snATAC-seq

tag: Sex

value: F

tag: age

tag: race

tag: egfr

tag: global glomerulosclerosis

tag: ifta


type: RNA

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

description: Gene expression data from MB231 cells expressing Non-silencing shRNA vector

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Breast adenocarcinoma

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

growth_protocol: MCF7 were cultured in 5% CO2 incubator at 37℃ and MB231 were cultured in 0% CO2 incubator at 37℃

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

tag: treatment


title: Primary-RPTEC_bulkATAC_1

city: St. Louis

first: Yoshiharu

last: Muto

department: Medicine / Nephrology

library_source: genomic

data_processing:
Fastq files were trimmed with Trim Galore and aligned with Bowtie2 with --very-sensitive -X 2000 using hg38. PCR duplicates were removed with Picard's MarkDuplicates function.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format

molecule: genomic DNA

source_name: Primary RPTEC (Lonza, P3)

extract_protocol:
Adherent cells were scraped from culture dishes and centrifuged at 500 × g for 5 min.
50,000 cells were suspended in 50 μL of ice-cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin), followed by incubation on ice for 4 min. Subsequently, 450 μL of ice-cold wash buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20) was added and centrifuged at 600 × g for 6 min. Pellets were resuspended in 25 μL of ATAC-seq transposition mix [12.5 μL 2× Illumina Tagment DNA (TD) buffer; 10.5 μL nuclease-free water; 2.0 μL Tn5 transposase (Illumina/Nextera, FC-121-1030)] and incubated at 37°C for 1 h on a thermomixer. The transposed DNA was purified with QIAGEN MinElute kit and amplified with dual indexes.

tag: cell type

value: primary RPTEC


title: Primary-RPTEC_bulkATAC_2

source_name: Primary RPTEC (Lonza, P4)


title: hTERT-RPTEC_bulkATAC_2

source_name: hTERT-RPTEC (ATCC, P10)

value: hTERT-RPTEC


title: hTERT-RPTEC_cut-and-run_IgG_2

data_processing:
Library strategy: CUT&RUN
Fastq files were trimmed with Trim Galore and aligned with Bowtie2 (parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700) using hg38. Peak calling was performed on each sample separately using MACS2 with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig format

extract_protocol:
Adherent cells were scraped from culture dishes and centrifuged at 500 × g for 5 min.
CUT&RUN assay libraries for cultured cells or human kidneys were generated with the CUTANA kit (EpiCypher, 14-1048). 500,000  cells were then mixed and incubated with Concanavalin A (ConA) conjugated paramagnetic beads. Antibodies were added to each sample (0.5μg of rabbit glucocorticoid receptor antibody [abcam, ab225886 ,1:20] or rabbit IgG negative control antibody [Epicypher, 13-0041k, 1:50]). The remaining steps were performed according to manufacturer’s instructions. Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645S) with manufacturer’s instructions, including minor modifications indicated by CUTANA described above.


title: hTERT-RPTEC_cut-and-run_GR_2


title: Osteoblast-Vehicle-2

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

hyb_protocol: Fragmented and Labeled ss-DNA (3.5 ug) was hybridized to Affymetrix Mouse Gene 2.0 ST GeneChips overnight at 45oC. Hybridized GeneChips were washed and stained in an Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using an Affymetrix 7G Scanner

data_processing: CEL files were imported into Affymetrix Expression Console software and data were anayzed by RMA (Gene Level Default RMA sketch) to obtain probe set expression values

organism: Mus musculus

source_name: osteoblast, vehicle 4 hr

label_protocol: Total RNA (100 ng) converted to fragmented and biotin-labeled ssDNA by WT Plus kit (Affymetrix)

growth_protocol: Dissected strips of calvaria from 7-10 day old C57BL/6J mice were incubated at 37oC with shaking for 20 min in a solution of 0.1% collagenase II (Worthington) and 0.05% trypsin (Invitrogen) in αMEM (Invitrogen). Supernatants were neutralized with 25% heat-inactivated fetal bovine serum (FBS, Invitrogen), and the digestion of calvarial strips was repeated twice. Supernatants from the three digestions were combined and centrifuged, and pellets were reconstituted in growth medium consisting of αMEM containing 10% heat-inactivated FBS and 0.1% Primocin (Invivogen). After 24 hours in culture, Primocin was reduced to 0.05%. Cells were sub-cultured at 90% confluency and at passage 2 differentiated post-confluence (Day 3). Cells were differentiated starting on Day 3 in αMEM containing 10% heat-inactivated FBS and 0.05% Primocin supplemented with 5 mM β-glycerophosphate (Millipore Sigma) and 50mg/L ascorbic acid (Millipore Sigma). On Day 10 cells were serum deprived in medium containing 0.5% BSA (Millipore Sigma) for 24 hrs before experimental treatment.

extract_protocol: RNA was prepared with the RNeasy Plus Mini Kit (Qiagen).  RNA quality was assessed by Bioanalyzer 2100 (Agilent).

treatment_protocol: Cells were treated with vehicle or hormone for 4 hours in serum-free medium containing 0.5% BSA. Following treatment, cells were washed with PBS prior to RNA isolation

tag: strain

value: Osteoblast

value: Vehicle


title: Osteoblast-hPTH-2

source_name: osteoblast, human parathyroid hormone (1-34) 4hr

value: human parathyroid hormone


title: Treated mimic experiment 2 [R2127]

city: Clemson

first: Susan

last: Duckett

state: South Carolina

address: 105 Collings ST, RM 112 BRC

department: Animal and Veterinary Science

institute: Clemson University

data_processing:
fastqc/0.11.8
trimgalore/0.6.5
rsem/1.3.3
subread's feature Counts/2.0.2
edgeR/3.34.1
Assembly: Ovis aries (TEXEL) ensembl release 96
Supplementary files format and content: tab-delimited text of raw gene counts

organism: Ovis aries

source_name: Ovine primary cells

growth_protocol: Satellite cells were cultured in high glucose (4.5g/L) DMEM with 20% fetal bovine serum (FBS), 1% penecilline/ streptomycin, and 0.1% gentamicin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using Trizol, and then shipped on dry ice to Novogene for sequencing.
mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads. Purified mRNA was fragmented, and first strand cDNA was synthesized with random hexamer primers and followed by second strand cDNA synthesis. Libraries then had end repair, A-tailing, adapter ligation, size selection, amplification, and purification and were then ready for quality control. Libraries were checked for quality, quantity, and size distribution with Qubit and RT-PCR. Libraries were then pooled and sequenced on an Illumina NovaSeq 6000 platform.

treatment_protocol:
miRNA treatments (mimiic miR-127 or AntagomiR-22-3p) were andministered using RNAiMAX lipofectamine when cells reached 60% confluence at 100nM or 500nM concentration, respectively, according to manufacturer specifictions.
Cells were transfected on d 0 and RNA was harvested 4 d following transfection.

tag: cell line

value: Ovine primary cells

value: skeletal muscle satellite cells

tag: genotype

value: SuffolkxTexel

value: mimic miR-127 at 100 nM

tag: time

value: 4 d after transfection


description: Gene expression data from MB231 cells expressing CCL2 shRNA vector


title: MCF7 cells expressing control vector

description: Gene expression data from MCF7 cells expressing control vector

value: MCF7 cells expressing control vector


title: Osteoblast-Vehicle-1


title: hTERT-RPTEC_cut-and-run_IgG_1

source_name: hTERT-RPTEC (ATCC, P8)


title: Control mimic experiment 2 [CMIMR2]

value: Control


title: Treated AntagomiR experiment 1 [R1223P]

value: AntagomiR-22-3p at 500 nM


title: Cells_IHSF115 and Actynomicin D_1h_ replicate 2

city: Madrid

first: Nuria

last: Vilaboa

state: Madrid

address: Edificio IdiPAZ segunda planta, Hospital Universitario La Paz, Paseo de la Castellana 261

country: Spain

institute: Fundación para la Investigación Hospital La Paz, G83727057

hyb_protocol: Biotinylated cRNA was hybridized with GeneChip Human Gene 2.0 ST Array (Applied Biosystems), following the manufacturer´s instructions.

scan_protocol: Arrays were scanned with a GeneChip scanner 3000 7G (Applied Biosystems).

data_processing: Raw data were normalized and gene levels analyzed using the RMA algorithm (Transcriptome Analysis Console Software; Applied Biosystems).

source_name: Cells treated for 10min with 25mM IHSF115 and then exposed for 1h to 10mg/ml actinomycin D.

label_protocol: Total RNA was processed using the GeneChip WT PLUS Reagent kit (Applied Biosystems, Waltham, MA).

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (Lonza, Basel, Switzerland) supplemented with 10%(v/v) fetal bovine serum, 10U/ml penicillin and 0.01mg/ml streptomycin.

extract_protocol: Total RNA prepared using the RNeasy Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: Samples C-1,2,3 and IHSF115-1,2,3 were prepared from cells treated for 6h with 0.25% DMSO or 25mM IHSF, respectively. Medium was replaced with fresh medium containing 0.25% DMSO or 25mM IHSF115 at 2h and 4h. Samples ActD-1,2 and IHSF115 + ActD-1,2 were prepared from cells treated for 10min with 0,25% DMSO or 25mM IHSF115 and then exposed for 1h to 10mg/ml actinomycin D.

value: HeLa cells (ATCC CCL-2)


title: MCF7 cells expressing CCL2

description: Gene expression data from MCF7 cells expressing CCL2

value: MCF7 cells expressing CCL2


title: Control AntagomiR experiment 2 [CANTR2]


title: VH1-2, mVHdel, VK1-33-CS, SP, IgK3

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

data_processing:
Library strategy: HTGTS-rep-seq
HTGTS-Rep-Seq data analysis was done by the HTGTS-Rep-Seq bioinformatics pipeline (Github address: https://github.com/Yyx2626/HTGTSrep), using IgBLAST with default parameters for qualified reads mapping. Only reads with more than 98% of the sequences having a sequencing Quality Score ≥20 were kept; only joined reads (R1 and R2 had an overlap region ≥10 bp and mismatch rate ≤8%) were kept.
Genome_build: mm9
Supplementary_files_format_and_content: .db.txt files were generated using HTGTS-Rep-Seq pipeline (IgBLAST)

source_name: splenic B220+ B cells

extract_protocol:
Splenic B cells were purified from 5-8 weeks old mice by MACS® Microbeads according to the manufacturer’s protocol. In brief, spleens were dissected out from unimmunized mice, prepared into single cell suspensions and stained with anti-B220 Microbeads for 20 minutes at 4°C. Then, the splenic B cells were collected using the LS column and MACSTM Separater and lysed for genomic DNA extraction.
10ug of genomic DNA from purified splenic B cells was used for generating HTGTS-rep-seq libraries as previously described (Lin et al. 2016). 4 bait primers that target mouse JH1, JH2, JH3 and JH4 were mixed to capture all IgH heavy chain repertoire in one library. And 4 bait primers that target mouse Jk1, Jk2, Jk4 and Jk5 were mixed to capture all Igk light chain repertoire in one library.

value: C57BL/6 and 129/Sv mix

tag: tissue

value: spleen

value: B220+ B cells

tag: locus (ig heavy-chain or light-chain)

value: IgK

tag: conditions

value: naïve

tag: primers

tag: sequencing method

value: HTGTS-Rep-Seq


title: Control mimic experiment 1 [CMIMR1]


title: Cells_IHSF115_6h_ replicate 3

source_name: Cells treated for 6h with 25mM IHSF115. Medium was replaced with fresh medium containing 25mM IHSF115 at 2h and 4h.


title: Treated mimic experiment 1 [R1127]


title: kidney_cut-and-run_IgG_2

source_name: Human Kidney Cortex 2

extract_protocol:
Nuclei were isolated with Nuclei EZ Lysis buffer (NUC-101; Sigma-Aldrich) supplemented with protease inhibitor (5892791001; Roche). Samples were cut into < 2 mm pieces, homogenized using a Dounce homogenizer (885302–0002; Kimble Chase) in 2 ml of ice-cold Nuclei EZ Lysis buffer, and incubated on ice for 5 minutes with an additional 2 ml of lysis buffer. The homogenate was filtered through a 40-μm cell strainer (43–50040–51; pluriSelect) and centrifuged at 500g for 5 minutes at 4°C. The pellet was resuspended, washed with 4 ml of buffer, and incubated on ice for 5 minutes. Following centrifugation, the pellet was resuspended in nuclei suspension buffer (1x PBS, 1% BSA), filtered through a 5-μm cell strainer (43–50020–50; pluriSelect)
CUT&RUN assay libraries for cultured cells or human kidneys were generated with the CUTANA kit (EpiCypher, 14-1048). 500,000  cells were then mixed and incubated with Concanavalin A (ConA) conjugated paramagnetic beads. Antibodies were added to each sample (0.5μg of rabbit glucocorticoid receptor antibody [abcam, ab225886 ,1:20] or rabbit IgG negative control antibody [Epicypher, 13-0041k, 1:50]). The remaining steps were performed according to manufacturer’s instructions. Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645S) with manufacturer’s instructions, including minor modifications indicated by CUTANA described above.

value: Human Kidney Cortex

tag: Sex

value: M

value: Non-hispanic White


title: hTERT-RPTEC_cut-and-run_GR_1

value: hTERT-RPTEC


title: Cells_IHSF115 and Actynomicin D_ 1h_replicate 1


title: kidney_cut-and-run_IgG_3

source_name: Human Kidney Cortex 3

tag: age

value: Hispanic


title: VH1-2, mVHdel, VK1-33-CS, SP, IgK2


title: Control AntagomiR experiment 1 [CANTR1]

value: Ovine primary cells

value: skeletal muscle satellite cells

value: SuffolkxTexel

value: 4 d after transfection


title: Cells_Actynomicin D_1h_ replicate 1

source_name: Cells treated for 10min with 0,25% DMSO and then exposed for 1h to 10mg/ml actinomycin D.

value: HeLa cells (ATCC CCL-2)


title: kidney_cut-and-run_IgG_1

source_name: Human Kidney Cortex 1

value: F

tag: race


title: kidney_cut-and-run_GR_1

tag: egfr


title: Cells_IHSF115_6h_ replicate 2


title: kidney_cut-and-run_GR_3

tag: global glomerulosclerosis


title: kidney_cut-and-run_GR_2

tag: ifta


title: hESCs shDAP5_total_rep4

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

data_processing:
Library strategy: Ribo-seq
CLIP-seq analysis: The obtained reads, Single-Read 60 bp long, were trimmed using cutadapt and mapped to the human genome (hg38) using STAR v2.4.2a (default parameters).
Counting proceeded over genes annotated in RefSeq, using htseq-count (intersection-strict mode)
Differential bound analysis was performed using DESeq2 with the betaPrior, cooksCutoff and independentFiltering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Pipeline was constructed using Snakemake.
Ribo-seq analysis: Reads were first trimmed from their linker and poly(A) using cutadapt, and filtered from rRNA reads by bowtie (v 1.2.3) alignment to rRNA library.
Reads that passed this filtration were aligned to human genome version hg38 using STAR version 2.7.3a.
Per gene, for translation calculation, reads were counted in the coding region excluding 15 and 6 nt from the beginning and end of each coding sequence (CDS), respectively. Reads were counted against GeneCode canonical transcripts, v32.
The read count normalization was with DEseq2. Translation efficiency was measured as log2(total).
Genome_build: hg38
Supplementary_files_format_and_content: M.David_CLIP-seq_2022.txt
Supplementary_files_format_and_content: M.David_Riboseq_2022.txt

source_name: Embryonic stem cells

growth_protocol: hESC H9 (Wa-09) cells were maintained on a feeder layer of iMEFs (irradiated mouse embryonic fibroblasts) in hESC medium (DMEM F-12, 20% knockout serum [ThermoFisher], 1% NEAA, 0.5% glutamine, 0.1 mM β-mercaptoethanol, 8 ng/mL bFGF). The cells were grown for one passage before experiments on Matrigel-coated plates containing mTeSR medium [STEMCELL technologies]. The medium was changed daily.

extract_protocol:
Lysated were treated with DNase and DAP5-bound mRNAs were pulled down with specific antibody
Libraries were prepared according to Illumina's instructions accompanying the SMARTer Ultra Low Input RNA kit (Clontech). Libraries were evaluated by Qubit and Bioanalyzer. Sequencing libraries were constructed with barcodes to allow multiplexing of all samples on one lane. The sequencing was run on an Illumina HiSeq 2000 instrument.
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted, and poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered.
RNA-seq: mRNA sample was subjected to DNAseI treatment and 3’ dephpsphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp. Ribo-seq:

treatment_protocol:
UV cross-linking at 0.15 mJ/cm2 (254 nm)
Cells were subsequently treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX.

value: hESC H9 (Wa-09)

tag: phenotype

tag: treatment

value: RNA


title: Cells_IHSF115_6h_ replicate 1


title: VH1-2, mVHdel, VK1-33-CS, SP, IgK1

tag: strain

value: C57BL/6 and 129/Sv mix

value: spleen

tag: cell type

value: B220+ B cells


title: Set1Δ +Fluconazole 2

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
FastQC v. 0.11.2  was used to observe read quality
Trimmomatic v. 0.32  was used to trim data
STAR  (v2.6.1d)  to align reads to the reference genome
HTSeq v.0.6.1  was used to count reads mapping to genes
DESeq2 Bioconductor package (v1.26.0) to identify differentially expressed genes
DAVID (the Database for Annotation, Visualization, and Integrated Discovery) was used in the annotation of genes and in performing the GO (gene ontology) enrichment analyses
Assembly: Candida glabrata CBS138 genome
Supplementary files format and content: count matrix

organism: Nakaseomyces glabratus

source_name: Candida glabrata cultures

growth_protocol: The CBS 138 Cg2001 WT and set1Δ strains were inoculated in SC media and grown to saturation overnight. Cells were diluted to an OD600 of 0.1 and recovered to log phase for 3 hours shaking at 30°. Prior to treatment, cells were collected for the untreated sample and zero time point.

extract_protocol:
Total RNA of three biological replicates for each condition and sample were isolated by standard acid phenol purification, treated with DNase (Ambion), and total RNA was purified using standard acid phenol purification.
The complementary DNA library was prepared by the Purdue Genomics Facility using the TruSeq Stranded Kit with poly(A) selection (Illumina) according to the manufacturer’s instructions.
2x150 on a NovaSeq 6000 PE150

treatment_protocol: Cultures were treated at an OD600 of 0.2 with 64 µg/ml fluconazole (Sigma-Aldrich, St. Louis, MO) dissolved in DMSO as previously described (69). Cells were collected after 3 hours.

value: Candida glabrata cultures

tag: genotype

value: Fluconazole


title: Set1Δ untreated 3

value: untreated


title: hESCs shDAP5_total_rep2


title: BM-CTMC

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description: CTMC

data_processing:
The sequenced reads were aligned to mouse genome using Tophat (version 2.0.8) with options: -g 20.
The genes epxression levels (FPKM) were calculated using Cuffdiff (version 2.1.1) with options: -u -b.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: connective tissue-type mast cells

growth_protocol: Bone marrow cells were cultured in RPMI 1640 medium containing FBS, NEAA, IL-3. The culture medium was replaced with fresh medium every 5 days. After 4 weeks of culture, we confirmed the cellular surface expression of both FceRI and c-kit on BMMCs. Then, BMMCs were cultured with IL-3, IL-9, and TGF-b1 to obtain BM-MMCs, or with IL-3, stem cell factor (SCF), and IL-4 to obtain BM-CTMCs. The culture medium was replaced with fresh medium every 5 days. After 4 weeks, cells were collected and used for further analysis.

extract_protocol:
Total RNA was isolated from mast cells by using NucleoSpin RNAXS. The cDNA was synthesized using SuperScript VILO cDNA synthesis kit.
The libraries were prepared according to the manufacture's protocol (NEBNext Ultra Directional RNA Library Prep Kit for Illumina).

value: BMMC-derived CTMCs


title: Set1Δ +Fluconazole 3


title: Set1Δ untreated 2


title: BM-MMC

description: MMC

source_name: mucosal-type mast cells

value: BMMC-derived MMCs


title: BMMC

description: BMMC

source_name: bone marrow derived mast cells

value: BMMCs


title: Cells_DMSO_6h_ replicate 3

source_name: Cells treated for 6h with 0.25% DMSO. Medium was replaced with fresh medium containing 0.25% DMSO at 2h and 4h.

tag: cell line


title: Set1Δ +Fluconazole 1


title: hESCs shDAP5_total_rep1


title: Cells_DMSO_6h_ replicate 2


title: Cells_Actynomicin D_1h_ replicate 2


title: hESCs shNT_total_rep4

value: shNT


title: Set1Δ untreated 1


title: Cells_DMSO_6h_ replicate 1


title: Nucleus pulposus, NP13, miRNA

city: Debrecen

first: Beáta

last: Scholtz

address: Nagyerdei krt. 98

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen, Faculty of Medicine

description: small RNA-seq

data_processing:
CASAVA 1.8.2 software to produce fastq.gz files
All preprocessing steps were done on the Galaxy platform. The sequencing quality of the raw data was first checked with FASTQC.
Adapter clipping: Galaxy Tool ID toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6; MIN_SIZE:16; MAX_SIZE:25; custom adapter sequence: TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGC
Trimmomatic: Galaxy Tool ID toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.1; Perform initial ILLUMINACLIP step? - No; SLIDINGWINDOW:4:20; MINLEN:16
The sequencing quality of the preprocessed data was checked again with FASTQC.
Preprocessed data were aligned to human miRNA hairpin sequences from miRBase using Chimira (default settings), and the resulting plain counts table was used in the subsequent analyses.
Assembly: hg19
Supplementary files format and content: tab-delimited text files for each sample, containing plain counts

source_name: Nucleus pulposus

growth_protocol: We established primary NP cell cultures from the NP tissue samples, applying the explantation method without any enzymatic digestions. NP cell cultures were maintained in Dulbecco’s Modified Eagle’s Medium/Ham’s Nutrient Mixture F12 (Sigma-Aldrich) containing 20% fetal bovine serum (Sig-ma-Aldrich), and penicillin-streptomycin (100 U and 100 mg/mL, respectively). Cells were cultured in 25 cm2 tissue culture flasks at 37ºC under a humidified atmosphere containing 5% (v/v) CO2.

extract_protocol:
Snap-frozen chordoma tissue samples were pulverized while frozen, the tissue powder was lysed immediately with TRIzolate Reagent (Sigma-Aldrich) (50 mg sample per 500 uL reagent), and the samples were homogenized with a rotor-stator homogenizer. An equal volume of chloroform was added to the homogenizates and vortexed, and the aqueous phase was separated using Phase Lock Gel™ (QuantaBio) (PLG 15 ml Heavy) tubes. RNA was isolated from the aqueous phase with the Direct-Zol RNA Miniprep kit (Zymo Research), according to the manufacturer's instructions, without DNase I treatment. RNA was prepared from the NP cell cultures with TRIzolate Reagent and Direct-Zol RNA Miniprep kit, according to the manufacturer's instructions. RNA quality was checked with Nanodrop 1000 spectrophotometer and Agilent 2100 Bioanalyzer.
Sequencing libraries were prepared with the Illumina TruSeq Small RNA SamplePrep kit.
miRNA-seq, 1x 50 bp

treatment_protocol: The chordoma samples were frozen in liquid nitrogen immediately after removal and stored at -80 ºC until processing.

tag: tissue

value: Nucleus pulposus

value: primary NP cell culture

value: Caucasian

tag: individual

value: patient diagnosed with degenerative disc disease (Pfirrmann grade III)


title: Nucleus pulposus, NP11, miRNA

description: small RNA-seq


title: Wild-type +Fluconazole 3

value: Wild-type


title: Nucleus pulposus, NP9, miRNA

description: small RNA-seq


title: Nucleus pulposus, NP6, miRNA

description: small RNA-seq


title: DMS_pladB_Rep1

value: +pladB, +DMS


title: Wild-type +Fluconazole 2


title: DMS_no_pladB

value: -pladB, +DMS


title: hESCs shNT_total_rep3

value: hESC H9 (Wa-09)

value: RNA


title: hESCs shNT_total_rep2


title: glh-4 glh-1 degron rep2

city: Worcester

first: Siyuan

last: Dai

address: 368 Plantation St.

department: RTI

institute: UMass Chan Medical School

data_processing:
cutadapt, trim 3' linkers
Bowtie2, mapping to C. elegans genome and transcriptome
Python, extract information from SAM files to csv files
WBcel235
Assembly: WS262
Supplementary files format and content: csv

organism: Caenorhabditis elegans

source_name: C. elegans yound adults

growth_protocol: C. elegans were grown on NGM plates with OP50 E. coli

extract_protocol:
Total RNAs were Trizol and isopropanol precipitation, small RNAs were enriched using mirVana miRNA isolation kit.
Purified small-RNAs were pre-treated with PIR-1 and ligated with 3' and 5' linkers. cDNA were generated by reverse transcribed and further amplified by PCR. A size selection procedure on native PAGE were carried out.

treatment_protocol: Animals were treated with auxin and taken away from it

tag: strains

value: degron::glh-4 glh-1

value: cultured with 500mM IAA


title: hESCs shDAP5_total_rep3


title: Nucleus pulposus, NP7, miRNA

description: small RNA-seq


title: Nucleus pulposus, NP5, miRNA

description: small RNA-seq


title: Wild-type untreated 3

value: Candida glabrata cultures


title: Nucleus pulposus, NP10, miRNA

description: small RNA-seq


title: Nomod

value: +pladB, -DMS


title: hESCs shNT_total_rep1


title: Chordoma tumor, CH13, miRNA

description: small RNA-seq

source_name: Chordoma tumor

value: Chordoma tumor


title: Wild-type +Fluconazole 1

value: Fluconazole


title: glh-4 degron rep2


title: hESCs shDAP5_RP_rep4


title: glh-4 glh-1 degron rep1


title: hESCs shDAP5_RP_rep3


title: hESCs shDAP5_RP_rep2


title: Chordoma tumor, CH11, miRNA

description: small RNA-seq


title: Chordoma tumor, CH12, miRNA

description: small RNA-seq


title: Wild-type untreated 1

value: untreated


title: Wild-type untreated 2


title: glh-4 degron rep1


title: Chordoma tumor, CH8, miRNA

description: small RNA-seq


title: glh-3 glh-1 degron rep2

value: degron::glh-3 glh-1


title: Chordoma tumor, CH10, miRNA

description: small RNA-seq


title: Chordoma tumor, CH7, miRNA

description: small RNA-seq


title: hESCs shDAP5_RP_rep1


title: hESCs shNT_RP_rep4

value: shNT


title: hESCs shNT_RP_rep3


title: glh-3 glh-1 degron rep1


title: Ovary, estrus

city: Lanzhou

first: Jie

last: Pei

state: Gansu

address: No. 335 Jiangouyan ST, Qilihe District

country: China

institute: Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq data was converted using the Cell Ranger analysis pipeline provided by 10X Genomics (v2.2.0) and reads were aligned to the yak genome version BosGru3.0 using the STAR aligner.
Assembly: BosGru3.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos grunniens

source_name: Ovary

extract_protocol:
The pieces of ovarian tissue were washed in cooled RPMI 1640 medium containing 0.04% bovine serum albumin twice. The ovarian samples were further minced into approximate 0.5 mm3 pieces with a sterile scalpel blade in RPMI 1640 medium containing 0.04% BSA. The pieces were incubated with 1 mg/ml collagenase Type II in 0.25% trypsin-EDTA on ice overnight. The digestion was stopped by adding 10% of fetal calf serum. Next, the dissociated cells were collected by centrifugation at 160 × g for 3 min and incubated with advanced DMEM/F12 Glutamax containing 1% insulin-transferrin-selenium , 1% penicillin-streptomycin, and 27 IU/ml RNase-free DNase I at 37 °C for 1 h. The ovarian cells were resuspended in DPBS containing 2% FBS and passed through a 40 μm cell strainer.
The cell suspensions containing high viability cells were prepared immediately. Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Chromium, PN-1000128) was used for gel beads in emulsion (GEM) formation. The cell suspensions, gel beads, and partitioning oil were loaded into a Chromium Single Cell Controller to produce single-cell GEM. Then, a primer containing Illumina TruSeq Read 1, 10X Barcode, and unique molecular identifier (UMI) was applied to produce barcoded full-length cDNA by reverse transcriptase reaction. The GEMs were broken and the pooled fractions were recovered. The first-strand cDNAs were purified with silane magnetic beads and amplified to generate sufficient mass for library construction. Enzymatic fragmention and size selection were used to optimize cDNA amplicon size. P5, P7, a sample index, and a TruSeq Read 2 were added to the amplicon via end repair, A-tailing, adaptor ligation, and PCR.

value: Ovary

value: 4 years


title: BOV15

city: Honolulu

first: MAHFUZ

middle: RAHMAN

last: ADNAN

state: HI

address: 1955 East-West Road

department: Human Nutrition, Food and Animal Sciences

institute: University of Hawaii at Manoa

data_processing:
hisat2-build was used too index genome (Bos_taurus.ARS-UCD1.2.dna.toplevel.fa)
hisat2 was used to align against the genome
samtools was used to sort SAM files
htseq_counts to produce raw counts instead of FPKM/TPM values
DESeq2 for differential gene expression analysis
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: xlsx, .fq.gz; contains raw read counts and DESeq2 results

organism: Bos taurus

source_name: Infectious

extract_protocol:
Total RNA was isolated from frozen tissues (60-100 mg) using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. The total RNA concentration was determined using NanoDrop One (Thermo Fisher Scientific, Madison, WI). RNA quality was determined with the Agilent 2100 Bioanalyzer (Agilent Technologies, Massy, France).
RNA libraries were prepared for sequencing using standard lllumina protocols

value: Intercaruncular Endometrium


title: glh-3 degron rep2


title: BOV14


title: female, normal, large intestine, 12-week-old C57BL/6 mice

city: Shinjuku

first: Mayumi

last: Oda

address: 35 Shinanomachi.

department: School of Medicine

institute: Keio University

description: 10x Genomics

data_processing:
Sequence data was mapped to the human genome (mm10) using CellRanger (version 3.1.0).
We quantified a proportion of reads mapped to the mitochondrial genome for each cell. Then, we excluded all cells with mitochondrial reads less than 1% or more than 10% from organoid data, and excluded all cells with mitochondrial reads less than 2.5% or more than 15% from tissue data.
Assembly: mm10
Supplementary files format and content: Tab-separated values file and matrix file (filtered_feature_bc_matrix)

organism: Mus

source_name: large intestine

extract_protocol:
Single cells were partitioned into Gel Beads in emulsion using the GemCode instrument.
Libraries were constructed using Single Cell 3' Library & Gel Bead Kit v2 and the A Chip Kit (10x genomics) according to the manufacturer's instructions. Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).

value: large intestine

value: epithelium

value: female


title: glh-3 degron rep1


title: hESCs shNT_RP_rep2

value: hESC H9 (Wa-09)


title: Chordoma tumor, CH6, miRNA

description: small RNA-seq

value: Caucasian


title: H9_CS_rep3

description:
M.David_CLIP-seq_2022.txt
81C-CS

data_processing:
CLIP-seq analysis: The obtained reads, Single-Read 60 bp long, were trimmed using cutadapt and mapped to the human genome (hg38) using STAR v2.4.2a (default parameters).
Counting proceeded over genes annotated in RefSeq, using htseq-count (intersection-strict mode)
Differential bound analysis was performed using DESeq2 with the betaPrior, cooksCutoff and independentFiltering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Pipeline was constructed using Snakemake.
Ribo-seq analysis: Reads were first trimmed from their linker and poly(A) using cutadapt, and filtered from rRNA reads by bowtie (v 1.2.3) alignment to rRNA library.
Reads that passed this filtration were aligned to human genome version hg38 using STAR version 2.7.3a.
Per gene, for translation calculation, reads were counted in the coding region excluding 15 and 6 nt from the beginning and end of each coding sequence (CDS), respectively. Reads were counted against GeneCode canonical transcripts, v32.
The read count normalization was with DEseq2. Translation efficiency was measured as log2(total).
Genome_build: hg38
Supplementary_files_format_and_content: M.David_CLIP-seq_2022.txt
Supplementary_files_format_and_content: M.David_Riboseq_2022.txt

tag: clip antibody

value: Anti-EIF4G2 (Cell Signaling, C-5169S)

value: UV crosslinking


title: BOV13


title: glh-2 glh-1 degron rep2

value: degron::glh-2 glh-1

value: cultured with 500mM IAA


title: BOV12


title: H9_MBL_rep3

description:
M.David_CLIP-seq_2022.txt
81C-MBL

value: Anti-EIF4G2 (MBL, RN003P)


title: BOV11


title: glh-2 degron rep2


title: H216R-dN

city: Madison

first: Sushmita

last: Roy

state: WI

address: 330 N. Orchard St.

department: Dept. of Biostatistics and Medical Informatics

institute: University of Wisconsin-Madison

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. The media was replenished daily on Days 7-10 with NMP media containing 30 ng/mL GDF11 (Peprotech) and 1 μM dorsomorphin (Tocris) to stimulate caudal NMP development. Cells were sub-culture on Day 9 at a 1:1 ratio, and pCNSPs were differentiated after 216hrs. + pCNSP DIFFERENTIATION + DORSAL DIFFERENTIATION (1 μM RA) + NEURONAL DIFFERENTIATION

data_processing:
Cell Ranger v3.1.0 and bcl2fastq v2.20.0.422 were used to perform demultiplexing, alignment, filtering, barcode counting, UMI counting, and gene expression estimation for each sample according to the 10x Genomics documentation. The gene expression estimates from each sample were then aggregated using Cellranger (cellranger aggr).
Genes that appeared in fewer than 5 cells and cells with fewer than 5000 UMIs from the dataset were filtered out from each sample.
Each cell’s expression value was depth normalized to a depth of 5000 followed by variance stabilizing normalization as implemented AdjustVariance in the pagoda2 package with default parameters except gam.k=10
Genome_build: GRCh38
Supplementary_files_format_and_content: MatrixMarket format matrix files include normalized (depth, variance stabilization) values, tar packed and gzipped for each sample
Supplementary_files_format_and_content: text files include barcode IDs, tar packed and gzipped for each sample
Supplementary_files_format_and_content: tab-delimited text files include HUGO symbol IDs of genes, tar packed and gzipped for each sample

molecule: polyA RNA

source_name: hESC-derived neurons (WA09)

growth_protocol: hESCs were maintained at 37°C in 5% CO2 in Essential 8 (E8) medium on 35 mm Matrigel (WiCell) coated tissue culture-treated plates and were passaged when 70-80% confluent. Briefly, cells were washed once with phosphate buffered saline (PBS, Invitrogen), then incubated at 37°C in Versene (Invitrogen) for 5 minutes. Versene was aspirated, the cells were gently dissociated from the well with fresh E8, and re-plated at a  1:12 seeding ratio. Media was replenished daily (Lippmann et. al. 2014).

extract_protocol:
Cells were singularized for scRNAseq by dissociation with Papain (Worthington). Briefly, cells were washed once with PBS and incubated in papain at 37°C for 1hr on an orbital shaker, then triturated vigorously with a wide-bore pipette. The cell suspension was centrifuged at 300g for 5 minutes, then quenched with ovomucoid solution for 10 minutes at room temperature. Quenched cells were centrifuged, gently resuspended in PBS containing 0.2% BSA and 10 μM Y27632, then passed through a 40 mm cell strainer (Mitenyi Biotec) to remove debris. Cells were kept on ice before being quantified and diluted for sequencing.
RNA libraries were prepared for sequencing according to the manufacturer’s recommendations using the Single Cell 30 Reagent v2/v3  kits (10X Genomics).

treatment_protocol:
HOX PROPAGATION: To initiate neuromesodermal progenitor (NMP) differentiation, hESCs were washed once with PBS, incubated at 37°C in Accutase (Invitrogen) for 5 mins, singularized by gentle trituration, and quenched with 1 volume E8 media. Following centrifugation for 5 mins at 300g, hESCs were replated onto 35 mm Matrigel-coated plates at a density of 1.5 x 105 cells/cm2 in E8 medium with 10 μM ROCK inhibitor (Y27632, Tocris). The media was replaced with Essential 6 (E6) medium (Lippmann et al., 2014) on the following day (Day 0), and then changed to E6 supplemented with 200 ng/mL FGF8b (Peprotech) 24 hours later (Day 1). On Day 2, Hox propagation was initiated by activation of Wnt signaling using NMP media comprised of E6 medium supplemented with 200 ng/mL FGF8b and 3 μM CHIR99021 (Tocris).
pCNSP DIFFERENTIATION: NMPs were cultured for 1 day in pCNSP media, comprising of E6 media supplemented with 1 µM retinoic acid (RA; Sigma), 10 µM SB-431542 (Abcam), and 100 nM µL LDN-193189 (Stemgent). Cells were singularized and replated at 5 x 105 cells/cm2 in pCNSP media containing 10 μM Y27632 for an additional 2 days. Media was replenished daily.
VENTRAL DIFFERENTIATION: Ventral progenitors were generated by culturing in E6 media containing 100 nM (1 µM for H216R-vN) RA, 10 µM SB-431542, 100 nM LDN-193189, 0.5 μM Pur, and 0.5 μM SAG for 4 days. Progenitors were cryopreserved to synchronize cultures.
DORSAL DIFFERENTIATION: pCNSPs were exposed to morphogens for 4 days to initiate dorsal patterning. Dorsal progenitors were generated by culturing in E6 media containing 100 nM (1 µM for H216R-dN) RA, 1 μM Cyc, 20 ng/mL BMP4 for 1 day, then E6 media containing 100 μM RA and 1 μM Cyc for 3 additional days. Media was replenished daily. Progenitors were cryopreserved to synchronize cultures.
NEURONAL DIFFERENTIATION: For neuronal differentiation and maturation prior to sequencing, cells were thawed in maturation media containing 10 μM Y27632 at 5 x 105 cells/cm2 overnight, with daily media changes for 6 days. Maturation media consisted of E6 containing 1x N2 Supplement (Thermofisher), 50x B27 Supplement (Thermofisher), 1 µM cAMP (Sigma), 10 ng/mL GDNF, 10 ng/mL BDNF, 10 ng/mL NT-3 (Peprotech), and 10 µM DAPT (Tocris). Media was switched to Neurobasal media (Gibco) containing 1x N2 Supplement, 50x B27 Supplement, 1x Glutamax (Thermofisher), 1x PenStrep (Invitrogen), 1 ng/mL laminin (Thermofisher), 1 µM cAMP, 10 ng/mL GDNF, 10 ng/mL BDNF, and 10 ng/mL NT-3 for 14 days. 2 days prior to sequencing, the media was supplemented with 10 µM AraC (Sigma) to eliminate proliferating cells.

value: hESC-derived neurons

value: 216 hrs of HOX propagation (11 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA (high)/Cyc/BMP4 treatment to generate dorsal progenitors. Cultures were matured for 6 days with DAPT/BMP7 then cultured for 14 days before sequencing.


title: H216-dN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. The media was replenished daily on Days 7-10 with NMP media containing 30 ng/mL GDF11 (Peprotech) and 1 μM dorsomorphin (Tocris) to stimulate caudal NMP development. Cells were sub-culture on Day 9 at a 1:1 ratio, and pCNSPs were differentiated after 216hrs. + pCNSP DIFFERENTIATION + DORSAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 216 hrs of HOX propagation (11 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/Cyc/BMP4 treatment to generate dorsal progenitors. Cultures were matured for 6 days with DAPT/BMP7 then cultured for 14 days before sequencing.


title: H9_Total_rep3

description:
M.David_CLIP-seq_2022.txt
81C-total


title: H168-dN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. The media was replenished daily on Days 7-9 with NMP media containing 30 ng/mL GDF11 (Peprotech) and 1 μM dorsomorphin (Tocris) to stimulate caudal NMP development. pCNSPs were differentiated after 168hrs. + pCNSP DIFFERENTIATION + DORSAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 168 hrs of HOX propagation (9 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/Cyc/BMP4 treatment to generate dorsal progenitors. Cultures were matured for 6 days with DAPT/BMP7 then cultured for 14 days before sequencing.


title: BOV05_normal

source_name: Normal


title: H9_CS_rep2

description:
M.David_CLIP-seq_2022.txt
81B-CS


title: Chordoma tumor, CH4, miRNA

description: small RNA-seq

value: Chordoma tumor


title: BOV04_normal


title: glh-1 degron rep1


title: H9_MBL_rep2

description:
M.David_CLIP-seq_2022.txt
81B-MBL


title: glh-2 glh-1 degron rep1


title: BOV02_normal


title: H9_Total_rep2

description:
M.David_CLIP-seq_2022.txt
81B-total


title: BOV01_normal


title: hESCs shNT_RP_rep1

value: shNT

value: RNA


title: H72-dN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. pCNSPs were differentiated after 72hrs. + pCNSP DIFFERENTIATION + DORSAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 72 hrs of HOX propagation (5 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/Cyc/BMP4 treatment to generate dorsal progenitors. Cultures were matured for 6 days with DAPT/BMP7 then cultured for 14 days before sequencing.


title: H120-dN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. pCNSPs were differentiated after 120hrs. + pCNSP DIFFERENTIATION + DORSAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 120 hrs of HOX propagation (7 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/Cyc/BMP4 treatment to generate dorsal progenitors. Cultures were matured for 6 days with DAPT/BMP7 then cultured for 14 days before sequencing.


title: BOV10

source_name: Short

value: Intercaruncular Endometrium


title: WT degron rep2

value: wild-type


title: WT degron rep1


title: Nucleus pulposus, NP12, miRNA

description: small RNA-seq

value: Nucleus pulposus

value: primary NP cell culture

value: Caucasian

value: patient diagnosed with degenerative disc disease (Pfirrmann grade III)


title: H48-dN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. pCNSPs were differentiated after 48hrs. + pCNSP DIFFERENTIATION + DORSAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 48 hrs of HOX propagation (4 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/Cyc/BMP4 treatment to generate dorsal progenitors. Cultures were matured for 6 days with DAPT/BMP7 then cultured for 14 days before sequencing.


title: BOV08


title: H9_CS_rep1

description:
M.David_CLIP-seq_2022.txt
81A-CS

value: hESC H9 (Wa-09)

value: Anti-EIF4G2 (Cell Signaling, C-5169S)

value: UV crosslinking


title: H9_MBL_rep1

description:
M.David_CLIP-seq_2022.txt
81A-MBL

value: Anti-EIF4G2 (MBL, RN003P)


title: glh-2 degron rep1

value: cultured with 500mM IAA


title: H216R-vN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. The media was replenished daily on Days 7-10 with NMP media containing 30 ng/mL GDF11 (Peprotech) and 1 μM dorsomorphin (Tocris) to stimulate caudal NMP development. Cells were sub-culture on Day 9 at a 1:1 ratio, and pCNSPs were differentiated after 216hrs. + pCNSP DIFFERENTIATION + VENTRAL DIFFERENTIATION (1 μM RA) + NEURONAL DIFFERENTIATION

value: hESC-derived neurons

value: 216 hrs of HOX propagation (11 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA (high)/SAG/Pur/SB/LDN treatment to generate ventral progenitors. Cultures were matured for 6 days with DAPT then cultured for 14 days before sequencing.


title: glh-1 degron rep2


title: H120-vN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. pCNSPs were differentiated after 120hrs. + pCNSP DIFFERENTIATION + VENTRAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 120 hrs of HOX propagation (7 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/SAG/Pur/SB/LDN treatment to generate ventral progenitors. Cultures were matured for 6 days with DAPT then cultured for 14 days before sequencing.


title: BOV09


title: BOV07


title: H24-dN

description: HOX PROPAGATION + pCNSP DIFFERENTIATION (after 24hr of HOX PROPAGATION) + DORSAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 24 hrs of HOX propagation (3 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/Cyc/BMP4 treatment to generate dorsal progenitors. Cultures were matured for 6 days with DAPT/BMP7 then cultured for 14 days before sequencing.


title: H9_Total_rep1

description:
M.David_CLIP-seq_2022.txt
81A-total


title: BOV02


title: H24-vN

description: HOX PROPAGATION + pCNSP DIFFERENTIATION (after 24hr of HOX PROPAGATION) + VENTRAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 24 hrs of HOX propagation (3 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/SAG/Pur/SB/LDN treatment to generate ventral progenitors. Cultures were matured for 6 days with DAPT then cultured for 14 days before sequencing.


title: H168-vN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. The media was replenished daily on Days 7-9 with NMP media containing 30 ng/mL GDF11 (Peprotech) and 1 μM dorsomorphin (Tocris) to stimulate caudal NMP development. pCNSPs were differentiated after 168hrs. + pCNSP DIFFERENTIATION + VENTRAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 168 hrs of HOX propagation (9 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/SAG/Pur/SB/LDN treatment to generate ventral progenitors. Cultures were matured for 6 days with DAPT then cultured for 14 days before sequencing.


title: BOV06

value: Intercaruncular Endometrium


title: H72-vN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. pCNSPs were differentiated after 72hrs. + pCNSP DIFFERENTIATION + VENTRAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 72 hrs of HOX propagation (5 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/SAG/Pur/SB/LDN treatment to generate ventral progenitors. Cultures were matured for 6 days with DAPT then cultured for 14 days before sequencing.


title: H216-vN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. Media was replenished on Day 4. Cells were sub-cultured again at a 2:3 ratio on Day 5. The media was replenished daily on Days 7-10 with NMP media containing 30 ng/mL GDF11 (Peprotech) and 1 μM dorsomorphin (Tocris) to stimulate caudal NMP development. Cells were sub-culture on Day 9 at a 1:1 ratio, and pCNSPs were differentiated after 216hrs. + pCNSP DIFFERENTIATION + VENTRAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 216 hrs of HOX propagation (11 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/SAG/Pur/SB/LDN treatment to generate ventral progenitors. Cultures were matured for 6 days with DAPT then cultured for 14 days before sequencing.


title: H48-vN

description: HOX PROPAGATION + Cells were sub-cultured at a 2:3 ratio. Briefly, cells were washed once with PBS, incubated in Accutase for 1.5-2 mins, and removed from the surface by gentle pipetting. After centrifugation, cells were gently resuspended in NMP Medium containing 10 μM Y27632 and seeded on 35 mm Matrigel-coated plates. pCNSPs were differentiated after 48hrs. + pCNSP DIFFERENTIATION + VENTRAL DIFFERENTIATION + NEURONAL DIFFERENTIATION

value: 48 hrs of HOX propagation (4 days), followed by 3 days of RA/SB/LDN treatment to generate pCNSPs, then 4 days of RA/SAG/Pur/SB/LDN treatment to generate ventral progenitors. Cultures were matured for 6 days with DAPT then cultured for 14 days before sequencing.


title: BOV05


title: CD4.VAT.Sp.ZT0.ZT12.bmal1WT.KO

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 and hash libraries were processed using cite-seq-count
Data analsysis was performed using Seurat v3 pipeline. Low-quality cells were defined as those with less than 700 or more than 3000 unique genes, or those with >10% mitochondrial gene reads and were removed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Visceral adipose tissue and spleen

extract_protocol:
34,000 VAT and 32,000 splenic CD4+ T cells were single-sorted and multiplexed using TotalSeq hashing antibodies. Cell encapsulation, RNA isolation, and hash library construction and sequencing were performed using the 10X Genomics platform.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: CD4+ T cells

value: Visceral adipose tissue and spleen

value: C57BL/6 Foxp3.Cre-YFP

tag: time

value: ZT0 or ZT12


title: BOV04


title: BOV01


title: hash.CD4.VAT.Sp.ZT0.ZT12.bmal1WT.KO

description: 10x Genomics


title: WT, S2

status: Public on Jul 27 2022

city: Shenyang

first: Xiaotong

last: Zhu

state: Liaoning

address: No. 77 Puhe Road Shenyang North NEW AREA

department: Department of Immunology

institute: China Medical University

data_processing:
Illumina Casava 1.7 software was used for basecalling.
Raw reads in the fastq format were first processed through in-house Perl scripts to remove low-quality reads, reads containing adapter, and poly-N. Meanwhile, the Q20, Q30 and GC content of the clean data were calculated.
The UMI (Unique Molecular Identifiers) was extracted by the UMI-tools (v2.0.4). Only clean UMI reads were kept for further analysis.
Strand-specific RNA-seq paired-end reads were mapped onto the P. falciparum 3D7 genome (assembly GCA_000002765) using Hisat2 v2.0.4
Assembly: GCA_000002765
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample.

organism: Plasmodium falciparum

source_name: WT, S

extract_protocol:
Samples for RNA-seq analyses were taken at 12, 24, and 36 hpi from highly synchronized cultures. For RNA analyses, erythrocyte pellets were rapidly lysed in 10× volumes of pre-warmed TRIzol (ThermoFisher, Waltham, USA) and stored at -80°C until RNA purification. The experiment was repeated at 4-week intervals to obtain three RNA samples as biological replicates. RNA purification and DNase treatment of the samples were performed as described previously (91). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform with paired-end 150 bp read chemistry. Raw reads in fastq format were firstly processed through in-house Perl scripts. The UMI (Unique Molecular Identifiers) was extracted by UMI-tools v1.0.0 (92). All the downstream analyses were based on high-quality UMI reads (92). Strand-specific RNA-seq paired-end reads were mapped onto the P. falciparum 3D7 genome (assembly GCA_000002765) using Hisat2 v2.0.4 (93). UMI-tools v1.0.0 were used to deduplicate reads based on the mapping coordinates and the UMI attached to the reads (92). HTSeq v0.9.1 was used to count the reads mapped to each gene. The FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of genes between the WT and NIF4iKD lines (three biological replicates per condition) was performed using the DESeq R package (1.18.0). The resulting P-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed. GO enrichment analysis of differentially expressed genes was implemented using the GOseq R package, in which gene length bias was corrected (94). GO terms with corrected P value less than 0.05 were considered significantly enriched by differentially expressed genes.
RNA libraries were prepared for sequencing using standard illumina protocols

value: whole parasite

tag: Stage

value: schizonts

value: WT


title: WT, T2

source_name: WT, T

value: trophozoites


title: WT, S3


title: WT, S1


title: WT, T1


title: WT, T3


title: WT, R3

source_name: WT, R

value: rings


title: WT, R2


title: WT, R1


title: KD, S3

source_name: KD, S

value: KD


title: KD, T3

source_name: KD, T


title: KD, T2


title: KD, R3

source_name: KD, R


title: KD, S2


title: KD, R2


title: KD, S1


title: KD, R1


title: TKO cells with 602 mutant Dnmt1, day 0

city: Chiba

first: Musashi

last: Kubiura-Ichimaru

address: 2-2-1 Miyama, Funabashi-shi

institute: Toho University

hyb_protocol: standard Affymetrix protocol

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

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

source_name: differenciated cells from mESCs

label_protocol: standard Affymetrix protocol

growth_protocol: Embryonic stem cells (day 0) were cultured in DMEM medium containing 10% FBS and LIF, and cell differentiation was induced by 3-day adherent cell culture of 1-day-old embryoid bodys in culture medium without LIF . The Day 4 cells were then cultured in 10% KSR-containing medium with Activin A for 3 days (Day 7).

extract_protocol: none provided by the submitter

value: Dnmt1/3a/3b triple knockout embryonic stem cells


title: TKO cells with full-length Dnmt1, day 0

source_name: Mouse embryonic stem cells (mESCs)


title: TKO cells with full-length Dnmt1, day 7


title: TKO cells with 602 mutant Dnmt1, day 4


title: TKO cells with 602 mutant Dnmt1, day 7


title: TKO cells with full-length Dnmt1, day 4


title: WT-none_R2

city: Los Angeles

first: Quen

last: Cheng

address: 10833 LeConte Ave

institute: UCLA

description: ChIPseqCounts.csv

data_processing:
Samples were sequenced and base calls performed on Illumina HiSeq 3000
Reads were trimmed of adapter sequences, then mapped to mm10 genome with bowtie2. For ChIP-seq, duplicated reads were removed using Picard MarkDuplicates.
For ChIP-seq, MACS2 version 2.1.0 was used in broad mode to identify peaks for each sample using pooled input samples as control, FDR < 0.01, and extension size of average fragment length. These peaks were merged to generate a single reference peak file, and the number of reads that fell into each peak was counted using deeptools multiBamSummary with extension size of average fragment length
Assembly: mm10
Supplementary files format and content: Raw count tables are provided (unnormalized). For ChIP data, genomic regions of interest were defined by peak-calling. For Fluidigm scRNA data, the RSEM package was used.

source_name: bone marrow-derived macrophage

growth_protocol: BMDMs were generated by isolating bone marrow from the femurs and tibias of age and sex-matched mice. Bone marrow cells were incubated in L929-conditioned media (RPMI + 30% L929 media, 10% FBS, 100 IU/ml penicillin, 100 ug/ml streptomycin, 2 mM L-glutamine, 55 µM 2-mercaptoethanol) at 37C in 15cm plates. On Day 4, cells were detached using a cell lifter and replated into experimental culture plates, unless otherwise indicated. Cells were stimulated on Day 7 or 8 with the indicated ligands.

extract_protocol:
H3K4me1 ChIP was performed on lysed and sonicated chromatin using rabbit anti-H3K4me1 (Abcam ab8895). scRNA-seq libraries were generated with the Fluidigm C1 system.
Libraries were prepared according to manufacturer's instructions: ChIP-seq with NEBNext Ultra II DNA Library Prep Kit (New England Biolabs E7645), Fluidigm scRNA-seq with the C1 system using 3 mRNA HT IFCs.

treatment_protocol: Cells were stimulated with TNF-alpha (aa 80 - 235) protein (410-MT-010, R&D Systems) or Pam3CSK4 (tlrl-pms, Invivogen) at the indicated doses and timepoints

tag: replicate

value: Replicate 2

tag: antibody

tag: stimulus

value: Unstimulated

tag: column header


title: WT-Pam3_R2

description: ChIPseqCounts.csv

value: Pam3CSK 100 ng/ml


title: WT-Pam3_R1

description: ChIPseqCounts.csv

value: Replicate 1


title: WT-TNF_R1

description: ChIPseqCounts.csv

value: TNF 10 ng/ml


title: WT-LPS_R1

description: ChIPseqCounts.csv

value: LPS 100 ng/ml


title: WT-input_R1

description: ChIPseqCounts.csv

value: n/a (background)


title: KO-TNF_R2

description: ChIPseqCounts.csv

value: Tnf-/-


title: KO-TNF_R1

description: ChIPseqCounts.csv


title: KO-none_R2

description: ChIPseqCounts.csv


title: WT-input_R2

description: ChIPseqCounts.csv


title: KD, T1


title: KO-Pam3_R2

description: ChIPseqCounts.csv


title: KO-LPS_R1

description: ChIPseqCounts.csv


title: WT-none_R1

description: ChIPseqCounts.csv


title: KO-input_R2

description: ChIPseqCounts.csv


title: KO-none_R1

description: ChIPseqCounts.csv


title: KO-Pam3_R1

description: ChIPseqCounts.csv


title: COL20_TNFkoP3CSKlo_R1

description: FluidigmCounts.csv

value: Pam3CSK 10 ng/ml


title: COL20_WTP3CSKlo_R1

description: FluidigmCounts.csv


title: COL18_WTP3CSKlo_R1

description: FluidigmCounts.csv


title: WT-TNF_R2

description: ChIPseqCounts.csv


title: COL19_TNFkoP3CSKlo_R1

description: FluidigmCounts.csv


title: COL19_WTP3CSKlo_R1

description: FluidigmCounts.csv


title: COL16_WTP3CSKlo_R1

description: FluidigmCounts.csv


title: COL18_TNFkoP3CSKlo_R1

description: FluidigmCounts.csv


title: COL17_TNFkoP3CSKlo_R1

description: FluidigmCounts.csv


title: COL17_WTP3CSKlo_R1

description: FluidigmCounts.csv


title: COL15_WTP3CSKlo_R1

description: FluidigmCounts.csv


title: COL16_TNFkoP3CSKlo_R1

description: FluidigmCounts.csv


title: COL13_WTP3CSKlo_R1

description: FluidigmCounts.csv


title: COL12_TNFkoP3CSKlo_R1

description: FluidigmCounts.csv


title: KO-input_R1

description: ChIPseqCounts.csv


title: COL15_TNFkoP3CSKlo_R1

description: FluidigmCounts.csv


title: COL11_WTP3CSKlo_R1

description: FluidigmCounts.csv


title: COL11_TNFkoP3CSKlo_R1

description: FluidigmCounts.csv


title: COL09_WTUT_R1

description: FluidigmCounts.csv


title: COL09_WTTNF_R1

description: FluidigmCounts.csv


title: COL08_WTTNF_R1

description: FluidigmCounts.csv


title: COL08_WTUT_R1

description: FluidigmCounts.csv


title: COL08_TNFkoTNF_R1

description: FluidigmCounts.csv


title: COL07_TNFkoTNF_R1

description: FluidigmCounts.csv


title: COL09_TNFkoTNF_R1

description: FluidigmCounts.csv


title: COL07_WTUT_R1

description: FluidigmCounts.csv


title: COL10_TNFkoTNF_R1

description: FluidigmCounts.csv


title: COL05_WTUT_R1

description: FluidigmCounts.csv


title: COL05_WTTNF_R1

description: FluidigmCounts.csv


title: COL04_TNFkoTNF_R1

description: FluidigmCounts.csv


title: COL05_TNFkoTNF_R1

description: FluidigmCounts.csv


title: COL06_WTTNF_R1

description: FluidigmCounts.csv


title: COL07_WTTNF_R1

description: FluidigmCounts.csv


title: COL06_WTUT_R1

description: FluidigmCounts.csv


title: COL06_TNFkoTNF_R1

description: FluidigmCounts.csv


title: COL03_TNFkoTNF_R1

description: FluidigmCounts.csv


title: COL02_TNFkoTNF_R1

description: FluidigmCounts.csv


title: COL13_TNFkoP3CSKlo_R1

description: FluidigmCounts.csv


title: COL14_TNFkoP3CSKlo_R1

description: FluidigmCounts.csv


title: Cortical neurons, hypoxia+10nMT3, 7hours, rep3

first: Kailtyn

middle: Yan-Yun

last: Liu

address: 10833 Le Conte Ave

department: Medicine

institute: UCLA/VA

data_processing:
The reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
The gene expression level was estimated using RSEM v1.2.15.
TMM (trimmed mean of M-values) was used to normalize the gene expression
Differentially expressed genes were identified using the edgeR program
Supplementary files format and content: MM10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: brain

growth_protocol: Cells were grown in poly-D-Lysin coated dish and in Neurobasal® medium containing 200 mM GluMAX™-1 and B27 supplement with 50% medium change every 3 days. After 6 days, cells were used for experiments.

extract_protocol:
RNA was extracted using RNease Plus (Qiagen). RNA QC was performed.
Library construction using Stranded mRNA (Poly-A)

treatment_protocol: Cells were exposed to hypoxia (0.2% oxygen, 5%CO2 and 94.8% N2) for 7 hours with or without 10 nM T3 present in the medium.

value: brain

value: Primary cells

value: Cortical neuronal cells

value: Wt

value: 0.2% oxygen + 10 nM T3 in the medium


title: Cortical neurons, hypoxia+10nMT3, 7hours, rep2


title: COL10_WTTNF_R1

description: FluidigmCounts.csv

value: WT


title: COL01_WTUT_R1

description: FluidigmCounts.csv


title: Cortical neurons, hypoxia+10nMT3, 7hours, rep1


title: COL10_WTUT_R1

description: FluidigmCounts.csv


title: Cortical neurons, hypoxia, 7hours, rep3

value: 0.2% Oxygen


title: Cortical neurons, hypoxia, 7hours, rep1


title: Cortical neurons, normoxia (control), rep3

value: Control


title: Cortical neurons, normoxia (control), rep2


title: Cortical neurons, normoxia (control), rep1


title: mESC2

city: Brisbane

first: Christian

last: Nefzger

state: Queensland

address: 306 Carmody Road

department: Institute for Molecular Biology

country: Australia

institute: The University of Queensland

data_processing:
Sample reads were aligned to the mouse genome (GENCODE GRCm38 primary assembly) using STAR version 2.4.2a ( --outFilterMatchNminOverLread 0.3 --outFilterScoreMinOverLread 0.3)
Reads with duplicated UMIs were removed using the software Je option markdupes
Transcript quantification was performed using feature Counts (exonic regions of GENCODE’s vM15 annotation version)75, and transcripts with more than 5 sequencing reads and 2 count per million of mapped reads in at least two sample were used for further analysis. This resulted in a filtered count matrix of 16154 genes.
ATAC-seq: Peak calling was performed using the MACS2 callpeak command with the following parameters “-g mm –shift -100 –extsize 200 –nomodel –call-summits –nolambda –keep-dup all -p 0.01” [34], [35]. Then, peak summits were extended by 250 bp on both sides  to a final width of 501 bp. Peaks were filtered for mm10 blacklisted regions [36]  (https://www.encodeproject.org/annotations/ENCSR636HFF/).
As in Corces et al. 2020 per sample overlapping peaks were handled using an iterative removal approach. That is in case of two overlapping peaks the most significant peak is kept and the other removed. This process is performed in an iterative manner, so all peaks have been kept or removed based on their overlap and significance score. This method results in a set of fixed-width peaks per sample.
Next, significance peak scores “(-log10(p-value))” were converted to a score per million value by dividing each individual peak score by the sum of all of the peak scores in the given sample divided by 1 million.  This normalized score per million value corrects the original peak calling scores for sample sequencing depth and quality, as higher quality samples yield higher number of peaks and higher significance scores overall. Thus, scores per million allow the direct comparison of peaks across biological replicates.
Next, we compiled a condition - MEF, mESC- and sequencer specific - BGI, Illumina - peak set containing reproducible peaks observed in a particular cell type and sequencing platform. For that, we generated a cumulative peak set per cell type and sequencing platform and performed the same iterative approach as mentioned above. Therefore, maintaining the peak with the highest significance or score per million. Only peaks with a score per million value >=3 observed in at least two samples (minimal overlap 50%) were further considered.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (*.txt) format for RNA-seq, bigwig for ATAC-seq samples, called peaks in (.gtf) format and counts per peak in .txt format.

source_name: mouse embryonic stem cells

extract_protocol:
RNA was extracted and purified from young and aged HSC (20,000-25,000 cells from individual mice) using Direct-zol RNA micro kit (Zymo Resarch) according to the manufacturer's instructions (RNA integrity number value >8)
3-prime biased approach was used to generate sequencing libraries. An 8bp sample index anda. 10bp unique molecular identifiery (UMI) were added during the initial poly(A) priming and pooled samples were amplified using a template swithcing oligonucleotide.  The Illumina P5 (5' AAT GAT ACG GCG ACC ACC GA 3') and P7 (5' CAA GCA GAA GAC GGC ATA CGA GAT 3') sequences were added by PCR and Nextera transposase, respectively. The library was designed so that the forward read (R1) utilizes a custom primer (5' GCC TGT CCG CGG AAG CAG TGG TAT CAA CGC AGA GTA C 3') to sequence directly into the index and then the 10 bp UMI. The reverse read (R2) uses the standard R2 primer to sequence the cDNA in the sense direction for transcript identification.

value: mouse embryonic stem cells

value: C57/Bl6 background


title: MEF2

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: mESC3


title: MEF4


title: MEF3


title: mESC1


title: COL03_WTUT_R1

description: FluidigmCounts.csv

value: Unstimulated


title: MEF1


title: NC_5mo

first: Sean

middle: M

last: Ronnekleiv-Kelly

state: Wisconsin

address: 1400 University Ave

department: Surgery

institute: University of Wisconsin

data_processing: Demultiplexing, barcode processing, gene counting and aggregation were made using Cell Ranger software v6.1.2

source_name: Pancreas

extract_protocol:
Five- and 9-month-old NC and CJ KC mice were sacrificed with cervical dislocation and the pancreas was rapidly dissected (< 60 seconds) and placed in cold PBS (Thermo Fisher Scientific, Waltham, MA). One male and female pancreas was pooled from each condition and time point. Pancreas samples were minced until the tissue was < 1 mm in diameter, and then centrifuged at 900 RPM for 5 minutes to remove fat contamination. Samples were then incubated with 5 mL of Collagenase P (Sigma Aldrich, St. Louis, MO) in HBSS (Thermo Fisher Scientific) at 37° C for 15 minutes while being shaken at 100 RPM. Additionally, samples were manually agitated every 2-3 minutes. The digestion reaction was quenched with 10 mL R10 media. Samples were then centrifuged at 900 RPM and washed twice with 10 mL of R10. Samples were then strained in a gradient fashion using 500 μm, 100 μm, and 40 μm strainers. Samples were then live/dead sorted into single-cell populations and were transferred to the University of Wisconsin Gene Expression Center (GEC) for Library Preparation.
Library preparation was performed according to the manufacturer’s instructions (single cell 3’ v3.1 protocol, 10X Genomics). Briefly, cell suspensions were added to master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). Cells were lysed within the GEMs and polyadenylated transcripts underwent reverse transcription to produce full-length cDNA containing an Illumina TruSeq Read 1 sequence; a unique molecular identifier (UMI); and a cell-specific 10X Barcode. The pooled barcoded cDNA was then cleaned up with Silane magnetic beads and amplified by PCR to produce enough mass for library construction. After fragmentation and size selection for appropriately-sized amplicons, a series of enzymatic steps were used to add P5 and P7 primer sequences; i5 and i7 sample indexes; and the Illumina TruSeq Read 2 sequence.

value: Pancreas

value: 5 Months

value: Normal Circadian


title: CJ_9mo

value: 9 Months

value: Chronic Jetlag


title: NC_9mo


title: PaCre+BMT_4

city: Osaka

first: Yu-Tung

last: Li

address: 2-2 Yamada-oka, Suita

institute: Osaka University

data_processing:
Sequencing outputs were demultiplexed using bcl2fastq2 (https://jp.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
Adapter sequence was trimmed using TrimGalore with the parameter (--nextera -–paired).
Trimmed reads were aligned on the mouse reference genome and the expression levels of transcripts was quantified using RSEM with the following parameters (rsem-calculate-expression –paired-end –star –output-genome-bam).
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data files are zipped RSEM output (.genes.results)

source_name: back skin

extract_protocol:
On day 14 post AD induction, skins were collected, flash frozen in liquid nitrogen, and RNA was harvested using ISOGEN reagent and was cleaned up using RNeasy Plus Mini Kit(Cat#74134).
Libraries were prepared according to KAPA RNA HyperPrep Kit with RiboErase (HMR) (Cat# KK8560). Briefly, total RNA was depleted of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase to remove rRNA duplexed on DNA and original DNA oligonucleotides. After fragmenting the RNA using heat and magnesium, the first strand cDNA was synthesized using random priming, followed by a combined second strand synthesis and A-tailing process. Libraries were amplified by PCR after the addition of adapters, and finally purified and size selected using magnetic beads. Libraries were sequenced on the Illumina NextSeq2000 following the manufacturer's protocols.

treatment_protocol: tdTomato-negative or positive femoral bone marrow cells sorted from Pdgfra-Cre;tdTomato mice were transplanted via tail vein after 10 Gy of irradiation. After 6-week recovery, AD was induced by repeated topical application of MC903 on back skin for six times.

tag: bmt

value: tdTomato-positive femoral bone marrow cells from Pdgfra-Cre

tag: age


title: PaCre+BMT_2


title: PaCre+BMT_3


title: CJ_5mo

tag: treatment


title: Cortical neurons, hypoxia, 7hours, rep2

value: brain

value: Primary cells

tag: strain


title: PaCre-BMT_7

value: tdTomato-negative femoral bone marrow cells from Pdgfra-Cre


title: PaCre+BMT_1


title: PaCre-BMT_6


title: PaCre-BMT_3


title: PaCre-BMT_4


title: LD15_EPS

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.58.0).

source_name: Myotubes from musculus obliquus internus after 7 days of differentiation. Cells were exposed to electrical pulse stimulation for 48h prior to harvesting.

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Human skeletal muscle cells (myotubes) grown from satellite cells were isolated from the M. obliquus internus abdominis of 4 healthy female donors. Body mass index, fasting glucose, insulin, plasma lipids and blood pressure of donors were within normal range. The biopsies were obtained with informed consent and the procedure was approved by the National Committee for Research Ethics (Oslo, Norway). The cells were cultured in DMEM-Glutamax (5.5 mM glucose), 2 % FCS, 2 % Ultroser G, P/S, and amphotericin B. At 70-80 % confluence the growth medium was replaced by DMEM-Glutamax supplemented with 2 % FCS, P/S, 1.25 µg/ml amphotericin B, and 25 pM insulin to induce differentiation. The cells were cultured in humidified 5 % CO2 atmosphere at 37 °C, and the medium was changed every 2–3 days.

extract_protocol: Total RNA was prepared using the Agilent Total RNA isolation kit. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Experiments were performed after 7 days of differentiation.  Cells were exposed to electrical pulse stimulation (EPS) for 48h prior to harvesting. Control cells were not stimulated.

tag: background

value: caucasian

tag: gender

value: female

tag: age(yr)


title: PaCre-BMT_5


title: LD8_Control

source_name: Myotubes from musculus obliquus internus after 7 days of differentiation. Cells were control treated.

tag: tissue

value: control


title: LD12_EPS

value: Myotubes from musculus obliquus internus

value: electrical pulse stimulation for 48h prior to harvesting


title: PaCre-BMT_1


title: LD31_EPS


title: LD8_EPS


title: LD15_Control


title: LD31_Control


title: PaCre-BMT_2


title: Adult (Adu)-Pto biological replicate 2

city: Athens

first: Lanxi

last: Hu

address: 120 Charlton street

institute: University of Georgia

description: Eukaryotic Strand-specific Transcriptome Resequencing

data_processing:
The data was filtered using SOAPnuke software in BGI. Specifically, the entire read was deleted in either of the following scenarios, 1) more than 28% of a read matches the adapter sequence, 2) more than 40% bases having a quality value lower than 20, 3) more than 3% N in the read. As results, ~48 M clean reads with average Q30 ≥ 88.81% per sample was obtained.
Differential expression analysis was done by comparing transcript levels using DEseq2 (LFC ≥ ±0.58, padj ≤ 0.05) {Love, 2014}. Gene ontology was analyzed against the whole Arabidopsis genome at TAIR Gene Ontology terms website, http://geneontology.org/ {Ashburner 2000, The Gene Ontology Consortium 2020}, and which was confirmed using total detected 22,622 (covers 88.7% of known genes in Arabidopsis genome) genes of the RNA-seq results on agriGO website http://systemsbiology.cau.edu.cn/agriGOv2/# {Tian, 2017}.
Figures were generated in R software. R scripts are available in the supplementary data of the paper.
Assembly: The clean RNA-seq data were aligned against the TAIR10 reference genome using with HiSAT2 (v.2.1.0, {Kim, 2019}) with following parameters, hisat2 -p 4 -x TAIR10indexed -1 sample_strand1.fq.gz -2 sample_strand2.fq.gz -S aligned_sample.sam. The aligned reads were assembled into transcripts according to the TAIR10 annotation {Lamesch, 2012;Swarbreck, 2008} using Stringtie {Pertea, 2016}. ~99% overall alignment rate was reached for each sample.
Supplementary files format and content: A combined gene count matrix sorted in .csv format

organism: Arabidopsis thaliana

source_name: Bulk

growth_protocol: We used 33 days old juvenile leaves or r10 leaves and 52 days old adult leaves. Detailed plant growth condition was described in the section of materials and methods.

extract_protocol:
Total RNAs were extracted using E.Z.N.A. Total RNA kit (Omega BIO-TEK). RNA quality was assessed with a 2100 Bioanalyzer instrument (Agilent, RIN score ≥ 7, 28S/18S ≥ 1). RNA concentration was measured using a Nanodrop spectrophotometer (Thermo Scientific, RNA concentration ≥ 50 ng/μL, 260/280 ~2.0). RNA samples were sequenced at BGI, San Jose lab.
Oligo dT based mRNA enrichment was followed by random N6 primer based reverse transcription. Synthesized cDNAs were then tailed with an Adenine each and then ligated with a bubble adapter. The DNA products were further amplified through PCR, separated with heat and cyclized using splint oligo. The synthesized DNA nanoballs were then sent for non-stranded mRNA sequencing (PE100) on a DNA Nanoball Sequencing (DNBseq) platform.

treatment_protocol: Pto DC3000 (1 x 108 CFU/mL suspended in 10mM MgCl2) was infiltrated into juvenile and adult wild type (Col-0) leaves and leaves 1-2 from rSPL10 plants. 10 mM MgCl2 was used as the mock treatment. Three hours after inoculation, 20 leaf discs with comparable size from 5-10 individual plants were cored and collected as one biological repeat per genotype per treatment. Three biological repeats were prepared for each genotype/treatment.

tag: cell type

value: Bulk

tag: genotype

value: Pto


title: Juvenile (Juv)-Pto biological replicate 2


title: Juvenile (Juv)-Pto biological replicate 3


title: rSPL10 (r10)-Pto biological replicate 1


title: Adult (Adu)-Pto biological replicate 3


title: Adult (Adu)-Pto biological replicate 1


title: Juvenile (Juv)-Pto biological replicate 1


title: rSPL10 (r10)-Pto biological replicate 2


title: Adult (Adu)-Mock biological replicate 3

value: Mock


title: ZT06

city: Hangzhou

first: zuorui

last: xie

address: Zhejiang Gongshang University

institute: ZFM

description: C57BL/6 mice

data_processing:
Total DNA extracted from the sample
Using FLASH v1.2.7 software, the reads of each sample were spliced by overlapping, and the obtained splicing sequence was the original Tag data (Raw Tags)
Using Trimmomatic v0.33 software to filter the spliced Raw Tags to obtain high-quality Tag data (Clean Tags)
Using UCHIME v4.2 software to identify and remove chimera sequences to obtain final effective data (Effective Tags)
Use Usearch software to cluster effective data at the 100% similarity to obtain Amplicon Sequence Variant (ASV). By comparing the representative sequences of OTUs with the Silva (bacteria) taxonomy database, the species classification information corresponding to each OTU can be obtained, and then the community composition of each sample can be counted at each level (phylum, class, order, family, genus, species). The QIIME software was used to generate species abundance tables at different taxonomic levels, and then the R language tool was used to draw the community structure map of the samples at each taxonomic level.
Assembly: V3-V4 region of the 16S rRNA gene
Supplementary files format and content: Clean gene for every gene and every sample
Supplementary files format and content: OTU_stat: Seqs detail of all samoles
Supplementary files format and content: OTU_stat_detail: Tag number and OTU number of all samples
Supplementary files format and content: OTU_shared_for_alpha_diversity: OTU shared for alpha diversity of all samples

organism: feces metagenome

source_name: gastric contents

growth_protocol: The experiment was performed in accordance with the ethical guidelines for animal use and with permission from Shanghai Public Health Clinical Center Animal Ethics Committee. Specific pathogen free C57BL/6 mice (6-week old, 18~20 g) were obtained from Sino-British SIPPR/BK Lab Animal Ltd. (Shanghai, China) and experiment was conducted in Laboratory Animal Department of Shanghai Public Health Clinical Center. The mice were grouped into two experimental groups: (i) Preventive group, and (ii) Therapeutic group.

extract_protocol:
Genomic DNA was extracted from thegastric contents with a QIAamp PowerFecal DNA extraction kit, according to the manufacturer’s instructions.
16S rRNA gene high-throughput sequencing of the V3-V4 region was performed by BGI Genomics Co., Ltd. (Shenzhen, China).

treatment_protocol: Mice model by administering L. paracasei ZFM54 before (pretreatment) and after (treatment) H. pylori challenge. The gastric contents were immediately collected from experimental mice.

value: mice challenged with Helicobacter pylori


title: ZT04

description: C57BL/6 mice


title: ZT02

description: C57BL/6 mice


title: rSPL10 (r10)-Mock biological replicate 2


title: Adult (Adu)-Mock biological replicate 2


title: rSPL10 (r10)-Pto biological replicate 3


title: Adult (Adu)-Mock biological replicate 1


title: rSPL10 (r10)-Mock biological replicate 3


title: ZT03

description: C57BL/6 mice


title: 7437-100pg

type: genomic

city: Fort Worth

first: Jianye

last: Ge

state: TX

address: 3500 Camp Bowie Blvd

department: Center for Human Identification

institute: University of North Texas Health Science Center

hyb_protocol: Following resuspension, the samples were combined back into their original wells, and 70µL was loaded onto the Omni5 beadchips (four samples per chip). Hybridization of the samples to the beadchips was carried out in a 48°C hybridization oven for about 24 hours. Beadchips were washed to prepare for the staining process and assembled into Flow-Through Chambers using LCG glass and LCG spacers.

scan_protocol: Flow-Through Chambers were placed into the Chamber Rack of a 44°C water circulator where RA1 reagent was used to wash away unhybridized DNA. Extension and staining (XStain) were performed on each beadchip:  the surface of the beadchips was conditioned for the extension reaction, primer extension was performed using labeled nucleotides, hybridized DNA was removed using 95% formamide/1mM EDTA, and the labeled extended primers underwent a multi-layer staining process. The stained beadchips were washed and coated, and then dried in a vacuum desiccator for approximately one hour before imaging on the Illumina iScan.

data_processing:
Initial data screening, including assessment of Illumina’s internal controls, was performed using GenomeStudio 2.0.5 software.
Processed data contains: Genotype: AA,AB,BB,or NC (no call)

label: cy3, cy5

source_name: UTAH/CEPH cell line

label_protocol: The DNA samples were denatured and neutralized before adding the Amplification Master Mix.  The amplification plate was incubated in a 37°C hybridization oven for approximately 23 hours. Samples were then split in half for subsequent processing, with both halves receiving the same treatment. Enzymatic fragmentation was carried out by adding FRG to each sample and incubating the plate at 37°C for one hour. The DNA was precipitated out using PA1 and 100% 2-propanol, which resulted in a blue pellet in the bottom of each well. Reagent RA1 was added to each sample to resuspend the precipitated DNA.

extract_protocol: DNA extraction protocol not provided.

tag: cell line

value: UTAH/CEPH

value: lymphoblastoid cell lines

tag: dna amount

value: 100pg DNA sample


title: LD12_Control