title: Embryo, E9.5, WT, Rep2

description:
Processed data for all E9.5 Embryo samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E9.5_Embryo_fpkm_sample.xlsx
E9.5_Embryo_Cmtr2WT2


title: PT32, C3D1

status: Public on Oct 31 2024

type: SRA

city: Crawley

first: Wee Loong

last: Chin

state: Western Australia

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

library_source: transcriptomic

data_processing:
Alignment was performed on paired-read samples using Kallisto (v0.43.0) for transcript abundance estimation.
sleuth_to_matrix was used to generate count and transcripts
Assembly: Gencode v34 reference.
Supplementary files format and content: csv file of counts (gzipped)
Supplementary files format and content: csv file of TPM (gzipped)

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: Not applicable

extract_protocol:
Peripheral blood was collected, processed and frozen at hospital sites within 90 minutes of phlebotomy as follows: (1) collected in PAXgene blood collection tubes containing RNA stabilizers and frozen upright at ‐70°C (or lower); (2) collected in CPT blood collection tubes to recover PBMCs; 1st centrifugation at 1500g, 30 minutes, 18‐25°C, no brake applied; buffy coat was transferred to a fresh centrifuge tube and volume brought to 15ml with PBS; 2nd centrifugation at 300g at 15 minutes, 18‐25°C, no brake applied; PBS was aspirated and pellet resuspended in fresh 10ml PBS, 3rd centrifugation 300g at 15 minutes, 18‐25°C, no brake applied; PBS was aspirated, cell pellet resuspended in freezing medium (RPMI, 10% FCS (v/v), 10% DMSO (v/v) on ice) at 2x105 cells/ml; frozen slowly at ‐70°C (or lower), then transferred into liquid nitrogen storage within 2 weeks.
Illumina NovaSeq S4, 300 cycles (150 bp paired-end reads). Samples were processed with Illumina’s TruSeq Stranded Total RNA protocol and sequenced across three lanes of the NovaSeq 6000 (NovaSeq S4 300 cycle reagent kit).

treatment_protocol: Not applicable

tag: tissue

value: Peripheral blood

tag: cell type

value: Peripheral blood mononuclear cells

tag: response (pfs)

value: Achieved PFS6M


title: Bulk RNA-seq, F99, ASCL1, GFPneg, rep2

city: Atlanta

first: Steven

last: Sloan

state: Georgia

address: 615 Michael Street, Room 375

country: USA

institute: Emory University

description:
20 million PE reads
ASCL1_fetal_feature_counts.xlsx
F99_ASCL1_rep2_GFPneg

data_processing:
Fastq files were first trimmed using Trimmomatic and mapped using STAR aligner with the paired end option selected (hg38). We used FeatureCounts to assemble transcripts and generate raw count matrices.
Assembly: hg38
Supplementary files format and content: xlsx count matrix

source_name: human fetal cortex

growth_protocol: Human cortical organoids: Following 3D formation, spheroids were treated daily in neural induction media (DMEM/F12, KSR, NEAA, Glutamax, Pen/Strep, Beta-mercaptoethanol) supplemented with Dorsomorphin (Sigma, Cat. 142 P5499-25MG, 5 μM) and SB-431542 (Selleck Chemicals, Cat. S1067, 10 μM) for 6 days.  Following this treatment, organoids were treated daily with neural media supplemented with EGF (R&D Systems, Cat. 236-EG-01M, 20 ng/mL) and FGF2 (R&D Systems, Cat. 233-FB-01M, 20 ng/mL) for 10 days, and every other day for days 16-24. At day 25, organoids were treated every other day with neural media supplemented with BDNF (PeproTech, Cat. 450-02- 1mg, 20 ng/mL) and NT-3 (R&D Systems, Cat. 267-N3-005/CF, 20 ng/mL) to promote differentiation of progenitors. From day 43 onwards, organoids were fed every 3 days with neural media only.

extract_protocol:
RNA was harvested using miRneasy kit (Qiagen).
Libraries were prepared with Takara Bio SMART-Seq v4 Ultra Low Input RNA Kit and NEBNext Ultra II kit.

treatment_protocol: Addition of D2HG or DMSO for several primary human fetal astrocyte samples

value: human fetal cortex

value: HepaCAM+ cells

tag: Sex

value: female

tag: genotype

value: GFP- cells

tag: treatment

value: TurboGFP:p2A:ASCL1 virus


title: iPSCCM_DGUC_F7_qEV_F02_6

city: La Jolla

first: Louise

middle: C

last: Laurent

state: CA

address: SCRM, 2880 Torrey Pines Scenic Drive

department: Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: induced pluripotent stem cell

extract_protocol:
RNA Isolation method was "500uL of biofluid was incubated with 100uL warmed Slurry and 900uL warmed Lysis Buffer A (containing 2-Mercaptoethanol) for 10 min at 60C. To this 1.5 mL of 100% ethanol was added and centrifuged for 2min at 1000rpm. To the pellet 300uL Lysis Buffer A was added and incubated for 10 min at 60C. 300uL 100% Ethanol was added, loaded onto the filter column and centrifuged for 30sec at 1000xg followed by 1 min at 16000xg. The column was washed thrice with 400uL Wash Solution for 1 min at 16000 xg and then centrifuged once again for 3 min to dry the membrane. RNA was eluted in 14uL water with a slow spin for 2 mins at 300 xg followed by a spin for 3 min at 16000 xg.". RNA Isolation kit was Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were multiplexed. Type of Starting Material was total RNA.

tag: disease

value: Healthy Subject

tag: anatomical location

value: Entire mesoderm

tag: rna source

value: other

tag: rna isolation kit


title: Yolk Sac, E9.5, KO, Rep1

city: Boston

first: Alena

last: Yermalovich

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description:
Processed data for all E9.5 Yolk Sac samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E9.5_Yolksac_fpkm_sample.xlsx
E9.5_Yolksac_Cmtr2KO1

data_processing:
Differential expression analysis was performed using the DESeq2 R package (Anders et al. 2015). Genes with an adjusted p-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO enrichment analysis of DEGs was implemented by the clusterProfiler R package (Yu et al. 2012). GO terms with corrected p-value <0.05 were considered significantly enriched by differentially expressed genes.
KEGG Pathway enrichment analysis used the R package clusterProfiler to test the statistical enrichment of differential expression genes in KEGG pathways (Kanehisa and Goto 2000). KEGG terms with adjusted corrected p=value <0.05 were considered significantly enriched.
Assembly: GRCm38/mm10
Supplementary files format and content: FPKM values per gene for each sample

organism: Mus musculus

source_name: yolk sac

extract_protocol:
Total RNA was isolated by TRIzol from embryos using Direct-zol RNA Micro Prep Kit and treated with DNase
Library construction and sequencing was performed using Novogene Co., Ltd. sequencing service. Briefly, sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina

tag: developmental stage

value: yolk sac

value: Cmtr2 WT


title: PT32, C2D1


title: Embryo, E9.5, WT, Rep1

description:
Processed data for all E9.5 Embryo samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E9.5_Embryo_fpkm_sample.xlsx
E9.5_Embryo_Cmtr2WT1

source_name: embryo

value: embryo

value: Cmtr2 KO


title: iPSCCM_IgG_B1_3

value: Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)


title: PT32, Baseline


title: Embryo, E9.5, KO, Rep3

description:
Processed data for all E9.5 Embryo samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E9.5_Embryo_fpkm_sample.xlsx
E9.5_Embryo_Cmtr2KO3


title: Embryo, E9.5, KO, Rep4

description:
Processed data for all E9.5 Embryo samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E9.5_Embryo_fpkm_sample.xlsx
E9.5_Embryo_Cmtr2KO4


title: Bulk RNA-seq, F99, ASCL1, GFPpos, rep2

description:
20 million PE reads
ASCL1_fetal_feature_counts.xlsx
F99_ASCL1_rep2_GFPpos

value: GFP+ cells


title: Bulk RNA-seq, F99, ASCL1, GFPpos, rep1

description:
20 million PE reads
ASCL1_fetal_feature_counts.xlsx
F99_ASCL1_rep1_GFPpos


title: iPSCCM_DGUC_F8_qEV_F09_5


title: Bulk RNA-seq, F99, ASCL1, GFPneg, rep1

description:
20 million PE reads
ASCL1_fetal_feature_counts.xlsx
F99_ASCL1_rep1_GFPneg


title: PT31, C2D1

value: Peripheral blood

value: Did not achieved PFS6M


title: PT31, C3D1

value: Peripheral blood mononuclear cells


title: Bulk RNA-seq, line 8858, Doxycycline control

description:
20 million PE reads
ASCL1_8858_feature_counts.xlsx
ASCL1_8858_Doxpos

source_name: human cortical organoid

value: human cortical organoid

tag: cell line

value: whole organoid

value: male


title: Embryo, E9.5, KO, Rep1

description:
Processed data for all E9.5 Embryo samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E9.5_Embryo_fpkm_sample.xlsx
E9.5_Embryo_Cmtr2KO1


title: iPSCCM_DGUC_F7_qEV_F12_5


title: PT30, C3D1

value: Achieved PFS6M


title: iPSCCM_DGUC_F7_qEV_F06_6


title: PT31, Baseline


title: iPSCCM_DGUC_F01_1


title: iPSCCM_DGUC_F8_qEV_F03_6


title: Embryo, E9.5, KO, Rep2

description:
Processed data for all E9.5 Embryo samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E9.5_Embryo_fpkm_sample.xlsx
E9.5_Embryo_Cmtr2KO2


title: Embryo, E8.5, WT, Rep4

description:
Processed data for all E8.5 samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E8.5_fpkm_sample.xlsx
E8.5_Cmtr2WT4


title: PT30, C2D1


title: Embryo, E8.5, WT, Rep3

description:
Processed data for all E8.5 samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E8.5_fpkm_sample.xlsx
E8.5_Cmtr2WT3


title: Bulk RNA-seq, line 8858, ContGFP, GFPneg

description:
20 million PE reads
ASCL1_8858_feature_counts.xlsx
ContGFP_8858_GFPneg

value: GFP- cells


title: iPSCCM_DGUC_F8_qEV_F07_6

value: Healthy Subject


title: PT30, Baseline


title: Bulk RNA-seq, line 8858, ContGFP, GFPpos

description:
20 million PE reads
ASCL1_8858_feature_counts.xlsx
ContGFP_8858_GFPpos


title: Bulk RNA-seq, line 8858, ASCL1, GFPneg

description:
20 million PE reads
ASCL1_8858_feature_counts.xlsx
ASCL1_8858_GFPneg


title: Bulk RNA-seq, line 8858, no treatment

description:
20 million PE reads
ASCL1_8858_feature_counts.xlsx
ASCL1_8858_notreat


title: iPSCCM_IgG_B1_2

value: Entire mesoderm


title: Embryo, E8.5, WT, Rep1

description:
Processed data for all E8.5 samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E8.5_fpkm_sample.xlsx
E8.5_Cmtr2WT1


title: PT29, C2D1


title: Embryo, E8.5, WT, Rep2

description:
Processed data for all E8.5 samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E8.5_fpkm_sample.xlsx
E8.5_Cmtr2WT2


title: iPSCCM_DGUC_F7_qEV_F06_5

value: other


title: Bulk RNA-seq, line 0524, ASCL1, GFPneg

description:
20 million PE reads
ASCL1_0524_feature_counts.xlsx
ASCL1_0524_rep2_GFPneg

tag: cell subtype


title: Bulk RNA-seq, line C4.1, Doxycycline control

description:
20 million PE reads
ASCL1_C4_feature_counts.xlsx
ASCL1_C4_Doxpos

value: female


title: iPSCCM_DGUC_F12_5


title: Embryo, E8.5, KO, Rep2

description:
Processed data for all E8.5 samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E8.5_fpkm_sample.xlsx
E8.5_Cmtr2KO2

value: Cmtr2 WT


title: iPSCCM_DGUC_F8_qEV_F03_5


title: Embryo, E8.5, KO, Rep3

description:
Processed data for all E8.5 samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E8.5_fpkm_sample.xlsx
E8.5_Cmtr2KO3

value: embryo


title: Embryo, E8.5, KO, Rep1

description:
Processed data for all E8.5 samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E8.5_fpkm_sample.xlsx
E8.5_Cmtr2KO1


title: PT28, C2D1


title: iPSCCM_DGUC_F7_qEV_F10/I11_6


title: Bulk RNA-seq, line 8858, ASCL1, GFPpos

description:
20 million PE reads
ASCL1_8858_feature_counts.xlsx
ASCL1_8858_GFPpos


title: iPSCCM_DGUC_F12_1


title: Rag2-/-γc-/-_3

city: Tianjin

first: Xue

last: Dong

state: TIANJIN

address: Qixiangtai Road

department: Department of Pharmacology

country: China

institute: Tianjin Medical University

data_processing:
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each sample

source_name: retina+choroid

extract_protocol:
Total RNAs of mouse retina-choroid complex were extracted using the TRIzol reagent following the manufacturer’s instructions.
RNA libraries for RNA-seq were completed by Novogene company (Beijing,China).

treatment_protocol: 6-8 adult C57BL/6J mice were induced CNV with laser photocoagulation (532 nm, 200 mW, 0.150 s, 100 μm; Vovus Spectra, Lumenis, US) using a slit lamp delivery system and a cover glass as a contact lens.

value: retina+choroid

value: laser-induced CNV

tag: timepoint

value: 3 days after injury


title: Bulk RNA-seq, line C4.1, ASCL1, GFPpos

description:
20 million PE reads
ASCL1_C4_feature_counts.xlsx
ASCL1_C4_GFPpos

value: GFP+ cells


title: PT28, Baseline

value: Peripheral blood

value: Did not achieved PFS6M


title: iPSCCM_DGUC_F7_qEV_F10_5

value: Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)


title: iPSCCM_IgG_FT2_1


title: Rag2-/-γc-/-_2


title: PT26, C3D1

value: Peripheral blood mononuclear cells


title: PT29, Baseline


title: Rag2-/-γc-/-_1


title: iPSCCM_IgG_FT1_3


title: dRNA Seq  ∆modT 9 hours, biol rep 2

city: Würzburg

first: Johannes

last: Suzer

state: Bavaria

address: Josef Schneider Straße D15

department: Institute of Molecular Infection Biology Würzburg

country: Germany

institute: Universität Würzburg

data_processing:
Raw reads of RNA-seq libraries were trimmed and filtered using BBDuk (ktrim = r, k = 23, mink = 11, hdist = 1, tpe, tbo, qtrim = r, trimq = 20, minlength = 25). Mapping and read counting was conducted with READemption 0.4.3 (READemption align: --poly_a_clipping, --realign, READemption gene_quanti: --skip_antisense, --no_count_splitting_by_gene_no) Reads were mapped to C. difficile 630 CP010905.2 with additional annotations of UTRs and ncRNAs.
Assembly: CP010905.2
Supplementary files format and content: wiggle

organism: Clostridioides difficile

growth_protocol: Trypton-Yeast medium containing 1% Glucose (TYG) was inoculated to an OD of 0.05 from exponentially growing day cultures of C. difficile 630 wild type or  ∆modT in biological triplicates.

extract_protocol:
RNA was extracted using the Hot Phenol method: Samples were thawed on ice, centrifuged for 20 min, 4500 rpm at 4 °C and the supernatant was completely discarded. Cells were suspended in 600 μl of 10 mg/ml lysozyme in TE buffer (pH 8.0) and incubated at 37 °C for 10 min. Next, 60 μl of 10 % w/v SDS was added and mixed by inversion. Samples were heated in a water bath at 64 °C, 1-2 min before adding 66 μl 3 M NaOAc, pH 5.2. Next, 750 μl acid phenol was added and phases were mixed by shaking followed by an incubation step at 64 °C  for 6 minutes with intermediate mixing. Samples were briefly placed on ice to cool before centrifugation for 15 min, 13,000 rpm at 4 °C. The aqueous layer was transferred into a 2 ml phase lock gel tube (Eppendorf), 750 μl chloroform (Roth, #Y015.2) was added, and everything centrifuged for 12 min, 13,000 rpm at room temperature. The aqueous layer was transferred to a fresh tube, 2 volumes of 30:1 mix (EtOH:3 M NaOAc, pH 6.5) was added and incubated overnight at -20 °C. Precipitated RNA was harvested by centrifugation, washed with cold 75 % v/v ethanol twice and air-dried. Purified RNA was resuspended in 50 µl RNase-free water and stored at -80 °C. From each sample 5 µg RNA were treated with 5U DNaseI (Thermo Fisher) according to the manufacturer's instructions, with 1U/µl RNase Inihibitor (Takara) in a volume of 50 µl and subsequently digested at 37°C for 30 minutes. The sample was adjusted to 100 µl with RNase free water and aliquoted to a phase lock gel tube, along with 100 µl P:C:I for RNA extraction. Phases were mixed by shaking and separated again by centrifugation at 16000 x g, 4 °C for 15 minutes. The aqueous phase was transferred to a new tube, 2.5 volumes of 30:1 Ethanol to NaOAc (3M pH 6.5) and samples were stored at -20 °C overnight for precipitation.  RNA was collected by centrifugation for 30 minutes at 16000 x g, 4 °C, washed twice with 200 µl 75% EtOH and 10 minutes centrifugation steps at 16000 x g, 4 °C. Finally, RNA pellets were air dried for 5 minutes at room temperature, dissolved in 20 µl RNase-free water and stored at -80°C until further processing.
Library preparation was performed by vertis Biotechnologie AG. First, ribosomal RNA was depleted using an in-house protocol. Subsequently, RNA was fragmentated by ultrasound (1 pulse of 30 s at 4°C) and an oligonucleotide adapter was ligated to the 3' end. First-strand cDNA synthesis was performed with the M-MLV reverse transcriptase using the appended 3’ adapter as primer. The first strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/µl using a high fidelity DNA polymerase with 15 PCR cycles. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). For Illumina NextSeq sequencing, the samples were pooled in approx. equimolar amounts and the cDNA pool was size fractionated in the range of 200 – 600 bp using a preparative agarose gel.

treatment_protocol: After 3.5 hours and 9 hours of growth, a volume equal to 4 OD was aliquoted to falcons. Aliquots were fixed by adding 0.2 volumes of Stop mix (95% ice cold ethanol, 5% acid phenol for RNA extraction) and immediately frozen liquid nitrogen.

tag: strain

value: {delta}modT

tag: growth stage

value: transition phase

tag: time

value: 9 hours post inoculation


title: PT26, C2D1

tag: tissue

value: Achieved PFS6M


title: PT28, C3D1

tag: cell type


title: Bulk RNA-seq, line 0524, ASCL1, GFPpos

description:
20 million PE reads
ASCL1_0524_feature_counts.xlsx
ASCL1_0524_rep2_GFPpos

value: human cortical organoid

value: whole organoid


title: Embryo, E8.5, KO, Rep4

description:
Processed data for all E8.5 samples -- column headers: gene_id, Cmtr2WT1, Cmtr2WT2, Cmtr2WT3, Cmtr2WT4, Cmtr2KO1, Cmtr2KO2, Cmtr2KO3, Cmtr2KO4
E8.5_fpkm_sample.xlsx
E8.5_Cmtr2KO4


title: PT29, C3D1

tag: response (pfs)


title: iPSCCM_DGUC_F8_qEV_F12_5

value: Healthy Subject

value: Entire mesoderm

value: other


title: dRNA Seq  ∆modT 9 hours, biol rep 3


title: PT26, Baseline


title: Bulk RNA-seq, line C4.1, ASCL1, GFPneg

description:
20 million PE reads
ASCL1_C4_feature_counts.xlsx
ASCL1_C4_GFPneg

tag: Sex

value: female

value: GFP- cells


title: iPSCCM_DGUC_F8_qEV_F07_5


title: dRNA Seq  ∆modT 9 hours, biol rep 1

tag: genotype


title: dRNA Seq  wild type 9 hours, biol rep 3

value: wild type


title: PT25, C3D1


title: Rag2-/-_2

value: retina+choroid

tag: treatment

value: laser-induced CNV

value: 3 days after injury


title: Rag2-/-_1


title: PT25, C2D1

value: Peripheral blood


title: iPSCCM_DGUC_F8_qEV_F12_6

tag: disease

value: Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek)


title: Placental biopsy, Preterm, SFJR9

city: SAN FRANCISCO

first: Joshua

middle: F

last: Robinson

address: 513 Parnassus Ave HSE16

department: Obstretrics, Gynecology and Reproductive Sciences

institute: University of California, San Francisco

description:
SFJR9_S9
salmon.merged.gene_counts_length_scaled_final.txt

data_processing:
We implemented the established Nextflow nf-core rnaseq pipeline (v 3.2) to obtain transcript counts from raw FASTQ files. In brief, quality control was performed on merged FASTQ files using FastQC (v 0.11.9). To process the raw RNA-Seq reads into transcript counts, we performed adapter and quality-based trimming (Trim Galore! V 0.6.6), removed genome (BBSplit) and rRNA contaminants (SortMeRNA v 4.2.0), and then aligned reads (STAR, v 2.6.1b; GRCh38/hg38). SAMtools (v 1.10) and Picard (v 2.18.23) were used for intermediate processing steps, including sorting as well as indexing of aligned reads and marking, respectively. Expression of each transcript was then quantified (Salmon v 1.4.0). Additional quality control was performed with RSeQC (v3.0.0) , Qualimap (v 2.2.2d), dupRadar (v 1.18.0), Preseq and DESeq2 (v 1.28.0).
Assembly: aligned reads (STAR, v 2.6.1b; GRCh38/hg38)
Supplementary files format and content: salmon.merged.gene_counts_length_scaled_final.txt

source_name: placenta

extract_protocol:
RNA was isolated from the biopsies preserved in RNAlater by using a spin column-based nucleic acid purification approach. Frozen specimens were dissected free of chorionic and basal plates, which were inconsistently present in the samples. Then they were placed in 2 mL tubes with 2.8 mm ceramic beads (Fisherbrand) and 600 µl lysis buffer (RLTplus; Qiagen), containing 1% (v/v) beta-mercaptoethanol (Sigma-Aldrich) and 0.5% (v/v) Reagent DX (Qiagen). Then, samples were homogenized at 4˚C using a Bead Mill 24 device (Fisherbrand), which enabled delivery of two 20 sec pulses with a 10 sec rest in between. Debris was pelleted by centrifugation at 15,000 xg for 2 min (Eppendorf 5415 R microcentrifuge). The supernatants were transferred to 1.5 mL tubes (Eppendorf) and the centrifugation step was repeated. Total RNA was purified following the manufacturer’s protocol (Qiagen RNeasy Plus Mini Kit). Absorbance at 280, 260 and 230 nm was measured (Nanodrop 2000; Thermo Scientific) to determine concentration and purity; 5 µL was aliquoted to measure integrity, and the remaining sample was stored at -80˚C.  The integrity of the RNA  was determined via microfluidic electrophoresis (Agilent Tapestation 4200) using either an RNA ScreenTape Assay or High Sensitivity ScreenTape Assay, depending on the concentration. Aliquots with concentrations exceeding the dynamic range were diluted to 500 ng/uL immediately prior to the assay, which was performed using the manufacturer’s protocol. A RNA Integrity Number (RIN) was automatically assigned on a 0-10 scale according to a standardized assessment of the electrophoretic trace of the 18S and 28S rRNAs. Samples having a RIN ≥ 7 were considered suitable for sequencing (RNA-Seq).
A portion of each sample (500 ng) was used for cDNA synthesis and library construction.
A genomic DNA cleanup step was performed to remove contaminants. Next, libraries were prepared using the Kapa Biosystems adapter kit. RNA sequencing was performed on a 150PE NovaSeq S4 flowcell to obtain ~25 million reads per sample.

value: placenta

tag: site

value: AMANHI Pakistan

tag: gestational age

tag: group

value: Preterm


title: CNV_14D_4

value: WT

value: 14 days after injury


title: PT25, Baseline

value: Peripheral blood mononuclear cells

value: Achieved PFS6M


title: CNV_14D_3


title: PT23, C3D1


title: Placental biopsy, Preterm, SFJR7

description:
SFJR7_S7
salmon.merged.gene_counts_length_scaled_final.txt


title: Rag2-/-_3


title: dRNA Seq  ∆modT 3.5 hours, biol rep 3

value: {delta}modT

value: exponential

value: 3.5 hours post inoculation


title: PT23, C2D1


title: dRNA Seq  ∆modT 3.5 hours, biol rep 2


title: CNV_14D_2


title: CNV_14D_1


title: PT21, C3D1


title: PT23, Baseline


title: dRNA Seq  wild type 3.5 hours, biol rep 3


title: Placental biopsy, Preterm, SFJR62

description:
SFJR62_S62
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Tanzania


title: CNV_7D_4

value: 7 days after injury


title: dRNA Seq  ∆modT 3.5 hours, biol rep 1


title: Placental biopsy, Term, SFJR5

description:
SFJR5_S5
salmon.merged.gene_counts_length_scaled_final.txt

value: GAPPS Bangladesh

value: Term


title: dRNA Seq  wild type 3.5 hours, biol rep 2

value: wild type


title: PT21, C2D1

value: Peripheral blood


title: dRNA Seq  wild type 9 hours, biol rep 2

value: transition phase

value: 9 hours post inoculation


title: PT21, Baseline


title: dRNA Seq, wild type 3.5 hours, biol rep 1


title: CNV_7D_2

value: retina+choroid

value: laser-induced CNV


title: Placental biopsy, Preterm, SFJR59

description:
SFJR59_S59
salmon.merged.gene_counts_length_scaled_final.txt

value: placenta

value: GAPPS Zambia

value: Preterm


title: dRNA Seq  wild type 9 hours, biol rep 1


title: CNV_7D_1

value: WT


title: Placental biopsy, Preterm, SFJR6

description:
SFJR6_S6
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Pakistan


title: MDA-MB-468_Combination_LT_Rep9

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by cutadapt (v 2.8) with parameters -m 75 -q 30
Reads were aligned to a hybrid reference genome consisting of both the human GRCh38.p13 primary assembly genome and the mouse GRCm39 primary assembly genome, utilizing STAR (v 2.7.2b) with parameter --outFilterMismatchNoverReadLmax 0.01 --outFilterMultimapNmax 1
Read counts over annotated genes were obtained using featureCount (subreads | version: 2.0.3) with parameters -T 12 -B -O --fraction -s 2 -p --countReadPairs -d 50 -D 800 -g gene_id
Assembly: GRCh38.p13 & GRCm39
Supplementary files format and content: comma-delimited text files include human and mouse gene counts for each sample

source_name: xenograft

growth_protocol: MDA-MB-468 were cultured in DMEM high glucose media supplemented with 10% FBS, 1% penicillin/streptomycin, 2 mM glutamine and 1 x non-essential amino acids.   Cells were inoculated orthotopically under fat pad (2x10^6 cells in 0.1 mL 50% Matrigel per animal) in female NSG mice to form xenograft tumors.

extract_protocol:
Tumor tissues were first submerged in 500 μL RNA-Later stabilization solution (Thermo Fisher Scientific) at room temperature. After stabilization, RNA samples were extracted from tumor tissues using the mRNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.  RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit

treatment_protocol: Animals were randomly allocated to study groups when the mean tumor size reached 50-100 mm^3. For everolimus treament, animals were dosed with everolimus (0.4mg/mL solution in the vehicle 70% PEG-400/30% Propylene Glycol, 5 mL/kg, p.o., q.d.).  For SNX631 treatment, animals received SNX631-medicated diet (350 ppm, producing 30-45 mg/kg/day dosage on average).   For the combination treatment, animals were put on SNX631 mediacated diet (350ppm) four days prior to daily oral gavage with everolimus to accommondate food flavor.

value: xenograft

value: triple-negative breast cancer cells

value: MDA-MB-468 xenograft growing in female NSG, treated with everolimus+SNX631 combination for 148 days


title: PT20, C2D1

value: Peripheral blood mononuclear cells

value: Achieved PFS6M


title: CNV_3D_4

value: 3 days after injury


title: Placental biopsy, Preterm, SFJR57

description:
SFJR57_S57
salmon.merged.gene_counts_length_scaled_final.txt


title: Placental biopsy, Preterm, SFJR61

description:
SFJR61_S61
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Tanzania


title: Placental biopsy, Preterm, SFJR58

description:
SFJR58_S58
salmon.merged.gene_counts_length_scaled_final.txt


title: PT20, Baseline

value: Peripheral blood


title: MDA-MB-468_Combination_LT_Rep7


title: CNV_3D_2


title: Placental biopsy, Preterm, SFJR60

description:
SFJR60_S60
salmon.merged.gene_counts_length_scaled_final.txt


title: CNV_3D_3


title: Placental biopsy, Preterm, SFJR55

description:
SFJR55_S55
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Pemba


title: CNV_7D_3

value: 7 days after injury


title: Placental biopsy, Preterm, SFJR56

description:
SFJR56_S56
salmon.merged.gene_counts_length_scaled_final.txt


title: MDA-MB-468_Combination_LT_Rep8


title: PT19, C3D1

value: Did not achieved PFS6M


title: PT19, C2D1


title: MDA-MB-468_Combination_LT_Rep5


title: C4 (without CNV)

value: retina+choroid

value: laser-induced CNV


title: PT19, Baseline


title: CNV_3D_1


title: MDA-MB-468_Combination_LT_Rep6


title: MDA-MB-468_Combination_LT_Rep4


title: Placental biopsy, Preterm, SFJR53

description:
SFJR53_S53
salmon.merged.gene_counts_length_scaled_final.txt

value: placenta


title: C3 (without CNV)


title: MDA-MB-468_Combination_LT_Rep3


title: PT20, C3D1


title: Placental biopsy, Preterm, SFJR52

description:
SFJR52_S52
salmon.merged.gene_counts_length_scaled_final.txt

value: Preterm


title: C2 (without CNV)

value: WT


title: MDA-MB-468_Combination_LT_Rep2


title: PT18, C2D1


title: Placental biopsy, Term, SFJR51

description:
SFJR51_S51
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Pakistan

value: Term


title: MDA-MB-468_Combination_LT_Rep1

value: xenograft

value: triple-negative breast cancer cells


title: PT18, Baseline

value: Peripheral blood mononuclear cells


title: C1 (without CNV)


title: Placental biopsy, Term, SFJR50

description:
SFJR50_S50
salmon.merged.gene_counts_length_scaled_final.txt


title: Embryo_9, E9.5, WT

description: instrument model: 10x Chromium Controller

library_source: transcriptomic single cell

data_processing:
Raw fastq files were aligned to mouse genome reference mm10 using CellRanger v5.0.0 (10X Genomics).
Count matrices filtered by CellRanger algorithm were further filtered by discarding cells with < 400 genes, < 800 UMI, and > 25% mitochondrial genes expressed.
Data was processed and analyzed using R package Seurat v4.0.5 (Hao et al. 2021).
Assembly: mm10
Supplementary files format and content: Tarball containing barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz for each sample

molecule: nuclear RNA

extract_protocol:
Slyper et al., Nature Medicine, 2020 (“TST protocol” described here:https://www.nature.com/articles/s41591-020-0844-1)
10x Genomics Chromium Single Cell 3' v3.1 Chemistry, Revision D

tag: developmental stage

value: embryo

value: Cmtr2 WT

value: male


title: PT15, C3D1

value: Peripheral blood


title: Placental biopsy, Term, SFJR4

description:
SFJR4_S4
salmon.merged.gene_counts_length_scaled_final.txt

value: GAPPS Bangladesh


title: Embryo_13, E9.5, WT


title: Placental biopsy, Term, SFJR49

description:
SFJR49_S49
salmon.merged.gene_counts_length_scaled_final.txt


title: Embryo_8, E9.5, WT


title: PT15, Baseline


title: MDA-MB-468_Everolimus_LT_Rep8

tag: cell line

value: MDA-MB-468 xenograft growing in female NSG, treated with everolimus (2mg/kg q.d.) for 148 days


title: MDA-MB-468_Everolimus_LT_Rep9


title: Embryo_2, E9.5, WT


title: Placental biopsy, Preterm, SFJR54

description:
SFJR54_S54
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Pemba


title: MDA-MB-468_Everolimus_LT_Rep7


title: PT18, C3D1

value: Did not achieved PFS6M


title: PT13, C3D1

value: Achieved PFS6M


title: Placental biopsy, Term, SFJR48

description:
SFJR48_S48
salmon.merged.gene_counts_length_scaled_final.txt

value: placenta


title: MDA-MB-468_Everolimus_LT_Rep10


title: Placental biopsy, Term, SFJR47

description:
SFJR47_S47
salmon.merged.gene_counts_length_scaled_final.txt


title: PT15, C2D1


title: PT13, C2D1


title: Embryo_4, E9.5, KO

value: Cmtr2 KO


title: MDA-MB-468_Everolimus_LT_Rep6

value: WT


title: Placental biopsy, Preterm, SFJR46

description:
SFJR46_S46
salmon.merged.gene_counts_length_scaled_final.txt

value: Preterm


title: PT13, Baseline


title: MDA-MB-468_Everolimus_LT_Rep5


title: Placental biopsy, Term, SFJR45

description:
SFJR45_S45
salmon.merged.gene_counts_length_scaled_final.txt

value: Term


title: PT11, C3D1


title: Embryo_18, E9.5, KO


title: Embryo_19, E9.5, KO


title: MDA-MB-468_Everolimus_LT_Rep4

value: xenograft


title: Placental biopsy, Term, SFJR44

description:
SFJR44_S44
salmon.merged.gene_counts_length_scaled_final.txt


title: Embryo_16, E9.5, KO

value: female


title: MDA-MB-468_Everolimus_LT_Rep3

value: triple-negative breast cancer cells


title: PT11, C2D1

value: Peripheral blood mononuclear cells


title: PT11, Baseline


title: Placental biopsy, Term, SFJR43

description:
SFJR43_S43
salmon.merged.gene_counts_length_scaled_final.txt


title: PT10, C3D1


title: Placental biopsy, Preterm, SFJR42

description:
SFJR42_S42
salmon.merged.gene_counts_length_scaled_final.txt


title: Embryo_15, E9.5, KO

value: embryo


title: MDA-MB-468_Everolimus_LT_Rep1


title: PT10, C2D1


title: Placental biopsy, Term, SFJR41

description:
SFJR41_S41
salmon.merged.gene_counts_length_scaled_final.txt

value: GAPPS Zambia


title: Control,scRNA

city: Wuhan

first: Boxin

last: Zhang

address: 237 Luoyu Road

institute: Wuhan University

description: MobiCube

data_processing:
Normalized aggregate data was generated across the samples using the MobiVision software pipeline (version 1.1, MobiDrop). This process involved demultiplexing cellular barcodes, mapping reads to the genome and transcriptome using STAR solo, and down-sampling reads as needed.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: s.c tumor

extract_protocol:
Following 4T1 tumor establishment, AIE COF were administered for 4T1-tumor bearing mice. On day 7 post-phototherapy, the C57BL/c mice were euthanized, and the tumors were harvested. The tumors were then processed into single-cell suspensions, with a cell concentration of 700-1200 cells μL-1 for each sample for scRNA-seq.
The MobiCube Single-Cell 3’ RNA-seq Kit v1.0 (MobiDrop) was used to prepare the library, which was subsequently sequenced using Illumina NovaSeq 6000 Systems.

value: s.c tumor

value: PBS


title: MDA-MB-468_SNX631_LT_Rep8

value: MDA-MB-468 xenograft growing in female NSG, treated with SNX631 (350ppm chow) for 96 days


title: AIE COF,scRNA

description: MobiCube

value: AIE COF-medidated phototherapy


title: Placental biopsy, Preterm, SFJR40

description:
SFJR40_S40
salmon.merged.gene_counts_length_scaled_final.txt


title: GA tissue, GB_3

city: Taichung

first: Chien-Wei

last: Lee

address: 2 Yuh-Der Road

country: Taiwan

institute: CMUH

data_processing:
Illumina Casava1.7 software used for basecalling.
The evaluation of quality for raw fastq data was conducted using FastQC. Subsequent processing involved the application of FastP to eliminate adapters and poly tails.
To address ribosomal RNA contamination, an alignment procedure was executed against NCBI_GRCm39_rRNA using Hisat2, and unmapped sequences were selected. After the filtering step, FastQC was rerun to ensure ongoing quality.
The alignment of filtered reads was accomplished using Hisat2 to the GENCODE_GRCm39, and the resulting mappings were sorted with SAMtools.
FeatureCounts153 was employed for annotation purposes using the GENCODE_GRCm39. Normalization was achieved through DESeq2.
Assembly: mm10
Supplementary files format and content: a csv file includes raw counts for each sample

source_name: Aged GA + GB

extract_protocol:
RNA was purified using TRIzol® and chloroform.Further, RNA is precipitated by isopropanol adn dissolved by RNase-free water.A total amount of 1 μg total RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

value: gastrocnemius muscle

tag: age

value: aged

value: administered 12 mg/kg body weight GB daily via oral gavage for two months


title: PT10, Baseline

value: Peripheral blood

value: Achieved PFS6M


title: GA tissue, GB_2


title: MDA-MB-468_SNX631_LT_Rep7

value: WT


title: Placental biopsy, Term, SFJR3

description:
SFJR3_S3
salmon.merged.gene_counts_length_scaled_final.txt

value: placenta

value: GAPPS Bangladesh

value: Term


title: PT09, C3D1


title: MDA-MB-468_SNX631_LT_Rep6

value: xenograft

value: triple-negative breast cancer cells


title: Placental biopsy, Term, SFJR38

description:
SFJR38_S38
salmon.merged.gene_counts_length_scaled_final.txt


title: PT09, C2D1

value: Peripheral blood mononuclear cells


title: GA tissue, GB_1


title: MDA-MB-468_SNX631_LT_Rep5


title: Placental biopsy, Term, SFJR37

description:
SFJR37_S37
salmon.merged.gene_counts_length_scaled_final.txt


title: MDA-MB-468_SNX631_LT_Rep4


title: PT09, Baseline


title: MDA-MB-468_Everolimus_LT_Rep2

value: MDA-MB-468 xenograft growing in female NSG, treated with everolimus (2mg/kg q.d.) for 148 days


title: Placental biopsy, Term, SFJR36

description:
SFJR36_S36
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Bangladesh


title: PT07, C3D1


title: GA tissue, CON_23M_2

source_name: Aged GA + Vehicle

value: administered vehicle (saline) daily via oral gavage for two months


title: GA tissue, CON_23M_3


title: MDA-MB-468_SNX631_LT_Rep3

value: MDA-MB-468 xenograft growing in female NSG, treated with SNX631 (350ppm chow) for 96 days


title: PT07, C2D1


title: GA tissue, CON_23M_1


title: MDA-MB-468_SNX631_LT_Rep2


title: GA tissue, CON_3M_3

source_name: Young GA + Vehicle

value: young


title: MDA-MB-468_SNX631_LT_Rep1


title: Placental biopsy, Preterm, SFJR33

description:
SFJR33_S33
salmon.merged.gene_counts_length_scaled_final.txt

value: Preterm


title: PT06, C3D1


title: Placental biopsy, Term, SFJR35

description:
SFJR35_S35
salmon.merged.gene_counts_length_scaled_final.txt


title: GA tissue, CON_3M_2

value: gastrocnemius muscle


title: Placental biopsy, Preterm, SFJR32

description:
SFJR32_S32
salmon.merged.gene_counts_length_scaled_final.txt


title: GA tissue, CON_3M_1


title: MDA-MB-468_Ctrl_LT_Rep7

value: MDA-MB-468 xenograft growing in female NSG, treated with vehicle for 78 days


title: PT06, C2D1

value: Peripheral blood


title: MDA-MB-468_Ctrl_LT_Rep8


title: PT06, Baseline

value: Achieved PFS6M


title: Placental biopsy, Preterm, SFJR30

description:
SFJR30_S30
salmon.merged.gene_counts_length_scaled_final.txt


title: P7sham_d3_FB

city: Oxford

first: Judy

middle: R

last: Sayers

address: Institute of Developmental and Regenerative Medicine, IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Dr, Headington

country: United Kingdom

institute: University of Oxford

description:
10X Genomics Single Cell 3' V3.1 feature barcode library
P7sham_d3_barcodes.tsv.gz
P7sham_d3_features.tsv.gz
P7sham_d3_matrix.tsv.gz

library_source: other

data_processing:
Data processed using the 10X Cell Ranger Multi pipeline (version 7.0.0)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: post-natal heart

growth_protocol: Samples harvested 3 days following MI or sham surgery

extract_protocol:
Enzymatic digestion and FACS isolation of CX40+ CD31- cardiac cells.
Gene Expression (GEX) and Cell Multiplexing Feature Barcode (FB) Libraries were constructed using the Single Cell 3' with Cell Multiplexing Reagent Kit (V3.1). Cell Multiplexing Oligos used as follows: P1MI_d3 (CMO301-308); P1sham_d3 (CMO307-312); P7MI_d3 (CMO301-305); P7sham_d3 (CMO306-310).

treatment_protocol: See samples

value: post-natal heart

value: Cell Multiplexing Oligo Barcode related to cells in Sample 4

value: P7 sham surgery


title: P7MI_d3_FB

description:
10X Genomics Single Cell 3' V3.1 feature barcode library
P7MI_d3_barcodes.tsv.gz
P7MI_d3_features.tsv.gz
P7MI_d3_matrix.tsv.gz

value: Cell Multiplexing Oligo Barcode related to cells in Sample 3

value: P7 MI surgery


title: Placental biopsy, Preterm, SFJR2

description:
SFJR2_S2
salmon.merged.gene_counts_length_scaled_final.txt

value: placenta

value: GAPPS Bangladesh


title: MDA-MB-468_Ctrl_LT_Rep5

value: xenograft

value: triple-negative breast cancer cells

value: WT


title: MDA-MB-468_Ctrl_LT_Rep6


title: PT05, C3D1

value: Peripheral blood mononuclear cells

value: Did not achieved PFS6M


title: PT07, Baseline


title: Placental biopsy, Preterm, SFJR34

description:
SFJR34_S34
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Bangladesh

value: Preterm


title: MDA-MB-468_Ctrl_LT_Rep4

value: MDA-MB-468 xenograft growing in female NSG, treated with vehicle for 78 days


title: MDA-MB-468_Ctrl_LT_Rep3


title: PT03, C3D1

value: Peripheral blood


title: MDA-MB-468_Ctrl_LT_Rep2


title: PT05, Baseline


title: P7MI_d3_GEX

description:
10X Genomics Single Cell 3' V3.1 gene expression library
P7MI_d3_barcodes.tsv.gz
P7MI_d3_features.tsv.gz
P7MI_d3_matrix.tsv.gz

molecule: polyA RNA

value: FACS isolated CX40+ CD31- cardiac cells


title: PT03, C2D1

value: Achieved PFS6M


title: MDA-MB-468_Ctrl_LT_Rep1


title: P7sham_d3_GEX

description:
10X Genomics Single Cell 3' V3.1 gene expression library
P7sham_d3_barcodes.tsv.gz
P7sham_d3_features.tsv.gz
P7sham_d3_matrix.tsv.gz

value: post-natal heart


title: Placental biopsy, Term, SFJR26

description:
SFJR26_S26
salmon.merged.gene_counts_length_scaled_final.txt

value: GAPPS Zambia

value: Term


title: Placental biopsy, Preterm, SFJR29

description:
SFJR29_S29
salmon.merged.gene_counts_length_scaled_final.txt


title: Placental biopsy, Preterm, SFJR25

description:
SFJR25_S25
salmon.merged.gene_counts_length_scaled_final.txt


title: Placental biopsy, Preterm, SFJR28

description:
SFJR28_S28
salmon.merged.gene_counts_length_scaled_final.txt


title: MDA-MB-468_Everolimus_ST_Rep8

value: MDA-MB-468 xenograft growing in female NSG, treated with everolimus (2mg/kg q.d.) for 38 days


title: P1sham_d3_GEX

description:
10X Genomics Single Cell 3' V3.1 gene expression library
P1sham_d3_barcodes.tsv.gz
P1sham_d3_features.tsv.gz
P1sham_d3_matrix.tsv.gz

value: P1 sham surgery


title: PT03, Baseline


title: P1MI_d3_FB

description:
10X Genomics Single Cell 3' V3.1 feature barcode library
P1MI_d3_barcodes.tsv.gz
P1MI_d3_features.tsv.gz
P1MI_d3_matrix.tsv.gz

value: Cell Multiplexing Oligo Barcode related to cells in Sample 1

value: P1 MI surgery


title: Placental biopsy, Term, SFJR21

description:
SFJR21_S21
salmon.merged.gene_counts_length_scaled_final.txt

value: placenta

value: AMANHI Pakistan


title: P1MI_d3_GEX

description:
10X Genomics Single Cell 3' V3.1 gene expression library
P1MI_d3_barcodes.tsv.gz
P1MI_d3_features.tsv.gz
P1MI_d3_matrix.tsv.gz


title: P1sham_d3_FB

description:
10X Genomics Single Cell 3' V3.1 feature barcode library
P1sham_d3_barcodes.tsv.gz
P1sham_d3_features.tsv.gz
P1sham_d3_matrix.tsv.gz

value: Cell Multiplexing Oligo Barcode related to cells in Sample 2


title: PT05, C2D1

value: Peripheral blood mononuclear cells

value: Did not achieved PFS6M


title: Placental biopsy, Preterm, SFJR27

description:
SFJR27_S27
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Bangladesh

value: Preterm


title: PT02, C3D1

value: Peripheral blood


title: PT02, C2D1


title: MDA-MB-468_Everolimus_ST_Rep6

value: xenograft

value: triple-negative breast cancer cells

value: WT


title: Placental biopsy, Term, SFJR20

description:
SFJR20_S20
salmon.merged.gene_counts_length_scaled_final.txt


title: MDA-MB-468_Everolimus_ST_Rep7


title: kidney, FA

city: Fuzhou

first: Zhimin

last: Chen

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

description: FA-data-matrix.txt

data_processing:
The data matrix processed by Seurat is output through R language
Assembly: mm10
Supplementary files format and content: tab delimited text file includes data value for each sample
Supplementary files format and content: text file includes data value for each sample

source_name: kidney

extract_protocol:
Harvested cells at the required densities were combined with gel beads  containing the barcoded information along with a mixture of cells and  enzymes. Oil surfactant droplets in a microfluidic double-cross system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence.
The cDNA fragment was then reverse transcribed before the sample was labeled. The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200300 base pairs (bp), together with the library building process of traditional secondgeneration sequencing such as sequencing junction and primers. Finally, the DNA library was generated by PCR amplification

value: kidney

value: wild type

value: FA

tag: disease state

value: FA-induced nephropathy


title: Placental biopsy, Preterm, SFJR1

description:
SFJR1_S1
salmon.merged.gene_counts_length_scaled_final.txt

value: GAPPS Bangladesh


title: MDA-MB-468_Everolimus_ST_Rep5

value: MDA-MB-468 xenograft growing in female NSG, treated with everolimus (2mg/kg q.d.) for 38 days


title: kidney, Ctrl

description: FA-data-matrix.txt

value: control


title: PT02, Baseline

value: Achieved PFS6M


title: Placental biopsy, Preterm, SFJR19

description:
SFJR19_S19
salmon.merged.gene_counts_length_scaled_final.txt

value: placenta


title: PT01, C3D1

value: Peripheral blood mononuclear cells


title: db/db 20B, db/db, 20weeks old, replicate2

city: Xi'an

first: Yan

address: 127 Changle West Road

institute: Xijing Hospital

description: 10x Genomics

data_processing:
Reads were processed using the Cell Ranger 6.0.1 pipeline with default and recommended parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
Heart tissue were transported in In sterile culture dish with 10 ml 1× DPBS solution (Solarbio, cat. no. D1040) on ice to remove the residual MACS Tissue Storage Solution (Miltenyi Biotec, cat. no. 130-100-008), then minced on ice. We used dissociation enzyme 0.25% Trypsin (Hyclone, cat. no. SH30042.01) and 10 ug/mL Recombinant DNase I (RNase-free) (TaKaRa, cat. no. 2270B) dissolved in DPBS with 5% Fetal Bovine Serum (FBS, Thermo Fisher Scientific, cat. no. SV30087.02) to digest the tissues. XX tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 μm nylon cell strainer and red blood cells were removed by 1× Red Blood Cell Lysis buffer (Thermo Fisher Scientific, cat. no. 00-4333-57) . Dissociated cells were washed with 1× DPBS containing 2% FBS. Cells were stained with AO/PI, and viability was assessed using a Countstar Fluorescence Cell Analyzer (Aber Instruments).
Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM). After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription. On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification.Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3.1). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina), and 150 bp paired-end reads were generated. The sequencing and bioinformatics analysis were performed by Majorbio Co., Ltd (Shanghai, China).

value: heart

value: db/db

value: 20weeks old


title: Placental biopsy, Term, SFJR18

description:
SFJR18_S18
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Bangladesh

value: Term


title: PT01, C2D1

value: Peripheral blood


title: MDA-MB-468_Everolimus_ST_Rep3

value: xenograft

value: triple-negative breast cancer cells

value: WT


title: db/db 20A, db/db, 20weeks old, replicate1

description: 10x Genomics


title: MDA-MB-468_Everolimus_ST_Rep2


title: db/db 14B, db/db, 14weeks old, replicate2

description: 10x Genomics

value: 14weeks old


title: Placental biopsy, Preterm, SFJR17

description:
SFJR17_S17
salmon.merged.gene_counts_length_scaled_final.txt

value: Preterm


title: MDA-MB-468_Everolimus_ST_Rep1


title: db/db 14A, db/db, 14weeks old, replicate1

description: 10x Genomics


title: 35_BL

city: Nedlands

first: Nicola

last: Principe

state: WA

address: 6 Verdun St

data_processing:
Alignment of 5’ VDJ sequencing data was performed with cell ranger. Sequences spanning the third complementary determining region (CDR3) of TRA, TRB, TRD and TRG genes from individual cells were derived. We focused on conventional TCRαβ T cells with productive rearrangements of the TRA, TRB CDR3 region. We used TraCeR56, a computational method to identify clonally related cells. We removed individual cells that produced >= 2 unique TRB CDR3 sequences, and cells that produced > 2 unique TRA CDR3 sequences. We called clones as individual T cells with identical combination of TRA/TRB CDR3 amino acid sequences, or cells with an identical TRB, or TRA CDR3 sequence.
Assembly: Cellranger v7.1.0
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0
Supplementary files format and content: Processed data files are output from CellRanger for each sample.
Library strategy: scTCR-Seq

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were thawed by immersing the cryotube in a 37°C water bath until a small ice shard remained. The cryotube contents were then mixed using a 1 mL pipette and transferred to a 50 mL centrifuge tube. Additionally, 1 mL of media was mixed with the cryovial and then transferred to the same 50 mL tube. Four sequential dilutions were performed by incrementally adding media to the centrifuge tube while gently agitating the mixture. Specifically, 2 mL, 4 mL, 8 mL, and 16 mL were added in succession, with a 30-second interval between each step. The PBMCs were subsequently centrifuged at 400g for 5 minutes. The supernatant was removed, leaving approximately 1 mL, in which the cells were resuspended. An additional 9 mL of media was added, followed by another 5-minute centrifugation at 400g. The supernatant was once again removed and discarded. The cells were finally resuspended in 1xDPBS+0.04% BSA. Cell count and viability were assessed using a Cellometer K2 and Acridine Orange/Propidium Iodide (AO/PI) staining.
Single cell libraries were constructed using the 10x Genomics chromium 5′ v2 workflow according to the manufacturer’s protocol. All experiments and conditions aimed for a capture of approximately 6000 cells. Libraries were quantified with Qubit and checked for fragment size using the TapeStation D1000 kit (Agilent). Libraries were pooled in equimolar concentration for a total pooled concentration of 1.8 nM. The libraries were sequenced using S4 (200 cycle) sequencing kits on the Illumina NovaSeq 6000 with a read one length of 100 cycles, and a read two length of 100 cycles. TCR libraries were constructed from the cDNA generated for each sample during the 5’ v2 workflow according to the manufacturers protocol (CG000331 REV A). The TCR libraries were then quantified using the QUBIT DNA HS kit (cat# Q32854) and fragment size determined using the TapeStation D1000 kit (Agilent). The libraries were then pooled in equimolar concentration for a total pooled concentration of 2nM. The libraries were sequenced using SP (100 cycle) sequencing kits on the Illumina NovaSeq 6000 with a read one length of 26 cycles, and a read two length of 90 cycles.

value: peripheral blood mononuclear cells

tag: patient

tag: timepoint

value: BL

tag: pfs 6m_response

value: NO

tag: gender

value: Male

tag: epithelioid


title: db/db 8B, db/db, 8weeks old, replicate2

description: 10x Genomics

tag: tissue

value: 8weeks old


title: Placental biopsy, Preterm, SFJR15

description:
SFJR15_S15
salmon.merged.gene_counts_length_scaled_final.txt

value: placenta


title: 34_BL

value: YES


title: MDA-MB-468_Ctrl_ST_Rep7

tag: cell type

value: MDA-MB-468 xenograft growing in female NSG, treated with vehicle for 30 days


title: Placental biopsy, Term, SFJR14

description:
SFJR14_S14
salmon.merged.gene_counts_length_scaled_final.txt


title: db/m B, db/m, 8weeks old, replicate2

description: 10x Genomics

value: heart

tag: genotype

value: db/m


title: MDA-MB-468_Ctrl_ST_Rep5

tag: treatment


title: 27_C2D1


title: MDA-MB-468_Everolimus_ST_Rep4

value: MDA-MB-468 xenograft growing in female NSG, treated with everolimus (2mg/kg q.d.) for 38 days


title: db/db 8A, db/db, 8weeks old, replicate1

description: 10x Genomics

value: db/db


title: MDA-MB-468_Ctrl_ST_Rep6

value: xenograft


title: 5_C2D1


title: Placental biopsy, Preterm, SFJR13

description:
SFJR13_S13
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Pakistan


title: db/m A, db/m, 8weeks old, replicate1

description: 10x Genomics


title: Placental biopsy, Preterm, SFJR12

description:
SFJR12_S12
salmon.merged.gene_counts_length_scaled_final.txt


title: MDA-MB-468_Ctrl_ST_Rep4

value: triple-negative breast cancer cells

value: WT


title: 36_C2D1


title: Placental biopsy, Preterm, SFJR16

description:
SFJR16_S16
salmon.merged.gene_counts_length_scaled_final.txt

value: AMANHI Bangladesh

value: Preterm


title: PT01, Baseline

source_name: Peripheral blood

value: Peripheral blood

value: Peripheral blood mononuclear cells

tag: response (pfs)

value: Achieved PFS6M


title: MDA-MB-468_Ctrl_ST_Rep3


title: Placental biopsy, Preterm, SFJR11

description:
SFJR11_S11
salmon.merged.gene_counts_length_scaled_final.txt

tag: site


title: Placental biopsy, Preterm, SFJR10

description:
SFJR10_S10
salmon.merged.gene_counts_length_scaled_final.txt

tag: gestational age


title: Naïve WT 43

city: Woolloongabba

first: Timothy

middle: Ryan

last: McCulloch

state: QLD

address: 37 Kent St

department: Frazer Institute

institute: University of Queensland

data_processing:
Sequence reads were trimmed using Trimomatic
Trimmed reads were mapped to GrCM38/mm10 mouse genome using HISAT2
Transcripts assembled and quantified using StringTie
Assembly: mm10
Supplementary files format and content: Tabular file includes raw counts for each sample

source_name: Spleen

extract_protocol:
RNA was extracted using Maxwell RSC simplyRNA Cells RNA extraction kit (Promega)
Libraries were prepped using an Illumina Stranded mRNA prep kit (Illumina)

treatment_protocol: Mice were infected with 1 x 10^6 CFU of Salmonella Typhimurium SL3261 by i.p. injection, and splenic CD4+ T cells isolated on day 10

value: Spleen

value: CD4+ T cells

value: Naïve


title: Naïve WT 42


title: MDA-MB-468_Ctrl_ST_Rep2

value: MDA-MB-468 xenograft growing in female NSG, treated with vehicle for 30 days


title: 21_C3D1

value: peripheral blood mononuclear cells

value: YES

value: Male


title: Naïve WT 41


title: 18_BL

value: BL

value: NO


title: Naive WT 40


title: 51_C3D1


title: Pcif1-KO_PCIF1-CD-rescue_anabolicSLAM

city: Shenzhen

first: Wee Siong Sho

last: Goh

state: Guangdong

address: Shenzhen Bay Laboratory, No. 5, Kelian Road, Goh Lab, A1819, Guangming District

department: Institute of Molecular Physiology

institute: Shenzhen Bay Laboratory

data_processing:
Basecalling was performed using Illumina RTA, with further demultiplexing performed by Illumina bcl2fastq 2.20.
Fastq sequences were first trimmed of 5' and 3' adapter sequences and poly(A) tails using Cutadapt 3.7 -q 20 -m 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AAAAAAAAAAAAAAAAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Reads were mapped to hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR 2.7.10a --outMultimapperOrder Random --outSAMmultNmax 1. T to C conversion in the reverse complement of read1 was counted and nascent reads were defined as reads with T to C conversion count >= 2.
Bedgraphs (in RPM) of the reverse complement of the first nucleotide of read 1 were constructed using custom Python scripts.
Reads were counted using htseq-count 2.0.1 -s reverse -t UTR, with gencode.v28.chr_patch_hapl_scaff.annotation.gtf obtained from gencodesgenes.org. Read counts were subjected to DESeq2 1.30.1 with lfcshrink to quantify differential transcriptional output. Cumulative log2fold-change plots and box-and-whiskers plots were generated with custom Python scripts.
Assembly: hg38
Supplementary files format and content: bedgraph

growth_protocol: ATCC HEK293T CRL-3216 cells were cultivated in a sterile 5% CO2 incubator at 37°C, and in DMEM supplemented with 10% FBS. Cells within passage 3–25 were used for experiments. HEK293T cells were regularly subjected to MycoAlert Plus Mycoplasma kit (Lonza LT07) to verify that they were mycoplasma-free.

extract_protocol:
48hr later, cells were harvested by scraping and nuclei was enriched using Nuclei EZ (Sigma NUC-101). Nuclei were homogenized in Trizol-LS and nuclear RNA was isolated using Phase-Lock (HEAVY) tubes according to manufacturer’s protocol. Residual genomic DNA was removed using RQ1 RNase-free DNAse (Promega M6101) before RNA was purified with RNA concentrator (Zymo R1015).
RNA-seq library was prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit-REV (Lexogen 016).
3’ mRNA-Seq

treatment_protocol: Cells were seeded in 6-well plates 24hr prior to transfection. Cells were then transfected with 5pmol siRNA against Dis3 (Silencer Select S229660), against scrambled control (Silencer Select 4390843) and/or against PCF11 (Silencer Select S28362); using Lipofectamine RNAimax (Invitrogen 13778030) according to manufacturer’s instructions.

value: Human embryonic kidney

value: PCIF1-CD overexpression


title: sr45 seedlings new rep2

city: Bellaterra

first: Alvaro

middle: Santiago

last: Larran

state: Barcelona

address: C/ de la Vall Moronta s/n, Campus UAB

country: Spain

institute: CRAG

data_processing:
Gene expression (GE) quantification is performed using vast-tools. vast-tools maps the first 50 nucleotides of the forward read (if longer and paired end) to a library with one reference transcript per gene, the *.1 transcript according to the TAIR 10 nomenclature or else that with the lowest suffix (33,602 genes in total). GE levels are provided using the cRPKM metric (corrected [for mappability] Reads Per Kilobasepair and Million mapped reads), as detailed in Labbé et al., Stem Cells 2012. cRPKM can be converted to TPMs applying the following formula: TPM = 10^6 * cRPKM/sum_all(cRPKM).
Assembly: tair10
Supplementary files format and content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Seeds were stratified at 4 °C for 48 hours in MS media and plants were grown under 16:8 photoperiod at 22 °C for 11 days.

extract_protocol:
RNA was extracted from 100 mg of seedlings using RNeasy plant mini kit (Qiagen) following manufacturer’s instructions. 2 μg of RNA per sample was used for library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole seedling


title: sr45 seedlings new rep1


title: Pcif1-KO_PCIF1-WT-rescue_anabolicSLAM

value: PCIF1-WT overexpression


title: 18_C3D1


title: sap18sr45 seedlings rep1


title: sap18sr45 seedlings rep2


title: Naïve WT 20


title: Col0 seedlings new rep2

value: wildtype


title: Naïve WT 22


title: siPcif1+ATRA BE(2)-C m6ACE-input 3

data_processing:
Basecalling is performed using Illumina RTA, with further demultiplexing performed by Illumina bcl2fastq 2.20.
Fastq sequences were first filtered for a quality score of 20, then trimmed of 5′ and 3′ adapter sequences and poly(A) tails using Cutadapt 3.7 -q 20 -m 30 -a TGGAATTCTCGGGTGCCAAGG -A GATCGTCGGACTGTAGAACTCTGAAC.
The 8-mer UMI located at the first 8 nucleotides of read 1 was registered and trimmed. Any complementary UMI sequence in read 2 was also trimmed.
Reads were mapped to the methylated spike-in using Bowtie2, or to the hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR. Aligned pairs that had the same mapping coordinates and UMIs were filtered out as PCR duplicates.
Read-start coordinates in hg38-mapped reads that began with an adenosine nucleotide, and had a minimum mean read count of 1 across the triplicate samples were collated. m6A or m6Am sites were identified as read starts that were at least 2-fold enriched in m6ACE libraries than in the corresponding input libraries. This enrichment was calculated using DESeq2 performed on A-only sites across triplicate pairs of m6ACE and corresponding input libraries (FDR < 0.1, padj < 0.05). Identified sites that were 1–4 nucleotides upstream of another identified significant Rm6AC site or sites found within clustered read-starts were filtered out.
To calculate the relative methylation level (RML) of each site in each sample: The read-start counts at positions –4 to 0 of each site in the m6ACE library were summed and divided by the read-start counts at positions –51 to 0 of the same site in the input library to give ‘X’. Similarly, the read-start counts at positions -4 to 0 of the spike-in m6A site in the m6ACE library were summed and divided by the read-start counts at positions –21 to 0 of the same spike-in m6A site in the input library to give ‘Y’. X was normalized to Y to give RML. RML values of each site was averaged across triplicates for each sample condition.
Assembly: hg38
Supplementary files format and content: bedgraph

growth_protocol: ATCC BE(2)-C CRL-2268 cells were cultivated in a sterile 5% CO2 incubator at 37°C, and in DMEM supplemented with 10% FBS. Cells within passage 3–20 were used for experiments. Cells were regularly subjected to MycoAlert Plus Mycoplasma kit (Lonza LT07) to verify that they were mycoplasma-free.

extract_protocol:
Cells were washed twice with cold PBS and RNA extracted using Trizol LS (Ambion 10296) according to manufacturer’s protocol with an additional ethanol precipitation step.
Library was prepared using m6ACE

treatment_protocol: BE(2)-C cells were seeded into T75 flasks and transfected with siRNA against Pcif1 (Silencer Select S34301) or against scrambled control (Silencer Select 4390843) for 24hr using Lipofectamine RNAimax (Invitrogen 13778030) as per manufacturer's protocol. For differentiation by ATRA treatment, BE(2)-C cells were subsequently treated with 10µM ATRA for 4day with ATRA-containing media replaced freshly every 24hr.

value: Human neuroblastoma cell line

value: WT

value: siPcif1 + ATRA


title: 26_C2D1


title: siPcif1+ATRA BE(2)-C m6ACE-input 2


title: 10_BL


title: Naïve KO 43

value: Spleen

value: TIGIT KO (C57)

value: S. Typhimurium infected


title: Col0 seedlings new rep1


title: 32_C3D1

value: Female


title: Naïve KO 42

value: CD4+ T cells


title: siScram+ATRA BE(2)-C m6ACE-input 3

value: siScram + ATRA


title: 41_C3D1

value: peripheral blood mononuclear cells

value: YES

value: Male


title: Bulk RNA-seq, GBM40, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM40T_RNA

data_processing:
Fastq files were first trimmed using Trimmomatic and mapped using STAR aligner with the paired end option selected (hg38). We used FeatureCounts to assemble transcripts and generate raw count matrices.
Assembly: hg38
Supplementary files format and content: xlsx count matrix

source_name: human glioblastoma

extract_protocol:
RNA was harvested using miRneasy kit (Qiagen).
Libraries were prepared with Takara Bio SMART-Seq v4 Ultra Low Input RNA Kit and NEBNext Ultra II kit.

value: human glioblastoma

value: HepaCAM+ cells


title: siPcif1+ATRA BE(2)-C m6ACE-input 1


title: Naïve KO 41


title: MDA-MB-468_Ctrl_ST_Rep1

value: xenograft

value: triple-negative breast cancer cells

value: MDA-MB-468 xenograft growing in female NSG, treated with vehicle for 30 days


title: 22_C2D1


title: siScram+ATRA BE(2)-C m6ACE-input 2

value: Human neuroblastoma cell line


title: Bulk RNA-seq, GBM40, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM40M_RNA


title: 36_BL

value: BL

value: NO


title: Naïve KO 22

value: Spleen


title: Bulk RNA-seq, GBM38, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM38T_RNA

tag: Sex

value: male

value: IDHwt


title: siScram+ATRA BE(2)-C m6ACE-input 1

value: WT


title: Bulk RNA-seq, GBM38, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM38M_RNA


title: 43_BL


title: Bulk RNA-seq, GBM37, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM37T_RNA


title: siPcif1+ATRA BE(2)-C m6ACE 3

value: siPcif1 + ATRA


title: Naïve KO 20

value: CD4+ T cells

value: TIGIT KO (C57)

value: S. Typhimurium infected


title: Infected WT 33

value: Naïve


title: siPcif1+ATRA BE(2)-C m6ACE 2


title: 47_C2D1

value: peripheral blood mononuclear cells

value: Male


title: Infected WT 32


title: Bulk RNA-seq, GBM33, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM33T_RNA

value: human glioblastoma

value: HepaCAM+ cells


title: siScram+ATRA BE(2)-C m6ACE 3

value: siScram + ATRA


title: 47_BL


title: siPcif1+ATRA BE(2)-C m6ACE 1

value: Human neuroblastoma cell line


title: Infected WT 31


title: 44_C3D1

value: YES


title: Bulk RNA-seq, GBM33, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM33M_RNA


title: Infected WT 30


title: 41_C2D1


title: Bulk RNA-seq, GBM32, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM32T_RNA

value: female


title: Naive KO 40

value: Spleen


title: siScram+ATRA BE(2)-C m6ACE 2


title: Infected WT 12


title: 37_C3D1

value: Female


title: siScram+ATRA BE(2)-C m6ACE 1


title: Bulk RNA-seq, GBM32, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM32M_RNA


title: 49_C2D1

value: NO


title: Infected WT 11


title: Bulk RNA-seq, GBM31, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM31T_RNA

value: male


title: 22_BL

value: BL


title: Infected KO 33

value: CD4+ T cells


title: 5_C3D1


title: Bulk RNA-seq, GBM37, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM37M_RNA


title: Bulk RNA-seq, GBM31, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM31M_RNA


title: siPcif1+ATRA BE(2)-C RNAseq 1

description:
BE2-C_+ATRA_siPcif1_RNAseq_minus.bw
BE2-C_+ATRA_siPcif1_RNAseq_plus.bw

data_processing:
Basecalling is performed using Illumina RTA, with further demultiplexing performed by Illumina bcl2fastq 2.20.
Fastq sequences were first trimmed of 5' and 3' adapter sequences and poly(A) tails using Cutadapt 3.7 --q -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Reads were mapped to hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR 2.7.10a --outMultimapperOrder Random --outSAMmultNmax 1.
Bigwig files (in RPM) were generated using bamCoverage --effectiveGenomeSize 2913022398 --normalizeUsing CPM -e --maxFragmentLength 300 --scaleFactor 1.0, with --samFlagInclude 99 and --sameFlagInclude 83 for plus and minus strand bigwig files respectively
Output BAM files from STAR was used for htseq-count -q -s reverse -t exon, using hg38 assembly transcriptome gtf (Gencode v28 comprehensive gene annotations). htseq-count output files were used in DESeq2 with lfcshrink option.
Assembly: hg38
Supplementary files format and content: bigwig and DESeq2 output

extract_protocol:
Cells were washed twice with cold PBS and RNA extracted using Trizol LS (Ambion 10296) according to manufacturer’s protocol.
RNA was treated with RQ1 RNaseFree DNase (Promega M6101) as per manufacturer’s protocol. Poly(A)+ cDNA libraries were subsequently generated from the DNase-free RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina 20020596).

value: WT

value: siPcif1 + ATRA


title: Bulk RNA-seq, GBM30, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM30T_RNA

value: IDHwt


title: Infected KO 31

value: TIGIT KO (C57)

value: S. Typhimurium infected


title: siScram+ATRA BE(2)-C RNAseq 3

description:
BE2-C_+ATRA_siScram_RNAseq_minus.bw
BE2-C_+ATRA_siScram_RNAseq_plus.bw


title: Bulk RNA-seq, GBM30, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM30M_RNA

value: human glioblastoma


title: Bulk RNA-seq, GBM28, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM28T_RNA

value: HepaCAM+ cells


title: 29_BL

value: peripheral blood mononuclear cells

value: Male


title: Infected KO 12


title: 37_BL

value: YES


title: Bulk RNA-seq, GBM25, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM25T_RNA

value: female


title: siScram+ATRA BE(2)-C RNAseq 1

value: Human neuroblastoma cell line

value: siScram + ATRA


title: Infected KO 30

value: Spleen


title: Infected KO 11


title: siPcif1+ATRA BE(2)-C RNAseq 3


title: Pcif1-KO_catabolicSLAM_12hPost-s4U

data_processing:
Basecalling is performed using Illumina RTA, with further demultiplexing performed by Illumina bcl2fastq 2.20.
Fastq sequences were first trimmed of 5' and 3' adapter sequences and poly(A) tails using Cutadapt 3.7 --q -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
SLAM-PILE v1.0, a T > C alignment software package based on STAR and Rsamtools to recover T > C conversions from SLAM-Seq datasets. Briefly, trimmed reads were first mapped to hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR 2.7.10a --outMultimapperOrder Random --outSAMmultNmax 1. The counts of each of the four nucleotides in every genomic location were analyzed using Rsamtools Pileup (version 2.6.0). T > C conversions in each gene were calculated by comparing the counts of each of the four nucleotide to the sequence in hg38, and the mRNA half-life for each gene was calculated by fitting the T > C conversion rates at time 0, 3, 6 and 12h (post removal of s4U) to the equation of exponential decay with power 2.
Assembly: hg38
Supplementary files format and content: This file includes the half-lives of mRNA of each gene derived from fitting T > C conversion rate at different timepoint to a function of exponential decay with base 2, the r-squared of the fitting included. The HEK293T cells were either Pcif1-KO or WT. The m6Am status of each gene were also included, 'n' for non-m6Am gene and 'm' for m6Am gene. The T > C conversion rates of each gene were generated either using SLAM-PILE or SLAM-DUNK, as shown in the names of each sub-sheets.

extract_protocol:
At T=0, 3, 6, and 12hr post addition of U-containing media, the medium was removed, the cells were washed twice with cold PBS, and the cells were directly lysed with 350ul TRIzol®-LS. Cells were harvested with Trizol-LS. RNA was isolated and IAA-treatment was performed according to SLAM-seq catabolics module protocol (Lexogen 062.24). Residual genomic DNA was removed using RQ1 RNase-free DNAse (Promega M6101), purified with RNA concentrator (Zymo R1015)
RNA-seq library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina 20020596).
3’ mRNA-Seq

treatment_protocol:
Cells were seeded in 6-well plates and after 12hr, when the cells reached approximately 50% confluence, the medium was carefully removed and replaced with fresh medium containing 50uM 4SU. The cells were then incubated further in the dark at 37 degrees for 24hr, with the fresh medium containing 50uM 4SU being replaced every 3hr.
Next, the medium was carefully removed and the cells were washed twice with 1x PBS. Fresh medium containing 5M uridine (U) was then added and the cells were further incubated at 37 degrees in the dark.

value: Human embryonic kidney


title: 24_BL

value: BL

value: NO


title: siPcif1+ATRA BE(2)-C RNAseq 2

value: WT


title: 22_C3D1


title: Bulk RNA-seq, GBM24, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM24T_RNA


title: Aged+GB

city: Taichung City

address: No. 2, Yude Road, North District

department: Department of Medical Research

institute: Translational Cell Therapy Center, China Medical University Hospital, China Medical University, Taiwan

description: 10x Chromium Single Cell 3’ reagent kit v2

data_processing:
Barcoded processing and gene counting were completed using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix Format

source_name: Gastrocnemius muscle

extract_protocol:
GA muscles were isolated from mice immediately following euthanasia. The muscles were minced and homogenized with homogenization buffer, 0.25M sucrose and 1% BSA diluted in Mg2+-free, Ca2+-free, RNase-free PBS (#AM9624, Invitrogen, Grand Island, NY, USA). The homogenates were incubated with 2.5% Triton-X100/RNase-free PBS at a 1:6 ratio for 5 minutes. After filtering through a 100-μm strainer, samples were centrifuged at 3000 × g for 10 min at 4 °C, resuspended in 2% BSA/RNase-free PBS, and then filtered through a 40-μm strainer again. Nuclei were labeled by DAPI with 0.2 U/µL RNase inhibitor (#N8080119, Thermo Fisher Scientific). Labeled nuclei were sorted by FACS Aria II Cell Sorter with 70 μm nozzle (BD Biosciences, San Jose, CA, USA) into 2% BSA/RNase-free PBS with RNase inhibitor. Isolated nuclei were observed by confocal fluorescent microscope (Leica TCS SP8, Wetzlar, Germany) to confirm the integrity. To adjust the optimal concentration of nuclei for the 10X Chromium system, isolated nuclei were counted and diluted or concentrated by centrifugation at 250 × g for 5 min at 4 °C.
Single-nucleus RNA-sequencing libraries were constructed by the Chromium Single Cell 3’ reagent kit v2 (10X Genomics, Pleasanton, CA, USA) per the manufacturer’s protocol. Following the library preparation, the libraries were sequenced on the NovaSeq 6000 System (Illumina, San Diego, CA, USA)

value: Gastrocnemius muscle

value: myonuclei

tag: strain

value: wild-type

tag: developmental stage

value: 20 months

value: F

value: Ginkgolide B 12 mg/kg for 8 weeks


title: Pcif1-KO_catabolicSLAM_6hPost-s4U

tag: cell line

value: 24h s4U + 6h U


title: Infected KO 32

value: CD4+ T cells

value: TIGIT KO (C57)

value: S. Typhimurium infected


title: Aged+Vehicle

value: PBS for 8 weeks


title: 46_C3D1

institute: University of Western Australia

value: peripheral blood mononuclear cells

value: YES

value: Female


title: Pcif1-KO_catabolicSLAM_3hPost-s4U

value: Human embryonic kidney

value: 24h s4U + 3h U


title: 21_C2D1

value: Male


title: Bulk RNA-seq, GBM24, margin

city: Atlanta

address: 615 Michael Street, Room 375

institute: Emory University

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM24M_RNA

value: human glioblastoma

value: HepaCAM+ cells

value: female


title: Young+Vehicle

value: Gastrocnemius muscle

value: myonuclei

value: wild-type

value: 3 months


title: siScram+ATRA BE(2)-C RNAseq 2

value: Human neuroblastoma cell line

value: WT

value: siScram + ATRA


title: 29_C2D1


title: Pcif1-KO_catabolicSLAM_0hPost-s4U

value: 24h s4U + 0h U


title: Bulk RNA-seq, GBM22, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM22T_RNA

value: male


title: 13_C2D1

value: peripheral blood mononuclear cells

value: YES


title: WT_catabolicSLAM_12hPost-s4U

value: Human embryonic kidney


title: 26_C3D1


title: KO_gingiva infiltration immune cells

city: Beijing

first: Jia

last: Song

state: China

address: Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
The Cell ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 3.2.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 3000 or less than 300, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with SCTransform function.
IntegrateData function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 3.2.3). Top 50 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 3.2.3).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

source_name: murine gingiva infiltration immune cells

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

value: gingiva


title: WT_gingiva infiltration immune cells


title: 47_C3D1

value: NO

value: Male


title: Bulk RNA-seq, GBM21, tumor

first: Steven

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM21T_RNA

value: human glioblastoma

value: HepaCAM+ cells


title: WT_catabolicSLAM_6hPost-s4U

value: 24h s4U + 6h U


title: WT_catabolicSLAM_3hPost-s4U

value: 24h s4U + 3h U


title: Bulk RNA-seq, GBM25, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM25M_RNA

value: female


title: Bulk RNA-seq, GBM21, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM21M_RNA


title: 10_C2D1


title: DN, replicate 2, scRNAseq

first: Tingfei

last: Xie

address: Longjing 2nd Road, Xin'an Street

institute: Southern Medical University

description: Singleron Matrix

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Seurat v4.0.6
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol: GEXSCOPE® Single Cell RNA Library Kits

value: Kidney

tag: age

value: 4 weeks old

value: Wild type

value: STZ

tag: disease state

value: diabetic nephropathy


title: Bulk RNA-seq, GBM20, tumor

last: Sloan

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM20T_RNA

value: male

value: IDHwt


title: Pcif1-KO_siPCF11_anabolicSLAM

data_processing:
Basecalling was performed using Illumina RTA, with further demultiplexing performed by Illumina bcl2fastq 2.20.
Fastq sequences were first trimmed of 5' and 3' adapter sequences and poly(A) tails using Cutadapt 3.7 -q 20 -m 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AAAAAAAAAAAAAAAAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Reads were mapped to hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR 2.7.10a --outMultimapperOrder Random --outSAMmultNmax 1.
Bedgraphs (in RPM) of the reverse complement of the first nucleotide of read 1 were constructed using custom Python scripts.
Reads were counted using htseq-count 2.0.1 -s reverse -t UTR, with gencode.v28.chr_patch_hapl_scaff.annotation.gtf obtained from gencodesgenes.org. Read counts were subjected to DESeq2 1.30.1 with lfcshrink to quantify differential transcriptional output. Cumulative log2fold-change plots and box-and-whiskers plots were generated with custom Python scripts.
Assembly: hg38
Supplementary files format and content: bedgraph


title: DN, replicate 1, scRNAseq

description: Singleron Matrix


title: Bulk RNA-seq, GBM20, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM20M_RNA


title: 24_C3D1

value: peripheral blood mononuclear cells

tag: patient

tag: timepoint

value: YES


title: Bulk RNA-seq, GBM18, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM18T_RNA


title: Pcif1-KO_siScram_anabolicSLAM

value: Human embryonic kidney

value: siScram


title: Con, replicate 1, scRNAseq

description: Singleron Matrix

value: Male

value: Sodium citrate

value: control


title: 42_C2D1

tag: pfs 6m_response

value: NO

tag: gender


title: WT_siPCF11_anabolicSLAM

value: WT


title: Virgin, sample6, HSL

city: South San Francisco

first: Jackson

last: Liang

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

data_processing:
HTSeqGenie workflow
Assembly: GRCm38
Supplementary files format and content: TAB file representing counts, rpkms

source_name: Mammary gland

growth_protocol: Nulliparous animals were raised to 12 weeks of age. Mammary tissues were collected from these animals and processed as described in the 'Extraction protocol'.

extract_protocol:
Mammary glands were minced, then treated with collagenase/hyaluronidase/DNaseI for 1hr at 37C. Then, resulting parenchymal cells were isolated by centrifugation and further digested by dispase and trypsin successively. Cells were pipetted through a 40um filter, then blocked and stained with antibodies for FACS. FACS markers: CD49f, CD61, EpCAM, Lin (CD31/CD45/Ter119). By FACS, individual populations were isolated - basal cells, alevolar progenitors (AP, also called 'luminal progenitors'), and hormone-sensing luminal cells (HSL, HR+ population, also called 'mature luminal cells'). See Characteristics 'cell population' field for FACS markers per cell type.
cDNA library was generated from 2 nanograms of total RNA using Smart-Seq V4 Ultra Low Input RNA Kit (Takara, 634894). 150 picograms of cDNA was used to make sequencing libraries by Nextera XT DNA Sample Preparation Kit (Illumina, FC-131-1024).

treatment_protocol: No treatment

tag: tissue

value: Mammary gland

value: parenchymal cells

tag: cell population

value: HSL (CD49f-lo/CD61-)

value: MMTV-Cre


title: Bulk RNA-seq, GBM15, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM15T_RNA

value: human glioblastoma

tag: cell type

value: HepaCAM+ cells

tag: genotype


title: Bulk RNA-seq, GBM22, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM22M_RNA

value: male


title: DN, replicate 3, scRNAseq

description: Singleron Matrix

value: Kidney

value: 4 weeks old

value: Wild type

tag: treatment

value: STZ

value: diabetic nephropathy


title: 21_BL

value: peripheral blood mononuclear cells

value: BL

value: YES

value: Male

tag: epithelioid


title: Virgin, sample6, AP

value: AP (CD49f-lo/CD61+)


title: Pcif1-KO HEK293T siPCF11 PCT 3

data_processing:
Basecalling is performed using Illumina RTA, with further demultiplexing performed by Illumina bcl2fastq 2.20.
Fastq sequences were first trimmed of 5' and 3' adapter sequences and poly(A) tails using Cutadapt 3.7 -q 20 -m 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AAAAAAAAAAAAAAAAAAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT.
Reads were mapped to hg38 assembly transcriptome (Gencode v28 comprehensive gene annotations) using STAR 2.7.10a --outMultimapperOrder Random --outSAMmultNmax 1.
Bedgraphs (in RPM) of the reverse complement of the first nucleotide of read 1 were constructed using custom Python scripts.
For each gene/ENSG, a single PCT 3’end was identified by selecting the genome coordinate with the highest mean PCT-seq reads per million mapped reads (RPM) count both within the first intron and within 10kb from the TSS of the TSL1 ENST transcript, and without overlapping with the 3'UTR of any transcript. For each gene/ENSG, a single full-length RNA 3’end was identified by selecting the genome coordinate with the highest mean PCT-seq RPM read count within the 3'UTR of the TSL1 ENST transcript. PCT read counts and full-length RNA read counts are denoted as the RPM respectively at the identified PCT 3’end and full-length RNA 3’end. Only PCTs that passed the following cutoff filters were used in differential PCT analysis: Minimum PCT RPM of 1.0, minimum full-length RNA RPM of 5.0, mean WT_siScram PCT RPM > mean WT_no-siDis3 PCT RPM, and mean Pcif1-KO_siScram PCT RPM > mean Pcif1-KO_no-siDis3 PCT RPM.
For each gene/ENSG, a single PCT 3’end was identified by selecting the genome coordinate with the highest mean PCT-seq reads per million mapped reads (RPM) count both within the first intron and within 10kb from the TSS of the TSL1 ENST transcript, and without overlapping with the 3'UTR of any transcript. For each gene/ENSG, a single full-length RNA 3’end was identified by selecting the genome coordinate with the highest mean PCT-seq RPM read count within the 3'UTR of the TSL1 ENST transcript. PCT RPM and full-length RPM are denoted as the RPM respectively at the identified PCT 3’end and full-length RNA 3’end. Only PCTs that passed the following cutoff filters were used in differential PCT analysis: Minimum PCT RPM of 1.0, minimum full-length RNA RPM of 5.0, mean WT_siScram PCT RPM > mean WT_no-siDis3 PCT RPM, and mean Pcif1-KO_siScram PCT RPM > mean Pcif1-KO_no-siDis3 PCT RPM.
Assembly: hg38
Supplementary files format and content: bedgraph

treatment_protocol: Cells were seeded in 12-well plates 24hr prior to transfection. Cells were then transfected with 5pmol siRNA against Dis3 (Silencer Select S229660), against scrambled control (Silencer Select 4390843) and/or against PCF11 (Silencer Select S28362); using Lipofectamine RNAimax (Invitrogen 13778030) according to manufacturer’s instructions.

value: Human embryonic kidney

value: siPcf11 + siDis3


title: 55_C3D1


title: Bulk RNA-seq, GBM15, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM15M_RNA


title: Pcif1-KO HEK293T siPCF11 PCT 2


title: Virgin, sample6, basal

value: Mammary gland

value: parenchymal cells

value: Basal (CD49f-hi/CD61+)


title: 7_BL

value: Female


title: WT_catabolicSLAM_0hPost-s4U

value: WT

value: 24h s4U + 0h U


title: 54_BL

value: NO


title: 42_C3D1


title: Con, replicate 2, scRNAseq

description: Singleron Matrix

value: Kidney

value: 4 weeks old

value: Wild type

value: Sodium citrate

value: control


title: Bulk RNA-seq, GBM12, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM12M_RNA

value: human glioblastoma

value: HepaCAM+ cells

value: male


title: Virgin, sample5, HSL

value: HSL (CD49f-lo/CD61-)

value: MMTV-Cre


title: Bulk RNA-seq, GBM11, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM11T_RNA

value: IDHwt


title: 35_C3D1

value: peripheral blood mononuclear cells

value: Male


title: Pcif1-KO HEK293T siPCF11 PCT 1

value: Human embryonic kidney

value: siPcf11 + siDis3


title: Virgin, sample5, AP

value: Mammary gland

value: parenchymal cells

value: AP (CD49f-lo/CD61+)


title: Pcif1-KO HEK293T siScram PCT 3

value: siScram + siDis3


title: Bulk RNA-seq, GBM11, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM11M_RNA


title: 34_C2D1

value: NO

value: YES


title: WT_siScram_anabolicSLAM

value: WT

value: siScram


title: Virgin, sample5, basal

value: Basal (CD49f-hi/CD61+)


title: 32_C2D1

value: Female


title: Virgin, sample4, HSL

value: HSL (CD49f-lo/CD61-)


title: Bulk RNA-seq, GBM10, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM10T_RNA

value: human glioblastoma

value: HepaCAM+ cells

value: male


title: Pcif1-KO HEK293T siScram PCT 1


title: Bulk RNA-seq, GBM12, tumor

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM12T_RNA

value: IDHwt


title: 8_BL

value: peripheral blood mononuclear cells

value: BL

value: Male


title: Bulk RNA-seq, GBM10, margin

description:
20 million PE reads
GBM_feature_counts.xlsx
GBM10M_RNA


title: Virgin, sample4, AP

value: Mammary gland

value: parenchymal cells

value: MMTV-Cre


title: 6_BL


title: WT HEK293T siPCF11 PCT 3

value: Human embryonic kidney

value: siPcf11 + siDis3


title: Virgin, sample4, basal


title: WT HEK293T siPCF11 PCT 2

value: WT


title: Bulk RNA-seq, line C3.1, HepaCAM+, d550

description:
20 million PE reads
hCS_feature_counts.xlsx
C3_d550_RNA

source_name: human cortical organoid

value: human cortical organoid


title: 4_BL

value: YES


title: WT HEK293T siPCF11 PCT 1


title: Virgin, sample3, HSL


title: 46_BL

value: Female


title: Bulk RNA-seq, line C4.1, HepaCAM+, d450

description:
20 million PE reads
hCS_feature_counts.xlsx
C4_d450_RNA

value: female


title: WT HEK293T siScram PCT 3

value: siScram + siDis3


title: 9_BL


title: Virgin, sample3, AP

value: AP (CD49f-lo/CD61+)


title: Bulk RNA-seq, line C3.1, HepaCAM+, d450

description:
20 million PE reads
hCS_feature_counts.xlsx
C3_d450_RNA

value: HepaCAM+ cells

value: male


title: Pcif1-KO HEK293T siScram PCT 2


title: Virgin, sample3, basal

value: Basal (CD49f-hi/CD61+)


title: WT HEK293T siScram PCT 2


title: Bulk RNA-seq, line C4.1, HepaCAM+, d400

description:
20 million PE reads
hCS_feature_counts.xlsx
C4_d400_RNA


title: 7_C2D1

value: peripheral blood mononuclear cells


title: 4_C3D1

value: Male


title: Virgin, sample2, HSL

value: Mammary gland

value: HSL (CD49f-lo/CD61-)


title: WT HEK293T siScram PCT 1


title: Bulk RNA-seq, line C3.1, HepaCAM+, d400

description:
20 million PE reads
hCS_feature_counts.xlsx
C3_d400_RNA


title: Virgin, sample2, AP

value: parenchymal cells

value: MMTV-Cre


title: Bulk RNA-seq, line C4.1, HepaCAM+, d550

description:
20 million PE reads
hCS_feature_counts.xlsx
C4_d550_RNA


title: 55_BL

value: BL


title: Virgin, sample2, basal


title: Bulk RNA-seq, line C3.1, HepaCAM+, d350

description:
20 million PE reads
hCS_feature_counts.xlsx
C3_d350_RNA


title: T Cells, CHRONIC exhaustion, H3K27me3, rep R3

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

library_source: genomic

data_processing:
Alignment: reads were aligned to the mm10 reference genome using Bowtie (v2.4.1).
Filtering: only uniquely mapped reads were kept and duplicates were removed using Picard (v1.141) MarkDuplicates.
Peak Calling: peaks were called using MACS2 (v2.1.2) with parameters -p 1e-8 --min-length 500 --max-gap 800 --broad for H3K27me3 and -q 0.05 --broad for H3K27ac. For both marks, peaks that only occurred in one replicate were removed. Peaks were then merged across replicates per condition and mark using bedtools merge (v2.26.0) then annotated using HOMER annotatePeaks (v4.11.1).
Track Creation: bigWig files were generated using deepTools2 bamCoverage (v3.5.4) and average bigWigs across replicates were generated using deepTools2 bigwigAverage then displayed using the UCSC Genome Browser.
Assembly: mm10 / GRCm38
Supplementary files format and content: Supplemental bigWigs represent single samples or else replicates averaged using bigWigAverage (*avg.bw).
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: P14 CD8+ T cells transgenic for a TCR recognizing the DbGP33-41 epitope of LCMV

growth_protocol: Mice were housed at the University of Pennsylvania in a specific pathogen–free facility and experiments and procedures were performed in accordance with Institutional Animal Care and Use Committee. For the in vitro model, P14 transgenic mice expressing a TCR specific for the LCMV peptide DbGP33–41 were backcrossed to C57BL/6 mice (Charles River), transferred from the lab of John Wherry, and bred in house. Mice were between 8 and 24 weeks old, randomly assigned to experimental groups, and sexes were alternated between experiments.

extract_protocol:
The CUT&RUN assay was performed as previously described with some modifications. In brief, after sorting for live CD8 positive T cells from the in vitro model, 20,000 cells per antibody were washed twice with cell wash buffer, bound to 40 ul of concanavalin A-coated magnetic beads, and then split to incubate overnight rotating at 4 °C in 250 ul of antibody buffer with either H3K27me3 (Cell Signaling, #9733) or H3K27ac (Active Motif, #39133) antibodies. Cells were then washed and resuspended in 0.1% digitonin buffer with pA-MN fusion protein at 700 ng/ml and incubated rotating at 4 °C for 1 hour. Cells were then washed, resuspended in the digitonin buffer, brought down to 0 °C, and CaCl2 was added to a final concentration of 2mM for digestion at 0 °C for 30 minutes. 2X stop buffer was then added to the reaction and incubated at 37°C for 10 minutes to release the fragments followed by centrifugation. SDS (0.1%) and proteinase K (0.2 mg/ml) were then added to the supernatant, incubated at 70°C for 10 minutes, and followed by phenol-chloroform DNA extraction.
Library preparation was performed according to manufacturer’s guidelines using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645L). The NEBNext® Library Quant Kit for Illumina® (E7630L) and bioanalyzer were used to assess library quality and concentration. Libraries were sequenced using the Illumina® NextSeq 500.

treatment_protocol: Complete RPMI (cRPMI) in this protocol is RPMI 1640 (Corning Cellgro) supplemented with 10% fetal bovine serum, 50 μM β-mercaptoethanol, 2 mM glutamine (Gibco), penicillin (100 U/ml; Sigma-Aldrich), streptomycin (100 μg/ml; Sigma-Aldrich), 100 μM nonessential amino acids (Invitrogen), 1 mM sodium pyruvate (Invitrogen), and 20 mM Hepes buffer (Invitrogen). CD8 T cells were isolated from spleens of naïve P14 transgenic mice by homogenizing against a 70-μm cell strainer, washing with cRPMI, passing through a 70-μm cell strainer again, and then isolation via a negative selection kit (STEMCELL Technologies) per the manufacturer’s instructions. DCs were isolated from spleens of naïve C57BL/6 mice by cutting samples into small pieces, incubating at 37°C for 30-45 min with deoxyribonuclease I (1 U/ml; Roche) and collagenase D (10 U/ml; Roche) in cRPMI, then homogenization against a 70-μm cell strainer. Red blood cells were lysed with ammonium-chloride-potassium (ACK) lysis buffer (Gibco) for 5 min, the cell suspension was quenched and washed with phosphate-buffered saline (PBS) and then passed through a 70-μm cell strainer again. DCs were isolated with CD11c+ Microbeads (Miltenyi) per the manufacturer’s instructions and then pulsed with DbGP33–41 peptide (0.1 μM, GenScript) in cRPMI for 30 min-1 hour at 37°C. CD8 P14 cells and DCs were then cocultured in cRPMI at a 1:1 ratio (105 DCs + 105 P14 cells per well) in a flat-bottom 96-well plate. At day 2, 4, and 6 of coculture, P14 cells were counted via BD Accuri and normalized to a concentration of 0.5 × 106 P14 cells/ml (105 P14 cells per well) to be replated into in vitro culture. Chronically stimulated P14 cells received DbGP33–41 peptide (1 nM) at day 2, 4, and 6 and both in vitro conditions (chronic and acute) received recombinant human IL-2 (10 U/ml; PeproTech) at day 2, 4, and 6. For EED inhibition experiments, EED226 (#22031) was bought from Cayman Chemical, resuspended in DMSO to make a stock concentration of 10mM and added to in vitro cell culture media at a concentration of 4uM. Control conditions were given an equivalent amount of DMSO.

tag: group

value: CHRONIC exhaustion

value: Clone 13 strain of the LCMV

tag: antibody

tag: antibody catalog

value: Cell Signaling, #9733

tag: replicate


title: T Cells, CHRONIC exhaustion, H3K27me3, rep R2

tag: strain

value: P14 CD8+ T cells transgenic for a TCR recognizing the DbGP33-41 epitope of LCMV


title: Virgin, sample1, HSL


title: Bulk RNA-seq, line C4.1, HepaCAM+, d300

description:
20 million PE reads
hCS_feature_counts.xlsx
C4_d300_RNA

value: human cortical organoid

tag: cell line

tag: Sex

value: female


title: 51_C2D1

tag: patient

value: YES


title: T Cells, CHRONIC exhaustion, H3K27me3, rep R1


title: Virgin, sample1, AP

value: AP (CD49f-lo/CD61+)


title: Bulk RNA-seq, line C3.1, HepaCAM+, d300

description:
20 million PE reads
hCS_feature_counts.xlsx
C3_d300_RNA

value: HepaCAM+ cells

value: male


title: Bulk RNA-seq, line C4.1, HepaCAM+, d250

description:
20 million PE reads
hCS_feature_counts.xlsx
C4_d250_RNA


title: T Cells, CHRONIC exhaustion, H3K27ac, rep R4

value: Active Motif, #39133


title: 45_BL

value: peripheral blood mononuclear cells

tag: timepoint

value: Male


title: 37_C2D1

tag: pfs 6m_response

value: Female


title: 15_C3D1

value: NO

tag: gender


title: 35_C2D1

tag: tissue


title: Virgin, sample1, basal

value: Mammary gland

value: parenchymal cells

tag: cell population

value: Basal (CD49f-hi/CD61+)

value: MMTV-Cre


title: Bulk RNA-seq, line C3.1, HepaCAM+, d250

description:
20 million PE reads
hCS_feature_counts.xlsx
C3_d250_RNA

tag: cell type


title: T Cells, CHRONIC exhaustion, H3K27ac, rep R1

value: CHRONIC exhaustion

tag: genotype

value: Clone 13 strain of the LCMV


title: T Cells, CHRONIC exhaustion, H3K27ac, rep R2

value: P14 CD8+ T cells transgenic for a TCR recognizing the DbGP33-41 epitope of LCMV


title: WT, N, sample3

data_processing:
HTSeqGenie pipeline
Assembly: GRCm38
Supplementary files format and content: TAB (Raw counts and rpkm per gene)

source_name: Mammary mature luminal cells

growth_protocol: Animals were raised under standard husbandry methods until 6 months of age.

extract_protocol:
Mammary glands were dissected from treated animals; mature luminal cells were isolated from tissues by FACS. RNA was isolated from mature luminal cells via Qiagen Rneasy Micro Plus kit.
Libraries were prepared from cDNA using the Nextera XT DNA Sample Preparation kit.

treatment_protocol: Animals were implanted with hormone pellets (E2 & P4), then dosed daily with giredestrant (30 mg/kg, p.o.) for four days

tag: er mutation

value: WT

tag: treatment

value: E2/P4 + giredestrant

value: Novel


title: T Cells, CHRONIC exhaustion, H3K27ac, rep R3

tag: group


title: WT, N, sample2