title: WS, brain organoid, day56 [RNA-seq]

city: hangzhou

first: zhao

last: xingsen

address: kaixuan road 268

institute: zhejiang university

description: RNAseq

data_processing:
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Assembly: Genome_build: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: neuron

extract_protocol:
Human organoids were homogenized in TRIzol reagent (Thermo Fisher Scientific) to extract total RNA and was purified with chloroform following the manufacturer’s protocol. The concentration of RNA was quantified using a NanoDrop spectrophotometer 2000 (Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: tissue/cell type

value: brain organoids

value: neuron

value: ws


title: L56A

status: Public on Sep 01 2025

type: SRA

city: São Paulo

first: Luciana

middle: Cezar de Cerqueira

last: Leite

state: SP

address: Avenida Vital Brasil, 1500

department: Desenvolvimento de Vacinas

country: Brazil

institute: Instituto Butantan

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.7dpc.8

library_source: transcriptomic

data_processing:
Raw paired-end RNA-Seq data were subjected to quality control using FastQC.
Trimmomatic v.0.36 was used to remove the adaptors and filter low quality bases at termini (quality below 25) (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36).
The filtered reads were aligned to the Mus musculus genome assembly Version GRCm39 using Bowtie2 v.2.3.5.1, with "--very-sensitive" preset, keeping other parameters at default.
The mapped and aligned reads were quantified to obtain the gene-level counts using featureCounts from the package Subread v.2.12 with “is PairedEnd” and “allow MultiOverlap” parameters set to true and the remaining at default settings.
Raw counts were processed using the Bioconductors package DESeq2 v.1.36.0 in R v.4.2.3 and normalized using the DESeq method to remove the library-specific artifacts.
Assembly: Mus musculus genome assembly Version GRCm39 using Bowtie2 v.2.3.5.1
Supplementary files format and content: tab-delimited csv file includes raw counts for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Lung

growth_protocol: Total lung and lymph node tissue were maintained in RNAlater (ThermoFisher) at -80ºC until extraction.

extract_protocol:
Total RNA was extracted and purified individually from left lung and accessory lobe samples or from lymph node samples stored in RNAlater (samples from 8 mice per group per time point) using the “RNA Extraction Protocol for Animal Tissue” Document number SOP-SMM-J003, Version A0 (BGI Genomics, Shenzhen, China) according to the manufacturer’s instructions.
Purified RNA integrity was estimated by capillary electrophoresis (Fragment Analyzer; Agilent Technologies, Santa Clara, CA, USA), and samples showed RIN scores 7.0. Non-stranded libraries were constructed using the BGI in-house Library Prep Kit

tag: tissue

value: Lung

tag: genotype

value: WT

tag: vaccination status

value: Not immunized

tag: vaccine

value: Saline

tag: vaccine dose

tag: vaccine route

value: subcutaneous

tag: days post_immunization

value: day 97

tag: challenge

value: Yes

tag: challenge strain

value: Mtb H37Rv

tag: challenge dose

value: 500 cfu

tag: challenge route

value: Intranasal

tag: disease

value: Tuberculosis

tag: disease stage

value: Early infection


title: Basal_CTL_2

city: Paris

first: Sebastien

last: Dussaud

address: 91 bd de l'hopital

country: France

institute: UPMC

description: Library name: Sample 2

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained using in-house scripts based on MACS and HTSeq (https://github.com/ctlab/quant3p).
Assembly: mm10
Supplementary files format and content: raw_counts.txt

growth_protocol: BMDMs were obtained from Gls1-/- and control mice. PCMs were obtained from atherosclerosis-prone Ldlr-/- mice backcrossed with or without Gls2-/- and transplanted with Gls1-/- or control bone marrow.

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and amount was assessed by Nanodrop (Ozyme)
Library construction were conducted by BGI Hong Kong Company Limited using a DNBseqTM platform

treatment_protocol: Bone marrow-derived macrophages were generated from Gls1-/- and control mice and cultured for the last 24h in presence or absence of interleukin-4 and glutamine synthase inhibitor (MSO). Atherosclerosis-prone Ldlr-/-  mice were backrossed with or without Gls2-/- mice and served as recipients for transplantation of Gls1-/- or control bone marrow. Then, hyperlipidemia was induced in these mice by feeding them with an atherogenic diet (Western diet, TD88137, Ssniff) for 11 weeks. Peritoneal macrophages were obtained from all four genotypes at the end of the study.

tag: cell line

tag: cell type

value: Cell culture


title: PrS-MOK20125P-C10-hyp, KO

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: TP63_PTC_C10_3_O2_GT25-00013_CCAAGTCT-TCATCCTT_S720_L004
KOLF2.2J derived knockout cell line, TP63 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: study8_featureCounts.csv study8_genesCounts.csv study8_genesRawCounts.csv study8_genesTPM.csv study8_stats.csv study8_txCounts.csv study8_txRawCounts.csv study8_txTPM.csv

organism: Homo sapiens

extract_protocol:
Arcturus PicoPure RNA isolation Kit Applied biosystems
KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina NovaSeq X

value: iPSC

tag: editing strategy

value: Termination codon

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

tag: condition

value: hypoxia

tag: parental cell_line


title: Basal_CTL_1

description: Library name: Sample 1


title: L55A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.7dpc.7

tag: tissue

value: Lung

tag: genotype

value: WT

tag: vaccination status

tag: vaccine

tag: vaccine dose

tag: vaccine route


title: PrS-MOK20105P-A06-hyp, KO

description:
Library name: HIF1a_PTC_A06_3_O2_GT25-00012_CTCTCGTC-AGGTTATA_S708_L004
KOLF2.2J derived knockout cell line, HIF1A PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: cct1-2 DMSO Rep2

city: Boston

first: Zlata

last: Gvozdenov

state: MA

address: 240 Longwood Ave

department: BCMP

country: USA

institute: Harvard Medical School

description: cct1-2 DMSO Rep2 (final processed files are derived from WT and cct1-2 data, as well as prior usage of both 4tU and DMSO files)

data_processing:
Reads were mapped to the S. cerevisiae genome using bowtie2 -5 25 -3 25 –no-mixed –no-discordant –dovetail.
bedtools bamtobed
Bed files were used to compute fragment locations for correctly aligned paired-end reads.
Per nucleotide coverage from the fragment locations were derived.
Normalized nt coverages were used to subtract background from the 4tU sample to obtain active transcription measurements.
Regions with differential active transcription were derived with Interval_identifier.py. Once background was subtracted (4tU signal – DMSO signal) and replicates were combined, deferentially regulated active transcription regions were identified with Interval_identifier.py. Cct1-2-specific interval identifier regions with elevated active transcription upon CCT inactivation. WT-specific interval identifier regions is a vise versa run (downregulated active transcripts upon CCT inactivation).
Half-life calculations were performed from the combined RNA-Seq and 4tU-Seq values (Schwalb et al., 2016, Blumberg et al., 2021).
Assembly: Per nucleotide coverage/count has 3 columns: chromosome name, position, and count.
Supplementary files format and content: Interval_identifier.py-generated tab-separated files contain information about the chromosome, coordinate start, coordinate end, transcript signal fold change, directionality.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

growth_protocol: WT and cct1-2 strains were grown in YPD to log phase at 30°C and shifted to 37°C for 4 h.

extract_protocol:
Biotinylated RNA was collected using glycogen blocked MyOne Streptavidin C1 Dynabeads (Invitrogen).
Libraries were constructed as described in Gvozdenov et al. 2023. Briefly, 5’ and 3’ primers were ligated onto RNA fragments, cDNA was made and amplified with index primers. Total RNA was subjected to polyA selection and fragmentation using Magnesium RNA Fragmentation Module (NEB) before biotinylation.

treatment_protocol:
WT and cct1-2 were treated with either 4-thiouracil (4tU, Sigma Aldrich; 5mM final) or DMSO for 5min (YPD, 37°C).
Fragmented polyA RNA was biotinylated with activateddisulfidemethane thiosulfonate (MTS) biotin (Biotium Biotin-XX MTSEA).

tag: strain

value: JFY148 (cct1-2 ts mutant)

tag: treatment

value: 7 h at 37C, 5 min DMSO


title: 7KQ, replicate2,scRNAseq

city: Beijing

first: Donglai

last: Wang

address: #5 Dong Dan San Tiao

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10 × Cell Ranger 2.1.0 software was used to generate fastq files and gene barcode matrices. Loupe Cell Browser 2.0.0, the Seurat R package and SPRING were used for clustering and further analyses.
Assembly: mm10
Supplementary files format and content: .h5

source_name: Cd45+ cells

extract_protocol:
1×106 MC38 cells were inoculated into the flanks of the indicated mice and allowed to grow for approximately 19 days. Tumors were isolated and digested with 1 mg/ml collagenase I (Merck, C0130) and 200 μg/ml DNase I (Sigma, DN25), and the live Cd45+ tumor-infiltrating cells were sorted via flow cytometry.
Library was performed according to the manufacter's instructions (Single Cell 3’ Reagent Kits v3.1 (Dual Index, 10× genomics, 1000268). Briefly,  Cd45+ cells were resuspended in the master mix  and loaded together with partitioning oil and gel beads into chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained  in every single GEM was retrotranscripted to cDNA, which contains an IIumina R1 pimer sequence, Unique Molecular Identifier (UMI) and 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction IIumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Cd45+ cells

value: p53 fl7KQ/-, Lck-cre

value: xenograft Mc38 cells


title: L54A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.7dpc.6

value: Not immunized

value: Saline

value: subcutaneous

tag: days post_immunization

value: day 97

tag: challenge

value: Yes

tag: challenge strain

value: Mtb H37Rv

tag: challenge dose

value: 500 cfu

tag: challenge route

tag: disease

tag: disease stage


title: PrS-MOK20105P-A05-hyp, KO

description:
Library name: HIF1a_PTC_A05_3_O2_GT25-00011_TCTCTACT-GAACCGCG_S700_L004
KOLF2.2J derived knockout cell line, HIF1A PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

tag: cell line

tag: cell type

value: iPSC

tag: editing strategy

value: Termination codon

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

tag: condition


title: cct1-2 4tU Rep2

description: cct1-2 4tU Rep2  (final processed files are derived from WT and cct1-2 data, as well as prior usage of both 4tU and DMSO files)

tag: strain

tag: genotype

value: 7 h at 37C, 5 min 4tU


title: MSO_CTL_2

description: Library name: Sample 6

value: Cell culture


title: WT DMSO Rep2

description: WT DMSO Rep2 (final processed files are derived from WT and cct1-2 data, as well as prior usage of both 4tU and DMSO files)

value: JFY143 (CCT WT W303, matA)

tag: treatment

value: 6 h at 37C, 5 min DMSO


title: L53A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.7dpc.5

tag: tissue

value: Lung

value: WT

tag: vaccination status

tag: vaccine

tag: vaccine dose

tag: vaccine route

tag: days post_immunization

tag: challenge

value: Intranasal

value: Tuberculosis

value: Early infection


title: PrS-MOK20105P-A04-hyp, KO

description:
Library name: HIF1a_PTC_A04_3_O2_GT25-00010_GACCTGAA-CTCACCAA_S729_L004
KOLF2.2J derived knockout cell line, HIF1A PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

tag: cell line

tag: cell type

value: primitive syncytium

value: hypoxia

tag: parental cell_line


title: WT 4tU Rep2

description: WT 4tU Rep2 (final processed files are derived from WT and cct1-2 data, as well as prior usage of both 4tU and DMSO files)

value: 6 h at 37C, 5 min 4tU


title: WT, replicate2, scRNAseq

description: 10x Genomics

value: Cd45+ cells

value: p53+/-, Lck-cre

value: xenograft Mc38 cells


title: L51A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.7dpc.3

value: Not immunized

value: Saline

value: subcutaneous

value: day 97

value: Yes

tag: challenge strain

value: Mtb H37Rv

tag: challenge dose

value: 500 cfu

tag: challenge route

tag: disease

tag: disease stage


title: L52A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.7dpc.4

value: Lung

tag: genotype

value: WT


title: WT, replicate1, scRNAseq

description: 10x Genomics

tag: treatment


title: PrS-MOK20125P-G12-hyp, KO

description:
Library name: TP63_PTC_G12_3_O2_GT25-00015_CAGTAGGC-ATTCGTCA_S724_L004
KOLF2.2J derived knockout cell line, TP63 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: iPSC

tag: editing strategy

value: Termination codon

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

tag: condition


title: PrS-MOK20105_125-WT2-nor, WT

description:
Library name: KOLF2_2J_20_O2_REP2_GT25-00038_AATGCCTC-TGGATCGA_S730_L004
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: Not applicable

value: primitive syncytium

value: normoxia


title: CTRL, brain organoid, day56 [RNA-seq]

description: RNAseq

tag: tissue/cell type

value: brain organoids

value: neuron

value: wt


title: cct1-2 DMSO Rep1

description: cct1-2 DMSO Rep1 (final processed files are derived from WT and cct1-2 data, as well as prior usage of both 4tU and DMSO files)

tag: strain

value: JFY148 (cct1-2 ts mutant)

value: 5 h at 37C, 5 min DMSO


title: ++Oxtr-9

city: Shenyang,China

first: Dan

last: Li

address: No. 146, Huanghe North Street, Yuhong District, Shenyang City, Liaoning Province，China

institute: Shenyang Medical College

data_processing:
Illumina Hiseq platform
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: white adipose tissue

extract_protocol:
Total RNA was purified from mouse white adipose tissue using Trizol reagent (Takara).1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

tag: tissue

value: white adipose tissue

value: ++Oxtr


title: cct1-2 4tU Rep1

description: cct1-2 4tU Rep1 (final processed files are derived from WT and cct1-2 data, as well as prior usage of both 4tU and DMSO files)

value: 5 h at 37C, 5 min 4tU


title: L50A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.7dpc.2

tag: vaccination status

value: Not immunized

tag: vaccine

value: Saline

tag: vaccine dose

tag: vaccine route

value: subcutaneous

tag: days post_immunization

value: day 97

tag: challenge

value: Yes

value: Mtb H37Rv

value: 500 cfu

value: Intranasal

value: Tuberculosis

value: Early infection


title: ++Oxtr-8

tag: genotype


title: L49A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Inf.7dpc.1

value: Lung

value: WT

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage


title: WT DMSO Rep1

description: WT DMSO Rep1 (final processed files are derived from WT and cct1-2 data, as well as prior usage of both 4tU and DMSO files)

value: JFY143 (CCT WT W303, matA)

tag: treatment

value: 4 h at 37C, 5 min DMSO


title: L48A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.90dpi.8

value: Immunized

value: 10e6 cfu

value: day 90

value: No

value: No disease


title: WT 4tU Rep1

description: WT 4tU Rep1 (final processed files are derived from WT and cct1-2 data, as well as prior usage of both 4tU and DMSO files)

value: 4 h at 37C, 5 min 4tU


title: PrS-MOK20125P-G12-nor, KO

description:
Library name: TP63_PTC_G12_20_O2_GT25-00030_TTACAGGA-GCTTGTCA_S701_L004
KOLF2.2J derived knockout cell line, TP63 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

tag: cell line

tag: cell type

value: iPSC

tag: editing strategy

value: Termination codon

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

tag: condition

value: normoxia

tag: parental cell_line


title: PrS-MOK20125P-C07-nor, KO

description:
Library name: TP63_PTC_C07_20_O2_GT25-00029_CCGTGAAG-ATCCACTG_S715_L004
KOLF2.2J derived knockout cell line, TP63 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: 7KQ, replicate1,scRNAseq

description: 10x Genomics

value: Cd45+ cells

value: p53 fl7KQ/-, Lck-cre

value: xenograft Mc38 cells


title: WT-12

tag: tissue

value: white adipose tissue

value: WT


title: L47A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.90dpi.7

value: Lung

tag: genotype

tag: vaccination status

tag: vaccine

tag: vaccine dose

tag: vaccine route

value: subcutaneous

tag: days post_immunization

tag: challenge


title: PrS-MOK20125P-C10-nor, KO

description:
Library name: TP63_PTC_C10_20_O2_GT25-00028_TCCAACGC-AAGTCCAA_S711_L004
KOLF2.2J derived knockout cell line, TP63 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

tag: cell line


title: Cells containing condensin fusion Brn1-cdc5KD arrested in metaphase with nocodazole replicate 2

city: London

first: Jonay

last: Garcia-Luis

state: London

address: Du Cane Road

department: London Institute of Medical Sciences

institute: UKRI

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB76

library_source: genomic

data_processing:
HiC: Alignment of the reads and processing of the contact data was done with Hicstuff using the S288C reference genome (Matthey-Doret et al. 2020, 10.5281/zenodo.4066351). Hicstuff pipeline was launched with the following parameters: filter out spurious 3C events, filter out PCR duplicates based on read positions. The “view” mode of Hicstuff ICE function was used to generate normalized contact maps as described in Imakaev et al. 2012, 10.1038/nmeth.2148).
ChIP-seq: Calibrated Chip-seq: The quality of the raw sequence data was assessed using FastQC (version 0.11.5). The reads were mapped to the S. cerevisiae genome (sacCer3) as the experimental genome or C. glabrata genome (CBS138) as the calibration genome using Bowtie 2 (version 2.3.4) with default parameters. To generate an alignment in which all the sequences exclusively map to the sacCer3 genome, the whole reads were first mapped to CBS138 genome and the unmapped reads were retrieved as a separate Fastq file. Subsequently, these unmapped reads were re-aligned to sacCer3 genome and the generated aligned BAM file therefore contained reads that were unique to sacCer3. The same method was used to generate alignments unique to CBS138. The occupancy ratio (ORi) was calculated as in Hu, B. et al.2015 (DOI: 10.1093/nar/gkv670). For each sample, the alignment BAM file was converted to Wig format using bedtools (version 2.27.1). To obtain a calibrated version, the Wig file with the conventional ChIP-seq profile was multiplied by the OR corresponding to each sample. Subsequently, these calibrated BigWig files were used to generate average profile plots for regions in ±10 kb of centromeres for 16 chromosomes in the sacCer3 genome
Genome_build: S288C reference genome
Supplementary_files_format_and_content: HiC: .cool   ChIP-seq: .bw

molecule: genomic DNA

extract_protocol:
Cells were fixed with 3% formaldehyde (Sigma-Aldrich, F8775) as detailed in Dauban et al. 2020 (DOI: 10.1016/j.molcel.2020.01.019). Formaldehyde was quenched with 300 mM of glycine at room temperature for 20 min.Hi-C  experiments  were performed  with  a  Hi-C  kit  (Arima  Genomics)  involving  a double DpnII + HinfI restriction digestion.
Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was done with Collibri™ ES DNA Library Prep Kit for Illumina Systems (Thermo Fisher, A38605024).

tag: treatment

value: To arrest cells in G2/M, Nocodazole (1.5 mg/mL stock in 100% DMSO) was added to cultures with an OD600=0.5 to a final concentration of 0.015 mg/mL for 3 hours at 30⁰C. Nocodazole was topped-up after 1.5 incubation at a concentration of 0.0075 mg/ml


title: L46A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.90dpi.6

value: Immunized

value: 10e6 cfu

value: day 90

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage


title: PrS-MOK20105_125-WT3-nor, WT

description:
Library name: KOLF2_2J_20_O2_REP3_GT25-00039_TACCGAGG-AGTTCAGG_S703_L004
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

tag: cell type

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

tag: condition


title: WT-11

tag: tissue

tag: genotype


title: WT-10


title: Cells containing condensin fusion Brn1-cdc5KD arrested in metaphase with nocodazole replicate 1

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB75


title: Cells containing condensin fusion Brn1-Cdc5 arrested in metaphase with nocodazole replicate 2

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB59


title: PrS-MOK20105_125-WT1-nor, WT

description:
Library name: KOLF2_2J_20_O2_REP1_GT25-00037_GGCATTCT-CAAGCTAG_S710_L004
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: iPSC

tag: parental cell_line


title: L45A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.90dpi.5

tag: vaccination status

tag: vaccine

tag: vaccine dose

tag: vaccine route

tag: days post_immunization

tag: challenge

value: No

value: No disease


title: PrS-MOK20105P-A06-nor, KO

description:
Library name: HIF1a_PTC_A06_20_O2_GT25-00027_CTTGGTAT-GGACTTGG_S726_L004
KOLF2.2J derived knockout cell line, HIF1A PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

tag: cell line

value: Termination codon

value: day 6

value: primitive syncytium


title: L44A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.90dpi.4

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage


title: Cells containing condensin fusion Brn1-Cdc5 arrested in metaphase with nocodazole replicate 1

description:
Hi-C matrix filtered and PCR duplicate-free binned at 1 kb in cooler format
HB58

tag: treatment


title: ++Oxtr-7

value: ++Oxtr


title: VTA - Ogtflox-/Y,6

city: Shanghai

first: Shao

middle: Ming

last: Shuo

address: 138 Yixueyuan Road

institute: Fudan university

data_processing:
Raw FASTQ files were processed using FastQC for quality control
Adapter sequences were removed and low-quality reads (Phred score < 30) were filtered out using Trimmomatic.
Cleaned reads were aligned to the mm10 using STAR  with default parameters
Aligned reads were quantified using featureCounts to obtain gene-level count matrices.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Ventral tegmental area

extract_protocol:
RNA was harvested using RNA-seq Library Prep Kit  (Vazyme). 2.0 ug of total RNA was used for the construction of sequencing libraries RNA
RNA libraries for RNA-seq were prepared using Universal V10 RNA-seq Library Prep Kit  following the manufacturer's protocols RNA-seq

value: Ventral tegmental area

value: dopaminergic neuronal cell

tag: cell type

value: neuronal cell

value: Ogtflox-/Y

value: Virus injection


title: PrS-MOK20105P-A05-nor, KO

description:
Library name: HIF1a_PTC_A05_20_O2_GT25-00026_GTCGGAGC-TTATAACC_S706_L004
KOLF2.2J derived knockout cell line, HIF1A PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

tag: editing strategy

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

tag: condition

value: normoxia


title: L43A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.90dpi.3

tag: tissue

value: Lung

tag: genotype

value: WT

tag: vaccination status

value: Immunized

tag: vaccine

tag: vaccine dose

tag: vaccine route

value: subcutaneous


title: PrS-MOK20105P-A04-nor, KO

description:
Library name: HIF1a_PTC_A04_20_O2_GT25-00025_ACTAAGAT-CCGCGGTT_S705_L004
KOLF2.2J derived knockout cell line, HIF1A PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

tag: cell line

value: iPSC

tag: parental cell_line


title: VTA - Ogtflox-/Y,5


title: PrS-MOK20062_101_98-WT3-nor, WT

description:
Library name: ELF5_NR2F2_ASCL2_WT_20__3_GT25-01225_CTCTCGTC-AGGTTATA_S150_L004
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: Not applicable


title: VTA - Ogtflox-/Y,4


title: PrS-MOK20062_101_98-WT2-nor, WT

description:
Library name: ELF5_NR2F2_ASCL2_WT_20__2_GT25-01224_TCTCTACT-GAACCGCG_S140_L004
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen


title: TestisJuv

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

description:
Library name: TestisJuv
Column name in gene_count.xls: TestisJuv

data_processing:
The RNA seq reads were mapped to the genome (Lv3.0) using STAR and analyzed using FeatureCounts. Differential gene expressions were analyzed with Deseq2 and the PCA plots were obtained with the command plotPCA
Assembly: Lvar 3.0
Supplementary files format and content: tab delimited excel file include feature count for each sample

organism: Lytechinus variegatus

source_name: Testis at 4.5 mpf

growth_protocol: Adult Lytechinus variegatus are obtained from Pelagic Corp, FL. The animals were either dissected to obtain the adult tissues or were spawned to get eggs and sperm. The resulting embryos were raised in a closed aquarium system at 26C where they were fed using standard rearing protocols with Rhodomonas salina CCMP1319, and Tisochrysis lutea CCMP1324. At metamorphosis the animals were moved to a closed water table where they were fed diatoms Amphora sp. CCMP129 and turf macroalgae algae i.e. Ulva sp. When they reached 4.5 month post fertilization, the gonads or presumptive gonads were extracted.

extract_protocol:
Tissues were stored in Trizol and RNA was extracted
Novogene polyA library from total RNA for adult tissues, AdmeraHealth polyA library from total RNA for juvenile tissues (4.5 mpf)

value: Testis at 4.5 mpf

value: wild type


title: Ovary5Stage1

description:
Library name: Ovary5Stage1
Column name in gene_count.xls: Ovary5Stage1, Illumina Novaseq PE150

source_name: Ovary Stage 1

value: Ovary Stage 1


title: VTA - Ogtflox-/Y,3


title: L41A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.90dpi.1

value: 10e6 cfu

tag: days post_immunization

value: day 90

tag: challenge

value: No

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage

value: No disease


title: OvaryJuv

description:
Library name: OvaryJuv
Column name in gene_count.xls: OvaryJuv

source_name: Ovary at 4.5 mpf

value: Ovary at 4.5 mpf


title: VTA - Ogtflox+/Y,5

value: Ventral tegmental area

value: dopaminergic neuronal cell

tag: cell type

value: neuronal cell

value: Ogtflox+/Y

tag: treatment


title: L40A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.90dpi.8

tag: tissue

value: Lung

value: WT

value: BCG


title: PrS-MOK20062_101_98-WT1-nor, WT

description:
Library name: ELF5_NR2F2_ASCL2_WT_20__1_GT25-01223_GACCTGAA-CTCACCAA_S143_L004
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: iPSC

tag: editing strategy

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

tag: condition

value: normoxia


title: IndetJuv3

description:
Library name: IndetJuv3
Column name in gene_count.xls: IndetJuv3

source_name: Indetermined gonad at 4.5 mpf

value: Indetermined gonad at 4.5 mpf

tag: genotype

value: wild type


title: VTA - Ogtflox+/Y,4

tag: cell line

value: Virus injection


title: IndetJuv2

description:
Library name: IndetJuv2
Column name in gene_count.xls: IndetJuv2


title: PrS-MOK20098P-B06-nor, KO

description:
Library name: ASCL2_PTC_B06_20_O2_GT25-01218_ATCCACTG-ACGCACCT_S136_L004
KOLF2.2J derived knockout cell line, ASCL2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: Termination codon

tag: parental cell_line


title: VTA - Ogtflox+/Y,3


title: L38A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.90dpi.6

tag: vaccination status

value: Immunized

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

tag: vaccine route

value: subcutaneous

tag: days post_immunization

value: day 90

tag: challenge

value: No

tag: challenge strain

value: No disease


title: PrS-MOK20098P-A01-nor, KO

description:
Library name: ASCL2_PTC_A01_20_O2_GT25-01217_AAGTCCAA-TACTCATA_S138_L004
KOLF2.2J derived knockout cell line, ASCL2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

tag: cell type


title: L37A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.90dpi.5

tag: tissue

value: Lung

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage


title: Tubefoot4

description:
Library name: Tubefoot4
Column name in gene_count.xls: Tubefoot4

source_name: Tube foot

value: Tube foot


title: PrS-MOK20101P-H01-nor, KO

description:
Library name: ELF5_PTC_H01_GT25-01216_GGACTTGG-CGTCTGCG_S145_L004
KOLF2.2J derived knockout cell line, ELF5 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

tag: editing strategy

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

tag: condition


title: VTA - Ogtflox+/Y,2

value: Ventral tegmental area

tag: cell line

value: dopaminergic neuronal cell

value: neuronal cell

tag: genotype

value: Ogtflox+/Y

tag: treatment


title: VTA, Stess,5

value: WT

value: Acute Restraint


title: L42A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.90dpi.2

tag: vaccination status

tag: vaccine

tag: vaccine dose

tag: vaccine route

tag: days post_immunization

tag: challenge


title: L36A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.90dpi.4

tag: tissue

value: BCG

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease


title: VTA, Stess,4

tag: cell type


title: Tubefoot3

description:
Library name: Tubefoot3
Column name in gene_count.xls: Tubefoot3

value: wild type


title: PrS-MOK20101P-E01-nor, KO

description:
Library name: ELF5_PTC_E01_GT25-01215_TTATAACC-TCGATATC_S148_L004
KOLF2.2J derived knockout cell line, ELF5 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

value: iPSC

tag: editing strategy

value: Termination codon

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

value: normoxia

tag: parental cell_line


title: Tubefoot2

description:
Library name: Tubefoot2
Column name in gene_count.xls: Tubefoot2

tag: genotype


title: L35A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.90dpi.3

tag: vaccination status

value: Immunized

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

value: subcutaneous

value: day 90

value: No

tag: disease stage


title: VTA, Stess,3

tag: tissue

value: Ventral tegmental area

tag: cell line

value: dopaminergic neuronal cell

tag: treatment


title: Tubefoot1

description:
Library name: Tubefoot1
Column name in gene_count.xls: Tubefoot1

value: Tube foot


title: PrS-MOK20062P-H02, KO

description:
Library name: NR2F2_PTC_H02_GT25-01222_AGTTCAGG-TCTGTTGG_S137_L004
KOLF2.2J derived knockout cell line, NR2F2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: condition

value: Not applicable


title: L39A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.90dpi.7

value: Lung

value: WT

tag: vaccine route

tag: days post_immunization

tag: challenge

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

value: No disease


title: PrS-MOK20098P-D02-nor, KO

description:
Library name: ASCL2_PTC_D02_20_O2_GT25-01219_GCTTGTCA-GTATGTTC_S142_L004
KOLF2.2J derived knockout cell line, ASCL2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

tag: cell type

value: iPSC

tag: editing strategy

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

tag: parental cell_line


title: Testis4

description:
Library name: Testis4
Column name in gene_count.xls: Testis4

source_name: Testis

tag: tissue

value: Testis

tag: genotype

value: wild type


title: PrS-MOK20101P-B06-nor, KO

description:
Library name: ELF5_PTC_B06_GT25-01214_CCGCGGTT-CTAGCGCT_S149_L004
KOLF2.2J derived knockout cell line, ELF5 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 20% oxygen

tag: cell line

value: Termination codon

value: day 6

value: primitive syncytium

tag: condition


title: VTA, Stess,2

value: neuronal cell

tag: treatment

value: Acute Restraint


title: L34A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.90dpi.2

tag: vaccination status

value: Immunized

tag: vaccine

value: BCG

tag: vaccine dose

value: 10e6 cfu

tag: vaccine route

value: subcutaneous

tag: days post_immunization

value: day 90

tag: challenge

tag: disease stage


title: L32A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.90dpi.8

value: Not immunized

value: Saline

value: No

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease


title: PrS-MOK20062P-E02, KO

description:
Library name: NR2F2_PTC_E02_GT25-01221_TGGATCGA-TATCGCAC_S141_L002
KOLF2.2J derived knockout cell line, NR2F2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: cell type

tag: editing strategy

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

value: Not applicable

tag: parental cell_line


title: VTA, Stess,1

tag: tissue

value: Ventral tegmental area

tag: cell line

value: dopaminergic neuronal cell

tag: genotype

value: WT

tag: treatment


title: Testis3

description:
Library name: Testis3
Column name in gene_count.xls: Testis3

value: Testis

value: wild type


title: L33A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.90dpi.1

value: Lung

tag: vaccination status

tag: vaccine

tag: vaccine dose

tag: vaccine route

tag: days post_immunization

tag: challenge

value: No disease


title: IndetJuv1

description:
Library name: IndetJuv1
Column name in gene_count.xls: IndetJuv1

value: Indetermined gonad at 4.5 mpf


title: VTA, Normal,5

tag: cell type

value: neuronal cell

value: Ctrl


title: PrS-MOK20062P-A02, KO

description:
Library name: NR2F2_PTC_A02_GT25-01220_CAAGCTAG-CGCTATGT_S146_L004
KOLF2.2J derived knockout cell line, NR2F2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

tag: editing strategy

value: Termination codon

value: day 6

value: primitive syncytium

tag: condition


title: Testis2

description:
Library name: Testis2
Column name in gene_count.xls: Testis2


title: L30A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.90dpi.6

value: Not immunized

value: Saline

value: subcutaneous

value: day 90

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage


title: ExM-MOK20108-WT2, WT

description:
Library name: MAFB_WT_2_GT24-12091_GCAGAATT-TGGCCGGT_S58_L007
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation

tag: cell line

value: Not applicable

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

value: fibroblast of villous mesenchyme (CL:0002558)

tag: parental cell_line


title: VTA, Normal,4

tag: tissue

value: Ventral tegmental area

value: dopaminergic neuronal cell

tag: genotype

value: WT

tag: treatment


title: L29A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.90dpi.5

value: Lung

tag: vaccination status

tag: vaccine

tag: vaccine dose

tag: vaccine route

tag: days post_immunization

tag: challenge

value: No

value: No disease


title: ExM-MOK20108-WT3, WT

description:
Library name: MAFB_WT_3_GT24-12092_ATGAGGCC-CAATTAAC_S62_L007
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation

tag: cell type

tag: editing strategy

tag: condition


title: ExM-MOK20108-WT1, WT

description:
Library name: MAFB_WT_1_GT24-12090_AACGTTCC-AGTACTCC_S47_L007
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation

tag: cell line

tag: altered gene_symbol


title: SpineWht

description:
Library name: SpineWht
Column name in gene_count.xls: SpineWht

source_name: White spine

value: White spine

value: wild type


title: Testis1

description:
Library name: Testis1
Column name in gene_count.xls: Testis1

value: Testis


title: L31A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.90dpi.7

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage


title: VTA, Normal,2

tag: tissue

value: neuronal cell

tag: genotype

tag: treatment

value: Ctrl


title: L28A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.90dpi.4

tag: vaccination status

value: Not immunized

tag: vaccine

tag: vaccine dose


title: ExM-MOK20108P-D05, KO

description:
Library name: MAFB_PTC_D05_GT24-12089_GGTACCTT-GACGTCTT_S48_L007
KOLF2.2J derived knockout cell line, MAFB PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation

value: iPSC

value: Termination codon

value: MAFB

tag: altered locus

tag: time

value: day 6

tag: model system

tag: parental cell_line


title: VTA, Normal,1

tag: cell line

tag: cell type


title: L27A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.90dpi.3

value: Saline

tag: vaccine route

value: subcutaneous

tag: days post_immunization

value: day 90

tag: challenge

tag: challenge strain


title: Spinemix

description:
Library name: Spinemix
Column name in gene_count.xls: Spinemix

source_name: Mixed color spines

value: Mixed color spines


title: VTA, Ogtflox+/Y,6

data_processing:
Raw FASTQ files were processed using FastQC for quality control
Adapter trimming and low-quality read removal (Phred score < 30) were performed using Trimmomatic
Reads were aligned to the mouse genome (mm10) using BWA
Mitochondrial reads and duplicate reads were removed using Samtools (v1.9) and Picard MarkDuplicates
Peak calling was performed using MACS2 with a p-value threshold of 1e-5
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
chromatin was harvested using Universal Plus DNA Library Prep Kit for Illumina  (Vazyme). 1.0 ug of total DNA was used for the construction of sequencing libraries DNA
libraries for ATAC-seq were prepared using Universal Plus DNA Library Prep Kit for Illumina following the manufacturer's protocols ATAC-seq

value: Ventral tegmental area

value: dopaminergic neuronal cell

value: Ogtflox+/Y

value: Virus injection


title: L26A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.90dpi.2

value: Lung

value: WT

value: No

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage

value: No disease


title: ExM-MOK20108P-C04, KO

description:
Library name: MAFB_PTC_C04_GT24-12088_GCACGGAC-TGCGAGAC_S41_L007
KOLF2.2J derived knockout cell line, MAFB PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation

tag: editing strategy

tag: altered gene_symbol

value: fibroblast of villous mesenchyme (CL:0002558)

tag: condition

value: Not applicable


title: SpineGrn

description:
Library name: SpineGrn
Column name in gene_count.xls: SpineGrn

source_name: Green spine

tag: tissue

value: Green spine

tag: genotype

value: wild type


title: VTA, Ogtflox+/Y,4

value: neuronal cell

tag: treatment


title: ExM-MOK20108P-A02, KO

description:
Library name: MAFB_PTC_A02_GT24-12087_ATGTAAGT-CATAGAGT_S33_L007
KOLF2.2J derived knockout cell line, MAFB PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation

value: iPSC

value: Termination codon

value: MAFB

tag: altered locus

tag: time

value: day 6

tag: model system

tag: parental cell_line


title: L25A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.90dpi.1

tag: vaccination status

value: Not immunized

tag: vaccine

value: Saline

tag: vaccine dose

tag: vaccine route

value: subcutaneous

tag: days post_immunization

value: day 90


title: VTA, Ogtflox-/Y,2

value: Ventral tegmental area

tag: cell line

value: dopaminergic neuronal cell

tag: cell type

value: Ogtflox+/Y

value: Virus injection


title: L24A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpi.8

value: Lung

value: WT

value: Immunized

value: 10e6 cfu

value: day 7

tag: challenge

value: No

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage

value: No disease


title: Rectum2

description:
Library name: Rectum2
Column name in gene_count.xls: Rectum2

source_name: Rectum

tag: tissue

value: Rectum

tag: genotype

value: wild type


title: VTA, Normal,3

value: neuronal cell

tag: treatment

value: Ctrl


title: PrS-MOK20046_72_80-WT2, WT

description:
Library name: WT_PrS_2_GT24-08506_GCAGAATT-TGGCCGGT_S38_L006
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

tag: condition

tag: parental cell_line


title: PrS-MOK20080P-H04, KO

description:
Library name: VGLLI_PTC_H04_GT24-08504_GGTACCTT-GACGTCTT_S34_L006
KOLF2.2J derived knockout cell line, VGLL1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: cell line

tag: cell type

value: Termination codon


title: PrS-MOK20046_72_80-WT1, WT

description:
Library name: WT_PrS_1_GT24-08505_AACGTTCC-AGTACTCC_S22_L006
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: L23A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpi.7

tag: vaccination status

tag: vaccine

tag: vaccine dose

tag: vaccine route

value: subcutaneous

tag: days post_immunization

tag: challenge

tag: challenge strain


title: Rectum1

description:
Library name: Rectum1
Column name in gene_count.xls: Rectum1

tag: tissue

tag: genotype


title: L22A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpi.6

value: Lung

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage


title: RadialNerve4

description:
Library name: RadialNerve4
Column name in gene_count.xls: RadialNerve4

source_name: Radial Nerve

value: Radial Nerve


title: VTA, Ogtflox-/Y,3

value: Ventral tegmental area

value: dopaminergic neuronal cell

value: Ogtflox-/Y

tag: treatment

value: Virus injection


title: SpineRed

description:
Library name: SpineRed
Column name in gene_count.xls: SpineRed

source_name: Red spine

value: Red spine


title: PrS-MOK20080P-F06, KO

description:
Library name: VGLLI_PTC_F06_GT24-08503_GCACGGAC-TGCGAGAC_S44_L006
KOLF2.2J derived knockout cell line, VGLL1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: editing strategy

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

tag: condition

tag: parental cell_line


title: L21A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpi.5

value: WT

tag: vaccination status

value: Immunized

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

tag: vaccine route

tag: days post_immunization

value: day 7

value: No

value: No disease


title: RadialNerve3

description:
Library name: RadialNerve3
Column name in gene_count.xls: RadialNerve3

tag: tissue

tag: genotype

value: wild type


title: VTA, Ogtflox-/Y,1

tag: cell line

tag: cell type

value: neuronal cell


title: PrS-MOK20080P-B05, KO

description:
Library name: VGLLI_PTC_B05_GT24-08502_ATGTAAGT-CATAGAGT_S29_L006
KOLF2.2J derived knockout cell line, VGLL1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: Termination codon

value: day 6

value: primitive syncytium

value: Not applicable


title: RadialNerve2

description:
Library name: RadialNerve2
Column name in gene_count.xls: RadialNerve2

value: Radial Nerve


title: Rectum3

description:
Library name: Rectum3
Column name in gene_count.xls: Rectum3

value: Rectum


title: L20A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpi.4

value: Lung

value: subcutaneous

tag: challenge

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage


title: PrS-MOK20072P-C05, KO

description:
Library name: MSX2_PTC_C05_GT24-08501_CGGCGTGA-ACAGGCGC_S45_L006
KOLF2.2J derived knockout cell line, MSX2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: editing strategy

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system

tag: condition


title: RadialNerve1

description:
Library name: RadialNerve1
Column name in gene_count.xls: RadialNerve1


title: Cortex_TG-DTMB 3

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

description: Cortex_TG DTMB treated group_replicate 3

data_processing:
Adapter sequences were trimmed with cutadapt-v2.10
Reads were mapped to the genome (Ensembl GRCm38 release100) using STAR-v2.7.2b with ENCODE option.
RSEM-v1.2.31 was used to calculate read counts and normalization.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated RSEM results:

source_name: Cortex

growth_protocol: 5xFAD (Tg6799) mice were purchased from the Jackson Laboratory (Bar Harbor, ME, USA) and male transgenic mice were bred with B6/SJL hybrid female mice. Genotyping was conducted by PCR analysis of tail cut samples. Only the female mice were used for behavior experiments in this study and wild type littermates were used as controls.

extract_protocol:
Brain was extracted after perfusion with cold PBS. Hippocampus and cortex was dissected from brain after brain extraction. Dissected tissues were frozen with liquid nitrogen and kept at -80°C until further use. RNA was extracted with Trizol reagent. Extracted RNA was treated with DNase to remove remaining DNA in extracted RNA. Then RNA was extracted again through phenol:chloroform extraction. Extracted RNA was confrimed of its concentration and purity through Nanodrop and agarose gel electrophoresis by confirming clear two bands of 28S and 18S rRNA. Extracted RNA was treated with 1/10 volume of 3M sodium acetate (pH 5.2) and 2~2.5 volumes of cold 100% ethanol and kept at -80°C until library construction. Among the extracted RNA, 1μg of RNA was used for library construction.
RNA-Seq libraries were prepared by using NEXTflex Rapid Directional mRNA-Seq Kit Bundles (Bioo Scientific, TX, USA) and sequenced on Illumina HiSeq 2500 platform (San Diego, CA, USA).

treatment_protocol: To evaluate the effects of DTMB on 5xFAD mice, DTMB (10 mg/kg) and vehicle (1% carboxymethylcellulose) were orally administrated to four groups (wild-type, wild-type + DTMB, 5xFAD, and 5xFAD + DTMB) for 3 months.

tag: age

tag: treatment

value: DTMB


title: Cortex_TG-DTMB 2

description: Cortex_TG DTMB treated group_replicate 2

tag: genotype


title: Cortex_TG-DTMB 1

description: Cortex_TG DTMB treated group_replicate 1


title: PrS-MOK20072P-B06, KO

description:
Library name: MSX2_PTC_B06_GT24-08500_TAATACAG-GTGAATAT_S39_L006
KOLF2.2J derived knockout cell line, MSX2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: cell line

tag: parental cell_line


title: PrS-MOK20072P-A12, KO

description:
Library name: MSX2_PTC_A12_GT24-08499_TGACGAAT-GCCTACTG_S26_L006
KOLF2.2J derived knockout cell line, MSX2 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: cell type


title: L17A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpi.1

source_name: Lung

tag: tissue

value: WT

tag: vaccination status

value: Immunized

tag: vaccine

tag: vaccine dose

tag: vaccine route

tag: days post_immunization

tag: challenge

tag: challenge strain


title: L18A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpi.2

value: 10e6 cfu

value: day 7

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage


title: Cortex_TG-V_3

description: Cortex_TG Vehicle group_replicate 3

tag: age

tag: treatment

value: Vehicle


title: VTA, Ogtflox-/Y,5

value: Ventral tegmental area

tag: cell line

value: dopaminergic neuronal cell

tag: genotype

value: Ogtflox-/Y

value: Virus injection


title: RadialCanal3

description:
Library name: RadialCanal3
Column name in gene_count.xls: RadialCanal3

source_name: Radial Canal

value: Radial Canal

value: wild type


title: RadialCanal4

description:
Library name: RadialCanal4
Column name in gene_count.xls: RadialCanal4


title: Cortex_TG-V_1

description: Cortex_TG Vehicle group_replicate 1


title: L15A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpi.7

value: BCG

value: No

value: No disease


title: RadialCanal1

description:
Library name: RadialCanal1
Column name in gene_count.xls: RadialCanal1


title: Cortex_TG-V_2

description: Cortex_TG Vehicle group_replicate 2


title: RadialCanal2

description:
Library name: RadialCanal2
Column name in gene_count.xls: RadialCanal2


title: PrS-MOK20046P-F02, KO

description:
Library name: DLX3_PTC_F02_GT24-08497_TTGGACTC-CTGCTTCC_S35_L006
KOLF2.2J derived knockout cell line, DLX3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: cell type

value: iPSC

tag: editing strategy

value: Termination codon

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

tag: condition

value: Not applicable

tag: parental cell_line


title: PrS-MOK20046P-C03, KO

description:
Library name: DLX3_PTC_C03_GT24-08496_CCAAGTCT-TCATCCTT_S21_L006
KOLF2.2J derived knockout cell line, DLX3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: Cortex_WT-DTMB 2

description: Cortex_WT DTMB treated group_replicate 2

value: DTMB


title: Peristomemb3

description:
Library name: Peristomemb3
Column name in gene_count.xls: Peristomemb3

source_name: Peristomial membrane

tag: tissue

value: Peristomial membrane


title: L16A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpi.8

value: Lung

value: WT

tag: vaccination status

value: Immunized

tag: vaccine

tag: vaccine dose

value: 10e6 cfu

tag: vaccine route

value: subcutaneous

tag: days post_immunization

value: day 7

tag: challenge

tag: challenge strain

tag: challenge dose


title: L19A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.rBCG.7dpi.3

tag: genotype

tag: challenge route

tag: disease

tag: disease stage


title: Thyroid, PTC with HT 9

city: Goyang

first: Dong-Woo

last: Lim

address: Dongguk-ro 32

institute: Dongguk university

description:
Library name: Sample 18
TH_31

data_processing:
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Homo sapiens (GRCh38) using HISAT v2.1.0.
After alignment, the relative abundances of gene were measured in Read Count using StringTie.
Genes with one more than zeroed Read Count values in the samples were excluded. 1 was added to each Read Count value of filtered genes. Filtered data were log2-transformed and subjected to RLE normalization.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts, FPKM, TPM for each Sample

source_name: Thyroid

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen) according to the manufacturer's protocol.
RNA library was 1.0 ug of total RNA was used to construct the sequencing libraries. RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA library preparation kit (Illumina). Only RNA preparations with RIN greater than 7.0 were used for RNA library construction.

value: Thyroid

tag: Sex

value: Female


title: L13A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpi.5

value: BCG

value: No


title: Peristomemb2

description:
Library name: Peristomemb2
Column name in gene_count.xls: Peristomemb2

value: wild type


title: Thyroid, PTC with HT 7

description:
Library name: Sample 16
TH_20


title: PrS-MOK20046P-H01, KO

description:
Library name: DLX3_PTC_H01_GT24-08498_CAGTAGGC-ATTCGTCA_S46_L006
KOLF2.2J derived knockout cell line, DLX3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

tag: cell line

tag: cell type

value: iPSC

tag: editing strategy

value: Termination codon

tag: altered gene_symbol

tag: altered locus

tag: time

tag: model system


title: Cortex_WT-V_2

description: Cortex_WT Vehicle group_replicate 2

tag: age

tag: treatment

value: Vehicle


title: L12A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpi.4

tag: tissue

tag: vaccination status

tag: vaccine

tag: vaccine dose

tag: vaccine route

tag: days post_immunization

tag: challenge

value: No disease


title: L11A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpi.3

tag: genotype

tag: challenge strain

tag: challenge dose

tag: challenge route

tag: disease

tag: disease stage


title: Ovary4

description:
Library name: Ovary4
Column name in gene_count.xls: Ovary4

source_name: Ovary

value: Ovary


title: Thyroid, PTC with HT 5

description:
Library name: Sample 14
TH_9

tag: Sex


title: Cortex_WT-V_1

description: Cortex_WT Vehicle group_replicate 1


title: L14A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpi.6


title: L10A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpi.2


title: Ovary3

description:
Library name: Ovary3
Column name in gene_count.xls: Ovary3


title: Thyroid, PTC with HT 6

description:
Library name: Sample 15
TH_14


title: Cortex_WT-DTMB 1

description: Cortex_WT DTMB treated group_replicate 1

value: DTMB


title: Hippocampus_TG-DTMB 3

description: Hippocampus_TG DTMB treated group_replicate 3

source_name: Hippocampus


title: Hippocampus_TG-DTMB 2

description: Hippocampus_TG DTMB treated group_replicate 2


title: Ovary2

description:
Library name: Ovary2
Column name in gene_count.xls: Ovary2


title: L9A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.BCG.7dpi.1

value: Lung


title: L8A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.7dpi.8

value: WT

value: Not immunized

value: Saline


title: Thyroid, PTC with HT 3

description:
Library name: Sample 12
TH_4


title: Ovary1

description:
Library name: Ovary1
Column name in gene_count.xls: Ovary1


title: Thyroid, PTC with HT 4

description:
Library name: Sample 13
TH_8


title: Thyroid, PTC with HT 2

description:
Library name: Sample 11
TH_2


title: Mouth3

description:
Library name: Mouth3
Column name in gene_count.xls: Mouth3

source_name: Mouth

value: Mouth


title: L7A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.7dpi.7

value: subcutaneous

value: day 7


title: L6A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.7dpi.6


title: Thyroid, PTC with HT 8

description:
Library name: Sample 17
TH_29

value: Thyroid

value: Female


title: Hippocampus_TG-V 2

description: Hippocampus_TG Vehicle group_replicate 2


title: Cortex_WT-V_3

description: Cortex_WT Vehicle group_replicate 3


title: Peristomemb1

description:
Library name: Peristomemb1
Column name in gene_count.xls: Peristomemb1

value: Peristomial membrane


title: Hippocampus_TG-V 1

description: Hippocampus_TG Vehicle group_replicate 1


title: Thyroid, PTC with HT 1

description:
Library name: Sample 10
TH_1


title: L5A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.7dpi.5

value: No


title: Thyroid, PTC without HT 9

description:
Library name: Sample 9
NG_35


title: L4A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.7dpi.4


title: Hippocampus_WT-DTMB 3

description: Hippocampus_WT DTMB treated group_replicate 3


title: LanternMusc4

description:
Library name: LanternMusc4
Column name in gene_count.xls: LanternMusc4

source_name: Lantern muscle

value: Lantern muscle

value: wild type


title: LanternMusc3

description:
Library name: LanternMusc3
Column name in gene_count.xls: LanternMusc3


title: Mouth1

description:
Library name: Mouth1
Column name in gene_count.xls: Mouth1


title: Hippocampus_WT-DTMB 2

description: Hippocampus_WT DTMB treated group_replicate 2


title: L3A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.7dpi.3


title: Thyroid, PTC without HT 7

description:
Library name: Sample 7
NG_22


title: L2A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.7dpi.2


title: Hippocampus_TG-DTMB 1

description: Hippocampus_TG DTMB treated group_replicate 1


title: Thyroid, PTC without HT 8

description:
Library name: Sample 8
NG_32


title: LanternMusc2

description:
Library name: LanternMusc2
Column name in gene_count.xls: LanternMusc2


title: Thyroid, PTC without HT 6

description:
Library name: Sample 6
NG_21


title: Hippocampus_WT-DTMB 1

description: Hippocampus_WT DTMB treated group_replicate 1


title: LanternMusc1

description:
Library name: LanternMusc1
Column name in gene_count.xls: LanternMusc1


title: L1A

description:
Organs were asseptically collected and kept in RNAlater at -80C until extraction
L.Sal.7dpi.1


title: Intambplate4

description:
Library name: Intambplate4
Column name in gene_count.xls: Intambplate4

source_name: Interambulacral plates

value: Interambulacral plates


title: S24, WT_V_M, rep 3

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

data_processing:
The clean reads were aligned to mouse genome mm10 by HISAT2. Sam filles were sorted as bam files and indexed by samtools.
The transcript count (number of reads per gene) were extract using stingTie (v1.3.5)  in default setting.
The transcript count data was further normalized and used to identify the differentially expressed genes by DEseq2 tool.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized count (in log2 scale) for each Sample.

source_name: brain

extract_protocol:
RNA extracted by using the RNeasy Mini Kit (Qiagen). The quality and quantity of purified RNA was estimated on Nanodrop 1000 Spectrophotometer (ThermoFisher).
total RNA libraries were prepared using DNBSEQ Eukaryotic Strand-specific mRNA library kit.

treatment_protocol: Mice aged between 1 to 4 months, were randomly assigned to either the vehicle group (1X PBS) or the lactate group (Sodium L-lactate). Mice received equal doses four times a week for 11 weeks. The lactate group received 2 g/kg body weight of sodium L-lactate (18 mmol/kg) dissolved in 1X PBS (pH 7.4) at 100 mg/ml.  The AD mice used here were hemizygous transgenic (Tg) mice for expressing human APP and PSEN1 mutation generated from the 5xFAD model, along with non-transgenic wild-type (WT) littermates.

value: brain

value: Vehicle


title: Hippocampus_WT-V_2

description: Hippocampus_WT Vehicle group_replicate 2


title: Thyroid, PTC without HT 4

description:
Library name: Sample 4
NG_16

value: Male


title: Mouth2

description:
Library name: Mouth2
Column name in gene_count.xls: Mouth2


title: Hippocampus_WT-V_1

description: Hippocampus_WT Vehicle group_replicate 1


title: Intambplate3

description:
Library name: Intambplate3
Column name in gene_count.xls: Intambplate3


title: Thyroid, PTC without HT 3

description:
Library name: Sample 3
NG_12


title: S23, WT_V_M, rep 2


title: S22, WT_V_M, rep 1


title: S21, WT_V_F, rep 3


title: Intambplate1

description:
Library name: Intambplate1
Column name in gene_count.xls: Intambplate1


title: S20, WT_V_F, rep 2


title: Gut4

description:
Library name: Gut4
Column name in gene_count.xls: Gut4

source_name: Gut

value: Gut


title: Intambplate2

description:
Library name: Intambplate2
Column name in gene_count.xls: Intambplate2


title: Thyroid, PTC without HT 1

description:
Library name: Sample 1
NG_10


title: Hippocampus_WT-V_3

description: Hippocampus_WT Vehicle group_replicate 3


title: Thyroid, PTC without HT 5

description:
Library name: Sample 5
NG_18


title: Gut3

description:
Library name: Gut3
Column name in gene_count.xls: Gut3


title: Purified HEK293T (ISBM-083) NTVE from co-culture with Neuro2a (ISBM-095) via FLAG-pull-down_spike-in_3

city: Munich

first: Gil

middle: Gregor

last: Westmeyer

address: Arcisstrasse 21

country: Germany

institute: Technical University Munich

description:
Library name: 24L010912
FLAG Purified sample of  co-cultivation of two stable NTVE lines

data_processing:
Deduplication via czid-dedup (paired-end mode)
featurecounts_harmonized.csv: Paired-end reads were aligned to the combined human-murine index via STAR  (star --readFilesCommand zcat --genomeDir {COMBINED_INDEX_STAR} --readFilesIn {R1} {R2} --runThreadN 8 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix {OUTPUT_NAME} --quantMode GeneCounts TranscriptomeSAM))
featurecounts_harmonized.csv: Gene level feature counting via featurecounts (featureCounts -a {COMBINED_INDEX_GTF} -o {OUTPUT_FILE}  -g gene_id -t exon -s 2 -p)
Quant files (*.sf.gz): Quantification via salmon (salmon quant -i {COMBINED_INDEX_SALMON} -l A -1 {R1} -2 {R2} --validateMappings -p 8 -o {OUT_PATH}")
Assembly: hg38, mm39, ARS-UCDI1.2
Supplementary files format and content: featurecounts_harmonized.csv: comma seperated plaintext file containing the raw counts mapping to features and metadata for all samples
Supplementary files format and content: Quant files (*.sf.gz): comma seperated plaintext file containing the TPMs and estimated number of reads for a specific sample, including metadata

growth_protocol: HEK293T cells were cultured in advanced DMEM supplemented wih 10% FCS and passaged by using Accutase at confluency

extract_protocol:
RNA from cell lysate was harvested using the NEB Monarch® Total RNA Miniprep Kit (T2010S). NTVE derived RNA was extracted from the supernatant using the Zymo Research Quick-RNA Viral Kit (R1040).
Libraries were constructed according to the protocols using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus for total RNA runs and Illumina Stranded mRNA Prep for polyA enriched runs

treatment_protocol: 500 ng/ml doycycline for NTVE induction; 50 ng/ml interferon-gamma or ASCL1 transactivation for pertubation.

tag: cell line

tag: cell type

value: immortalised cell line

value: NTVE Gag:PABP(ZF:Hibit):P2A:dVSVG:FLAG; CAG-TetON3g (ISBM-083)

tag: rna origin

value: Supernatant

tag: spike-in

value: 1pg mGL mRNA

value: doxycycline 500ng/ul


title: S18, WT_lac_M, rep 3

tag: tissue

value: WT

tag: treatment

value: lactate


title: Gut2

description:
Library name: Gut2
Column name in gene_count.xls: Gut2


title: S19, WT_V_F, rep 1


title: Purified HEK293T (ISBM-083) NTVE from co-culture with Neuro2a (ISBM-095) via FLAG-pull-down_spike-in_2

description:
Library name: 24L010911
FLAG Purified sample of  co-cultivation of two stable NTVE lines


title: Purified HEK293T (ISBM-083) NTVE from co-culture with Neuro2a (ISBM-095) via FLAG-pull-down_spike-in_1

description:
Library name: 24L010910
FLAG Purified sample of  co-cultivation of two stable NTVE lines


title: Gut1

description:
Library name: Gut1
Column name in gene_count.xls: Gut1


title: NTVE lysate-3_ISBM-083_spike-in

description:
Library name: 24L012565
Stable NTVE line

value: Cell Lysate


title: S17, WT_lac_M, rep 2


title: Esophagus4

description:
Library name: Esophagus4
Column name in gene_count.xls: Esophagus4

source_name: Esophagus

value: Esophagus


title: Thyroid, PTC without HT 2

description:
Library name: Sample 2
NG_11

value: Thyroid

value: Female


title: Healthy control skin HC3

type: RNA

first: Chloé

last: Grolleau

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

institute: INSERM U1342, eq 16

description:
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
HC3
HC3_(HTA-2_0).sst-rma-combined-dabg.chp Signal

hyb_protocol: Each sample was hybridized onto GeneChip® Human Transcriptome Array 2.0 (ThermoFisher Scientific), washed, and stained with the Affymetrix® Fluidics Station 450

scan_protocol: Scanning was performed with the Affymetrix® GeneChip Scanner 3000 7G (ThermoFisher Scientific)

data_processing:
The data were analyzed using the Affymetrix Transcriptome Analysis Console (TAC) software v.4 (ThermoFisher Scientific)
annotation=HTA-2_0.r3.na36.hg19.a1.transcript.csv

label: biotin

source_name: Biopsy of cutaneous plastic surgery waste

label_protocol: Ten nanogram of Total RNA was amplified, labeled, and fragmented using GeneChip WT Pico Reagent Kit (ThermoFisher Scientific)

extract_protocol: Total RNA was automatically extracted from tissue samples using the Maxwell RSC RNA FFPE kit according to the manufacturer’s protocol

value: Healthy control

value: skin


title: S16, WT_lac_M, rep 1

value: brain


title: Healthy control skin HC1

description:
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
HC1
HC1_(HTA-2_0).sst-rma-combined-dabg.chp Signal


title: Healthy control (HC) skin 2

description:
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
HC2_(HTA-2_0).sst-rma-combined-dabg.chp Signal

label_protocol: Ten nanogram of Total RNA was amplified, labeled, and fragmented using GeneChip WT Reagent Kit (ThermoFisher Scientific)

growth_protocol: A skin biopsy from one patient with active lichen planus and 3 skin biopsies from healthy control donnors were cut in half and cultured in RPMI enriched medium (10% FCS with 60UI/ml of IL2).

extract_protocol: RNAs were extracted using RNeasy microkit (Qiagen).

treatment_protocol: Each half of lichen planus biopsy was treated with either anti-IFNAR1 antibody (anifrolumab 10 mm/ml, AstraZeneca) or control isotype (IgG1 kappa 10 mm/ml, abcam) for 72h. Control biopsies were cultured in medium without antibody for 72h.

value: Medium, 72h


title: NTVE lysate-2_ISBM-083_spike-in

description:
Library name: 24L012564
Stable NTVE line


title: S15, WT_lac_F, rep 3


title: Lupus-lichen skin

description:
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
LL
Pre_(HTA-2_0).sst-rma-combined-dabg.chp Signal

source_name: lesional cutaneous biopsy

value: Lupus-lichen keratoderma


title: Lupus-lichen skin after 6 months treatment with anifrolumab

description:
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
LL-anifro
Post_(HTA-2_0).sst-rma-combined-dabg.chp Signal

source_name: post-lesional cutaneous biopsy

value: Anifrolumab 300mg/monthly since 6 months


title: Esophagus3

description:
Library name: Esophagus3
Column name in gene_count.xls: Esophagus3

value: wild type


title: Healthy control (HC) skin 3

description:
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
HC3_(HTA-2_0).sst-rma-combined-dabg.chp Signal


title: Healthy control skin HC2

description:
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
HC2
HC2_(HTA-2_0).sst-rma-combined-dabg.chp Signal


title: NTVE lysate-1_ISBM-083_spike-in

description:
Library name: 24L012563
Stable NTVE line

value: immortalised cell line

value: NTVE Gag:PABP(ZF:Hibit):P2A:dVSVG:FLAG; CAG-TetON3g (ISBM-083)


title: Esophagus2

description:
Library name: Esophagus2
Column name in gene_count.xls: Esophagus2


title: S14, WT_lac_F, rep 2


title: S13, WT_lac_F, rep 1


title: NTVE lysate-2_ISBM-083_noDOX_spike-in

description:
Library name: 24L012561
Stable NTVE line, no induction of export system

value: 1pg mGL mRNA


title: Eggs4

description:
Library name: Eggs4
Column name in gene_count.xls: Eggs4

source_name: Unfertilized eggs

value: Unfertilized eggs


title: Esophagus1

description:
Library name: Esophagus1
Column name in gene_count.xls: Esophagus1


title: S11, AD_V_M_rep 2

value: AD model

value: Vehicle


title: NTVE lysate-1_ISBM-083_noDOX_spike-in

description:
Library name: 24L012560
Stable NTVE line, no induction of export system

value: Cell Lysate


title: Eggs3

description:
Library name: Eggs3
Column name in gene_count.xls: Eggs3


title: Healthy control (HC) skin 1

description:
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
HC1_(HTA-2_0).sst-rma-combined-dabg.chp Signal


title: S12, AD_V_M_rep 3


title: Eggs2

description:
Library name: Eggs2
Column name in gene_count.xls: Eggs2


title: NTVE lysate-3_ISBM-083_noDOX_spike-in

description:
Library name: 24L012562
Stable NTVE line, no induction of export system


title: Supernatant Gag-2_ISBM-038_spike-in

description:
Library name: 24L011712
Stable exporter line without poly-A binding protein in the export system

value: Gag (ZF); Pgk-TetON3g  (ISBM-038)

value: Supernatant

value: doxycycline 500ng/ul


title: circulating donor T cells in vitro stimulated w/ host DC at 2yrs post-BMT2

city: Pittsburgh

first: Xiaohua

last: Chen

state: PA

address: 4401 Penn Ave

institute: UPMC CHP BMTCT

description: Library name: BBMT1_2YT_PllusDC2

data_processing:
CLC Genomic workbench software v25 was used for reading, mapping and gen expression profiling, following the protocol provided by company
Assembly: hg38 human genome, ENSEMBLv91 anotation
Supplementary files format and content: tab deliminated text files with both raw counts and normalized counts

source_name: Peripheral blood

growth_protocol: T cells grew in RPMI1640+10%HS for 7 days at 37C+5%CO2.

extract_protocol:
QIAGENÒ RNeasyÒ plus micro kit protocol
RNA libraries for RNAseq were prepared using Truseq stranded total RNA protocol for T cells and Illumina stranded total RNAseq protocol

treatment_protocol: T cells were either stimulated with or withour host Dendritic cells.

value: Peripheral blood

value: PB T cells

value: WT

value: stimulated w/ hDC

tag: batch

value: batch 1


title: S09, AD_V_F_rep 3

value: brain


title: Supernatant Gag-1_ISBM-038_spike-in

description:
Library name: 24L011711
Stable exporter line without poly-A binding protein in the export system


title: circulating donor T cells in vitro stimulated w/ host DC at 2yrs post-BMT1

description: Library name: BBMT1_2YT_PlusDC1


title: circulating donor T cells in host at clinical tolerance stage of 2yrs post-BMT3

description: Library name: BBMT1_2YT3


title: NTVE -3_ISBM-083_spike-in

description:
Library name: 24L011710
Stable NTVE line


title: CoelomicFluid

description:
Library name: CoelomicFluid
Column name in gene_count.xls: CoelomFluid

source_name: Coelomic Fluid

value: Coelomic Fluid

value: wild type


title: MyceliumDMM1_rep1

city: Thiverval-Grignon

first: Isabelle

last: Fudal

address: avenue Lucien Bretignieres

institute: INRA

hyb_protocol: Hybridization by PartnerChip Company

scan_protocol: Scanning by PartnerChip Company

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Plenodomus lingam

source_name: DMM1 silenced_mycelium

label_protocol: Labelling by PartnerChip Company

growth_protocol: Mycelium was grown during one week in Fries liquid medium.

extract_protocol: RNA extraction was carried out using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was treated with DNase I RNase-Free (New England Biolabs).

tag: strain/isolate background

tag: genotype/variation

value: silenced for DMM1

value: mycelium grown in in vitro liquid Fries medium

tag: culture duration

value: 7 days of growth


title: S07, AD_V_F_rep 1

tag: genotype

value: AD model


title: Supernatant Gag-3_ISBM-038_spike-in

description:
Library name: 24L011713
Stable exporter line without poly-A binding protein in the export system

value: immortalised cell line

value: 1pg mGL mRNA


title: Lichen planus treated with control isotype

description:
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
LP-Iso_(HTA-2_0).sst-rma-combined-dabg.chp Signal

value: Lichen planus

value: Control isotype IgG1 kappa 10 mg/ml 72h

value: skin


title: AxialGland4

description:
Library name: AxialGland4
Column name in gene_count.xls: AxialGland4

source_name: Axial Gland

value: Axial Gland


title: Lichen planus treated with anti-IFNAR1 antibody

description:
RMA expression value derived from Affymetrix Transcriptome Analysis Console  software v.4
LP-Ani_(HTA-2_0).sst-rma-combined-dabg.chp Signal

value: Anifrolumab 10 mg/ml 72h


title: S08, AD_V_F_rep 2

value: Vehicle


title: NTVE -2_ISBM-083_spike-in

description:
Library name: 24L011709
Stable NTVE line

value: NTVE Gag:PABP(ZF:Hibit):P2A:dVSVG:FLAG; CAG-TetON3g (ISBM-083)

value: Supernatant

value: doxycycline 500ng/ul


title: circulating donor T cells in host at clinical tolerance stage of 2yrs post-BMT2

description: Library name: BBMT1_2YT2

value: Peripheral blood

value: PB T cells

value: WT

value: batch 1


title: AxialGland3

description:
Library name: AxialGland3
Column name in gene_count.xls: AxialGland3

value: wild type


title: NTVE -1_ISBM-083_spike-in

description:
Library name: 24L011708
Stable NTVE line


title: MyceliumDMM1_rep2

value: silenced for DMM1

value: mycelium grown in in vitro liquid Fries medium

value: 7 days of growth


title: circulating donor T cells in host at clinical tolerance stage of 2yrs post-BMT1

description: Library name: BBMT1_2YT1


title: MyceliumDMM1_rep3


title: S10, AD_V_M_rep 1

value: brain

value: AD model


title: S05, AD_lac_M, rep 2

value: lactate


title: AxialGland2

description:
Library name: AxialGland2
Column name in gene_count.xls: AxialGland2

value: Axial Gland


title: Eggs1

description:
Library name: Eggs1
Column name in gene_count.xls: Eggs1

value: Unfertilized eggs


title: NTVE -2_ISBM-064_spike-in

description:
Library name: 24L006498
Stable NTVE line,  same SN sample as 24L006480

value: immortalised cell line

value: NTVE Gag:PABP(ZF:Hibit); Pgk-TetON3g (ISBM-064)

value: 1pg mGL mRNA


title: graft T cells stimulated w/ host DC3

description: Library name: BBMT1_gT_PlusDC3

source_name: Bone marrow

value: Bone marrow

value: BM T cells

value: stimulated w/ hDC


title: AxialGland1

description:
Library name: AxialGland1
Column name in gene_count.xls: AxialGland1


title: graft T cells stimulated w/ host DC2

description: Library name: BBMT1_gT_PlusDC2

value: WT


title: NTVE -1_ISBM-064_spike-in

description:
Library name: 24L006497
Stable NTVE line,  same SN sample as 24L006479

value: Supernatant

value: doxycycline 500ng/ul


title: S04, AD_lac_M, rep 1


title: S03, AD_lac_F, rep 3


title: dusA KO, rep3

city: Winnipeg

first: Sarah

last: Schultz

state: Manitoba

address: 144 Dysart Rd

department: Chemistry

country: Canada

institute: University of Manitoba

description: Library name: dusA KO 3

data_processing:
Bioinformatics was performed by MesoRNA (Chicago, IL, USA). Reads were demultiplexed and trimmed as appropriate in accordance with the MSR-seq library preparation protocol (PMID: 35513407). Quality control was performed with FastQC (https://www.bioinformatics.babraham.ac.uk/index.html). Reads were aligned to tRNA sequences adapted from GtRNAdb (https://gtrnadb.org/) with bowtie2 (PMID: 22388286). Further analysis and plots were generated with custom software developed by MesoRNA.
Assembly: Genome assembly ASM75055v1
Supplementary files format and content: tab delimited text files of abundance counts for each sample

organism: Escherichia coli BW25113

growth_protocol: E. coli cultures were grown from single colonies overnight in LB media containing 50 µg/mL kanamycin (ΔdusA strain) or lacking antibiotic (wildtype). Saturated cultures were centrifuged, resuspended in fresh LB media and cultures were prepared in LB media  at an OD600 of ~0.1. Cultures were grown at 37°C until reaching an OD600 between 0.3 and 0.4, when 15 mL of each culture was harvested by centrifugation, shock frozen, and stored at -80°C until RNA extraction.

extract_protocol:
total RNA was extracted in acidic conditions using TRIzol as per manufacturers instructions
Library was constructed by MesoRNA (Chicago, IL, USA) similar as in PMID: 35513407

treatment_protocol: no treatment - LB 37C

tag: strain

value: dusA KO


title: S06, AD_lac_M, rep 3


title: NTVE IFN-gamma-3_ISBM-064

description:
Library name: 24L006490
Stable NTVE line, 50 ng/ml IFN-gamma

value: 50 ng/ml interferone gamma + doxycycline 500ng/ul


title: graft T cells stimulated w/ host DC1

description: Library name: BBMT1_gT_PlusDC1

value: batch 1


title: dusA KO, rep2

description: Library name: dusA KO 2


title: dusA KO, rep1

description: Library name: dusA KO 1


title: graft T cells pre-BMT3

description: Library name: BBMT1_gT3


title: NTVE IFN-gamma-2_ISBM-064

description:
Library name: 24L006489
Stable NTVE line, 50 ng/ml IFN-gamma


title: S02, AD_lac_F, rep 2

value: brain


title: graft T cells pre-BMT1

description: Library name: BBMT1_gT1


title: S01, AD_lac_F, rep 1

value: AD model


title: BW25113 wildtype, rep2

description: Library name: WT 2


title: Pooled heads from 13 ints1-deficent zebrafish larvae - sample3

city: Tel Aviv

first: Shir

last: Confino

address: Chaim Levanon St 55, Tel Aviv-Yafo

department: Neurobiology, Biochemistry and Biophysics

country: Israel

institute: Tel Aviv University

description: Library name: KO3

data_processing:
Mapping. The following reference genomes and annotations were used for alignment: zebrafish genome GRCz11 (GenBank:GCA_000002035.4) and Ensembl annotations release. RNA-Seq reads were aligned to the relevant reference genome using STAR with default parameters. Expression. Annotation files were supplemented to include a single precursor mRNA for each gene. Precursors span the entire gene locus, from the earliest annotated isoform start point to the last annotated isoform end point. Isoform specific FPKM values were calculated using Cufflinks. Mature mRNA expression was calculated by summing the FPKM values of all mature mRNA isoforms.
Assembly: GRCz11
Supplementary files format and content: FPKM

organism: Danio rerio

source_name: Head

extract_protocol:
Total RNA was extracted from samples using the RNeasy Mini Kit, Qiagen (Qiagen, Catalog No.NC9677589), following the manufacturer’s instructions and including an on-column DNase treatment.  An additional ethanol precipitation was performed for extra purification. All samples had an RNA integrity number (RIN) score ranging from 9.3 to 9.5.
Libraries were prepared using the TruSeq Stranded mRNA protocol. A 9 bp of Unique Molecular Identifiers (UMIs) tags were add added before PCR amplification to reduce errors and quantitative bias introduced by the amplification. All samples passed quality control (QC) and pre-processing, and were used for further analyses

value: Head

value: CRISPR mutants

value: KO


title: graft T cells pre-BMT2

description: Library name: BBMT1_gT2


title: NTVE -6_ISBM-064

description:
Library name: 24L006484
Stable NTVE line

value: immortalised cell line


title: NTVE IFN-gamma-1_ISBM-064

description:
Library name: 24L006488
Stable NTVE line, 50 ng/ml IFN-gamma

value: NTVE Gag:PABP(ZF:Hibit); Pgk-TetON3g (ISBM-064)


title: Pooled heads from 13 ints1-deficent zebrafish larvae - sample4

description: Library name: KO4


title: NTVE -4_ISBM-064

description:
Library name: 24L006482
Stable NTVE line


title: WT-iMacs-3

city: Guangzhou

first: Baoqiang

last: Kang

address: Kaiyuan Avenue 190

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: Library name: Sample15

data_processing:
Illumina Casava1.7 software used for basecalling.
Briefly, reads were aligned to human genome (UCSC hg38) using HISAT2 (v2.0.4)
and gene expression was counted using samtools (v1.3.1) and htseq-count (v 0.6.0), filtered by a threshold of at least 20 averaged raw read counts among samples, and then normalized by GC-count and Gene-length using EDASeq (v2.12.0).
Differential expression and PCA plot were performed using DESeq (v 1.18.1) and genes with p-value < 0.05 and fold-change > 2 were considered as significant difference.
Correlation plot was performed using ggplot2 (v2.2.1) and heatmap was performed using pheatmap (v1.0.10).
Assembly: GRCh38/hg38
Supplementary files format and content: count

source_name: cord blood

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cord blood

value: induced pluripotent stem cell derived macrophage

value: macrophage differentiation


title: WT-iMacs-2

description: Library name: Sample14


title: BW25113 wildtype, rep1

description: Library name: WT 1


title: Pooled heads from 13 ints1-deficent zebrafish larvae - sample1

description: Library name: KO1


title: NTVE -3_ISBM-064

description:
Library name: 24L006481
Stable NTVE line


title: Pooled heads from 13 wild-type zebrafish larvae - sample4

description: Library name: WT4

value: WT sibs

value: CTRL


title: Pooled heads from 13 ints1-deficent zebrafish larvae - sample2

description: Library name: KO2


title: WT-iMacs-1

description: Library name: Sample13

value: WT


title: BW25113 wildtype, rep3

description: Library name: WT 3


title: NTVE -2_ISBM-064

description:
Library name: 24L006480
Stable NTVE line, same SN sample as 24L006498

value: Supernatant

value: doxycycline 500ng/ul


title: GFP-tumor-iMac-3

description: Library name: Sample12

value: GFP knock in

value: macrophage differentiation coculture with tumor


title: sheep hepatocyte,G90_100,scRNA-seq

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

institute: Peking University

description: gestational day 90 to 100

data_processing:
We employed Trimmomatic (v0.39) to remove index, primer, and adapter sequences from the paired-end reads. The resulting trimmed reads were aligned to the Ovis aries reference genome (oviAri3) using Hisat2 (v2.1.0)  with default parameters. Next, featureCounts (v2.0.1) with default parameters assigned the reads to genes. Gene expression values were then calculated as transcripts per 0.1 million (TP0.1M).
Assembly: oviAri3
Supplementary files format and content: Smart-seq3xpress output files: Tab-separated rexpression values matrix files

organism: Ovis aries

source_name: liver

extract_protocol:
Slaughtered sheep livers were cut into small cubes and stored in Belzer UW Cold Storage Solution at 4°C and transported to the laboratory. For isolation of sheep hepatocytes, livers were dissected into 1 mm3 cubes and digested with RPMI 1640 medium containing 2.5 mg/mL collagenase IV (Sigma‒Aldrich, C5138) and 2.5 mg/mL collagenase II at 37°C for 20 minutes. The cell suspension was centrifuged at 50 × g for 3 minutes at 4 °C, and then the cell pellets were resuspended and washed twice with RPMI 1640 medium containing 10% FBS at 4°C.
Smart-seq3xpress scRNA-seq experiments was performed according to the published procedure(Hagemann-Jensen et al., 2022). Briefly, purified single hepatocytes were manually picked with a microcapillary pipette under a microscope and transferred into the 384-well PCR plates containing 0.3 μL of lysis buffer and 3 μL of silicone oil (Merck, 317667). The mRNA was reverse transcribed into cDNA using 0.2 μL of dispensed RT mix. The cDNA was then amplified using 0.6 μL PCR mix. The library of each cell was constructed separately using the TruePrep DNA Library Prep Kit (Vazyme, TD501)

value: liver

value: hepatocyte

value: female

tag: Stage


title: NTVE -1_ISBM-064

description:
Library name: 24L006479
Stable NTVE line, same SN sample as 24L006497


title: Pooled heads from 13 wild-type zebrafish larvae - sample2

description: Library name: WT2

value: Head


title: GFP-tumor-iMac-1

description: Library name: Sample10


title: GFP-tumor-iMac-2

description: Library name: Sample11


title: NTVE -5_ISBM-064

description:
Library name: 24L006483
Stable NTVE line


title: Pooled heads from 13 wild-type zebrafish larvae - sample1

description: Library name: WT1


title: sheep hepatocyte,G50_70,scRNA-seq

description: gestational day 50 to 70


title: NTVE lysate IFN-gamma-2_ISBM-064

description:
Library name: 24L006470
Stable NTVE line, 50 ng/ml IFN-gamma

value: Cell Lysate

value: 50 ng/ml interferone gamma + doxycycline 500ng/ul


title: NTVE lysate IFN-gamma-3_ISBM-064

description:
Library name: 24L006471
Stable NTVE line, 50 ng/ml IFN-gamma

value: immortalised cell line

value: NTVE Gag:PABP(ZF:Hibit); Pgk-TetON3g (ISBM-064)


title: cct1-2 DNase-Seq

first: Zlata

last: Gvozdenov

address: 240 Longwood Ave

institute: Harvard Medical School

data_processing:
Quality control: fastQC (0.10.1)
Aligning the reads to the reference genome: bowtie (1.0.0), command: -m 1 -v 2 --sam ~/indexes/SacCer3. Only uniquely mapped reads were retained for further analyses.
DNase peak detection: Hotspot (v4)
Footprint detector/Footprint finder (Chen and Noble, 2008)
Assembly: sacCer3
Supplementary files format and content: DNaseI hypersensitive sites (DHSs) and footprints: tab separated chromosome, star coordinate, end coordinate, and hypersenssitivity score for DHSs.
Library strategy: DNase-Seq

source_name: JFY148 (cct1-2 ts mutant)

extract_protocol:
DNA was isolated, resolved on a 1% agarose gel, the DNAs in the size range of 100-650 bp were excised. Gel-excised DNA was purified using a QIAprep Spin Miniprep columns (Qiagen).
The libraries were prepared with Illumina's 'TruSeq DNAseq Sample Prep kit' with one modification: adaptors were diluted 1:20. The libraries were quantitated by qPCR, and sequenced on two lanes for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and processed with Casava 1.8.2. The samples were sequenced on Illumina HiSeq2000.

treatment_protocol: Nuclei were treated with DNaseI at room temperature.

value: JFY148 (cct1-2 ts mutant)

value: 4 h at 37C


title: sheep hepatocyte,P7L,scRNA-seq

description: postpartum day 7 with lactation


title: sheep hepatocyte,G40_50,scRNA-seq

description: gestational day 40 to 50


title: GFP-iMac-3

description: Library name: Sample9

value: cord blood

value: induced pluripotent stem cell derived macrophage

value: macrophage differentiation


title: GFP-iMac-2

description: Library name: Sample8


title: WT DNase-Seq

source_name: JFY143 (CCT WT W303, matA)

value: JFY143 (CCT WT W303, matA)


title: sheep hepatocyte,G140_150,scRNA-seq

description: gestational day 140 to 150


title: sheep hepatocyte,P15L,scRNA-seq

description: postpartum day 15 with lactation


title: cct1-2 RNA-Seq, HiSeq 2000

description: Rep 1 (final processed files are derived from WT and cct1-2 data)

data_processing:
RNA-Seq reads were trimmed using trimmomatic (Bolger et al., 2014) with TRAILING:20 MINLEN:40.
Reads were aligned to the reference genome sacCer3 (UCSC, April 2011) using STAR (Dobin 2013).
Differential expressed genes were computed using GFold (V1.1.0) (Feng et al. 2012); files with extensions *.read_cnt and *.diff. correspond to differential gene expression analysis.
Metagene profiles were generated using Galaxy deepTools (http://deeptools.ie-freiburg.mpg.de/).
Cryptic transcription regions were identified with Interval_identifier.py. cct12_over_cct_rep12.bed indicates regions with differential transcription upon CCT inactivation. cct_over_cct12_rep12.bed is a vise versa run (transcripts that got lost upon CCT inactivation). Only regions that intersect between HiSeq2000 and HiSeq4000 runs (i.e., are detectable in both replicates) were considered.
The aligned reads were visually displayed with IGV (2.3.25 and 2.3.94).
Assembly: sacCer3
Supplementary files format and content: Interval_identifier.py-generated tab-separated files contain information about the chromosome, coordinate start, coordinate end, transcript fold change (WT wrt. cct1-2 or vice versa), directionality.

growth_protocol: WT and cct1-2 strains were grown in YPD to log phase at 30°C and shifted to 37°C for 4 h. VDY1874 H2A.Z-FRB::KAN was grown in YPD at 30°C.

extract_protocol:
Total RNA was extracted with RiboPure Yeast kit (Ambion).
The RNA-Seq libraries were prepared with Illumina’s TruSeq Stranded mRNA Sample Prep kit.

treatment_protocol: VDY1874 with H2A.Z-FRB::KAN: cells were divided into two flasks – rapamycin was added at 1 µg/ml final concentration to first half (treated sample) and the same amount of ethanol without rapamycin was added to the second half of the culture (control).


title: sheep hepatocyte,G100_120,scRNA-seq

description: gestational day 100 to 120


title: GFP-iMac-1

description: Library name: Sample7


title: NTVE lysate-5_ISBM-064

description:
Library name: 24L006464
Stable NTVE line

value: doxycycline 500ng/ul


title: CAR-tumor-iMac-3

description: Library name: Sample6

value: CAR knock in


title: Pooled heads from 13 wild-type zebrafish larvae - sample3

description: Library name: WT3

value: WT sibs

value: CTRL


title: WT RNA-Seq, HiSeq 2000


title: sheep hepatocyte,G70_80,scRNA-seq

description: gestational day 70 to 80

value: liver

value: hepatocyte


title: NTVE lysate-4_ISBM-064

description:
Library name: 24L006463
Stable NTVE line


title: sheep hepatocyte,G0,scRNA-seq

description: Virgin

value: female


title: NTVE lysate IFN-gamma-1_ISBM-064

description:
Library name: 24L006469
Stable NTVE line, 50 ng/ml IFN-gamma

value: Cell Lysate


title: CAR-tumor-iMac-2

description: Library name: Sample5

value: macrophage differentiation coculture with tumor


title: CAR-tumor-iMac-1

description: Library name: Sample4


title: Control plants 3

city: Cambridge

first: Ignacy

last: Bonter

address: Downing site

institute: University of cambridge

data_processing:
Galaxy
Assembly: Tak 6.1
Supplementary files format and content: Count tables in .tabular files

organism: Marchantia polymorpha

source_name: thallus

growth_protocol: 21 celcius on either half gamborg plates or half gamborg + 2.5uM Sodium Arsenite

extract_protocol:
RNA easy plant kit from Qiagen
Novogene

value: thallus

value: Half B5