title: Patient D - Baseline (BOB40560WB_S39)


title: Patient E - Baseline (BOB40559WB_S57)

status: Public on Jun 22 2022

type: SRA

city: Boston

first: Livius

last: Penter

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description:
Targeted TCR sequencing
PatientE_Baseline_TCRalpha.xlsx
PatientE_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz

library_source: transcriptomic

data_processing:
Demultiplexing of raw sequencing data
Separation of TCR alpha and beta reads using BLAST
Assembly and annotation of reads using MiXCR
Quality control and error correction
Quantification of T cell clonotypes
Assembly: GRCh38
Supplementary files format and content: Excel files include T cell clonotype count values for each Sample
Library strategy: TCR-seq

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Total RNA was extracted from 5 x 10^6 PBMCs using the RNeasy Mini Kit (Qiagen)
Libraries were constructed using RNase H-dependent T-cell receptor sequencing with 40 ng input for each reaction in 4 replicates (PMID 31341290)
rhTCRseq

tag: tissue

value: peripheral blood

tag: cell type

value: T cells

tag: treatment

value: SOC chemotherapy

tag: time

value: Before therapy


title: Patient C - C3 after surgery (BOB40558WB_S6)

description:
Targeted TCR sequencing
PatientC_C3_TCRalpha.xlsx
PatientC_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: SOC chemotherapy and surgery

value: After 3 cycles and surgery


title: Patient C - C3 after surgery (BOB40558WB_S38)


title: Patient D - Baseline (BOB40560WB_S23)

description:
Targeted TCR sequencing
PatientD_Baseline_TCRalpha.xlsx
PatientD_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: oocyte, T2

city: Nanjing

first: Li

last: Yu

address: No. 1 Weigang, Nanjing City, Jiangsu Province

country: China

institute: College of Animal Science and Technology, Nanjing Agricultural University

data_processing:
Reads aligned with the genes are counted by cufflinks (v2.2.1). FPKM (FPKM_DEG_Summary.txt) uses cuffnorm for standardization. Differentially expressed genes (DEG_C_vs_H.High_in_C.txt and DEG_H_vs_T.High_in_T.txt) are calculated using cuffdiff.
Supplementary_files_format_and_content: FPKMs, DEGs

organism: Sus scrofa

source_name: oocyte

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
isolation and purify mRNA from total RNA
synthesis the first strand cDNA and synthesis the second strand cDNA
Purify the double-stranded cDNA with 1.8X  AMPure XP beads
cDNA were end repaired and added A base to the 3’ end and cDNA were ligated adaptors
Purify  and the adaptor purificated library with AMPure XP beads

tag: Stage

value: GV

value: 24 hours

value: heat stress+NMN


title: oocyte, H2

value: heat stress


title: Patient C - Baseline (BOB40557WB_S5)

description:
Targeted TCR sequencing
PatientC_Baseline_TCRalpha.xlsx
PatientC_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Patient C - C3 after surgery (BOB40558WB_S22)


title: Patient C - C3 after surgery (BOB40558WB_S54)


title: Patient D - Baseline (BOB40560WB_S55)


title: oocyte, C2

value: control


title: Patient E - Baseline (BOB40559WB_S41)


title: oocyte, C1


title: Patient B - C3 after surgery (BOB35132WB_S52)

description:
Targeted TCR sequencing
PatientB_C3_TCRalpha.xlsx
PatientB_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Patient D - C3 after surgery (BOB40561WB_S40)

description:
Targeted TCR sequencing
PatientD_C3_TCRalpha.xlsx
PatientD_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: ChIP-seq TFEB

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

country: Italy

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1  -S --sam-nohead -m 1
Data were filtered using the following specifications: duplicate reads were filtered out
peaks files were called by using MACS tool by using the following parameters: --nolambda -p 1E-5
Genome_build: mm9
Supplementary_files_format_and_content: processed data files in bed format, with the following fields: chromosome, start, stop, MACS_peak id, MACS_peak score

molecule: genomic DNA

organism: Mus musculus

source_name: MEC

growth_protocol: Mouse embryonic epicardial cells were derived from 11.5 dpc mouse hearts as described in (Li, P., et al., IGF signaling directs ventricular cardiomyocyte proliferation during embryonic heart development. Development, 2011. 138(9): p. 1795-805.)

extract_protocol:
For ChIP-seq, approximately 2 x 10E7 cells were cross-linked by addition of formaldehyde to 1% for 10 min at RT, quenched with 0.125 M glycine for 5 min at RT, and then washed twice in cold PBS. The cells were resuspended in Lysis Buffer 1 (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 and protease inhibitor) to disrupt the cell membrane and in Lysis Buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitor) to isolate nuclei. The isolated nuclei were then resuspended in SDS ChIP Buffer (20 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS and protease inhibitors). Extracts were sonicated using the Bioruptor H Twin (Diagenode) for 2 runs of 10 cycles [30 sec ‘‘ON’’, 30 sec ‘‘OFF’’] at high power setting. Cell lysate was centrifuged at 12,000 g for 10 min at 4°C. The supernatant was diluted with ChIP Dilution Buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton) before immunoprecipitation step. Magnetic beads (Dynabeads® Rat Anti-Mouse IgM for anti-PolII-phospho-S5, Dynabeads®Protein G for all the other ChIPs, Life Technologies) were saturated with PBS/1% BSA and the samples were incubated with 2 micrograms of antibody overnight at 4°C on a rotator.  Next day samples were incubated with saturated beads for two hours at 4°C on a rotator. Successively immunoprecipitated complexes were washed five times with RIPA buffer (50 mM Hepes-KOH pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0,7% Na-Deoxycholate) at 4°C for 5 minutes each on a rotator. Elution Buffer was added and incubated at 65°C for 15 minutes. The decrosslinking was performed at 65°C overnight. Decrosslinked DNA was purified using QIAQuick PCR Purification Kit (QIAGEN) according to the manufacture’s instruction.
For ChIP-seq, approximately 10 ng of purified ChIP DNA were end-repaired, dA-tailed, and adapter-ligated using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB), following manufacturer instructions.

treatment_protocol: MEC were infected with lentiviral vector pTripz-Tfeb and TFEB S142A expression was induced by doxycycline treatment for 8 hours.

value: Mouse epicardial cells

tag: chip antibody


title: Patient B - C3 after surgery (BOB35132WB_S4)


title: ChIP-seq IgG

value: IgG (12-370, Millipore)


title: Patient B - Baseline (BOB35142WB_S51)

description:
Targeted TCR sequencing
PatientB_Baseline_TCRalpha.xlsx
PatientB_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Patient B - C3 after surgery (BOB35132WB_S20)


title: Patient B - Baseline (BOB35142WB_S3)


title: oocyte, T1


title: Patient B - Baseline (BOB35142WB_S19)


title: Patient B - Baseline (BOB35142WB_S35)


title: Patient A - C3 after surgery (BOB33035WB-2_S34)

description:
Targeted TCR sequencing
PatientA_C3_TCRalpha.xlsx
PatientA_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Patient A - C3 after surgery (BOB33035WB-2_S2)


title: Patient A - C3 after surgery (BOB33035WB-2_S50)


title: Patient A - Baseline (BOB31848WB-3_S49)

description:
Targeted TCR sequencing
PatientA_Baseline_TCRalpha.xlsx
PatientA_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Patient A - C3 after surgery (BOB33035WB-2_S18)


title: Patient C - Baseline (BOB40557WB_S21)


title: Patient C - Baseline (BOB40557WB_S37)


title: Patient C - Baseline (BOB40557WB_S53)


title: Patient A - Baseline (BOB31848WB-3_S33)


title: Patient A - Baseline (BOB31848WB-3_S17)


title: Patient A - Baseline (BOB31848WB-3_S1)


title: oocyte, H1


title: Patient 10 - Follow-up

description:
Targeted TCR sequencing
Patient10_Post_TCRalpha.xlsx
Patient10_Post_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: Follow-up


title: Patient 10 - C6

description:
Targeted TCR sequencing
Patient10_C6_TCRalpha.xlsx
Patient10_C6_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: After 6 cycles


title: CP-1

city: Shanghai

first: Yang

middle: yang

last: Guo

address: Dongan Road

institute: 复旦大学

data_processing:
GEMs (Gel Bead in Emulsion) were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling
The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection
Each single-cell RNA-seq library was sequenced twice in two lanes of HiSeq 4000 (Illumina) to obtain single-end, 91 bp, approximately 300 million reads per library.
The 3' Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation, 聽adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined.聽
The final library pool was sequenced on the Illumina xx instrument using 150-base-pair paired-end reads.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Pancreas

extract_protocol:
For the quality check and counting of single cell suspension, the cell survival rate is generally above 80%. The cells that have passed the test are washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/ul for 10x Genomics ChromiumTM. The system is operated on the machine.
RNA libraries were prepared for sequencing with Single Cell 3′ library and Gel Bead Kit v.3 according to the manufacturer's protocol

tag: strain

value: pancreas

tag: disease state

value: chronic pancreatitis


title: Patient 10 - C3 before surgery

description:
Targeted TCR sequencing
Patient10_C3_TCRalpha.xlsx
Patient10_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: peripheral blood

value: After 3 cycles


title: M14 KO  input

city: Chicago

first: Jie

last: Du

address: 900 E. 57th Street

institute: University of Chicago

data_processing:
Sequencing raw data were preprocessed by trim_galore v0.6.5 and then mapped against mm10 reference genome by HISAT2 v2.1.0.
Peak calling was carried out using R package exomePeak.
Downstream analysis and visualization of data were accomplished using R v3.6.
Motif search was performed using HOMER v4.10.0.
The longest isoform was retained if a gene has more than one isoforms.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: colonic epithelial cells

extract_protocol:
Colonic epithelial cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. SMARTer Stranded RNA-seq Kit v2- Pico Input  Mammalian (Cat#634411) was used with 5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

tag: age

value: post natal week 6

tag: genotype

value: Mettl14 f/f; CDX-cre

tag: molecule subtype

value: total RNA

tag: rip antibody

value: none (input)


title: Patient B - C3 after surgery (BOB35132WB_S36)

value: T cells

value: SOC chemotherapy and surgery

value: After 3 cycles and surgery


title: M14 KO  m6A rep3

value: m6A antibody immunoprecipitated mRNA

value: anti-m6A (Synaptic Systems, catalog # 202003)


title: Patient 8 - Follow-up

description:
Targeted TCR sequencing
Patient8_Post_TCRalpha.xlsx
Patient8_Post_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: SOC chemotherapy


title: Patient 10 - Baseline

description:
Targeted TCR sequencing
Patient10_Baseline_TCRalpha.xlsx
Patient10_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: Before therapy


title: M14 KO  m6A rep2


title: M14 f/f  input

value: Mettl14 f/f


title: Patient 8 - C3 before surgery

description:
Targeted TCR sequencing
Patient8_C3_TCRalpha.xlsx
Patient8_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: M14 f/f  m6A rep3


title: Patient 8 - C6

description:
Targeted TCR sequencing
Patient8_C6_TCRalpha.xlsx
Patient8_C6_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: After 6 cycles


title: Patient 8 - Baseline

description:
Targeted TCR sequencing
Patient8_Baseline_TCRalpha.xlsx
Patient8_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Patient 7 - Follow-up

description:
Targeted TCR sequencing
Patient7_Post_TCRalpha.xlsx
Patient7_Post_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: Follow-up


title: M14 KO  m6A rep1


title: M14 f/f  m6A rep2


title: Patient 7 - C6

description:
Targeted TCR sequencing
Patient7_C6_TCRalpha.xlsx
Patient7_C6_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: peripheral blood


title: LOW tissue Week20 - 4

city: Bern

first: Daniel

last: Sanchez-Taltavull

address: Murtenstrasse 35

department: Department of BioMedical Research

country: Switzerland

institute: University of Bern

description:
rild_multi.txt
rild_unique.txt
X20WeLo_Ir4_

data_processing:
Raw reads were trimmed for adaptors and length using trimmomatic v. 0.36 via ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:60 parameters
Filtered reads were aligned to the mouse genome
Reads were aligned STAR v. 2.7.3a with --outFilterType BySJout --outFilterMultimapNmax 20 --outSAMtype BAM, SortedByCoordinate and otherwise default parameters
Readmaps were counted using featureCounts tool from subread v.2.0.1 package, once in unique and once in multi-mapping mode (-M)
Reads for genes COX2, ATP6, COX3, ND3, COX1, and ND4 were counted from multi-mapping, the rest - from unique mode
Genome_build: GRCm38, ENSEMBL version 102
Supplementary_files_format_and_content: .txt tables of readcounts

source_name: Liver tissue

extract_protocol:
RNA was extracted from snap-frozen tissue with RNeasy Micro Kit (Qiagen; 74004)
The library was prepared without size exclusion with the TruSeq Stranded mRNA kit (Illumina, 20020594)

treatment_protocol:
Tissue harvested on anhestetised mice (IP injection of fentanyl 50µg/kg, midazolam 5mg/kg, medetomidine 500µg/kg)
Mice were injected with 50 µl iv of ExiTronNano6000 contrast agent (Miltenyi Biotec; 130-095-147). One hour after contrast agent injection CT-imaging and irradiation were performed during the light phase under 2% isoflurane anesthesia using Xrad 225cx small animal irradiator. Dose calculation was realized by Monte Carlo dose calculation (SmART-Plan Xrad 225cx planning system), and delivery was performed using a Varian Tube NDI 226 (X-ray machine; 250 keV, tube current: 15 mA, beam filter: 5 mm Cu), with a dose rate of 1.08 Gy·min−1. Based on these CT images, we designed a 180º arc irradiation plan that using a 5mm diameter collimator to deliver 50Gy as a single dose to the right superior lobe and median lobes interface.

value: Balb/c

value: Week 20

tag: treatement

value: LOW

tag: mouse identifyer


title: Patient 7 - C3 before surgery

description:
Targeted TCR sequencing
Patient7_C3_TCRalpha.xlsx
Patient7_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: After 3 cycles


title: M14 f/f  m6A rep1

value: colon

value: post natal week 6


title: Patient 7 - Baseline

description:
Targeted TCR sequencing
Patient7_Baseline_TCRalpha.xlsx
Patient7_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: T cells


title: LOW tissue Week20 - 2

description:
rild_multi.txt
rild_unique.txt
X20WeLo_Ir2_


title: Patient 6 - Follow-up

description:
Targeted TCR sequencing
Patient6_Post_TCRalpha.xlsx
Patient6_Post_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Patient 6 - C6

description:
Targeted TCR sequencing
Patient6_C6_TCRalpha.xlsx
Patient6_C6_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: LOW tissue Week20 - 1

description:
rild_multi.txt
rild_unique.txt
X20WeLo_Ir1_


title: HIGH tissue Week20 - 4

description:
rild_multi.txt
rild_unique.txt
X20WeHi_Ir4_

value: HIGH


title: HIGH tissue Week20 - 1

description:
rild_multi.txt
rild_unique.txt
X20WeHi_Ir1_


title: Control tissue Week20 - L

description:
rild_multi.txt
rild_unique.txt
X20WeHi_Ct5_

value: Non irradiated (LOW location)


title: Control tissue Week20 - H

description:
rild_multi.txt
rild_unique.txt
X20WeLo_Ct5_

value: Non irradiated (HIGH location)


title: Patient 6 - C3 before surgery

description:
Targeted TCR sequencing
Patient6_C3_TCRalpha.xlsx
Patient6_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Patient 6 - Baseline

description:
Targeted TCR sequencing
Patient6_Baseline_TCRalpha.xlsx
Patient6_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: HIGH tissue Week20 - 2

description:
rild_multi.txt
rild_unique.txt
X20WeHi_Ir2_


title: Patient 5 - Baseline

description:
Targeted TCR sequencing
Patient5_Baseline_TCRalpha.xlsx
Patient5_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: LOW tissue Week6 - 3

description:
rild_multi.txt
rild_unique.txt
X06WeLo_Ir3_

value: Week 6


title: LOW tissue Week6 - 4

description:
rild_multi.txt
rild_unique.txt
X06WeLo_Ir4_


title: LOW tissue Week6 - 1

description:
rild_multi.txt
rild_unique.txt
X06WeLo_Ir1_


title: Patient 5 - C6

description:
Targeted TCR sequencing
Patient5_C6_TCRalpha.xlsx
Patient5_C6_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: SOC chemotherapy


title: HIGH tissue Week6 - 4

description:
rild_multi.txt
rild_unique.txt
X06WeHi_Ir4_


title: Patient 4 - Follow-up

description:
Targeted TCR sequencing
Patient4_Post_TCRalpha.xlsx
Patient4_Post_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: HIGH tissue Week6 - 3

description:
rild_multi.txt
rild_unique.txt
X06WeHi_Ir3_


title: HIGH tissue Week6 - 2

description:
rild_multi.txt
rild_unique.txt
X06WeHi_Ir2_


title: Patient 4 - C3 before surgery

description:
Targeted TCR sequencing
Patient4_C3_TCRalpha.xlsx
Patient4_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz


title: Control tissue Week6 - H

description:
rild_multi.txt
rild_unique.txt
X06WeLo_Ct5_


title: HIGH tissue Week6 - 1

description:
rild_multi.txt
rild_unique.txt
X06WeHi_Ir1_


title: Patient 4 - Baseline

description:
Targeted TCR sequencing
Patient4_Baseline_TCRalpha.xlsx
Patient4_Baseline_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: Before therapy


title: LOW tissue Day6 - 3

description:
rild_multi.txt
rild_unique.txt
X06DaLo_Ir3_

value: Day 6


title: U937_rep2

city: Cambridge

first: Johanna

last: Dahlqvist

address: 415 Main street

institute: Broad Institute of MIT and Harvard

data_processing:
library strategy: 4C-seq
In data analysis, we identified reads derived from ligation of distant chromatin interactions using the Bioconductor Basic4Cseq package. We determined regions that contact the FCGR2A promoter (chr1:161475029-161475562) according to enrichment of reads from NlaIII/DpnII fragments (from 4C BAM files), focusing on fragments within 600kb (chr1:161200000-161800000).
Genome_build: hg19
Supplementary_files_format_and_content: Each processed datafile is a bed file containing the location and count of loci interacting with the FCGR2A TSS.

growth_protocol: U937 cells were cultured in standard cell culture medium (RPMI-1640, 10% HIFBS (both Thermo Fisher Scientific), 2 mM L-glutamine, 100 units/ml streptomycin, 100 mg/ml penicillin) in 38 degrees Celsius with 5% CO2.

extract_protocol:
2-5 million U937 cells were cross-linked with 1% v/v formaldehyde for 10 minutes during mixing and reactions were quenched using 0.2M glycine. After washing, cells were lysed for 15 minutes using 300 ul ice-cold 4C lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% Igepal CA630) with 50 μl of protease inhibitors (Sigma, P8340). Pelleted nuclei were washed and resuspended in 50 μl of 0.5% sodium dodecyl sulfate (SDS) and incubated at 62 degrees for 5-10 minutes and reactions were then quenched using 145 μl of water and 25 μl of 10% Triton X-100 (Sigma, 93443). Next, chromatin was digested using DpnII and NlaIII restriction enzymes (New England Biolabs (NEB)) with the following procedure for each enzyme: restriction enzyme was added together with 10X NEB CutSmart and incubated for 2h at 37 degrees with rotation. Reactions were inactivated at 62 degrees, followed by ligation using the ligation master mix (663 μl of water, 120 μl of 10X T4 DNA ligase buffer (NEB), 100 μl of 10% Triton X-100, 12 μl of 10 mg/ml Bovine Serum Albumin (100X BSA), 5 μl of 400 U/ μl T4 DNA Ligase (NEB)) with samples at room temperature for 4h with rotation. Cells were then pelleted at 2,500 g for five minutes, and the supernatant discarded, followed by resuspension in 300 μl buffer (10 mM Tris 0.5 M NaCl, 1% SDS) and addition of 50 μl proteinase K with incubation at 55 degrees for 30 minutes. The temperature was then increased up to 68 degrees overnight. Samples were ethanol precipitated and then purified using 1X Agencourt XP beads (Beckman).
To quantify library, quantitative real-time RT-PCR (qPCR) was used to amplify using anchor primers 5’ and 3’ of the FCGR2A TSS (chr1:161475247; FANTOM5) with Nextera P5 and P7 sequencing adapters (primers: 5’:TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGTTACTGTTCTGCTGGCCGGT, 3’:GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGTCCATTCTGCACCAAACATTCA). The cycle number for the sample to cross threshold in the qPCR was used to determine the number of PCR cycles for library amplification and hence PCR was run for 23 cycles with 100 ng 4C DNA library and NEBNEXT 2X master mix (NEB). Samples were purified using 1X Agencourt XP beads, resuspended in 50 μl Buffer EB, quantified using Qubit (Thermo Fisher Scientific), quality assessed using tape station and finally sequenced using Illumina MiSeq.

tag: cell line

value: Monocytic leukemic cell line

tag: cross-linking

value: 1% v/v formaldehyde

tag: restriction enzymes

value: DpnII and NlaIII (New England Biolabs)

tag: primers for amplification


title: U937_rep1

tag: cell type


title: LOW tissue Day6 - 1

description:
rild_multi.txt
rild_unique.txt
X06DaLo_Ir1_

value: Balb/c


title: LOW tissue Day6 - 2

description:
rild_multi.txt
rild_unique.txt
X06DaLo_Ir2_


title: 293Freestyle_REG1A

city: La Jolla

first: Nathan

middle: E

last: Lewis

state: CA

address: 9500 Gilman Dr

institute: UCSD

data_processing:
The CHO-K1 (Rupp et al., 2018)  and the human GRCh38.p12 reference genomes were extended to incorporate the transgene sequences so that the transcripts of the heterologous secretome can be quantified.
Reads were then quasi-mapped to either the extended CHO-K1 or the human GRCh38.p12 genome based on the origin of cell line and quantified with Salmon(Patro et al., 2017).
Genome_build: C_griseus_v1.0 for CHO cells, GRCh38.p12 for HEK293
Supplementary_files_format_and_content: Excel (.xlsx) file of raw abundance (TPM) in matrix format, with sample names denoted by columns and genes by row. The tabs denote the cell line of origin.

source_name: Human embryonic kidney 293 (HEK293) cells

extract_protocol:
RNA was extracted using RNeasy plus Mini Kit (Qiagen) according to manufacturer’s guidelines and the quality of the isolated RNA was evaluated by BIOanalyzer 2100 (Agilent, Santa Clara, CA) using the Agilent RNA 6000 Nano Kit.
Library preparation was performed with Illumina’s TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: RS-122-2103), according to manufacturer’s protocol

tag: recombinant protein

tag: group

value: producer


title: 293Freestyle_ST6GAL1


title: 293Freestyle_RSPO1


title: 293Freestyle_POSTN

value: POSTN


title: HIGH tissue Day6 - 2

description:
rild_multi.txt
rild_unique.txt
X06DaHi_Ir2_

tag: time


title: 293Freestyle_THBS4


title: HIGH tissue Day6 - 4

description:
rild_multi.txt
rild_unique.txt
X06DaHi_Ir4_


title: 293Freestyle_PAMR1


title: Patient 4 - C6

description:
Targeted TCR sequencing
Patient4_C6_TCRalpha.xlsx
Patient4_C6_TCRbeta.xlsx
See Processed_data_files.tar.gz

tag: tissue

value: peripheral blood

tag: treatment

value: After 6 cycles


title: Patient 5 - C3 before surgery

description:
Targeted TCR sequencing
Patient5_C3_TCRalpha.xlsx
Patient5_C3_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: After 3 cycles


title: HIGH tissue Day6 - 1

description:
rild_multi.txt
rild_unique.txt
X06DaHi_Ir1_

tag: strain


title: Patient 5 - Follow-up

description:
Targeted TCR sequencing
Patient5_Post_TCRalpha.xlsx
Patient5_Post_TCRbeta.xlsx
See Processed_data_files.tar.gz

value: T cells

value: Follow-up


title: 293Freestyle_NRTN_PP


title: Control tissue Week6 - L

description:
rild_multi.txt
rild_unique.txt
X06WeHi_Ct5_

value: Non irradiated (LOW location)


title: Control tissue Day6 - L

description:
rild_multi.txt
rild_unique.txt
X06DaLo_Ct5_


title: 293Freestyle_LOX

value: LOX


title: LOW tissue Day1 - 3

description:
rild_multi.txt
rild_unique.txt
X01DaLo_Ir3_

value: Day 1

value: LOW


title: LOW tissue Day1 - 4

description:
rild_multi.txt
rild_unique.txt
X01DaLo_Ir4_


title: 293Freestyle_JAG2


title: LOW tissue Day1 - 2

description:
rild_multi.txt
rild_unique.txt
X01DaLo_Ir2_


title: 293Freestyle_GCG

value: GCG


title: 293Freestyle_HGF

value: HGF


title: LOW tissue Day1 - 1

description:
rild_multi.txt
rild_unique.txt
X01DaLo_Ir1_


title: HIGH tissue Day1 - 4

description:
rild_multi.txt
rild_unique.txt
X01DaHi_Ir4_

value: HIGH


title: 293Freestyle_FSTL3


title: HIGH tissue Day6 - 3

description:
rild_multi.txt
rild_unique.txt
X06DaHi_Ir3_

value: Day 6


title: HIGH tissue Day1 - 2

description:
rild_multi.txt
rild_unique.txt
X01DaHi_Ir2_


title: 293Freestyle_FN1


title: HIGH tissue Day1 - 1

description:
rild_multi.txt
rild_unique.txt
X01DaHi_Ir1_


title: 293Freestyle_PLG

value: PLG


title: 293Freestyle_FLT3LG


title: Control tissue Day1 - L

description:
rild_multi.txt
rild_unique.txt
X01DaHi_Ct5_

value: Balb/c


title: 293Freestyle_Control_pQMCF2

value: non-producer


title: Control tissue Day1 - H

description:
rild_multi.txt
rild_unique.txt
X01DaLo_Ct5_

value: Non irradiated (HIGH location)


title: 293Freestyle_NRTN

value: NRTN

value: producer


title: 293Freestyle_CCL28


title: 293Freestyle_CXCL13


title: 293Freestyle_BMP10


title: 293Freestyle_CCL20


title: 293Freestyle_ARTN

value: ARTN


title: 293Freestyle_ADM5


title: 293F_THBS4


title: 293Freestyle_AMBP

value: AMBP


title: 293F_RSPO1


title: 293F_ST6GAL1


title: 293Freestyle_ASGR1


title: 293F_REG1A


title: 293F_PLG


title: 293F_NRTN_PP


title: 293F_NRTN


title: 293F_PAMR1


title: HIGH tissue Day1 - 3

description:
rild_multi.txt
rild_unique.txt
X01DaHi_Ir3_


title: 293F_POSTN

value: POSTN


title: 293F_LOX


title: 293Freestyle_Control_pQMCF


title: 293F_JAG2


title: TET2 UA rep3

city: Bethesda

first: Taehoon

last: Shin

address: 9000 Rockville Pike

institute: National Institutes of Health

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina HiSeq 3000 per cycle basecall files were demultiplexed and converted to FASTQ files with adaptor masking using bcl2fastq
High-quality reads were mapped to the ENSEMBL Mmul_8.0.1 whole genome reference FASTA and annotated with the ENSEMBL Mmul_8.0.1 release 95 GTF
Tools from bioconductor in a standard workflow were used to produce BAM files and count matrices for primary analysis
Secondary analysis was carried out with a custom pipeline written in R
Genome_build: ENSEMBL Mmul_8.0.1
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample

organism: Macaca mulatta

source_name: CFU

growth_protocol: BM-derived single CD34+ HSPCs were plated with MethoCult H4435 Enriched medium and grown for 14 days.

extract_protocol:
Single colonies were picked and split for both RNA and DNA. RNA was extracted using Qiagen MicroKit from the colonies with predicted uniallelic TET2 mutation or WT on DNA analysis.
cDNA was synthesized using the SMART-Seq V4 Ultra Low Input RNA Kit and libraries were generated using the Nextera XT DNA Library Preparation Kit.

value: Bone marrow CD34+ HSPCs

tag: timing

value: 15 months post-transplantation


title: TET2 UA rep2

tag: genotype


title: 293F_HGF


title: 293F_GCG


title: 293F_FSTL3


title: 293F_Control_pQMCF2

value: Control


title: 293F_FN1


title: WT rep2

value: wild type


title: 293F_CCL28


title: 293F_Control_pQMCF


title: TET2 UA rep1


title: WT rep3


title: 293F_CCL20


title: 293F_BMP10


title: 293F_CXCL13


title: 293F_ASGR1


title: WT rep1


title: 293F_ARTN


title: Micorwell-seq datasets of Xenopus_testis_COL20

city: Hangzhou

first: Haide

last: Chen

address: 866 Yuhangtang road

institute: Zhejiang University

data_processing:
Base call files were performed with Illumina bcl2fastq.
Sequenced reads were trimmed for adaptor sequences. Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp); UMI:In read1, the bases 49-54 (6bp)
scRNA-seq reads were aligned to the Xenopus laevis J-strain 9.2 genome assembly using STAR (version 2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell/molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix (DGE) based on UMI counts. The cell barcode is tagged with XC, the UMI is tagged with XM, and the gene is tagged with GE.
Genome_build: Xenopus laevis J-strain 9.2
Supplementary_files_format_and_content: Tab-delimited text files of digital expression matrix (DGE) based on raw UMI counts, with genes as rows and cells as columns.

molecule: polyA RNA

organism: Xenopus laevis

extract_protocol:
Tissues or whole-body single-cell dissociation and lysate
Library preparations were performed with the Microwell-seq protocol

value: wild-type

tag: age

value: one year elder

value: testis


title: Micorwell-seq datasets of Xenopus_testis_COL23


title: Micorwell-seq datasets of Xenopus_stomach_COL18

value: stomach


title: 293F_AMBP


title: Micorwell-seq datasets of Xenopus_spleen_COL21

value: spleen


title: 293F_ADM5


title: Micorwell-seq datasets of Xenopus_pancreas_COL19

value: pancreas


title: 293F_FLT3LG


title: Micorwell-seq datasets of Xenopus_lung_COL21

value: lung


title: Micorwell-seq datasets of Xenopus_lung_COL24


title: Micorwell-seq datasets of Xenopus_kidney_COL22

value: kidney


title: Micorwell-seq datasets of Xenopus_kidney_COL19


title: case_4

type: RNA

city: Wuhan

first: Hua

last: Hu

address: 13 Hangkong Road

department: School of Public Health, Tongji Medical College

institute: Huazhong University of Science & Technology

description: To findout new differentially expressed miRNA in plasma among newly diagnosed diabetic cases and healthy controls

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.       a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first             denatured for 2 min at 95°C, incubated on ice for 2 min      b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization             System - Nimblegen Systems, Inc., Madison, WI, USA)        c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: a) The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been averaged.  b) We use Median Normalization Method to obtain “Normalized Data”, Normalized Data= (Foreground-Background)¬/¬median, the median is 50 percent quantile of microRNA intensity which is larger than 30 in all samples after background correction.  c) After normalization, the statistical significance of differentially expressed miRNA was analyzed by T-test.

source_name: diabetic case_4

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:      a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture             was incubated for 30 min at 37°C.         b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of             fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling             reaction was incubated for 1 h at 16°C      c, Terminated by incubation for 15 min at 65°C

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

value: plasma

tag: status of diabetic at 2013

value: newly diagnosed

tag: gender

value: female

value: 64 years


title: case_9

source_name: diabetic case_9

value: 55 years


title: case_6

source_name: diabetic case_6

value: 62 years


title: case_10

source_name: diabetic case_10

value: 69 years


title: case_1

source_name: diabetic case_1

value: 60 years


title: case_11

source_name: diabetic case_11


title: case_3

source_name: diabetic case_3

value: 59 years


title: Micorwell-seq datasets of Xenopus_intestine_COL23

value: wild-type

value: intestine


title: case_14

source_name: diabetic case_14

value: male

value: 61 years


title: Micorwell-seq datasets of Xenopus_kidney_COL17

value: one year elder


title: case_2

source_name: diabetic case_2

value: 83 years


title: case_7

source_name: diabetic case_7

value: 52 years


title: case_13

source_name: diabetic case_13


title: case_12

source_name: diabetic case_12

value: 73 years


title: case_8

source_name: diabetic case_8

value: plasma

value: 70 years


title: case_5

source_name: diabetic case_5

value: newly diagnosed

value: female

value: 57 years


title: Micorwell-seq datasets of Xenopus_intestine_COL22


title: case_15

source_name: diabetic case_15

value: 58 years


title: control_12

source_name: healthy control_12

value: healthy


title: control_10

source_name: healthy control_10


title: 15D_K2

city: Daegu

first: Ji Hwan

last: Park

state: Gyeongbuk

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Newbiology

country: South Korea

institute: DGIST

description: Gene expression of old human dermal fibroblasts in 15 days post treatment of KU60019. [rep2]

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Human dermal fibroblasts, old cell,15 days post treatment of KU60019, replicated 2

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: Human dermal fibroblasts originated from neonatal (PCS-201-010; ATCC) was used in this research. Cells were cultured in Dulbecco's modified Eagle's medium containing 25 mM glucose supplemented with 10% FBS (SH30919.03; Hyclone), 100 U/ml penicillin, and 100 μg/ml streptomycin (SV30079.01; Hyclone). Confluent cells were serially passaged with 1:4 split during early passages (~p45) and 1:3 (~p47) or 1:2 split during late passages (~p50). When the above 90% of cells were stained by SA-ß-galactosidase staining, and population-doubling time (PD) of the cells was longer than 14days, it was considered senescent cells. On the contrary, cells that possess population doubling time shorter than 2 days were regarded as young cells. Cells were tested for mycoplasma contamination with a Mycoalert mycoplasma-detection kit (LT07-318; Lonza).

extract_protocol: To extract RNA with high purity, cells were lysed with QIAzol lysis reagent (#79306 Qiazen), then precipitated with isopropanol. after washing with ethanol, RNA is diluted with DEPC, RNase free water. RNA Integrity Number (RIN) was checked using Bioanalyzer 2100, with Agilent RNA 6000 Nano Kit according to a standard protocol, average RIN value was 9.1.

treatment_protocol: For drug treatment, 2.5μM Y27632 and 0.5μM KU60019 were used each.

tag: condition

value: old cell (population-doubling time of the cells was longer than 14 days)

tag: time point

value: 15 days post treatment


title: 15D_combi2

description: Gene expression of old human dermal fibroblasts in 15 days post co-treatment of Y27632 and KU60019. [rep2]

source_name: Human dermal fibroblasts, old cell,15 days post co-treatment of Y27632 and KU60019, replicated 2

value: Human dermal fibroblasts originated from neonatal (PCS-201-010; ATCC)


title: 15D_combi1

description: Gene expression of old human dermal fibroblasts in 15 days post co-treatment of Y27632 and KU60019. [rep1]

source_name: Human dermal fibroblasts, old cell,15 days post co-treatment of Y27632 and KU60019, replicated 1


title: 15D_combi3

description: Gene expression of old human dermal fibroblasts in 15 days post co-treatment of Y27632 and KU60019. [rep3]

source_name: Human dermal fibroblasts, old cell,15 days post co-treatment of Y27632 and KU60019, replicated 3


title: Micorwell-seq datasets of Xenopus_intestine_COL19

value: wild-type

value: intestine


title: 15D_K1

description: Gene expression of old human dermal fibroblasts in 15 days post treatment of KU60019. [rep1]

source_name: Human dermal fibroblasts, old cell,15 days post treatment of KU60019, replicated 1


title: Micorwell-seq datasets of Xenopus_eye_COL21

value: eye


title: control_6

source_name: healthy control_6

value: male

value: 62 years


title: control_9

source_name: healthy control_9


title: control_15

source_name: healthy control_15

value: 66 years


title: 15D_Y3

description: Gene expression of old human dermal fibroblasts in 15 days post treatment of Y27632. [rep3]

source_name: Human dermal fibroblasts, old cell,15 days post treatment of Y27632, replicated 3


title: Micorwell-seq datasets of Xenopus_bladder_COL22

value: one year elder

value: bladder


title: 15D_Y2

description: Gene expression of old human dermal fibroblasts in 15 days post treatment of Y27632. [rep2]

source_name: Human dermal fibroblasts, old cell,15 days post treatment of Y27632, replicated 2


title: 15D_K3

description: Gene expression of old human dermal fibroblasts in 15 days post treatment of KU60019. [rep3]

source_name: Human dermal fibroblasts, old cell,15 days post treatment of KU60019, replicated 3


title: Micorwell-seq datasets of Xenopus_stomach_COL20

value: stomach


title: 15D_Y1

description: Gene expression of old human dermal fibroblasts in 15 days post treatment of Y27632. [rep1]

source_name: Human dermal fibroblasts, old cell,15 days post treatment of Y27632, replicated 1


title: control_4

source_name: healthy control_4

value: plasma


title: control_7

source_name: healthy control_7

value: 60 years


title: control_13

source_name: healthy control_13

value: 52 years


title: control_14

source_name: healthy control_14

value: 55 years


title: MHCC97H_RNC-nanopore

city: guangzhou

first: Gong

last: Zhang

address: Jinan University, No.601, West Huangpu Avenue ，Guangzhou, Guangdong, China.

institute: Jinan University

data_processing:
Base-calling was performed with MinKNOW(V 3.6.5).
Reads were aligned to GRCh38 no-alt analysis set (accession GCA_00001405.15) using minimap2 v2.7-r654 in spliced alignment mode with the command: minimap2 -ax splice -uf -k14 -secondary=no.
FLAIR correct (v1.5) was used to correct the splice-site boundaries of reads.
Genome_build: GRCh38, accession GCA_000001405.15
Supplementary files format and content: Flair correct data contains identified isoforms
Supplementary files format and content: count data

source_name: MHCC97H cells

growth_protocol: MHCC97H cells were cultured in the DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 10 μg/mL ciprofloxacin, and both of cells were detected mycoplasma negative during maintenance and upon experiments.

extract_protocol: Direct RNA Sequencing Kit (Oxford Nanopore Technologies plc, Oxford, UK) was used for full-length RNC-seq library preparation. The prepared library was load into a MinION flow cell (Oxford Nanopore Technologies plc, Oxford, UK) and sequenced on MinION device (Oxford Nanopore Technologies plc, Oxford, UK).

treatment_protocol: MHCC97H cells were pre-treated with 100 μg/mL cycloheximide (Acmec, Shanghai, China) for 10 min at 37°C, followed by 5 mL pre-colded PBS (Beyotime, Shanghai, China) washes twice and lysis for 30 min on ice by 2 mL pre-cooled human cell lysis buffer (20 mM Tris-HCl, 5 mM MgCl2, 150 mM KCl, 1 mM DTT, 100 μg/mL cycloheximide, 25 units/ml Turbo DNase I, 1% Triton X-100). Cell lysates were clarified by centrifuge at 17000 x g at 4°C for 15 min, supernatants were transferred on the surface of 14.5mL sucrose cushion (30% sucrose, 20 mM Tris-HCl, 5 mM MgCl2, 150 mM KCl, 1 mM DTT, 100 μg/mL cycloheximide). RNCs were purified by ultra-centrifugation in a Type 70Ti rotor (Beckman Coulter, Brea, CA, USA) at 185,000 x g for 5 h at 4°C.

value: liver cancer cells

tag: cell line

tag: molecule subtype

value: ribosome nascent-chain complex(RNC)


title: control_2

source_name: healthy control_2

value: healthy

value: 83 years


title: 009T

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

description: Saline-treated SIV-infected rhesus monkey with encephalitis, enriched microglia/brain macrophages

data_processing:
Cellranger pipeline (version 3.1.0) was used here. Cellranger mkfastq was used for demultiplexing and generate fastq files and cellranger count was used to align the reads to Mmul10 and M33262.1 reference genomes.
M33262.1 was split and annotated into 5 regions as described in the manuscript.
Genome_build: Mmul10
Genome_build: M33262.1
Supplementary_files_format_and_content: H5 files were created from cellranger count to store the matrix of UMI per gene per cell for each sample

source_name: Rhesus macaque CD11b enriched brain microgla and macrophages

extract_protocol:
Brains were removed at necropsy, microglia/macrophage enriched cells were isolated from the brain and cryopreserved. Isolates were immunomagnetically enriched for CD11b+ cells, and then flow cytometry sorted for CD11b positive, live events, and processed for scRNA.
scRNA10x Genomics Chromium GEM Chip and placed into Chromium Controller for library preparation. The prepared libraries  were sequenced using Illumina Nextseq550 sequencer.

value: Enriched brain microglia and macrophages

tag: agent

value: SIVmac251, SIVE, saline

tag: protocol

value: Saline before and after SIVmac251 infection


title: control_3

source_name: healthy control_3

value: male

value: 61 years


title: 83T

description: Saline-treated monkey, SIVmac251-infected, cART, latent SIV+I31:I33, enriched microglia/brain macrophages

tag: cell type

value: SIVmac251, SIV, cART, dolutegravir, tenofovir, emtricitabine


title: WT-T-3

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

data_processing:
Demultiplexing and FASTQ data generation was carried out on BaseSpace (Illumina’s cloud-base resource).
Reads were aligned to the Arabidopsis genome using the spliced-aligner STAR (version 2.5.2b, (45)). Reads were required to map to an unique location on the genome, whilst allowing up to 4% mismatched bp per read (--outFilterMismatchNoverLmax 0.04). STAR was run in the 2-pass mode to achieve sensitive discovery of splice junctions.
All resulting read alignments (.BAM) files were used for transcript discovery by performing a Araport11-guided transcript assembly using Scallop (version 1.3.3b, (76)) with option “—min_transcript_coverage 10”. The generated assemblies per sample were compared to the Araport11 reference annotation using gffcompare. In addition, in-house scripts were used to filter for transcripts having non-canonical splice junctions or splice junctions not supported by 20 unique reads in at least 3 samples. In addition, transcripts were required to solely match exon-intron junctions of one Araport11 gene locus, to avoid merging exons of different gene loci. In total, this resulted in 16,761 novel transcripts that were appended to the annotated Araport11 transcripts.
For transcript and gene quantification we used the pseudo-alignment tool Kallisto (version 0.43.0). Initially, a Kallisto index was created using the Araport11 and 16,761 novel assembled transcript sequences. Reads were quantified using 100 bootstraps and bias correction (“-b 100 --bias”).
kallisto_expression_matrix: Kallisto pseudocounts for all genes
Genome_build: Araport11 + Scallop assembled transcripts
Supplementary_files_format_and_content: GTF annotation file including Araport annotation and Scallop-assembled transcripts,  kallisto quantification matrix for transcripts and genes

organism: Arabidopsis thaliana

source_name: Col-0 total RNA

growth_protocol: For the in vitro stress assays, seeds were first sterilized using gas sterilization and stratified for 3 days. Seeds were then sown on growth medium containing half-strength MS salts, 1% (w/v) sucrose, 100 mg L−1 myo-inositol, 500 mg L−1 MES, 0.5 mg L−1 nicotinic acid, 0.5 mg L−1 pyridoxine, 1 mg L−1 thiamine and 7% plant tissue culture agar (Duchefa) at 21°C and long-day conditions (16 h light [80 μmol m−2 s−1]/8 h dark).

extract_protocol:
RNA was isolated from three-week-old seedling shoot tissue using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA).
The Illumina NextSeq 500 High sequencer was used to generate 150bp paired end reads at the VIB nucleomics core facility (http://nucleomics.be/). Sequencing libraries were constructed with the TruSeq Stranded LT mRNA Library Preparation Kit (Illumina).

treatment_protocol: Plants shoots were harvested at control conditions after three weeks of growth.

tag: ecotype background

tag: genotype/variation

value: wild type

value: Three-week-old seedling shoot tissue

value: total RNA


title: control_8

source_name: healthy control_8

tag: tissue

value: plasma

value: 70 years


title: 15D_Ct3

description: Gene expression of old human dermal fibroblasts in 15 days post treatment of DMSO (control). [rep3]

source_name: Human dermal fibroblasts, old cell,15 days post treatment of DMSO (control), replicated 3

value: Human dermal fibroblasts originated from neonatal (PCS-201-010; ATCC)

value: old cell (population-doubling time of the cells was longer than 14 days)

value: 15 days post treatment

tag: treatment

value: DMSO


title: WT-T-2


title: 82T


title: WT-T-1


title: KO-T-3

source_name: smeb-1 total RNA


title: control_11

source_name: healthy control_11

value: healthy

value: 57 years


title: control_5

source_name: healthy control_5

value: 58 years


title: control_1

source_name: healthy control_1

value: 59 years


title: 74T

value: Enriched brain microglia and macrophages

value: Saline before and after SIVmac251 infection


title: KO-T-1


title: CHO_THBS4

organism: Cricetulus griseus

source_name: Chinese hamster ovary (CHO) cells

value: CHO

tag: recombinant protein

tag: group

value: producer


title: 31T

description: Saline-treated monkey, SIVmac251-infected, enriched microglia/brain macrophages

value: SIVmac251, SIV


title: CHO_RSPO1


title: 15D_Ct2

description: Gene expression of old human dermal fibroblasts in 15 days post treatment of DMSO (control). [rep2]

source_name: Human dermal fibroblasts, old cell,15 days post treatment of DMSO (control), replicated 2


title: 8D_combi2

description: Gene expression of old human dermal fibroblasts in 8 days post co-treatment of Y27632 and KU60019. [rep2]

source_name: Human dermal fibroblasts, old cell,8 days post co-treatment of Y27632 and KU60019, replicated 2

value: 8 days post treatment


title: 8D_combi3

description: Gene expression of old human dermal fibroblasts in 8 days post co-treatment of Y27632 and KU60019. [rep3]

source_name: Human dermal fibroblasts, old cell,8 days post co-treatment of Y27632 and KU60019, replicated 3


title: CHO_POSTN

value: POSTN


title: 8D_K3

description: Gene expression of old human dermal fibroblasts in 8 days post treatment of KU60019. [rep3]

source_name: Human dermal fibroblasts, old cell,8 days post treatment of KU60019, replicated 3


title: 8D_K2

description: Gene expression of old human dermal fibroblasts in 8 days post treatment of KU60019. [rep2]

source_name: Human dermal fibroblasts, old cell,8 days post treatment of KU60019, replicated 2


title: 15D_Ct1

description: Gene expression of old human dermal fibroblasts in 15 days post treatment of DMSO (control). [rep1]

source_name: Human dermal fibroblasts, old cell,15 days post treatment of DMSO (control), replicated 1


title: KO-T-2

value: Three-week-old seedling shoot tissue

value: total RNA


title: CHO_REG1A


title: 8D_K1

description: Gene expression of old human dermal fibroblasts in 8 days post treatment of KU60019. [rep1]

source_name: Human dermal fibroblasts, old cell,8 days post treatment of KU60019, replicated 1

value: Human dermal fibroblasts originated from neonatal (PCS-201-010; ATCC)


title: CHO_NRTN_PP


title: 23T

source_name: Rhesus macaque CD11b enriched brain microgla and macrophages


title: 8D_combi1

description: Gene expression of old human dermal fibroblasts in 8 days post co-treatment of Y27632 and KU60019. [rep1]

source_name: Human dermal fibroblasts, old cell,8 days post co-treatment of Y27632 and KU60019, replicated 1

value: old cell (population-doubling time of the cells was longer than 14 days)


title: 25T


title: CHO_PLG

value: PLG


title: CHO_NRTN

value: NRTN


title: CHO_PAMR1


title: CHO_LOX

value: LOX


title: CHO_HGF

value: HGF


title: 41T

description: Saline-treated monkey, enriched microglia/brain macrophages

value: saline

value: saline for duration of study


title: 38T

value: Enriched brain microglia and macrophages


title: CHO_JAG2


title: CHO_ST6GAL1


title: 8D_Y3

description: Gene expression of old human dermal fibroblasts in 8 days post treatment of Y27632. [rep3]

source_name: Human dermal fibroblasts, old cell,8 days post treatment of Y27632, replicated 3


title: 16T

description: Saline-treated Monkey, enriched microglia/brain macrophages


title: CHO_GCG

value: GCG


title: CHO_FSTL3

value: CHO


title: 8D_Y2

description: Gene expression of old human dermal fibroblasts in 8 days post treatment of Y27632. [rep2]

source_name: Human dermal fibroblasts, old cell,8 days post treatment of Y27632, replicated 2


title: CHO_FN1

value: producer


title: CHO_Control_pQMCF2

value: Control

value: non-producer


title: CHO_CCL28


title: CHO_CXCL13


title: 8D_Ct2

description: Gene expression of old human dermal fibroblasts in 8 days post treatment of DMSO (control). [rep2]

source_name: Human dermal fibroblasts, old cell,8 days post treatment of DMSO (control), replicated 2

value: 8 days post treatment

value: DMSO


title: CHO_Control_pQMCF


title: CHO_CCL20


title: 8D_Y1

description: Gene expression of old human dermal fibroblasts in 8 days post treatment of Y27632. [rep1]

source_name: Human dermal fibroblasts, old cell,8 days post treatment of Y27632, replicated 1


title: CHO_BMP10


title: 8D_Ct1

description: Gene expression of old human dermal fibroblasts in 8 days post treatment of DMSO (control). [rep1]

source_name: Human dermal fibroblasts, old cell,8 days post treatment of DMSO (control), replicated 1


title: 8D_Ct3

description: Gene expression of old human dermal fibroblasts in 8 days post treatment of DMSO (control). [rep3]

source_name: Human dermal fibroblasts, old cell,8 days post treatment of DMSO (control), replicated 3


title: CHO_AMBP

value: AMBP


title: CHO_ADM5


title: CHO_FLT3LG


title: CHO_ASGR1


title: CHO_ARTN

value: ARTN


title: Healthy control_H2

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: PBMCs derived from healthy control_H2

data_processing:
Sequencing was performed on a DNBSEQ-G400RS platform in 2 x 100 bp paired-end mode.
The sequenced reads were mapped to the human reference genome  sequences (hg19) using TopHat, version 2.0.13, in combination with  Bowtie2, version 2.2.3, and SAMtools, version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM processed value in csv file

source_name: Healthy control_H2

extract_protocol:
Total RNA isolation of leukocytes from 31 COVID-19 patients on day1 and 16 healthy controls in the Osaka Covid-19 Cohort was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA). The collection tubes were stored after blood collection until further analysis at -30°C.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions. DNA libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

value: peripheral blood mononuclear cells

tag: diagnosis

value: healthy


title: HKb1

city: Kyoto

first: Munemasa

last: Nagao

state: Kyoto

address: 54 Kawaharacho, Shogoin, Sakyoku

department: Gastroenterology

institute: Kyoto University Graduate School of Medicine

description: gene expression of biliary spheroids derived from Hnf1bCreER;Kras;Ctnnb1 mice

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

label: biotin

source_name: biliary spheroid

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

extract_protocol: RNA was prepared using the RNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genotype


title: Healthy control_H9

description: PBMCs derived from healthy control_H9

source_name: Healthy control_H9


title: HKb2


title: Healthy control_H8

description: PBMCs derived from healthy control_H8

source_name: Healthy control_H8


title: Hb2

description: gene expression of biliary spheroids derived from Hnf1bCreER;Ctnnb1 mice


title: Healthy control_H25

description: PBMCs derived from healthy control_H25

source_name: Healthy control_H25


title: 3D_K3

description: Gene expression of old human dermal fibroblasts in 3 days post treatment of KU60019. [rep3]

source_name: Human dermal fibroblasts, old cell,3 days post treatment of KU60019, replicated 3

value: Human dermal fibroblasts originated from neonatal (PCS-201-010; ATCC)

value: old cell (population-doubling time of the cells was longer than 14 days)

value: 3 days post treatment


title: Healthy control_H7

description: PBMCs derived from healthy control_H7

source_name: Healthy control_H7


title: 3D_combi1

description: Gene expression of old human dermal fibroblasts in 3 days post co-treatment of Y27632 and KU60019. [rep1]

source_name: Human dermal fibroblasts, old cell,3 days post co-treatment of Y27632 and KU60019, replicated 1


title: Healthy control_H24

description: PBMCs derived from healthy control_H24

source_name: Healthy control_H24


title: 3D_combi2

description: Gene expression of old human dermal fibroblasts in 3 days post co-treatment of Y27632 and KU60019. [rep2]

source_name: Human dermal fibroblasts, old cell,3 days post co-treatment of Y27632 and KU60019, replicated 2


title: 3D_K2

description: Gene expression of old human dermal fibroblasts in 3 days post treatment of KU60019. [rep2]

source_name: Human dermal fibroblasts, old cell,3 days post treatment of KU60019, replicated 2


title: Hb3


title: 3D_K1

description: Gene expression of old human dermal fibroblasts in 3 days post treatment of KU60019. [rep1]

source_name: Human dermal fibroblasts, old cell,3 days post treatment of KU60019, replicated 1


title: HKb3


title: Hb1


title: 3D_combi3

description: Gene expression of old human dermal fibroblasts in 3 days post co-treatment of Y27632 and KU60019. [rep3]

source_name: Human dermal fibroblasts, old cell,3 days post co-treatment of Y27632 and KU60019, replicated 3


title: Healthy control_H22

description: PBMCs derived from healthy control_H22

source_name: Healthy control_H22


title: Healthy control_H23

description: PBMCs derived from healthy control_H23

source_name: Healthy control_H23


title: Healthy control_H19

description: PBMCs derived from healthy control_H19

source_name: Healthy control_H19


title: Healthy control_H1

description: PBMCs derived from healthy control_H1

source_name: Healthy control_H1


title: Healthy control_H21

description: PBMCs derived from healthy control_H21

source_name: Healthy control_H21


title: HK2

description: gene expression of biliary spheroids derived from Hnf1bCreER;Kras mouse

source_name: biliary spheroid


title: 3D_Y2

description: Gene expression of old human dermal fibroblasts in 3 days post treatment of Y27632. [rep2]

source_name: Human dermal fibroblasts, old cell,3 days post treatment of Y27632, replicated 2


title: Healthy control_H16

description: PBMCs derived from healthy control_H16

source_name: Healthy control_H16


title: Healthy control_H20

description: PBMCs derived from healthy control_H20

source_name: Healthy control_H20


title: Healthy control_H15

description: PBMCs derived from healthy control_H15

source_name: Healthy control_H15


title: Healthy control_H14

description: PBMCs derived from healthy control_H14

source_name: Healthy control_H14


title: COVID-19 patient_COV99

description: PBMCs derived from COVID-19 patient_COV99

source_name: COVID-19 patient_COV99


title: COVID-19 patient_COV97

description: PBMCs derived from COVID-19 patient_COV97

source_name: COVID-19 patient_COV97


title: Healthy control_H11

description: PBMCs derived from healthy control_H11

source_name: Healthy control_H11


title: HK1


title: COVID-19 patient_COV90

description: PBMCs derived from COVID-19 patient_COV90

source_name: COVID-19 patient_COV90


title: COVID-19 patient_COV87

description: PBMCs derived from COVID-19 patient_COV87

source_name: COVID-19 patient_COV87


title: BN_P3_RRBS

city: Loma Linda

first: Charles

last: Wang

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

description: bisulfite conversion

data_processing:
NextSeq 550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
RRBS fastq header contained 6 nt index sequence and 6 random nt (N6 NuGen RRBS duplicate information). Adaptors and low quality reads were trimmed with Trim_galore v0.4.5. and reads containing adapter were discarded. Following adaptor and quality trimming, the fastq files were further trimmed with NuGEN custom python script trimRRBSdiversityAdaptCustomers.py. Potential PCR or optical duplicates were removed using NuGEN python script Nudup.py
Trimmed reads was aligned to rat genome Rnor_6.0, allowing for 1 mismatch and retaining only uniquely mapped reads. Bam files were generated using Bismark v0.16.34. CpG coverage reports were generated using MethylKit (v1.16.1) from bam files.
RNA-seq fastq files were trimmed with trimmomatic, aligned to rat genome with STAR (v2.5.2), and reads were qunatified with Htseq_count (v0.6.1). Gene differential expression was analyzed using edgeR (v3.26.8) with FPKM threshold of 1.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Processed methylation data is uploaded as CpG reports in txt format. Process RNA-seq data is uploaded raw count matrix in csv format.

organism: Rattus norvegicus

source_name: BN, P18

growth_protocol: 6-8 week-old female rats

extract_protocol:
QIAGEN AllPrep DNA/RNA/miRNA Universal Kit protocol
RRBS: NuGen Ovation RRBS Methyl-Seq protocol with QIAGEN EpiTech Fast DNA Bisulfite Kit for bisulfite conversion. RNA-seq NuGen Universal RNA-seq library protocol for rat.
RRBS: Bisulfite-seq (reduced representation). RNA-seq: total stranded RNA with ribosomal RNA depletion.

treatment_protocol: pregnancy

tag: strain

value: BN

tag: developmental stage

value: pregnant (day18)

value: kidney

tag: age

value: two-month

tag: Sex

value: female


title: 3D_Y1

description: Gene expression of old human dermal fibroblasts in 3 days post treatment of Y27632. [rep1]

source_name: Human dermal fibroblasts, old cell,3 days post treatment of Y27632, replicated 1

tag: condition

tag: time point


title: H3

description: gene expression of biliary spheroids derived from Hnf1bCreER mouse


title: H2


title: HK3


title: 3D_Ct3

description: Gene expression of old human dermal fibroblasts in 3 days post treatment of DMSO (control). [rep3]

source_name: Human dermal fibroblasts, old cell,3 days post treatment of DMSO (control), replicated 3


title: young_2

description: Gene expression of young human dermal fibroblasts. [rep2]

source_name: Human dermal fibroblasts, young cell, replicated 2

value: young cell (population-doubling time of the cells was shorter than 2 days)


title: COVID-19 patient_COV86

description: PBMCs derived from COVID-19 patient_COV86

source_name: COVID-19 patient_COV86


title: BN_P1_RRBS

description: bisulfite conversion


title: 3D_Y3

description: Gene expression of old human dermal fibroblasts in 3 days post treatment of Y27632. [rep3]

source_name: Human dermal fibroblasts, old cell,3 days post treatment of Y27632, replicated 3


title: COVID-19 patient_COV81

description: PBMCs derived from COVID-19 patient_COV81

source_name: COVID-19 patient_COV81


title: COVID-19 patient_COV75

description: PBMCs derived from COVID-19 patient_COV75

source_name: COVID-19 patient_COV75


title: 3D_Ct1

description: Gene expression of old human dermal fibroblasts in 3 days post treatment of DMSO (control). [rep1]

source_name: Human dermal fibroblasts, old cell,3 days post treatment of DMSO (control), replicated 1


title: BN_P2_RRBS

description: bisulfite conversion


title: 3D_Ct2

description: Gene expression of old human dermal fibroblasts in 3 days post treatment of DMSO (control). [rep2]

source_name: Human dermal fibroblasts, old cell,3 days post treatment of DMSO (control), replicated 2


title: COVID-19 patient_COV78

description: PBMCs derived from COVID-19 patient_COV78

source_name: COVID-19 patient_COV78


title: BN_NP3_RRBS

description: bisulfite conversion

source_name: BN, non-pregnant

value: non-pregnant


title: COVID-19 patient_COV70

description: PBMCs derived from COVID-19 patient_COV70

source_name: COVID-19 patient_COV70


title: COVID-19 patient_COV73

description: PBMCs derived from COVID-19 patient_COV73

source_name: COVID-19 patient_COV73


title: BN_NP1_RRBS

description: bisulfite conversion


title: BN_NP2_RRBS

description: bisulfite conversion


title: COVID-19 patient_COV6

description: PBMCs derived from COVID-19 patient_COV6

source_name: COVID-19 patient_COV6


title: COVID-19 patient_COV68

description: PBMCs derived from COVID-19 patient_COV68

source_name: COVID-19 patient_COV68


title: CD_P3_RRBS

description: bisulfite conversion

source_name: CD, P18

value: CD


title: COVID-19 patient_COV59

description: PBMCs derived from COVID-19 patient_COV59

source_name: COVID-19 patient_COV59


title: COVID-19 patient_COV57

description: PBMCs derived from COVID-19 patient_COV57

source_name: COVID-19 patient_COV57


title: CD_P2_RRBS

description: bisulfite conversion


title: COVID-19 patient_COV53

description: PBMCs derived from COVID-19 patient_COV53

source_name: COVID-19 patient_COV53


title: COVID-19 patient_COV43

description: PBMCs derived from COVID-19 patient_COV43

source_name: COVID-19 patient_COV43


title: COVID-19 patient_COV50

description: PBMCs derived from COVID-19 patient_COV50

source_name: COVID-19 patient_COV50


title: COVID-19 patient_COV45

description: PBMCs derived from COVID-19 patient_COV45

source_name: COVID-19 patient_COV45


title: COVID-19 patient_COV72

description: PBMCs derived from COVID-19 patient_COV72

source_name: COVID-19 patient_COV72


title: human FLS cell line, 3D culture in matrigel, bio rep 2

city: Guangzhou

first: Jongdae

last: Lee

state: Guangdong

address: No.195, Dongfengxi Road,

department: School of Basic Medicines

institute: Guangzhou Medical University

data_processing:
HISAT2 (v2.0.4)
Sequencing quality was assessed using Agilent 4200 Bioanalyzer. The sequencing data was filtered with SOAPnuke (v1.5.2) to remove the reads containing the sequencing adapter; Reads whose low-quality base ratio (base quality less than or equal to 5) was more than 20% were removed; After removing reads whose unknown base ('N' base) ratio is more than 5%, the clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4), and then expression level of gene was calculated by STRING TIE (v1.2.3).
To get an insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by P value with a rigorous threshold (P value ≤ 0.05) by Bonferroni.
Assembly: hg18
Supplementary files format and content: csv file of read counts for all genes for each sample
Supplementary files format and content: csv file of read counts for all transcripts for each sample
Supplementary files format and content: csv file include FPKM values of all genes for each sample
Supplementary files format and content: csv file include FPKM values of all transcripts for each sample

source_name: Synovium

growth_protocol: 2D FLS were cultured in DMEM medium supplemented with 10% FBS, and antibiotics on plastic tissue culture plate, and 3D FLS were cultured in matrigel diluted 1:3 in complete growth medium. Cells were kept at proper confluency in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol (ThermoFisher Scientific).
RNAseq libraries were prepared using the VAHTS TM mRNAseq V2 Library Prep Kit for Illumina® (Vazyme #NR601), and libraries were sequenced on an Illumina Xten to a read depth of 25–35 million reads per sample.

treatment_protocol: FLS were cultured in plastic tissue culture plate (2D) for 2 days or Vitrogel for 7 days and stimulated with TNFα (1ng/ml) for 2h in duplicates. Total RNAs were collected and subjected to RNAseq.

value: Synovium

tag: cell line

value: Fibroblast-like synoviocytes

value: synoviocyte

value: WT

value: 3D culture


title: CD_P1_RRBS

description: bisulfite conversion


title: human FLS cell line, 3D culture in matrigel, bio rep 1


title: COVID-19 patient_COV41

description: PBMCs derived from COVID-19 patient_COV41

source_name: COVID-19 patient_COV41

value: peripheral blood mononuclear cells


title: COVID-19 patient_COV38

description: PBMCs derived from COVID-19 patient_COV38

source_name: COVID-19 patient_COV38


title: human FLS cell line, 3D culture in matrigel,TNFa stimulated,  bio rep 1

value: 3D culture+TNFa


title: human FLS cell line, 3D culture in matrigel,TNFa stimulated,  bio rep 2


title: COVID-19 patient_COV65

description: PBMCs derived from COVID-19 patient_COV65

source_name: COVID-19 patient_COV65


title: COVID-19 patient_COV35

description: PBMCs derived from COVID-19 patient_COV35

source_name: COVID-19 patient_COV35


title: COVID-19 patient_COV33

description: PBMCs derived from COVID-19 patient_COV33

source_name: COVID-19 patient_COV33


title: human FLS cell line, 2D culture (on plastic tissue culture plate), TNFa stimulated, bio rep 2

value: adherent culture+TNFa


title: young_3

description: Gene expression of young human dermal fibroblasts. [rep3]

source_name: Human dermal fibroblasts, young cell, replicated 3

value: Human dermal fibroblasts originated from neonatal (PCS-201-010; ATCC)


title: COVID-19 patient_COV27

description: PBMCs derived from COVID-19 patient_COV27

source_name: COVID-19 patient_COV27


title: COVID-19 patient_COV62

description: PBMCs derived from COVID-19 patient_COV62

source_name: COVID-19 patient_COV62


title: COVID-19 patient_COV1

description: PBMCs derived from COVID-19 patient_COV1

source_name: COVID-19 patient_COV1


title: BN_P3_RNAseq

description:
stranded, rRNA depletion
RNAseq_counts.csv

source_name: BN, P18

value: BN


title: H1

description: gene expression of biliary spheroids derived from Hnf1bCreER mouse

source_name: biliary spheroid


title: COVID-19 patient_COV112

description: PBMCs derived from COVID-19 patient_COV112

source_name: COVID-19 patient_COV112


title: human FLS cell line, 2D culture (on plastic tissue culture plate), bio rep 2

value: adherent culture


title: CD_NP3_RRBS

description: bisulfite conversion

source_name: CD, non-pregnant

value: kidney


title: CD_NP2_RRBS

description: bisulfite conversion

value: two-month


title: COVID-19 patient_COV108

description: PBMCs derived from COVID-19 patient_COV108

source_name: COVID-19 patient_COV108


title: young_1

description: Gene expression of young human dermal fibroblasts. [rep1]

source_name: Human dermal fibroblasts, young cell, replicated 1


title: BN_P2_RNAseq

value: pregnant (day18)

value: female


title: BN_P1_RNAseq


title: human FLS cell line, 2D culture (on plastic tissue culture plate), bio rep 1


title: COVID-19 patient_COV105

description: PBMCs derived from COVID-19 patient_COV105

source_name: COVID-19 patient_COV105


title: COVID-19 patient_COV102

description: PBMCs derived from COVID-19 patient_COV102

source_name: COVID-19 patient_COV102


title: human FLS cell line, 2D culture (on plastic tissue culture plate), TNFa stimulated, bio rep 1

source_name: Synovium


title: CD_NP1_RRBS

description: bisulfite conversion

value: non-pregnant


title: BN_NP3_RNAseq

source_name: BN, non-pregnant


title: 60_R

city: Fort Collins

first: Thomas

middle: J

last: LaRocca

state: CO

address: 1582 Campus Delivery

institute: Colorado State University

data_processing:
Adapters trimmed & file QC by Fastp
Reads aligned with STAR (hg38) and counting with LiBiNorm
Differential expression analyzed with DESeq2
Supplementary files format and content: count matrix

source_name: healthy adult woman

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns.
PolyA libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit

tag: pre or post

value: post

tag: r or nr

value: R

value: PBMC


title: 58_NR

value: NR

tag: cell type


title: Cells in preovulatory follicle of patient 6

city: Suzhou

first: Huihua

last: Wu

address: NO. 26, Daoqian road

institute: The Affiliated Suzhou Hospital of Nanjing Medical University

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Genome_build: Grch38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cells in preovulatory follicle of IVF

extract_protocol:
The first punctured follicle with 18-20mm diameter was used. The follicular fluid and  cumulus cells were collected for scRNA-seq
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).
scRNA_seq

treatment_protocol: IVF controlled ovarian stimulation

tag: organ

value: ovary

value: IVF treatment


title: 57_NR

value: pre


title: 59_R


title: Cells in preovulatory follicle of patient 5


title: Cells in preovulatory follicle of patient 4


title: 56_R


title: BN_NP1_RNAseq

tag: tissue


title: 54_R


title: Cells in preovulatory follicle of patient 3

tag: treatment


title: BN_NP2_RNAseq


title: 55_R


title: CD_P3_RNAseq

source_name: CD, P18

value: CD


title: 52_NR


title: 51_NR


title: Cells in preovulatory follicle of patient 1


title: CD_P2_RNAseq


title: CD_P1_RNAseq


title: Cells in preovulatory follicle of patient 2


title: 53_R


title: 50_NR


title: CD_NP3_RNAseq


title: CD_NP2_RNAseq


title: Bace1-fl/fl

city: Farmington

first: Marc

last: Benoit

address: 263 Farmington Ave

institute: UConn Health

description:
Global Bace1 deletion over age
JZ19018

data_processing:
Post-library quality inspection, libraries were sequenced using an Illumina Nextseq 500 sequencer
Raw sequencing was aligned and annotated using the CellRanger v3.1.0 pipeline. During FASTQ generation, reads with more than 1 mismatch in the 8bp i7 index were excluded
During alignment using STAR [PMC3530905], only reads with MAPQ scores greater than 255 aligned to annotated transcripts were retained. Reads containing bases with Q30 scores below 3 were also excluded
After alignment, cell barcodes were filtered up to 1 mismatch against a whitelist of 737,500 barcodes provided by 10X Genomics. Barcodes associated with cells were distinguished from ambient mRNA using an adaptively-computed UMI threshold. The raw counts matrix was filtered using cutoff values of mitochondrial transcripts below 10% and 600 to 6500 unique features
Assembly: mm10

source_name: purified microglia

extract_protocol:
Microglia were isolated from mouse brains using adult brain dissociation kits (MiltenyiBiotec, cat.no. 130-107-677). Briefly, forebrain was dissociated into a single-cell suspension, and myelin, cell debris, and erythrocytes were removed subsequently and cells were immunolabelled with CD11b microbeads (cat. No. 130-093-634). The cell suspension was allowed to pass though the magnetic column and retained CD11b-positive cells from the column, which were flushed out and used for analysis.
Microglia were loaded into capture plates (a droplet-based 10x Chromium controller) to perform single-cell partitioning and mRNA was barcoded and subsequently converted into cDNA.

treatment_protocol: Tamoxifen-treated mice received 5 doses of via injecting Tamoxifen i.p at 100mg/kg for five consecutive days

value: no treatment


title: Bace1-fl/fl;Ubc-cre;5xFAD

description:
Global Bace1 deletion over age
JZ19003


title: Bace1-fl/fl;5xFAD

description:
Global Bace1 deletion over age
JZ19004


title: 47_R


title: Bace1 KO

description:
Global Bace1 knock out
JZ18003

value: Bace1 -/-


title: CD_NP1_RNAseq


title: 46_NR


title: wildtype

description:
wildtype
JZ18001

value: Bace1 +/+


title: 48_R


title: 45_NR


title: A-9_Panc1_siSF3B1_Hx

city: Zurich

first: Patrik

last: Simmler

address: Otto-Stern-Weg 7

institute: ETH Zurich

data_processing:
The fastq data for the read pairs from the Illumina sequencer have been processed in abioinformatic workflow. First, the remains of the adapters and sub-standard quality reads have been trimmed with trimmomatic (v0.35).
For the pairs in which both reads have passed the trimming, they have been mapped to the GRCh38.p13 genome using STAR (v2.7.0a) and indexed BAM files obtained with samtools (v1.9).
The reads have been counted using featureCounts from subread package (v1.5.0) with the options for pairs of reads to be counted as RNA fragments. The counting used GRCh38.p13 genome annotation GTF file. The count vectors for all the samples have been combined into a count table. The table has been processed in the secondary (statistical) analysis with R scripts using edgeR (v3.24.3), in particular binomial generalized log-linear model with contrast tests. It resulted in lists of genes ranked for differential expression by p-value and used Benjamini-Hochberg adjusted p-value as the estimate of the false discovery rate.
Assembly: GRCh38.p13

source_name: PDAC cell line (ATCC)

extract_protocol:
Cells were harvested and RNA was extracted using the NucleoSpin® RNA kit (Macherey-Nagel) according to the manufacturer’s instructions. For each organoid line, 2-3 wells of organoids from a 24 well plate were harvested in lysis buffer RA1 (RNA extraction kit, MN) supplemented with TCEP (Tris(2-carboxyethyl)phosphine hydrochloride).
For library preparation, the quantity and quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (1 μg) were ribosome depleted and then reverse-transcribed into double-stranded cDNA with Actinomycin added during first-strand synthesis. The cDNA samples were fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters. The adapters contain the index for multiplexing. Fragments containing TruSeq adapters on both ends were selectively enriched with PCR. The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Bioanalyzer 2100 (Agilent, Waldbronn, Germany). The product is a smear with an average fragment size of approximately 360 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. Cluster generation and sequencing involved application of the TruSeq SR Cluster Kit v4-cBot-HS or TruSeq PE Cluster Kit v4-cBot-HS (Illumina, Inc, California, USA) using 8 pM of pooled normalized libraries on the cBOT.

treatment_protocol: Panc1 cells were treated either with control siRNA (siCtrl) or siRNA targeting SF3B1 (siSF3B1). siCtrl cells were exposed to 1% O2 or 21% O2, siSF3B1 cells to 1% O2 for 8 hours.

value: Hypoxia


title: human, umbilical cord-derived, MSC, rep1

city: Fujisawa

last: Kamiya

state: Kanagawa

address: 26-1 Muraoka-Higashi 2-chome

department: CiRA

institute: Kyoto University

data_processing:
Base calling was performed using standard parameters in build-in software provided with the Ion Torrent S5 XL sequencer (Torrent suite v5.16.1).
Sequenced reads were mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using standard parameters and build-in software provided with the Ion Torrent S5 XL sequencer (Torrent suite v5.16.1).
RPM were calculated using plug-in software provided with the Ion Torrent S5 XL sequencer (ampliSeqRNA v5.6.0.3)
Assembly: hg19
Supplementary files format and content: Tab-delimited text file include gene symbol and gene expression in RPM for each sample

source_name: human umbilical cord-derived primary culture cells

growth_protocol: XF-iMSC and human primary cultured MSCs were cultured in PRIME-XV MSC Expansion XSFM medium (Irvine Scientific)

extract_protocol:
Total RNA was purified using an RNeasy Mini Kit (Qiagen, Valencia, CA, USA)
10 ng of total RNA were reverse transcribed  to obtain single-stranded cDNA using the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific). cDNA libraries were  synthesised using the Ion AmpliSeq Transcriptome Human Gene Expression Core Panel (Thermo Fisher Scientific) and the Ion Ampliseq Library Kit Plus (Thermo Fisher Scientific), according to the manufacturer’s protocol. Barcode-labeled cDNA libraries were analyzed using the Ion S5 XL System (Thermo Fisher Scientific) and the Ion 540 Chip Kit (Thermo Fisher Scientific).

value: MSCs

value: WT


title: human, umbilical cord-derived, MSC, rep3

value: human umbilical cord-derived primary culture cells


title: human, bone marrow-derived, MSC, rep2

source_name: human bone marrow-derived primary culture cells


title: human, umbilical cord-derived, MSC, rep2


title: human, bone marrow-derived, MSC, rep1

value: human bone marrow-derived primary culture cells


title: human, adipose-derived, MSC, rep3

source_name: human adipose-derived primary culture cells


title: A-6_Panc1_siSF3B1_Hx


title: 49_NR

value: female


title: A-3_Panc1_siSF3B1_Hx


title: human, bone marrow-derived, MSC, rep3


title: 44_R

value: post


title: Bace1-fl/fl;Cx3cr1-CreER;5xFAD +TAM

description:
Conditional deletion of Bace1 in microglia
RY21004

value: tamoxifen


title: human, adipose-derived, MSC, rep2

value: human adipose-derived primary culture cells


title: 43_R

value: R

value: PBMC


title: Bace1-fl/fl;Cx3cr1-CreER;5xFAD -TAM

description:
Conditional deletion of Bace1 in microglia
RY21003


title: Bace1-fl/fl;Cx3cr1-CreER +TAM

description:
Conditional deletion of Bace1 in microglia
RY21002


title: human, adipose-derived, MSC, rep1


title: A-8_Panc1_siCtrl_Hx

value: siCtrl


title: 42_NR

value: NR


title: 1231A3, XF-iMSC, rep3

source_name: 1231A3 iPSC-derived MSCs

value: 1231A3 iPSC-derived MSCs


title: Bace1-fl/fl;Cx3cr1-CreER -TAM

description:
Conditional deletion of Bace1 in microglia
RY21001

value: no treatment


title: 41_NR

value: pre


title: 1231A3, XF-iMSC, rep2


title: Sample_FP1_F3

city: Dallas

first: Subhransu

middle: S

last: Sahoo

state: Texas

address: 5323 Harry Hines Blvd

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
Single-end 76 bp read length Fastq files were checked for quality using fastqc (v0.11.5) and fastq_screen (v0.11.4)
Fastq files were mapped to human genome using STAR(v2.5.3a)
Read counts were generated using featureCounts (subread, v1.4.6)
Differential expression was performed using edgeR
Normalized read counts generated using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited files that includes normalized read counts for each sample per gene

source_name: FP cells transduced with Foxa2 lentiviral particles (FP-Foxa2)

growth_protocol: FP cells with or without Foxa2 were cultured in Advanced DMEM/F12 medium supplemented with 10% FBS and antibiotics (50 U/mL penicillin and 50 mg/L streptomycin) in a humidified atmosphere at 370C containing 5% CO₂.

extract_protocol: Total RNA from FP cells with or without Foxa2 was isolated using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: FP cells with or without Foxa2 were treated with puromycin to select positively transduced cells.

value: FP cells

value: Uterine tumor

tag: genotype/variation


title: A-2_Panc1_siCtrl_Hx

value: Hypoxia


title: Sample_FP1_F1

value: transduced with Foxa2 lentiviral particles (FP-Foxa2)


title: Sample_FP1_F2


title: A-5_Panc1_siCtrl_Hx


title: 38_NR


title: A-4_Panc1_siCtrl_Nx

value: Normoxia


title: Sample_FP3

source_name: FP cells transduced with pLenti empty vector (FP)


title: 1231A3, XF-iMSC, rep1

value: MSCs

value: WT


title: MHCC97H_Ribo-seq

data_processing:
Library strategy: Ribo-seq
For MHCC97H RNC-seq datasets, reads were mapped to rRNA reference sequences using FANSe3(Release version 3.13) with the parameters –S14 -E4 in MHCC97H (100bp read lengths). For MHCC97H Ribo-seq dataset, reads were  mapped to rRNA reference sequences using FANSe3 with the parameters –S10 -E2 -U1.
The filtered reads from each sample were mapped to the NCBI RefSeq-RNA database using FANSe3 with unique mode based on the same parameters as above.
The UCSC refFlat annotation was used for isoform calling. Isoforms with uniquely-mapped read count >=10 were considered as detected.
Genome_build: GRCh38, accession GCA_000001405.15
Supplementary files format and content: abundance measurement, STAR Juntcions identification.
*-seq.txt files are Fanse3 output
*seq.final.out files are Star output

source_name: MHCC97H cells

extract_protocol:
RNA was isolated using TRIzol reagent . RNA less than 200 nt was isolated using Zymo RNA clean and concentrator kit (Zymo Research, Orange, CA, USA). RNAs with the length of 17~200nt were loaded on a 15% (w/v) Urea PAGE and resolved by gel electrophoresis. Ribosome footprints were purified by gel recovery according to the Zymo small-RNA PAGE Recovery kit (Zymo Research, Orange, CA, USA). The 3’ dephosphorylation reaction was performed using T4 PNK (New England Biolab, Hitchin, Hertfordshire, UK) without ATP. The 5’ phosphorylation reaction was performed using T4 PNK with 1 mM ATP. RNA was precipitated by adding 39 µL of nuclease free water, 1.0 µL of GlycoBlue coprecipitant (Invitrogen, Carlsbad, CA, USA)  and 10 µL of 3 M sodium acetate (pH5.5), 150 µl isopropanol, at -80°C overnight.
Ribosome footprints sequencing library was constructed by using MGIEasy Small RNA library preparation kit. Libraries were sequenced in a BGI-Seq 500 sequencer at SE50 mode.

treatment_protocol: In brief, MHCC97H cells were pre-treated with 100 μg/mL cycloheximide for 10 min at 37℃, and then washed twice using 5 mL pre-cooled PBS. The cells were lyzed for 30min on ice in 2 mL pre-colded human cell lysis buffer. Cell lysates were clarified by centrifuge at 17000 x g at 4℃ for 15 min. Purified lysates were treated with 7 units RNase I (Thermo Fisher, Waltham, MA, USA) per OD260. The RNase digestion was performed at 4°C with gentle mixing for 60 mins, and then stopped by adding 10 μl of SUPERase-in RNase inhibitor (Thermo Fisher, Waltham, MA, USA). Monosomes were pelleted using ultra-centrifugation in a Type 70Ti rotor at 185,000 x g for 3h at 4°C.

value: liver cancer cells

tag: molecule subtype

value: ribosome protected fragments (RPF)


title: RNA-seq_sOKC6_R1

city: Athens

first: Konstantinos

middle: I

last: Tosios

address: Thivon 2

country: Greece

institute: National and Kapodistrian University of Athens

data_processing:
The quality of sequencing reads was evaluated with FastQC (Galaxy Version 0.72+galaxy1). 3′ adapter trimming was performed with Trim Galore software and each read was trimmed to 75 bp length, while also removing reads that have an average quality score below 20. Reads were mapped to the hg19 reference genome using HISAT2 (Galaxy Version 2.1.0+galaxy6) with with "paired-end", “stranded” and “reverse” options. Htseq-count (Galaxy Version  0.9.1) was used to count reads inside genes with in union mode, with "stranded" and "reverse" parameters parameters. DESeq2 (Galaxy Version 2.11.40.6+galaxy1) was applied for differential gene expression analysis. RSeQC package was employed to evaluate the distribution of the reads across the genome with the command "bam mapping stats".
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using the bamCoverage command (Galaxy Version 3.3.2.0.0) from the deepTools package with default settings except for RPKM normalization.

extract_protocol:
For RNA extraction, 10μm sections were cut from each sample (the first 5 sections of each FFPE block were discarded to avoid contamination). The sections were stored in sterile 2ml eppendorfs (one eppendorf for each sample regardless the number of sections) and stored at -20˚C until RNA extraction. Total RNA was extracted via a spin-column based method, using the AllPrep DNA/RNA FFPE Kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s recommendations. Initial deparaffinization step was performed with 640μl of Zymo Research deparaffinization solution (Catalog # D3067-1-20) per sample. RNA was finally eluted in 15-25 μl RNasefree water and stored at -80˚C until library preparation.
cDNA libraries were prepared with 300ng total RNA input  using KAPA Stranded RNA-Seq Kit with RiboErase (catalogue number #KK8483, KAPA Biosystems, Wilmington, MA), according to the manufacturer’s specifications. As a high percentage of each sample was already in the 100-200 bp range, the fragmentation step was omitted. In brief, the workflow included rRNA depletion, cDNA synthesis, end repair to generate blunt ends, A-tailing, adapter ligation and PCR amplification. PCR amplification consisted of an initial denaturation step at 98°C for 45 sec, followed by 15 amplification cycles (denaturation at 98°C for 15 sec; annealing at 60°C for 30 sec; and extension at 72°C for 30 sec) and final extension at 72°C for 5 min.

value: Formalin-fixed and paraffin-embedded tissue (intraosseous in jawbones)


title: 40_NR

value: post

value: female


title: A-1_Panc1_siCtrl_Nx

value: siCtrl


title: MHCC97H_RNC-seq

data_processing:
Library strategy: RNC-seq
MHCC97H RNC-seq and Ribo-seq were mapped to the GRCh38 no-alt analysis set (accession GCA_00001405.15) using STAR (2.5.0a) with the gtf option (GRCh38 full analysis set, accession GCA_000001405.15).
The total number of splice junctions detected for each sample was taken from the *.final.out file printed by the aligner STAR
The UCSC refFlat annotation was used for isoform calling. Isoforms with uniquely-mapped read count >=10 were considered as detected.
Genome_build: GRCh38, accession GCA_000001405.15
Supplementary files format and content: abundance measurement, STAR Juntcions identification
*-seq.txt files are Fanse3 output
*seq.final.out files are Star output

extract_protocol:
Total MHCC97H RNC-RNA were isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). 1μg of total RNC-RNA were subjected for library construction. Brieﬂy, PolyA+ mRNAs were isolated using VAHTS mRNA Capture Beads (Vazyme, Jiangsu, Nanjing, China).
The sequencing library was constructed by MGIEasy RNA library Preparation kit (MGItech, Guangdong, Shenzhen, China) following the manufacturer’s instructions. Libraries were sequenced in a BGI-Seq 500 (MGItech, Guangdong, Shenzhen, China) sequencer at SE100 mode

value: ribosome nascent-chain complex(RNC)


title: 39_NR

value: NR

value: PBMC


title: 37_NR

value: pre


title: Sample_FP1

value: FP cells

value: transduced with pLenti empty vector (FP)


title: Sample_FP2

value: Uterine tumor


title: 27_R

value: R


title: RNA-seq_sOKC4_R1


title: RNA-seq_sOKC5_R1


title: 36_R


title: RNA-seq_sOKC2_R1


title: 34_NR


title: WM32-3

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
Image analysis and base calling performed by RTA 2.0
Reads were aligned to the mm10 version of the mouse genome as reference using STAR v2.7.3a after removal of contaminants  (rDNA, tRNA, mtrDNA) were removed using Bowtie2 (version 2.2.5)
Reads aligned to STAR were quantified to the mm10-RefSeq Transcripts v99 (released 2021-08-02)and normalized by TMM and transformed by log2 (TMM + 1 + log2)
Normalized counts were used to determine differential gene expression between the groupus by DESEQ2
All analyses were corrected for multiple comparisons at false discovery rate (FDR) 0.05 (at least)
Genome_build: mm10
Supplementary_files_format_and_content: txt files contain raw and normalized counts

source_name: Bone marrow from femur

extract_protocol:
Bone marrow was released from femurs by centrifugation at 5700 g for 30 seconds into RNAlater followed by TRI Reagent lysis and RNA isolation by the TRI Reagent protocol
Illumina Stranded mRNA Prep protocol, mRNA from total RNA via oligo-dt magnetic beads then converted to cDNA, fragmented and end repaired, then 3’ ends adenylated and ligated with pre-index anchors, ligated fragments amplified and indexed then multiplexed and sequenced on the Illumina NextSeq 500.

value: Male

value: 32 weeks old

value: Nox4 fl/fl


title: RNA-seq_sOKC1_R1


title: 35_NR


title: RNA-seq_sOKC3_R1


title: WM32-1


title: WM3

value: 3 weeks old


title: 33_NR


title: RNA-seq_OKC6_R1

source_name: Odontogenic keratocyst (sporadic)


title: 32_NR


title: WM2


title: 31_NR


title: RNA-seq_OKC4_R1


title: RNA-seq_OKC5_R1


title: WM1


title: RNA-seq_OKC3_R1


title: 29_NR


title: WM32-2


title: WF32-3

value: Female


title: RNA-seq_OKC1_R1

value: Formalin-fixed and paraffin-embedded tissue (intraosseous in jawbones)


title: WF32-2


title: 28_NR


title: WF32-1


title: WF3_S9


title: RNA-seq_DF6_R1

source_name: Dental Follicle


title: 25_NR


title: RNA-seq_DF5_R1


title: 26_NR

value: post


title: WF2_S8


title: DM_rep3

city: Provo

first: Clinton

last: Whipple

state: UT

institute: Brigham Young University

description: RNA-seq of laser-captured ear bract primordia, Hiseq 2500, 125bp single-end reads.

data_processing:
The overall quality of our sequencing data was assessed using FastQC and the raw reads were filtered using Trimmomatic v.0.36 to trim and remove low-quality reads and adapter sequences.
The filtered reads were mapped to the maize B73 reference genome version 3, release 31 (AGPv3.31) using STAR aligner v.2.6.0a with default parameter settings.
A read count matrix including all samples was generated by aggregating the raw counts of mapped reads for a given gene in each sample using featureCounts with reference to 39479 maize gene models in AGPv3.31.
The read count matrix was subjected to differential gene expression analysis using a Bioconductor R package edgeR v.3.22.5. Briefly, genes with ubiquitously low expression were filtered out from the read count matrix in order to improve differential expressed gene detection sensitivity and only the genes that had count-per-million (CPM) value >0.25 in at least three libraries were retained. This resulted in a filtered read count matrix containing 20168 expressed genes in the samples. The filtered read count matrix was normalized for compositional bias between libraries using a trimmed means of M values (TMM) method.
Genome_build: maize B73 reference genome version 3, release 31 (AGPv3.31)
Supplementary_files_format_and_content: a merged .txt file contaning a normalized read counts for each expressed genes in all samples

organism: Zea mays

source_name: ear bract primordium

growth_protocol: B73, tsh1, tsh4, and tsh1 tsh4 mutants used for LCM-RNA-seq assays were grown in 5 gallon pots in a greenhouse at 24 °C with supplemental lights for 16-h light/ 8-h dark period.

extract_protocol:
ear primordia were fixed overnight in 3.5% paraformaldehyde, dehydrated through an ethanol series, transferred to Histoclear before embedding in paraffin. Embedded samples were sectioned at 5 µm and mounted onto charged HistoBond slides . The slides were then subjected to laser microdissection by using a PALM microbeam system. Three biological replicates were prepared per genotype (B73, tsh1, tsh4, and tsh1 tsh4). Approximately 750 microns of cells were harvested for each biological replicate. RNA was extracted from microdissected tissues with the PicoPure RNA Isolation Kit and in vitro amplified using a TargetAmp 2-round aRNA Amplification Kit 2.0.
RNA-seq libraries were constructed using a TruSeq Stranded mRNA Library Prep Kit and quantified on an Agilent bioanalyzer (Agilent)

treatment_protocol: no treatment

value: ear bract primordium

value: The ear bract primordia used in this project were collected from the uppermost 2-3 nodes, the earliest stage where the bract ridge, but not the adjacent meristem is visible

value: tsh1;tsh4 double mutant


title: DM_rep2


title: WF1_S7


title: RNA-seq_DF3_R1


title: RNA-seq_DF4_R1


title: 23_NR

value: NR

value: female


title: 30_NR

value: pre

value: PBMC


title: DM_rep1


title: tsh4_rep3


title: 22_NR


title: RNA-seq_OKC2_R1


title: PM32-3

value: PrxCre +/ Nox4 fl/fl


title: PM32-2


title: 21_NR


title: RNA-seq_DF2_R1


title: PM32-1


title: RNA-seq_DF1_R1


title: 20_R


title: 19_R


title: tsh4_rep2


title: tsh1_rep3


title: 24_NR


title: tsh4_rep1


title: 17_R


title: tsh1_rep2


title: PF32-3


title: PM3


title: tsh1_rep1


title: 18_R


title: PM2


title: 16_R


title: B73_rep3


title: PF32-2


title: 15_R


title: PF32-1


title: PF3


title: B73_rep2


title: PF2


title: B73_rep1


title: 12_R


title: 13_NR


title: PF1