title: 3998720079_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720079_H

tag: title

tag: diagnosis

value: Active TB

value: PTB

value: Lung

value: TRUE

tag: age

tag: weight (kg)

tag: hiv positive

value: FALSE

value: Culture, PCR

tag: tst

tag: qtf-git

value: INDETERMINATE


title: NKT17_lung_E

status: Public on Jan 26 2021

type: SRA

city: San Diego

first: Mitchell

last: Kronenberg

state: CA

address: 9420 Athena Circle

country: USA

institute: La Jolla Institute for Immunology

description:
063_63_17E_NKT_120417_200_IsEn12_G8
all_counts.tsv

library_source: transcriptomic

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr).
Filtered reads were mapped against the mouse mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand).
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4).
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all_counts.tsv: Count matrix with rows as genes and columns as samples.

molecule: polyA RNA

organism: Mus musculus

source_name: individual lung

growth_protocol: Cells were enriched and sorted ex vivo from the indicated mouse tissues into 0.2% Triton-x-100 without cell culture.

extract_protocol:
Cells representing specific iNKT subsets were sorted directly into 0.2 ml PCR tubes containing 8 µL of low-input lysis buffer (0.2% Triton-X-100 and RNase inhibitor) and stored at -80oC until processed further. RNA extraction, reverse transcription, cDNA amplification, fragmentation, and additional PCR amplification were performed as previously described (Rosales et al. Methods Mol Biol 1799, p275).
We followed the Smart-Seq2 protocol as described previously (Picelli et al., 2013; Rosales et al., 2018). Libraries were then pooled at equal molar concentration and sequenced using the HiSeq 2500 and NovaSeq6000 Illumina platform (Illumina).
Samples from the experiment comparing splenic NKTFH and NKTeff cells from aGalCer-challenged mice with unchallenged splenic iNKT cells were sequenced via a paired-end read method using the Novaseq6000 sequencer according to supplied protocols (Illumina). Sequencing for all other samples was performed according to a single-end strategy using the HiSeq2500 sequencer (Illumina).

treatment_protocol: Cells were isolated from either pools of tissues from 15-20 6-week-old female C57Bl/6J mice, or from individual 6-7 week-old female C57Bl/6J mice. Mice were euthanized and perfused with 3-10ml liver perfusion media (Gibco) when liver or lung was harvested. Thymus, spleen and liver cell suspensions were prepared by physical disaggregation, and sedimentation at 400xg. Liver mononuclear cells were isolated by pelleting through centrifugation at 750g for 12’ in 34% Percoll/PBS. Spleen and liver suspensions were treated with RBC lysis buffer (Sigma). Lungs were homogenized in GentleMacs C tubes (Miltenyi Biotec) with 2 mL Spleen Dissociation Medium (STEMCELL Technologies) using the Miltenyi GentleMacs dissociator. Cell suspensions for all tissues except liver were enriched for iNKT cells by negative selection using biotinylated antibodies against CD8b.2 (53–5.8, BD Biosciences), CD19 (1D3, Tonbo Biosciences), CD24 (M1/69, BD Biosciences), CD62L (MEL-14, Invitrogen), CD11b (M1/70, Tonbo Biosciences), CD11c (N418, Tonbo Biosciences), F4/80 (BM5.1, Tonbo Biosciences), EpCam(G8.8, Invitrogen), and TER-119 (TER-119, Tonbo Biosciences) together with Rapidspheres (StemCell technologies) and either the Big Easy or Easy eight magnets (StemCell technologies) using protocols from the manufacturer. The cells were then suspended at up to 100 million cells/mL and incubated with 1 mg/mL of Streptavidin A (Sigma-Aldrich). Cells were stained with tetramers of CD1d loaded with αGalCer (BV421, in house preparation), live/dead yellow (ThermoFisher Scientific), anti-TCRb-APC-eF780 (H57-597, ThermoFisher Scientific), anti-CD8a-PE CF594 (53-6.7, BD Biosciences) and anti-CD19-PE CF594 (1D3, BD Biosciences), anti-CD4-AF700 (GK1.5, BioLegend), together with one of the following antibody panels, as indicated in column H. Panel A: anti-IL-17RB-AF488 (FAB10402G, R&D Systems), anti-ICOS-PerCP Cy5.5 (C398.4A, BioLegend), anti-CD122-BV650 (5H4, BD Biosciences), anti-CXCR3-APC (CXCR3-173, BioLegend), anti-SDC1-PE (281-2, BioLegend), and anti-FR4-PE Cy7 (ebio12A5, ThermoFisher Scientific). Panel B: anti-CXCR5-PE (L138D7, BioLegend), and anti-PD-1-APC, clone RMP1-30, BioLegend. Panel C: anti-TCRgd-FITC (GL3, BD Biosciences), and anti NK1.1 (PK136, BD Biosciences). Cells were sorted using a FACSAria III or a FACSAria Fusion. All NKT cells were sorted as lymphocyte-gated single cells, viability dye-low, CD8a-, CD19- , CD1d-tetramer-staining, TCRb+, in addition to the criteria indicated in column H (total NKT cells required no additional sorting criteria). gdT cells, CD4 T cells and NK cells were sorted as lymphocyte-gated single cells, viability dye-low, CD8a-, CD19- , and CD1d-tetramer-non-staining, in addition to the additional criteria indicated in column H.

tag: strain

tag: Sex

value: Female

tag: cell type

tag: stimulation

tag: sorting scheme / criteria

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: 3998703013_L

type: RNA

city: London

first: Long

last: Hoang

address: Dovehouse Street

department: Genomic Medicine

country: United Kingdom

institute: Imperial College London

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703013_L

hyb_protocol: For each sample, seven hundred and fifty nanograms of labelled cRNA were hybridised overnight to Illumina Human HT12 V4 BeadChip arrays (Illumina), which contained greater than 47,000 probes. The arrays were washed, blocked, stained and scanned on an Illumina iScan, as per the manufacturer’s instructions.

scan_protocol: The arrays were scanned on an Illumina iScan, as per the manufacturer’s instructions.

data_processing: GenomeStudio (Illumina) was used to perform quality control and generate signal intensity values.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol: RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion), as per the manufacturer’s instructions. 250 g of isolated total RNA was globin-reduced using the GLOBINclear 96-well format kit (Applied Biosystems/Ambion) according to the manufacturer’s instructions. Total and globin-reduced RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA yield was assessed using a NanoDrop8000 spectrophotometer (NanoDrop Products, Thermo Fisher Scientific). High-quality (>6.5 RIN) whole blood RNA was successfully obtained and processed by microarray in all cases. Biotinylated, amplified antisense complementary RNA (cRNA) targets were prepared from 200-250 ng of globin-reduced RNA using the Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion).

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

tag: site of infection

value: Lung, Lymph node

tag: smear microscopy

tag: culture result

value: Positive

tag: gender

value: Male

tag: height (cm)

tag: bmi

value: Indian

value: Culture

tag: pcr

tag: pcr result

value: Negative

value: POSITIVE


title: 200681360009_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360009_B

label_protocol: Biotinylated, amplified antisense complementary RNA (cRNA) targets were prepared from 200-250 ng of globin-reduced RNA using the Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion).

tag: title

tag: diagnosis

value: EPTB

value: Miliary TB (disseminated)

tag: age

tag: weight (kg)

tag: hiv positive

tag: tst

tag: qtf-git


title: 3998720110_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720110_F

tag: sampledate at t0

tag: dosanjh

value: Active TB

value: Lung, Miliary TB (disseminated)

value: MiddleEast


title: 3998734086_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734086_E

tag: eptborptb

tag: site of infection

value: Lymph node

value: TRUE

value: FALSE

tag: tst result

value: NEGATIVE


title: 3998734102_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734102_E

value: Abdomen, Bones, Spine

tag: smear microscopy

tag: culture result

tag: gender

value: Black


title: 200681360011_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
200681360011_J

value: Lung, Lymph node

value: Positive

tag: height (cm)

tag: bmi

tag: pcr


title: 3998675108_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675108_K

tag: title

tag: diagnosis

value: Lung, Lymph node, Pleura

value: Male

value: Indian


title: 3998703010_G

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703010_G

value: Bones, Kidneys

tag: age

value: Female

tag: weight (kg)

value: Culture


title: NKT17_lung_D

description:
055_55_17D_NKT_110917_200_IsEn12_G7
all_counts.tsv

tag: strain

tag: Sex

tag: cell type

tag: stimulation

tag: sorting scheme / criteria

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: SIX3 knockdown_D3

city: Stanford

first: Romina

middle: J

last: Bevacqua

address: 279 Campus Drive W

department: Developmental Biology

institute: Stanford University

description:
RB04
six3_TPM_3D_ordered.csv

data_processing:
Barcodes were trimmed using Trimgalore_0.5.0.
Reads were aligned to the human genome index (hg19) using STAR v2.6.1d (Dobin et al. 2013).
Transcripts per million (TPM) were quantified using RSEM v1.3.0 (Li and Dewey 2011).
Differentially expressed genes with fold change were detected using the DESeq2 R package (Love et al. 2014).
Genome_build: hg19 (GRCh37) transcriptome
Supplementary_files_format_and_content: *_csv: Comma-separated text files include TPM values.

source_name: primary islet cells

growth_protocol: Primary human islets were disersed/ transduced with lentiviruses and cultured for 5 days.

extract_protocol:
SMART-seq v4 Ultra Low input RNA kit (Clontech).
Low Input library preparation kit v2 (Clontech).
Paired-end 150-bp reads on the Illumina HiSeq4000 platform.

treatment_protocol: Lentiviral shRNAs against SIX2 or SIX3 versus non-target shRNA control.

value: Primary islet cells

tag: developmental stage

value: Adult

tag: genotype/variation

value: SIX3 knockdown


title: SIX3 knockdown_D2

description:
RB02
six3_TPM_3D_ordered.csv


title: NKT1_lung_F

description:
064_64_1F_NKT_120417_200_IsEn12_H8
all_counts.tsv

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-


title: SIX3 knockdown_D1

description:
s3665
six3_TPM_3D_ordered.csv


title: NKT1_lung_E

description:
062_62_1E_NKT_120417_200_IsEn12_F8
all_counts.tsv


title: SIX3 knockdown-Control_D2

description:
RB01
six3_TPM_3D_ordered.csv

value: Control


title: NKT1_lung_D

description:
054_54_1D_NKT_110917_200_IsEn12_F7
all_counts.tsv


title: SIX3 knockdown-Control_D1

description:
scr665
six3_TPM_3D_ordered.csv


title: NKT17_lung_C

description:
053_53_17C_NKT_110917_200_IsEn12_E7
all_counts.tsv


title: NKT1_lung_C

description:
052_52_1C_NKT_110917_200_IsEn12_D7
all_counts.tsv


title: SIX2 knockdown_D4

description:
rhHIP.133_SIX2.alleles.results
six2_TPM_4D_table.csv

value: SIX2 knockdown


title: 3998703010_D

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703010_D

tag: sampledate at t0

tag: dosanjh

value: Active TB

tag: eptborptb

value: EPTB

tag: site of infection

value: Intestine, Lymph node, Peritoneum

tag: smear microscopy

value: TRUE

tag: hiv positive

value: FALSE

tag: tst

tag: tst result

tag: pcr result

tag: qtf-git

value: POSITIVE


title: 3998734082_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734082_F

tag: title

tag: diagnosis

value: Lung, Lymph node

tag: culture result

value: Positive

tag: age

tag: gender

value: Male

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Indian

tag: pcr

value: Negative


title: NKT1_lung_B

description:
050_50_1B_NKT_110917_200_IsEn12_B7
all_counts.tsv

tag: strain

tag: Sex

value: Female

tag: cell type

tag: stimulation

tag: sorting scheme / criteria


title: NKT17_lung_B

description:
051_51_17B_NKT_110917_200_IsEn12_C7
all_counts.tsv

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: SIX2 knockdown-Control_D4

description:
rhHIP.133_SCR.alleles.results
six2_TPM_4D_table.csv

value: Primary islet cells

tag: developmental stage

value: Adult

tag: genotype/variation


title: 3998734084_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734084_A

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

tag: site of infection

value: Lymph node

tag: smear microscopy

tag: hiv positive

value: Culture

tag: tst

tag: tst result

tag: pcr result

tag: qtf-git


title: 3998734089_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734089_H

tag: title

tag: diagnosis

value: Active TB

value: PTB

value: Lung

tag: culture result

tag: age

tag: gender

tag: height (cm)

tag: weight (kg)

tag: bmi

value: Asian

tag: pcr


title: 3998675115_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675115_I

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

value: EPTB

value: FALSE

value: TRUE


title: 3998734082_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734082_C

tag: site of infection

tag: smear microscopy

value: Positive

tag: hiv positive

value: INDETERMINATE

value: POSITIVE


title: 3998734082_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734082_B

value: Male

value: Indian

tag: tst


title: 3998734089_E

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998734089_E

value: White

tag: qtf-git


title: 3998675110_A

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675110_A

tag: title

tag: tst result

tag: pcr result

value: Negative


title: 3998675098_F

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675098_F

tag: diagnosis

tag: culture result

tag: age

value: Female


title: NKT17_lung_A

description:
049_49_17A_NKT_110917_200_IsEn12_A7
all_counts.tsv

tag: strain

tag: Sex

tag: cell type

tag: stimulation

tag: sorting scheme / criteria

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: NKT1_lung_A

description:
048_48_1A_NKT_110917_200_IsEn12_H6
all_counts.tsv

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-


title: SIX2 knockdown-Control_D3

description:
R326_SCR.alleles.results
six2_TPM_4D_table.csv

value: Primary islet cells

tag: developmental stage

value: Adult

tag: genotype/variation

value: Control


title: SIX2 knockdown_D2

description:
R318_S2.alleles.results
six2_TPM_4D_table.csv

value: SIX2 knockdown


title: SIX2 knockdown_D3

description:
R326_SIX2.alleles.results
six2_TPM_4D_table.csv


title: Inf mom adults only D7 CD45 pos

city: Salt Lake City

first: Keke

middle: Celeste

last: Fairfax

state: UT

address: 15 N Medical Drive East

department: Pathology

institute: University of Utah

data_processing:
Sequencing reads were processed by using 10× Genomics CellRanger pipeline and further analyzed with the Seurat R package. The effect of mitochondrial generepresentation and the variance of unique molecular identifier (UMI) counts were regressed out from the data set prior to analysis. Gene expression signatures defining cell clusters were analyzed after aggregating 3 samples (uninfected mother, infected mother, single-sex infected mother).
Genome_build: mm10
Supplementary_files_format_and_content: filtered feature, barcode,matrix files from cell ranger for importation into R

source_name: popliteal lymph node

extract_protocol: Live CD45+ cells were sorted via BD FACSAria cell sorter and washed once in PBS containing 0.04% BSA. Samples were then processed for SCseq via a 10X platform (single cell 3'V2) according to the manufacturer's instructions (10X Genomics).

tag: strain background

value: Balb/c

tag: genotype

tag: immunization

value: D7 post tetanus/diphtheria immunization

tag: tissue

value: popliteal lymph node


title: Inf mom D7 CD45pos


title: NK_spleen_rep4

description:
034_IsEn15_NK_S_H_B6
all_counts.tsv

source_name: individual spleen

value: NK

value: C / NK1.1+ TCRb- gdTCR-


title: Uninf mom D7 CD45 pos


title: SIX2 knockdown-Control_D2

description:
R318_SCR.alleles.results
six2_TPM_4D_table.csv


title: SIX2 knockdown_D1

description:
Pitsb_SIX2.alleles.results
six2_TPM_4D_table.csv


title: 3998675115_H

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675115_H

tag: title

tag: sampledate at t0

tag: dosanjh

value: Active TB

tag: eptborptb

value: PTB

tag: site of infection

value: Lung

tag: smear microscopy

value: TRUE

value: Positive

tag: gender

tag: weight (kg)

value: Black

tag: hiv positive

value: FALSE

value: Culture

tag: tst

tag: pcr

tag: qtf-git

value: POSITIVE


title: 3998675110_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675110_L

tag: diagnosis

value: EPTB

value: Lymph node

tag: culture result

tag: age

value: Male

tag: height (cm)

tag: bmi

value: White

tag: pcr result

value: Negative


title: 3998703010_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998703010_I

tag: title

tag: sampledate at t0

value: Lung, Pleura


title: 3998720112_B

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998720112_B

tag: dosanjh

tag: eptborptb

value: Female

value: Indian

tag: tst result


title: SIX2 knockdown-Control_D1

description:
Pitsb_SCR.alleles.results
six2_TPM_4D_table.csv

tag: cell type

value: Primary islet cells

tag: developmental stage

value: Adult

tag: genotype/variation

value: Control


title: RAW_shGPS2_LPS_60min_rp1

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

country: China

institute: Nanjing University

data_processing:
Library strategy: GRO-Seq
GRO-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using bwa with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.

growth_protocol: Lentivirus-mediated GPS2 knockdown RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
shGFP and shGPS2  RAW cells were treated with 100 ng/ml LPS (0, 1 hour) and cell nuclei were extracted. The nuclear run-on reaction was performed for 7 minutes and RNA hydrolysis was allowed to proceed for 10 minutes. All GRO-seq library preparations were performed in parallel to avoid batch effects.
GRO-Seq library preparation was processed by the protocol from Minna U Kaikkonen lab (PMID: 23932714).

treatment_protocol: RAW264.7 cells were treated  with or without LPS treatment (0, 1hour)

tag: cell line

value: RAW264.7 cells

value: Macrophage

tag: strain

value: BALB/c

tag: genotype

value: GPS2 knockdown

tag: antibody

value: No antibody

tag: treatment

value: LPS 1 hour


title: 3998675095_K

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675095_K

tag: diagnosis

value: Active TB

tag: site of infection

tag: smear microscopy

value: TRUE

tag: culture result

value: Positive

tag: age

tag: gender

tag: weight (kg)

tag: hiv positive

value: FALSE

value: Culture

tag: tst

tag: pcr

tag: qtf-git

value: NEGATIVE

value: POSITIVE


title: 3998675096_I

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675096_I

tag: title

tag: sampledate at t0

tag: dosanjh

tag: eptborptb

value: EPTB

value: Lymph node

value: Male

tag: height (cm)

value: Indian


title: RAW_shGPS2_LPS_60min_rp2

tag: cell line

value: RAW264.7 cells

tag: cell type

tag: strain

tag: genotype

tag: antibody

tag: treatment


title: RAW_shGFP_LPS_60min_rp2

value: Macrophage

value: control


title: RAW_shGPS2_con_rp2

value: BALB/c

value: GPS2 knockdown

value: Ctrl


title: SW480 Time 72 Rep 2

city: Bethesda

first: Markus

middle: Alexander

last: Brown

state: Maryland

address: 50 South Drive, Room 1408

department: Center for Cancer Research

institute: National Institutes of Health

data_processing:
Fastq files were processed using the CCBRPIPELINER/3.0 found on github: https://github.com/CCBR/Pipeliner/blob/master/RNASeqDocumentation.pdf
Reads were aligned using STAR
Trimmomatic was used for adapter clipping
FastQC, FastQ Screen, RSeQC, Picard, Preseq, and Samtools were used to assess sequencing quality
Gene abundance was determined using RSEM
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files provide TPM values for each sample

source_name: SW480 - colorectal cancer

growth_protocol: SW480 cells were grown in RPMI medium supplemented to 10% FBS. Cells were split when they reached 70% confluency in a T75 flask, approximately three times a week.

extract_protocol:
RNA was extracted using the RNeasy kit from Qiagen. The optional DNAse incubation was performed.
Ribosomal RNA (rRNA) was removed using biotinylated, target-specific oliges combined with Ribo-Zero rRNA removal beads according to the Illumina total RNA sequencing protocol. The RNA was fragmented and copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The double-stranded cDNA was used as input to a standard Illumina library prep with end-repair, adapter ligation, and PCR.

treatment_protocol: Three replicates were treated with siRNA targeting TCF7L2 for the indicated amount of time. The siRNA was deliverd using the RNAiMAX lipofectamine reagent.

tag: timepoint

value: 72 hours

value: SW480 - colorectal cancer

value: siRNA TCF7L2


title: RAW_shGPS2_con_rp1

value: No antibody


title: RAW_shGFP_LPS_60min_rp1

value: LPS 1 hour


title: RAW_shGFP_con_rp2


title: 3998675098_L

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675098_L

tag: diagnosis

value: Active TB

tag: site of infection

value: Lung, Lymph node

tag: smear microscopy

value: TRUE

tag: culture result

value: Positive

tag: age

tag: gender

tag: weight (kg)

tag: bmi

value: FALSE

value: Culture

tag: tst result


title: RAW_shGFP_con_rp1

value: RAW264.7 cells


title: Gro_seq_RAW_GPS2_KO_LPS_60m_rp2

data_processing:
Library strategy: GRO-seq
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.
ChIP-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.
GRO-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using bwa with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.
4C-seq raw files (fastq, paired-end) were performed by the standard 4Cseqpipe protocol. The primer sequences were trimmed from the raw reads. The trimmed reads were mapped to the mm9 reference fragmented genome. The contact intensity was normalized by the fragment counts. The cis-interacting DNA contact profiles around the baits were plotted in the same chromosome window.
Genome_build: mm9
Supplementary_files_format_and_content: 4C-seq analysis does not provide processed data file.
RNA-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the tags for each condense gene
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. MACS2 was used for the peak calling. The differential changed peaks was done in R using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.

source_name: RAW264.7 cells

growth_protocol: CRISPR/cas9-mediated GPS2 knockout RAW264.7 cells were maintained normal 10% FBS DMEM medium.

extract_protocol:
WT and GPS2 KO RAW cells were treated with 100 ng/ml LPS (0, 30 min, 1 hour) and cell nuclei were extracted. The nuclear run-on reaction was performed for 7 minutes and RNA hydrolysis was allowed to proceed for 10 minutes. All GRO-seq library preparations were performed in parallel to avoid batch effects.
ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit.

treatment_protocol: RAW264.7 cells were treated  with or without LPS treatment (0,30min, 1hour)

value: Macrophage

tag: agent

value: LPS

tag: time point

value: 60 min


title: SW480 Time 72 Rep 1

tag: cell line


title: NKT_lung_rep3

description:
029_IsEn15_NKT_Lg_H_E5
all_counts.tsv

tag: strain

tag: Sex

value: Female

tag: cell type

value: NKT

tag: stimulation

tag: sorting scheme / criteria

value: C


title: SW480 Time 48 Rep 2

tag: timepoint

value: 48 hours

value: SW480 - colorectal cancer

tag: treatment


title: 3998675093_J

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675093_J

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

tag: eptborptb

value: PTB

tag: site of infection

value: Lung

tag: smear microscopy

value: Male

tag: height (cm)

value: White

tag: hiv positive

tag: tst

tag: pcr

tag: pcr result

tag: qtf-git

value: INDETERMINATE

value: POSITIVE


title: NK_lung_rep4

description:
027_IsEn15_NK_Lg_H_C5
all_counts.tsv

tag: strain

tag: Sex

tag: cell type

value: NK

tag: stimulation

value: C / NK1.1+ TCRb- gdTCR-


title: gdT_lung_rep3

description:
028_IsEn15_gd_Lg_H_D5
all_counts.tsv

tag: sorting scheme / criteria

value: C / gdTCR+ TCRb-


title: gdT_spleen_rep3

description:
033_IsEn15_gd_S_H_A6
all_counts.tsv


title: Gro_seq_RAW_Con_LPS_60m_rp1

value: Macrophage

value: BALB/c

tag: agent

tag: time point


title: NKT_spleen_rep3

description:
025_IsEn15_NKT_S_G_A5
all_counts.tsv


title: SW480 Time 24 Rep 2

tag: timepoint

value: 24 hours

tag: cell line

tag: treatment

value: siRNA TCF7L2


title: 3998675098_C

description:
RNA was isolated using 1.5 ml whole blood and the MagMAX-96 Blood RNA Isolation Kit (Applied Biosystems/Ambion)
3998675098_C

tag: title

tag: sampledate at t0

tag: dosanjh

tag: diagnosis

value: Active TB

tag: eptborptb

tag: site of infection

tag: smear microscopy

value: FALSE

tag: culture result

value: Positive

tag: age

tag: gender

tag: weight (kg)

tag: bmi

value: Black

value: Culture

value: TRUE

tag: tst result


title: Gro_seq_RAW_Con_rp2

tag: cell type

tag: strain

tag: agent

value: No treatment


title: SW480 Time 24 Rep 1

tag: timepoint

tag: cell line

value: SW480 - colorectal cancer

tag: treatment


title: Gro_seq_RAW_GPS2_KO_rp2


title: Gro_seq_RAW_GPS2_KO_LPS_60m_rp1

value: LPS

tag: time point

value: 60 min


title: NK_spleen_rep3

description:
031_IsEn15_NK_S_H_G5
all_counts.tsv

tag: Sex

value: Female

value: NK

tag: stimulation

tag: sorting scheme / criteria


title: shSMRT_H3K27ac_rp2

library_source: genomic

data_processing:
ChIP-seq raw files (fastq or txt files, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.
ChIP-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.
GRO-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using bwa with default parameters. HOMER were then used for the tag directories construction from SAM files, duplicated reads removal, peak calling, peaks annotation, raw tag counts extraction and Bed file generation. Only peaks with fold enrichment over input tag count and local tag count > 4 and fdr< 0.001 (default -F -L -C -fdr) are kept.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.
4C-seq raw files (fastq, paired-end) were performed by the standard 4Cseqpipe protocol. The primer sequences were trimmed from the raw reads. The trimmed reads were mapped to the mm9 reference fragmented genome. The contact intensity was normalized by the fragment counts. The cis-interacting DNA contact profiles around the baits were plotted in the same chromosome window.
Genome_build: mm9
Supplementary_files_format_and_content: 4C-seq analysis does not provide processed data file.
RNA-seq raw files (fastq, single-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using HISAT2 with default parameters. Read counts were imported by HOMER and analyzed using analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for four replicates per condition.  Differential gene expression was performed with DESeq2 using HOMER’s getDiffExpression.pl using default parameter. Transcripts with an adjusted p-value < 0.05 were considered as differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the tags for each condense gene
ATAC-seq raw files (fastq, paired-end) were aligned to the NCBI37/mm9 version of the mouse reference genome, using Bowtie2 with default parameters. MACS2 was used for the peak calling. The differential changed peaks was done in R using edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files contain the genomic coordinates and p value of each peak.

molecule: genomic DNA

growth_protocol: CRISPR/cas9-mediated enhancer/promoter knockout or lentivius-mediated gene knockdown  RAW264.7 cells were maintained normal 10% FBS DMEM medium

extract_protocol:
Fresh cells were crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 30 min, followed by 1% formaldehyde for 10 min at room temperature. Nuclei were isolated, sonicated and incubated with magnetic bead-antibody complexes.
ChIPed DNA was processed using Takara SMRTer ThruPLEX DNA-seq Kit. Briefly, DNA was end-repaired and ligated to stem-loop adaptors. Then DNA was PCR amplified with Illumina-compatible primers for 7-11 cycles and library fragments of 200 to 400 bp were selected using Ampure XP beads.

treatment_protocol: RAW264.7 cells were treated  with or without LPS treatment (2 hours)

tag: antibody


title: Gro_seq_RAW_GPS2_KO_rp1


title: SW480 Time 0 Rep 2

value: 0 hours

value: siRNA Negative Control


title: CD4T_spleen_rep4

description:
026_IsEn15_CD4_T_S_G_B5
all_counts.tsv

value: C / TCRb+ CD4+


title: shSMRT_H3K27ac_rp1

value: Macrophage

value: BALB/c


title: SW480 Time 0 Rep 1


title: shGPS2_H3K27ac_rp2


title: NKT_lung_rep2

description:
021_IsEn15_NKT_Lg_G_E4
all_counts.tsv

value: NKT

value: C


title: gdT_spleen_rep2

description:
024_IsEn15_gd_S_G_H3
all_counts.tsv

value: C / gdTCR+ TCRb-


title: SW480 Time 48 Rep 1

value: 48 hours

value: siRNA TCF7L2


title: RAW264.7_input

description: ChIP-seq_Sample (input)

value: input


title: Gro_seq_RAW_Con_LPS_60m_rp2


title: NK_spleen_rep2

description:
023_IsEn15_NK_S_G_G3
all_counts.tsv

value: C / NK1.1+ TCRb- gdTCR-


title: CD4T_lung_rep3

description:
022_IsEn15_CD4_T_Lg_G_F4
all_counts.tsv


title: Gro_seq_RAW_Con_rp1

value: No treatment


title: SYC221

city: Chicago

first: Xiao

last: Song

state: IL

address: 303 E Superior St, Lurie 6-250

department: Neurology

institute: Northwestern University Feinberg School of Medicine

data_processing:
Reads were aligned to the human genome GRCh38 using HISAT2 (Version 2.1.0).
Read counts for each gene were quantified using HTSeq-count (Version 0.10.0) and then normalized by DESeq2 (r package, version 1.20.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files include raw counts for each gene of each sample generated from HTSeq-count; csv file includes normalized counts for each gene of all samples for generated from DESeq2.

source_name: lower grade glioma tissues

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini kit or Trizol reagent according to the manufacturer's instruction.
Stranded, rRNA-deleted libraries were prepared using the Illumina stranded Total RNA TruSEQ kit according to the manufacturer's instruction.

tag: idh1 status

value: Mut

tag: tissue type

value: lower grade glioma tissues


title: GPS2_CRISPR_WT_LPS_2_hour

value: LPS

value: 2 hours


title: shGFP_for_smrt_H3K27ac_rp2


title: shGFP_for_gps2_H3K27ac_rp2


title: SYC220


title: NK_lung_rep3

description:
019_IsEn15_NK_Lg_G_C3
all_counts.tsv

value: Female

value: NK


title: shGFP_for_smrt_H3K27ac_rp1


title: shGFP_for_gps2_H3K27ac_rp1


title: NKT_spleen_rep2

description:
016_IsEn15_NKT_S_F_H2
all_counts.tsv


title: H3K27ac_CRISPR_WT_Ctrl


title: SYC218


title: SYC219


title: RAW264.7_WT_H3K27ac


title: gdT_lung_rep2

description:
013_IsEn15_gd_Lg_F_E3
all_counts.tsv


title: shGPS2_H3K27ac_rp1


title: H3K27ac_CRISPR_E1.1_KO_Ctrl


title: NK_spleen_rep1

description:
010_IsEn15_NK_S_E_B3
all_counts.tsv


title: CD4T_spleen_rep3

description:
015_IsEn15_CD4_S_F_G3
all_counts.tsv

value: C / TCRb+ CD4+


title: RAW264.7_LPS_1_hour_H3K27ac

value: Macrophage

value: 1 hours


title: NK_lung_rep2

description:
014_IsEn15_NK_Lg_F_F3
all_counts.tsv


title: 75c_U7_5_LTL

city: Edinburgh

first: Oliver

last: Teenan

state: Midlothian

address: 47 Little France Crescent

department: Cardiovascular Sciences

institute: University of Edinburgh

data_processing:
Quality control was examined by FASTQC
Raw reads ere trimmed using TrimGalore(Ver 0.4.1)/ Cutadapt (version 1.1) to remove primer/adaptor contamination and low quality reads (<20 Phred Score)
Alignment was performed using Bowtie wrapper Shortsack to mouse genome GRCm38 and MiRBase (Ver 22)
CPM was generated using EdgeR software on RStudio.
Genome_build: GRCm38 and MiRBase (Ver 22)

source_name: UUO-7_LTL+ cells

extract_protocol:
Mice were perfused with PBS immediately after culling and kidneys were removed, before being digested into a single cells suspension and before being labelled with pre-conjugated antibodies for flourescently activated cell sorting into PDGFRB, CD31, F4/80 and LTL cell suspensions.
These  sorted cell suspsions were homogenized by vortexing for 10 seconds, the lysate pipetted onto a gDNA Eliminator spin column and centrifuged at 10,000g for 30 seconds.  The gDNA column was discarded and 1.5 times volume pure ethanol was added to the lysate and placed on a RNeasy MinElute column.  The column was spun at 10,000g for a further 30 seconds, 700ul RWT buffer was added and the extraction continued as per manufacturers protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: injury model

tag: tissue

value: Sorted kidney tissue

value: LTL+ cells

tag: molecule type

value: small RNA


title: 76c_U7_5_PDGFRB

source_name: UUO-7_PDGFRβ+ cells

value: PDGFRbeta+ cells


title: SYC214


title: 70c_U7_4_f480

source_name: UUO-7_F480+ cells

value: F480+ cells


title: SYC209


title: 74c_U7_5_f480


title: H3K27ac_CRISPR_E1.2_E_KO_Ctrl

value: BALB/c


title: 71c_U7_4_LTL


title: H3K27ac_CRISPR_S_KO_Ctrl


title: CD4T_spleen_rep2

description:
007_IsEn15_CD4_S_E_G2
all_counts.tsv


title: SYC213


title: SYC212


title: SYC206

source_name: glioblastoma tissues

value: glioblastoma tissues


title: 66c_U7_3_f480


title: 73c_U7_5_CD31

source_name: UUO-7_CD31+ cells

value: CD31+ cells


title: 72c_U7_4_PDGFRB


title: 65c_U7_3_CD31


title: SYC211

value: Mut


title: NKT_spleen_rep1

description:
008_IsEn15_NKT_S_E_H1
all_counts.tsv

value: NKT

value: C


title: 69c_U7_4_CD31


title: 64c_U7_2_PDGFRB


title: 67c_U7_3_LTL


title: NK_lung_rep1

description:
006_IsEn15_NK_Lg_E_F1
all_counts.tsv

value: C / NK1.1+ TCRb- gdTCR-


title: gdT_spleen_rep1

description:
009_IsEn15_gd_S_E_A3
all_counts.tsv

value: Female

value: C / gdTCR+ TCRb-


title: SYC204


title: 62c_U7_2_f480


title: 63c_U7_2_LTL


title: SYC203


title: gdT_lung_rep1

description:
005_IsEn15_gd_Lg_E_E2
all_counts.tsv


title: 54c_SH_4_f480

source_name: Sham_F480+ cells

value: Sham


title: NKT_lung_rep1

description:
004_IsEn15_NKT_Lg_E_D2
all_counts.tsv


title: CD4T_lung_rep2

description:
003_IsEn15_CD4_Lg_E_C2
all_counts.tsv

value: C / TCRb+ CD4+


title: SYC205


title: 61c_U7_2_CD31


title: SYC202

value: lower grade glioma tissues


title: 55c_SH_4_LTL

source_name: Sham_LTL+ cells

value: Sorted kidney tissue


title: 56c_SH_4_PDGFRB

source_name: Sham_PDGFRβ+ cells


title: SYC208


title: CD4T_lung_rep1

description:
002_IsEn15_CD4T_Lg_B1
all_counts.tsv


title: SYC201


title: 52c_SH_3_PDGFRB


title: 53c_SH_4_CD31

source_name: Sham_CD31+ cells


title: 51c_SH_3_LTL

value: LTL+ cells


title: 50c_SH_3_f480

value: small RNA


title: CD4T_spleen_rep1

description:
001_IsEn15_CD4T_S_A2
all_counts.tsv


title: 49c_SH_3_CD31


title: NKTFH_rep10

description:
074_74_6FH_NKT_11618_200_IsEn12_B10
all_counts.tsv

value: NKTFH

value: 2 mg i.v.agalcer in vivo 6d prior to isolation

value: B / CXCR5+ PD-1+


title: SYC200


title: 48c_SH_2_PDGFRB

value: PDGFRbeta+ cells


title: NKTFH_rep9

description:
072_72_5FH_NKT_11618_200_IsEn12_H9
all_counts.tsv


title: 47c_SH_2_LTL


title: SYC199

value: glioblastoma tissues


title: NKTFH_rep8

description:
070_70_4FH_NKT_11618_200_IsEn12_F9
all_counts.tsv


title: 46c_SH_2_f480

value: F480+ cells


title: SYC197


title: NKT1_liver_rep3B

description:
058_Lv1_Exp2_Li_NKT1_2
all_counts.tsv

source_name: pooled liver

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-


title: 45c_SH_2_CD31

value: CD31+ cells


title: SYC196


title: 38c_U2_4_f480

source_name: UUO-2_F480+ cells


title: 39c_U2_4_LTL

source_name: UUO-2_LTL+ cells


title: SYC195


title: 37c_U2_4_CD31

source_name: UUO-2_CD31+ cells


title: SYC193


title: 36c_U2_3_PDGFRB

source_name: UUO-2_PDGFRβ+ cells


title: 35c_U2_3_LTL


title: SYC192


title: NKTFH_rep6

description:
057_57_hs2FH_NKT_111617_200_IsEn12_A8
all_counts.tsv

source_name: individual spleen


title: NKTFH_rep7

description:
058_58_hs3FH_NKT_111617_200_IsEn12_B8
all_counts.tsv


title: 34c_U2_3_f480


title: NKT17_lung_rep4B

description:
056_Lg17_Exp2_Lu_NKT17_2
all_counts.tsv

source_name: pooled lung

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: 40c_U2_4_PDGFRB


title: NKT2_lung_rep3B

description:
055_Lg2_Exp2_Lu_NKT2_2
all_counts.tsv

value: Female


title: NKT1_lung_rep3B

description:
054_Lg1_Exp2_Lu_NKT1_2
all_counts.tsv


title: 33c_U2_3_CD31


title: SYC189

source_name: lower grade glioma tissues

value: Mut


title: 32c_U2_2_PDGFRB


title: SYC188


title: NKT17_thymus_rep4B

description:
052_T_17_Exp2_Th_NKT17_2
all_counts.tsv

source_name: pooled thymus


title: Rolling_RNAseq_3

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

description:
All_data_normalized_and_res.csv
Rolling_denovo_Trinity.fasta

data_processing:
Sequenced reads were mapped to mm10 reference using bwa
Counts were normalized by DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: csv file with gene counts normalized by DEseq2, Rolling_denovoTrinity.fasta, Stretching_denovoTrinity.fasta

organism: Oniscidea

source_name: Oniscidea

growth_protocol: Fresh tissue

extract_protocol:
RNA was extracted with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq with fresh tissue

treatment_protocol: No treatment

tag: status

value: Rolling

tag: replicates


title: SYC190


title: 31c_U2_2_LTL

tag: strain

tag: cell type


title: NKT2_thymus_rep3B

description:
051_T_2_Exp2_Th_NKT2_2
all_counts.tsv


title: Rolling_RNAseq_2


title: SYC187


title: 30c_U2_2_f480


title: SYC186


title: Rolling_RNAseq_1


title: 29c_U2_2_CD31


title: NKT1_thymus_rep3B

description:
050_T_1_Exp2_Th_NKT1_2
all_counts.tsv


title: SYC191


title: 28c_U2_1_PDGFRB


title: NKT2_spleen_rep5B

description:
047_S_2_Exp2_Sp_NKT2_2
all_counts.tsv

source_name: pooled spleen


title: NKT17_spleen_rep5B

description:
048_S_17_Exp2_Sp_NKT17_2
all_counts.tsv


title: 27c_U2_1_LTL


title: SYC184


title: 26c_U2_1_f480


title: Stretching_RNAseq_2

description:
All_data_normalized_and_res.csv
Stretching_denovo_Trinity.fasta

value: Stretching


title: Stretching_RNAseq_3


title: SYC183

value: lower grade glioma tissues


title: SYC182


title: 25c_U2_1_CD31

value: Sorted kidney tissue


title: NKT17_lung_rep2B

description:
047_47_Lg17_NKT_80817_200_IsEn12_G6
all_counts.tsv


title: NKT1_spleen_rep5B

description:
046_S_1_Exp2_Sp_NKT1_2
all_counts.tsv


title: Stretching_RNAseq_1


title: NKTFH_rep5

description:
056_56_hs1FH_NKT_111617_200_IsEn12_H7
all_counts.tsv


title: NKT17_lung_rep2A

description:
046_46_Lg17_NKT_80817_200_IsEn12_F6
all_counts.tsv


title: SYC177

source_name: glioblastoma tissues

tag: patient gender

tag: patient age


title: 24c_SH_1_PDGFRB

value: Sham


title: NKT2_spleen_rep4B

description:
043_S_2_Exp1_Sp_NKT2_2
all_counts.tsv


title: SYC176

value: WT


title: 23c_SH_1_LTL

value: LTL+ cells

value: small RNA


title: 22c_SH_1_f480


title: SYC175

value: Male


title: 21c_SH_1_CD31


title: NKT1_spleen_rep4B

description:
042_S_1_Exp1_Sp_NKT1_2
all_counts.tsv


title: NKT2_lung_rep1A

description:
042_42_Lg2_NKT_80817_200_IsEn12_B6
all_counts.tsv


title: SYC179


title: 19c_RU_5_LTL

source_name: rUUO_LTL+ cells

value: rUUO


title: 20c_RU_5_PDGFRB

source_name: rUUO_PDGFRβ+ cells

value: PDGFRbeta+ cells


title: SYC171

value: glioblastoma tissues


title: 17c_RU_5_CD31

source_name: rUUO_CD31+ cells


title: NKT2_lung_rep1B

description:
043_43_Lg2_NKT_80817_200_IsEn12_C6
all_counts.tsv


title: SYC167


title: NKT17_lung_rep3B

description:
041_Lung_or_Lg_17_Exp1_Lu_NKT17_2
all_counts.tsv


title: NKT1_lung_rep2B

description:
039_Lung_or_Lg_1_Exp1_Lu_NKT1_2
all_counts.tsv

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-


title: NKT2_lung_rep2B

description:
040_Lung_or_Lg_2_Exp1_Lu_NKT2_2
all_counts.tsv


title: NKT17_thymus_rep3

description:
039_39_T17_NKT_80817_200_IsEn12_G5
all_counts.tsv


title: Patient 7: right anterior section 5

city: Calgary

first: Jacob

last: Kennard

state: CA-AB

address: 2500 university drive

department: Chemical Engineering

country: Canada

institute: University of Calgary

hyb_protocol: Affymetrix Clariom D Array.

scan_protocol: Affymetrix Clariom D Array.

data_processing: Samples were normalised (log2) with Affymetrix Expression Console Software (v1.4) using SST-RMA algorithm and annotated on exon/gene level with the library for Clariom D Array (human).

label: biotin

source_name: Human abdominal aortic aneurysm tissue

label_protocol: Affymetrix WT PLUS Labeling Kit.

growth_protocol: Entire AAA was resected during open repair surgery. Aneurysm was then segmented and preserved.

extract_protocol: Thermofisher MirVana miRNA isolation kit.

treatment_protocol: After AAA segmentation tissue samples were suspended in MirVana Lysis/Binding buffer.

tag: subject id

value: Patient 7

value: abdominal aortic aneurysm (AAA) tissue

tag: tissue section

value: right anterior section

tag: ilt thickness

tag: tawss

tag: raw


title: Patient 7: right posterior section 6

value: right posterior section


title: Patient 7: left anterior section 6

value: left anterior section


title: 16c_RU_4_PDGFRB


title: Patient 5: left posterior section 1

value: Patient 5

value: left posterior section


title: Patient 7: left anterior section 3


title: SYC166

value: Female


title: SYC174


title: Patient 7: right posterior section 4


title: SYC173


title: NKT2_thymus_rep2

description:
037_37_T2_NKT_80817_200_IsEn12_E5
all_counts.tsv

tag: Sex

tag: stimulation

tag: sorting scheme / criteria


title: 15c_RU_4_LTL

tag: injury model

value: Sorted kidney tissue


title: iNeurons_astrocytes_well_W09

city: Nijmegen

first: Nael

last: Nadif Kasri

address: Geert Grooteplein Zuid 10

department: Department of Human Genetics

country: Netherlands

institute: Radboudumc

description:
Cultured on 24-well plate
Count_table_iNeurons_astrocytes.txt

data_processing:
Base calls converted to fastq and demultiplexed using Illumina's bcl2fastq conversion software (v2.16.0.10)
Reads trimmed using Trimmomatic (version 0.33)
Mapping performed with STAR with default settings (--outReadsUnmapped None, --outFilterType Normal, --outFilterScoreMin 0, outFilterMultimapNmax 10, --outFilterMismatchNmax 10, --alignIntronMin 21, --alignIntroMax 0, --alignMatesGapMax 0, --alignSJoverhangMin 5, --alignSJDBoverhangMin 3, --sjdbOverhang 100).
Uniquely mapped reads (mapping quality = 255) extracted
Htseq count (version 0.9.1) was performed to generate count matrices (parameters: --order=pos, --stranded=yes, --mode=union, --type=exon, --idattr=gene_id)
The samples for which the fastq files are not demultiplexed are RNA-seq samples from co-cultures, i.e. human iNeurons and rat astrocytes. I cannot separate these samples using demultiplexing because the libraries have the same library barcodes, but they are separated further in the pipeline when mapping to a combined human and rat genome. Reads mapping to the human genome represent iNeuron reads and reads mapping to the rat genome represent astrocyte reads.
Genome_build: GRCh38.p12 for HUVECs, combined GRCh38.p12/Rnor6.0 for iNeurons and astrocytes
Supplementary_files_format_and_content: Count tables with raw gene counts for every gene and every sample

organism:
Homo sapiens
Rattus norvegicus

source_name: iNeurons

growth_protocol: On DIV0, well plates were coated with 20 µg/ml laminin and 20,000 iPSCs were seeded per well of a 24-well plate using Essential E8 Flex Basal medium (Gibco), supplemented with 1x RevitaCell™ Supplement (Gibco), and 4 µg/ml doxycyclin (Sigma Aldrich). On DIV1 cell medium was changed to DMEM/F12 medium (Gibco), supplemented with 0.1 mg/ml primocin (InvivoGen), 4 µg/ml doxycyclin, 1x N-2 (Gibco),  1x MEM Non-Essential Amino Acids Solution (NEAA, GIbco), 10 ng/ml NT-3 Recombinant Human Protein (NT-3, Promocell) and 10 ng/ml BDNF Recombinant Human Protein (BDNF, Promocell). On DIV2, the rat astrocytes (isolated according to earlier described protocols26) were added in a 1:1 ratio with the hiPSCs, similar to the hiPSC seeding. On DIV3, medium was removed and switched to Neurobasal medium (Gibco) supplemented with 0.1 mg/ml primocin, 1X B-27 Supplement, serum free (Gibco),  1X GlutaMAX™ Supplement (Gibco), 4 µg/ml doxycyclin, 10 ng/ml NT-3, 10 ng/ml BDNF and 2 µM Cytosine β-D-arabinofuranoside hydrochloride (Sigma Aldrich). Starting from day 5, 50% of the medium was refreshed every 2 days with Neurobasal medium, supplemented with 0.1 mg/ml primocin, 1X B-27,  1X GlutaMAX™, 4 µg/ml doxycyclin, 10 ng/ml NT-3 and 10 ng/ml BDNF. From DIV9 onwards, medium was refreshed every 2 day with this medium, which was then supplemented with Fetal Calf Serum (Sigma Aldrich) to sustain the rat astrocytes. iNeurons were kept in culture up to DIV38.

extract_protocol:
RNA was isolated and purified using the Quick-RNA Microprep kit (Zymo Research, R1051)
RNA-seq libraries were prepared using the SMARTer Stranded Total RNA Sample Prep Kit (low input mammalian) (Takara Bio, 634861)

tag: origin

value: iPSC-derived neurons (co-cultured with rat astrocytes)

tag: treatment

value: untreated

tag: disease state/genotype

value: healthy


title: Patient 4: left anterior section 1

value: Patient 4

tag: tissue


title: 18c_RU_5_f480

source_name: rUUO_F480+ cells

tag: strain

value: rUUO

value: F480+ cells

tag: molecule type

value: small RNA


title: Patient 4: right anterior section 2


title: 14c_RU_4_f480

tag: cell type


title: SYC162

tag: patient gender

value: Male

tag: patient age

tag: idh1 status

value: Mut

tag: tissue type

value: glioblastoma tissues


title: iNeurons_astrocytes_chip_C30

description:
Cultured on microfluidic chip
Count_table_iNeurons_astrocytes.txt

growth_protocol: On DIV0, channels from the chip were coated with 20 µg/ml laminin and approximately 10,000 iPSCs were seeded per channel. The top channels were first filled with culture medium by open-microfluidic flow, after which a droplet containing a high concentration of cell suspension (calculated to contain the correct number of cells) was pipetted into the channels to disperse the cells. Two hours after seeding the cells in the channels, the wells containing the microfluidic chips were filled with Essential E8 Flex Basal medium (Gibco), supplemented with 1x RevitaCell™ Supplement (Gibco), and 4 µg/ml doxycyclin (Sigma Aldrich). On DIV1 cell medium was changed to DMEM/F12 medium (Gibco), supplemented with 0.1 mg/ml primocin (InvivoGen), 4 µg/ml doxycyclin, 1x N-2 (Gibco),  1x MEM Non-Essential Amino Acids Solution (NEAA, GIbco), 10 ng/ml NT-3 Recombinant Human Protein (NT-3, Promocell) and 10 ng/ml BDNF Recombinant Human Protein (BDNF, Promocell). On DIV2, the rat astrocytes (isolated according to earlier described protocols26) were added in a 1:1 ratio with the hiPSCs, similar to the hiPSC seeding. On DIV3, medium was removed and switched to Neurobasal medium (Gibco) supplemented with 0.1 mg/ml primocin, 1X B-27 Supplement, serum free (Gibco),  1X GlutaMAX™ Supplement (Gibco), 4 µg/ml doxycyclin, 10 ng/ml NT-3, 10 ng/ml BDNF and 2 µM Cytosine β-D-arabinofuranoside hydrochloride (Sigma Aldrich). Starting from day 5, 50% of the medium was refreshed every 2 days with Neurobasal medium, supplemented with 0.1 mg/ml primocin, 1X B-27,  1X GlutaMAX™, 4 µg/ml doxycyclin, 10 ng/ml NT-3 and 10 ng/ml BDNF. From DIV9 onwards, medium was refreshed every 2 day with this medium, which was then supplemented with Fetal Calf Serum (Sigma Aldrich) to sustain the rat astrocytes. iNeurons were kept in culture up to DIV38.


title: NKT17_spleen_rep3

description:
035_35_S17_NKT_80817_200_IsEn12_C5
all_counts.tsv

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: 8c_RU_2_PDGFRB

value: PDGFRbeta+ cells


title: SYC161

value: WT


title: NKT17_lung_rep4A

description:
034_Lg17_Exp2_Lu_NKT17_1
all_counts.tsv


title: SYC163


title: iNeurons_astrocytes_chip_C29


title: SYC172


title: Patient 1: left anterior section 5

tag: subject id

value: Patient 1

value: abdominal aortic aneurysm (AAA) tissue

tag: tissue section

value: left anterior section

tag: ilt thickness

tag: tawss


title: 7c_RU_2_LTL

value: Sorted kidney tissue

value: LTL+ cells


title: Patient 4: right anterior section 1

value: right anterior section

tag: raw


title: NKT1_liver_rep3A

description:
036_Lv1_Exp2_Li_NKT1_1
all_counts.tsv

source_name: pooled liver

tag: Sex

value: Female

tag: stimulation

tag: sorting scheme / criteria

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-


title: NKT2_lung_rep3A

description:
033_Lg2_Exp2_Lu_NKT2_1
all_counts.tsv


title: ApoE shRNA input DNA

city: Hefei

first: Qiang

last: Liu

state: Anhui

address: 443 Huangshan Road

institute: University of Science and Technology of China

data_processing:
bcl2fastq2 V2.2 software used for basecalling and parameter is default
inhouse scripts used for filtering
bowtie2 V2.1.0 used for alignment
MACS2 V2.1.1 used for peak-calling
normalization also used inhouse scripts and cauculated
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: mice hippocampus input ApoE knockdown

extract_protocol:
Hippocampus Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for ChIP-seq.
Libraries were prepared according to Illumina's instructions，including DNA fragment,End repair,dA-Tailing,Adaptor ligation and the KAPA HiFi DNA Polymerase for PCR amplification

value: brain; hippocampus

tag: chip antibody


title: control shRNA input DNA

source_name: mice hippocampus input control

tag: tissue


title: SYC159


title: 6c_RU_2_f480

tag: strain

tag: injury model

value: rUUO

value: F480+ cells


title: ApoE shRNA H3K27ac

source_name: mice hippocampus H3K27ac ApoE knockdown

value: H3K27ac (Abcam,ab4729, lot )


title: NKT1_lung_rep3A

description:
032_Lg1_Exp2_Lu_NKT1_1
all_counts.tsv

tag: cell type


title: SYC157

tag: patient gender

value: Male


title: 5c_RU_2_CD31

value: CD31+ cells

tag: molecule type

value: small RNA


title: control shRNA H3K27ac

source_name: mice hippocampus H3K27ac control


title: 4c_RU_1_PDGFRB

value: PDGFRbeta+ cells


title: tfh_ko3: Bach2-cKO rep3

city: Shanghai

first: Heng

last: Zhang

address: No.227 Sounth Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Alignment: We used STAR (version 2.5.2b) to align raw reads to mouse genome (Gencode, GRCm38) and annotated transcripts and genes using Gencode mouse genome gtf file (vM10). Read abundance was quantified by STAR quantification mode '--quantMode GeneCounts'
Gene filtering: Raw read counts were loaded in R statistical environment and created a deseq object using DESeq2 package (R version 3.5.1, DESeq2 version 1.20.0). Read counts for individual samples were compiled by genes, low read count genes (total read count ≤ number of biological samples) were removed from downstream analyses. Mitochondrial genes and ribosomal genes were also removed.
Read normalization: Raw read counts were then normalized using DESeq2 command 'counts(deseq.df, normalized = T)'.
Genome_build: mm10
Supplementary_files_format_and_content: tfh_normalized_readcount.csv; CSV file; Normalized read count for all samples

source_name: mesenteric lymph nodes

extract_protocol:
10,000-3,0000 Tfh Cells (CD4+B220-CD44+PD-1+CXCR5+) were sorted from the MLNs of WT and Bach2fl/flCd4-cre mice using a FACSAria II cell sorter (BD Biosciences).cDNA was synthesized and amplified using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech).
The library for mRNA sequencing was generated using Illumnia TruSeq Preparation Kit (RS-122-2001)

value: mesenteric lymph nodes


title: SYC160

tag: patient age

tag: idh1 status

value: WT

value: glioblastoma tissues


title: 3c_RU_1_LTL


title: NKT1_spleen_rep3

description:
032_32_S1_NKT_80817_200_IsEn12_H4
all_counts.tsv


title: SYC156

tag: tissue type


title: NKT17_thymus_rep4A

description:
030_T_17_Exp2_Th_NKT17_1
all_counts.tsv

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: NKT2_thymus_rep3A

description:
029_T_2_Exp2_Th_NKT2_1
all_counts.tsv


title: 2c_RU_1_f480

value: Sorted kidney tissue


title: tfh_ko1: Bach2-cKO rep1


title: 13c_RU_4_CD31


title: SYC153


title: tfh_wt3: WT rep3


title: 1c_RU_1_CD31


title: NKT1_thymus_rep3A

description:
028_T_1_Exp2_Th_NKT1_1
all_counts.tsv


title: SYC158


title: flower buds, pep1-1

city: Köln

first: Maria

last: Albani

address: Carl-von-Linné-Weg 10

department: Botanical institute

country: Germany

institute: University of Cologne

data_processing:
Reads derived from the Illumina library were aligned to the reference genome (A. alpina_V5) using Bowtie 2
SAMtools and BCFtools were used to identify variations
Differential expression between samples was determined using DESeq
SHOREmap v3.6 was used to extract the SNPs information and to visualise the allele frequency (AF) for eop055BC1F2
Homozygous SNPs found in the pep1-1 resequencing data reference were used for background correction. SNPs which originated the pep1-1 resequencing data  and were filtered out from eop055BC1F2 and SNPs with a quality score higher than 40 were kept for further analysis to visualise the AF.
Genome_build: Arabis alpina V5 genome
Supplementary_files_format_and_content: tab-delimited text files include variations compared with wild type reference genome

organism: Arabis alpina

source_name: plants at the beginning of reproductive stage

growth_protocol: Plants are grown at long days

extract_protocol:
Genomic DNA was extracted with the DNeasy Plant Maxi Kit (Qiagen)
Libraries were generated using the Illumina Genomic DNA sample kit.

value: flower buds

tag: genotype

tag: accession

value: Pajares


title: SYC152


title: NKT17_spleen_rep5A

description:
026_S_17_Exp2_Sp_NKT17_1
all_counts.tsv

value: Female


title: NKT1_liver_rep2B

description:
027_27_Lv1_NKT_62917_200_IsEn12_C4
all_counts.tsv

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-


title: flower buds, eop055BC1F2


title: tfh_wt2: WT rep2


title: tfh_wt1: WT rep1


title: SYC150


title: tfh_ko2: Bach2-cKO rep2


title: SYC155


title: rpoB M1304R 3

city: St. Paul

first: Arkady

last: Khodursky

address: 1479 Gortner Ave

institute: University of Minnesota

data_processing:
Illumina Casava1.7 software used for basecalling
De-multiplexing was performed using Illumina’s bcl2fastq software 2.20
The reads were mapped to the reference genome (GCF_000005845.2_ASM584v2) using HISAT2
The final per feature read counts were obtained with Rsubread
Genome_build: GCF_000005845.2_ASM584v2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Escherichia coli

source_name: MG1655 exponential

growth_protocol: Overnight cultures were diluted 1:1,000 into 50ml LB; 10-12 generations maintained under OD600 of 0.3 in LB

extract_protocol:
10ml samples were transferred into 15ml conical tubes containing 1.25 ml of the “stop” solution (ethanol v/v 95%, and phenol v/v 5%). Cells were then spun down and decanted. Pellets were flash frozen in liquid nitrogen and kept at -80°C until all samples were collected. Pellets were thawed on ice and resuspended in 200µl of TE buffer containing 20,000 mg/L of lysozyme and incubated at 37°C for 10 min. Total RNA was purified following a standard RNAeasy mini prep kit protocol (Qiagen, Hilden, Germany).
rRNA was removed using a RiboZero kit from Illumina (Cat. # MRZB12424). The library was made using TruSeq mRNA library prep kit

tag: phase

value: early exponential near steady state

value: rpoB mutant


title: SYC149


title: SEAM-Control

city: Kgs. Lyngby

first: Anne

middle: Zebitz

last: Eriksen

address: Produktions Torvet 423

department: Health Technology

country: Denmark

institute: Technical University of Denamrk

description: Whole eye organoid from hESCs

data_processing:
 Raw reads were aligned to the human genome (hg19) using the RNA express app on Basespace (Illumina) and differential gene expression was determined using the DEseq2 protocol [REF: PMID 25516281].
Featuer, barcode and matrix files from the two data sets (infected and not infected) were loaded into R 4.0.2 using the Seurat package
Data entries with <200 and >7000, or more than 30% mitocondrial RNA were filtered out from both data sets seperately
Data was normalized with verbose set to false, and variable features in the two seperate data sets were found using the "vst" metods, and the number of variable features to find set to 2000.
Integration ancors were found using the "FindIntegrationAncors" function and Integration of the two data sets were preformed with dims = 1:20
Default assay was run, and the data was scaled before funning UMAP, FindNeighbors and FindClusters, using "pca", dims=1:20 and resulution=0.75
Genome_build: Enricher: Mouse Gene Atlas
Supplementary_files_format_and_content: SEAM-Control. Filter files: barcodes.tsv.gz.gz; feature.tsv.gz.gz; matrix.mtx.gz
Supplementary_files_format_and_content: SEAM-Infected Filter files: barcodes.tsv.gz.gz; feature.tsv.gz.gz; matrix.mtx.gz
rds file of a Seurat object called SEAM.combined consisting of two data sets "ctrl" and "stim", and a total of 22 clusters. 18464 features across 10821 samples within 2 assays   Active assay: RNA (16464 features, 0 variable features)   1 other assay present: integrated   2 dimensional reductions calculated: pca, umap
CSV file of cluster marker for cluster 0 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 1 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 2 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 3 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 4 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 5 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 6 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 7 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 8 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 9 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 10 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 11 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 12 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 13 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 14 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 15 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 16 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 17 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 18 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 19 list of genes, relative expression and p-value: gene, STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 20 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
CSV file of cluster marker for cluster 21 list of genes, relative expression and p-value: gene, CTRL_p_val; CTRL_avg_logFC; CTRL_pct.1; CTRL_pct.2; CTRL_p_val_adj;  STIM_p_val; STIM_avg_logFC;  STIM_pct.1; STIM_pct.2; STIM_p_val_adj; max_pval;  minimump_p_val
HTML file with R-code of analysis

source_name: eye organoid

growth_protocol: hESCs were seeded as single cells onto Matrigel-coated dishes at 500cells cm-2 (5,000 cells in one well of a 6 Well plate), after which they were cultured in mTeSR1 media for 10 days to achieve round small-to-medium-sized separate colonies. Half of the culture medium was then changed to SEAM differentiation media; GMEM (Life Technologies), 10% knockout serum replacement (KSR, Life Technologies) and supplemented with 1X L-Glutamine (Life Technologies), 1X MEM Non-Essential Amino Acids Solution (Life Technologies), 1X Penicillin-Streptomycin (10,000 U/mL, Life Technologies), Sodium Pyruvate (100mM, Life Technologies) and 0.1 m 2-mercaptoethanol (Sigma). Media changes were performed three times per week throughout the differentiation, in which half of the media was changed for the first week of differentiation, after which full media changes were made. After four to seven weeks of differentiation, SEAM structures were mature and pigmented, at which point they were analyzed and/or harvested.

extract_protocol:
differentiated SEAM cultures were dissociated in the incubator for 1-hour at 37 °C, 20% O2, 5% CO2 using 2.5 mg/ml Collagenase 2 (Worthington Biochemical Corporation) in Hanks’ Balanced Salt Solution with 3mg/ml DNase I Solution (STEMCELL Technologies) and 2uM Thiazovivin ROCK Inhibitor. The harvested cells were washed with Dulbecco’s Modified Eagle Medium: Nutrient Mix F-12 (DMEM/F12, Life Technologies), containing 0.1% BSA, 3mg/ml DNase I Solution and 2 uM Thiazovivin and then filtered with a 40um cell strainer (Corning). Cells were frozen down prior to single-cell RNA sequencing in 90% Heat Inactivated Fetal Bovine Serum (FBS, Sigma) and 10% DMSO (COMPANY) using Mr. Frosty containers.
Chromium Single Cell 3’ Library and Gel Bead Kit v3.0 using an input of ~10,000 cells, The samples were sequenced on the Novaseq 6000 Illumina sequencer with S4 flow cell, (100/paired end reads) targeting a depth of 50,000-100,000 reads per cell using v3 chemistry
10X Genomics Chromium controller v3.16 alined to GRCh38.100 and SARS-CoV-2 USA-WA1

treatment_protocol: The Infected SEAM culture was exposted to live SARS-CoV2 virus at 1MOI added to the media and incubated for 24h.

tag: source cells

value: H9 ESC

value: eye organoid

tag: rna population

value: cytoplasmic RNA

tag: disease state

value: not infected


title: NKT1_liver_rep2A

description:
026_26_Lv1_NKT_62917_200_IsEn12_B4
all_counts.tsv

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr).
Filtered reads were mapped against the mouse mm10 reference using Tophat v1.4.1 (--library-type fr-firststrand).
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4).
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: all_counts.tsv: Count matrix with rows as genes and columns as samples.

extract_protocol:
Cells representing specific iNKT subsets were sorted directly into 0.2 ml PCR tubes containing 8 µL of low-input lysis buffer (0.2% Triton-X-100 and RNase inhibitor) and stored at -80oC until processed further. RNA extraction, reverse transcription, cDNA amplification, fragmentation, and additional PCR amplification were performed as previously described (Rosales et al. Methods Mol Biol 1799, p275).
We followed the Smart-Seq2 protocol as described previously (Picelli et al., 2013; Rosales et al., 2018). Libraries were then pooled at equal molar concentration and sequenced using the HiSeq 2500 and NovaSeq6000 Illumina platform (Illumina).
Samples from the experiment comparing splenic NKTFH and NKTeff cells from aGalCer-challenged mice with unchallenged splenic iNKT cells were sequenced via a paired-end read method using the Novaseq6000 sequencer according to supplied protocols (Illumina). Sequencing for all other samples was performed according to a single-end strategy using the HiSeq2500 sequencer (Illumina).

tag: Sex

tag: stimulation

tag: sorting scheme / criteria


title: SEAM-Infected

description: Whole eye organoid from hESCs infected with SARS-CoV2

tag: tissue

value: infected with SARS-CoV2


title: SYC154

value: Male

value: Mut


title: NKT2_spleen_rep5A

description:
025_S_2_Exp2_Sp_NKT2_1
all_counts.tsv

source_name: pooled spleen

tag: strain


title: MCF-7 RNA-seq PRL+ ACY241+ biological rep 3

city: Richmond

first: Justin

middle: Michael

last: Craig

state: Virginia

address: 1201 E Marshall St

department: Massey Cancer Center

institute: Virginia Commonwealth University

description: ACY241_PRL_RNAseq_no_rRNA_Kallisto_Gene_Counts_matrix.txt

data_processing:
NovaSEQ 6000 basecalling for ChIP- and RNA-seq performed by standard Illumina pipeline/software.
ChIP-seq and RNA-seq: ChIP-seq and RNA-seq data were analyzed using the R statistical computing environment and the Galaxy web platform via the public server at usegalaxy.org. Raw reads in .FASTQ file format were assessed for sequence quality, GC content, the presence of adaptors, overrepresented k-mers and duplicated reads utilizing FastQC v0.11.2. Adapters, polyG tails, and 15 bases from 5’ and 3’ tails were trimmed and any low quality reads (>20% bases with phred quality <Q20) or reads less than 60 bases in length (after trimming) were filtered using fastp v0.20.1.
ChIP-seq: Filtered reads were aligned to the hg38 reference genome (GRCh38; excluding the Y chromosome and alternate scaffolds) using Bowtie2 v2.3.4.3. The resultant .BAM files from technical replicates were merged and duplicate reads were removed before biological replicates and corresponding input samples were passed to MACS2 v2.1.1.20160309.6 for peak detection in paired-end mode (-BAMPE) with FDR<0.01.  Peaks in ENCODE blacklist regions were removed. The .BAM files of biological replicates were normalized to sequencing depth and combined to create counts per million (CPM) normalized .BIGWIG files using deepTools bamCoverage module v3.3.2.0.0.
RNA-seq: Filtered reads were aligned to curated RefSeq transcripts (refMrna.fa downloaded from UCSC Table Browser July 27, 2020) utilizing Kallisto quant v0.46.0.4. Gene level summaries of transcript counts were obtained using tximport v0.1. Normalization and differential expression analysis were conducted with limma-voom v3.38.3 using “robust settings” and an FDR<0.05 (Benjamini-Hochberg).
Genome_build: hg38
Supplementary_files_format_and_content: .bigwig files for each experimental condition represent merged technical and biological replicate .BAM files with duplicate reads removed and normalized for sequencing depth as read counts per million (CPM)
Supplementary_files_format_and_content: RNA-seq matrix with gene level read counts for each sample

growth_protocol: MCF-7 cell line was obtained from the American Type Culture Collection (ATCC) and cells were cultured in Dulbecco’s modified Eagles’s medium (DMEM; Life Technologies #11965092) supplemented with 10% fetal bovine serum (FBS; Corning #MT35011CV) and 1% penicillin-streptomycin (ThermoFisher Scientific #15140-122).

extract_protocol:
ChIP-seq:  Approximately 1.0 x 108 cells were used for each experimental condition and biological replicate (n=2 per condition and ChIP target). At the conclusion of ACY-241 treatment and/or prolactin stimulation, chromatin was cross-linked in 1% formaldehyde for 12 minutes, followed by neutralization with 1/20 volume of 2.5 M glycine. Cells were washed twice with ice-cold PBS, scraped and collected in a third volume of PBS, and briefly spun down before pellets were snap-frozen in liquid nitrogen. With the exception of sonication, which was performed using the Covaris M220 Focused-ultrasonicator (Covaris, Inc.), chromatin isolation, immunoprecipitation, and DNA extraction were performed as previously described [Lee, T.I., S.E. Johnstone, and R.A. Young, Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat Protoc, 2006. 1(2): p. 729-48]. DNA purity was assessed by spectrophotometry at 260, 270, and 280 nm, and integrity was assessed by capillary electrophoresis utilizing the Agilent 2100 Bioanalyzer.  RNA-seq:  RNA was extracted in phenol: chloroform: isoamyl alcohol (PCA) followed by ethanol precipitation. DNA was enzymatically digested prior to a second round of PCA and ethanol precipitation. RNA purity was assessed by spectrophotometry at 260, 270, and 280 nm, and integrity was assessed by capillary electrophoresis utilizing the Agilent 2100 Bioanalyzer. All samples possessed RIN (RNA Integrity Number) values ≥9.
ChIP-seq:  Library preparation was performed on ≥100 ng DNA using the Ovation Ultralow V2 DNA-Seq Library Preparation Kit (NuGEN) according to the manufacturer’s instructions.  RNA-seq:  Library preparation was performed on ≥500 ng RNA using the Universal Plus mRNA-Seq Library Preparation Kit (NuGEN) according to the manufacturer’s instructions.

treatment_protocol: ChIP-seq:  MCF-7 cells were grown in 150-mm plates to ~60% confluency in complete medium (as described above) before serum starvation (DMEM, 0.1% BSA) for 20 hours. Cells were treated with either 2 µM ACY-241 or 0.1% DMSO for two hours prior to stimulation with prolactin (250 ng/mL) or an equal volume of 1X PBS for 30 minutes, followed by cell harvest. For each ACY-241/prolactin experimental condition (DMSO/PRL-, DMSO/PRL+, ACY-241/PRL-, ACY-241/PRL+), pooled chromatin was aliquoted for incubation with each antibody immediately prior to the immunoprecipitation step to ensure sampling from an identical cell population and enable robust comparison of the chromatin occupancy of each ChIP target  RNA-seq:  MCF-7 cells were grown in 150-mm plates to ~60% confluency in complete medium (as described above) before serum starvation (DMEM, 0.1% BSA) for 20 hours. Cells were treated with either 2 µM ACY-241 or 0.1% DMSO for two hours prior to stimulation with prolactin (250 ng/mL) or an equal volume of 1X PBS for an additional 2 hours, followed by cell harvest.

tag: cell type

value: ER+ breast cancer cells derived from pleural effusion of pt with breast adenocarcinoma

tag: chip antibody

tag: cell line

tag: treatment

value: 120 minutes 250 ng/mL prolactin, 120 minutes 2 uM ACY-241 (Citarinostat)


title: NKT1_spleen_rep5A

city: San Diego

first: Mitchell

last: Kronenberg

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description:
024_S_1_Exp2_Sp_NKT1_1
all_counts.tsv


title: rpoB M1304R 1


title: NKT17_thymus_rep2B

description:
023_23_T17_NKT_62917_200_IsEn12_G3
all_counts.tsv

source_name: pooled thymus

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: SYC147

source_name: glioblastoma tissues

tag: patient gender

tag: patient age

tag: idh1 status

value: WT

value: glioblastoma tissues


title: SYC146

tag: tissue type


title: MCF-7 RNA-seq PRL+ ACY241+ biological rep 2


title: NKT17_thymus_rep2A

description:
022_22_T17_NKT_62917_200_IsEn12_F3
all_counts.tsv


title: MCF-7 RNA-seq PRL+ ACY241+ biological rep 1


title: rpoB wild type 2

tag: phase

tag: genotype

value: wild type


title: NKT17_spleen_rep4

description:
020_S_17_Exp1_Sp_NKT17_1
all_counts.tsv

value: Female


title: SYC151


title: SYC145


title: SYC144


title: MCF-7 RNA-seq PRL- ACY241+ biological rep 3

value: 120 minutes 2 uM ACY-241 (Citarinostat)


title: rpoB wild type 1

value: early exponential near steady state


title: NKT2_spleen_rep4A

description:
019_S_2_Exp1_Sp_NKT2_1
all_counts.tsv


title: rpoB M1304R 2

value: rpoB mutant


title: SYC143


title: NKT1_thymus_rep2B

description:
019_19_T1_NKT_62917_200_IsEn12_C3
all_counts.tsv

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-


title: cardiomyocytes tansfected with siHoxa5, repeat3

first: Zhiguang

last: Shi

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

data_processing:
NovaSeq Control Software 1.7.0  used for basecalling.
Raw RNA-seq data was quality controlled with FastQC (v0.11.8), aligned with STAR (v.2.6.1b) and counted with HTseq to the mouse genome (Mm10) genome and gene annotations.
All downstream statistical analyses were performed using R (v3.5.3). After RNA-seq data was aligned to the transcriptome, counts were transformed to TPM (transcript per million).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Adult mouse cardiomyocytes

extract_protocol:
Adult mouse  cardiomyocytes  were isolated and plated as follows: In brief, heart was exposed first, and EDTA buffer is injected steadily into the right ventricle after cutting of descending artery. The heart then was removed from the mice , perfused with EDTA buffer and collagenase buffer. After digestion completed, cardiac myocytes may be collected by gravity settling, then treated with calcium re-introduction. Adult mouse cardiac myocytes were plated on laminated culture dishes(Nest, 801002) as described. One hours post-plating, myocytes are washed once with pre-equilibrated culture media, and then replaced with the M199 Culture media（gibco,12340-030）.
Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesize dusing random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 380 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on a NovaSeq 6000 platform (Illumina).

treatment_protocol: Adult mouse cardiomyocytes were isolated and cultured, and transfected with Small interfering RNA targetting to Negtive control or Hoxa5. After  24 hours, cardiomyocytes were treated  with phenylephrine for 24 hours

value: Adult mouse cardiomyocytes

value: phenylephrine

tag: transfection


title: MCF-7 RNA-seq PRL- ACY241+ biological rep 1


title: cardiomyocytes tansfected with siHoxa5, repeat4


title: MCF-7 RNA-seq PRL- ACY241+ biological rep 2


title: SYC141


title: SYC142


title: NKT1_spleen_rep4A

description:
018_S_1_Exp1_Sp_NKT1_1
all_counts.tsv


title: cardiomyocytes tansfected with siHoxa5, repeat2


title: MCF-7 RNA-seq PRL+ ACY241- biological rep 3

value: 120 minutes 250 ng/mL prolactin, 120 minutes 0.1% DMSO


title: NKT1_thymus_rep2A

description:
018_18_T1_NKT_62917_200_IsEn12_B3
all_counts.tsv


title: cardiomyocytes tansfected with siHoxa5, repeat1


title: NKT17_lung_rep3A

description:
017_Lung_or_Lg_17_Exp1_Lu_NKT17_1
all_counts.tsv

source_name: pooled lung


title: SYC139


title: rpoB wild type 3


title: MCF-7 RNA-seq PRL+ ACY241- biological rep 1


title: MCF-7 RNA-seq PRL+ ACY241- biological rep 2


title: SYC137


title: NKT2_lung_rep2A

description:
016_Lung_or_Lg_2_Exp1_Lu_NKT2_1
all_counts.tsv


title: SYC138


title: cardiomyocytes tansfected with siN ,repeat4

value: siN


title: NKT17_spleen_rep2

description:
016_16_S17_NKT_62917_200_IsEn12_H2
all_counts.tsv


title: SYC134


title: MCF-7 RNA-seq PRL- ACY241- biological rep 3

value: 120 minutes 0.1% DMSO


title: MCF-7 RNA-seq PRL- ACY241- biological rep 2


title: cardiomyocytes tansfected with siN ,repeat2


title: NKT1_lung_rep2A

description:
015_Lung_or_Lg_1_Exp1_Lu_NKT1_1
all_counts.tsv


title: MCF-7 RNA-seq PRL- ACY241- biological rep 1


title: cardiomyocytes tansfected with siN ,repeat1


title: SYC132

value: Male


title: MCF-7 ChIP-seq HMGN2 PRL- ACY241- biological rep 2 technical rep 2

value: ER+ breast cancer cells derived from pleural effusion of pt with breast adenocarcinoma

value: HMGN2 Cell Signaling Technology #9437


title: SYC133


title: NKT1_spleen_rep2

description:
014_14_S1_NKT_62917_200_IsEn12_F2
all_counts.tsv


title: NKT2_spleen_rep2

description:
015_15_S2_NKT_62917_200_IsEn12_G2
all_counts.tsv


title: MCF-7 ChIP-seq HMGN2 PRL- ACY241- biological rep 2 technical rep 1


title: cKIf/+, single cells from P0 telencephalic tissue

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Cell Ranger software used for basecalling.
STAR performs splicing-aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic, intronic, and intergenic, and by whether the reads align (confidently) to the genome. The adopted alignment are as follows: 1) A read is exonic if at least 50% of it intersects an exon, intronic if it is non-exonic and intersects an intron, and intergenic otherwise. 2) Reads that align to a single exonic locus but also align to 1 or more non-exonic loci, the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. 3) Reads that are confidently mapped to the transcriptome are used for UMI counting.
In Cell Ranger v2.x and earlier, the following algorithm is used to determine the cutoff for calling a barcode cell-associated: 1) Rank-sort the total UMI counts across all of the detected barcodes that passed the 16bp barcode whitelist filtering criteria. 2)Determine the 99th percentile of the UMI counts among the top N barcodes where N is the provided 'expected recovered cell' parameter passed to the pipeline (--expect-cells=3000 by default). 3) All barcodes with total UMI counts greater than or equal to 10% of the 99th percentile value are classified as cells.
The Seurat R package was applied to identify major cell types. RandomForest was applied to identify subtypes.
The graphs of principal component analysis (PCA) and T-distributed stochastic neighbor embedding (t-SNE) were produced following the scaling process, t
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: barcodes.tsv.gz, genes.tsv.gz, matrix.mtx.gz, all_cell.csv, all_UMI.csv

source_name: P0 cerebral cortex

extract_protocol:
Cerebral cortex tissue was digested into single cell suspensions. Then, these suspensions were carried out with 10x Genomics Chromium Single Cell Kit for single cell RNA-seq.
RNA libraries sequencing was performed using standard Illumina protocols.

value: serpina3 conditional knock-in mice

tag: age

value: cerebral cortex


title: SYC130

value: WT

value: glioblastoma tissues


title: MCF-7 ChIP-seq HMGN2 PRL- ACY241- biological rep 1 technical rep 2


title: SYC129

value: Mut


title: cardiomyocytes tansfected with siN ,repeat3


title: WT, single cells from P0 telencephalic tissue

value: Wildtype


title: unstim_NKT_rep3

description:
012_RSS96_IsEn16
all_counts.tsv

source_name: individual spleen

tag: Sex

value: Female

value: total NKT

value: C


title: unstim_NKT_rep4

description:
013_RSS96_IsEn16
all_counts.tsv

tag: stimulation


title: MCF-7 ChIP-seq HDAC6 PRL+ ACY241+ biological rep 2 technical rep 2

value: HDAC6 Cell Signaling Technology #7558

value: 30 minutes 250 ng/mL prolactin, 120 minutes 2 uM ACY-241 (Citarinostat)


title: NKT17_lung_rep1

description:
010_10_Lg17_NKT_61417_200_IsEn12_B2
all_counts.tsv

tag: sorting scheme / criteria

value: A / CXCR3-ICOS+CD122-SDC1+IL-17RB+FR4-


title: SYC127


title: SYC128


title: unstim_NKT_rep2

description:
011_RSS96_IsEn16
all_counts.tsv


title: MCF-7 ChIP-seq HMGN2 PRL- ACY241- biological rep 1 technical rep 1


title: MCF-7 ChIP-seq HDAC6 PRL+ ACY241+ biological rep 2 technical rep 1


title: unstim_NKT_rep1

description:
010_RSS96_IsEn16
all_counts.tsv


title: SYC126


title: NKT2_thymus_rep1

description:
006_6_T2_NKT_61417_200_IsEn12_F1
all_counts.tsv


title: MCF-7 ChIP-seq HDAC6 PRL+ ACY241+ biological rep 1 technical rep 2


title: NKT1_liver_rep1

description:
011_11_Lv1_NKT_61417_200_IsEn12_C2
all_counts.tsv

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-


title: SYC125


title: SYC122


title: NKT1_thymus_rep1

description:
005_5_T1_NKT_61417_200_IsEn12_E1
all_counts.tsv


title: NKTFH_rep4

description:
007_RSS96_IsEn16
all_counts.tsv

value: 2 mg i.v.agalcer in vivo 6d prior to isolation

value: B / CXCR5+ PD-1+


title: NKT17_spleen_rep1

description:
003_3_S17_NKT_61417_200_IsEn12_C1
all_counts.tsv


title: NKT1_lung_rep1

description:
009_9_Lg1_NKT_61417_200_IsEn12_A2
all_counts.tsv


title: NKTnonFH_rep3

description:
006_RSS96_IsEn16
all_counts.tsv

value: B / CXCR5- PD-1-


title: MCF-7 ChIP-seq HDAC6 PRL- ACY241+ biological rep 2 technical rep 2

value: ER+ breast cancer cells derived from pleural effusion of pt with breast adenocarcinoma

value: 120 minutes 2 uM ACY-241 (Citarinostat)


title: SYC121


title: SYC120

value: Male


title: NKT17_thymus_rep1

description:
007_7_T17_NKT_61417_200_IsEn12_G1
all_counts.tsv


title: NKTFH_rep3

description:
005_RSS96_IsEn16
all_counts.tsv


title: SYC119


title: SYC118

value: WT


title: NKTFH_rep2

description:
003_RSS96_IsEn16
all_counts.tsv


title: MCF-7 ChIP-seq HDAC6 PRL- ACY241+ biological rep 2 technical rep 1


title: MCF-7 ChIP-seq HDAC6 PRL- ACY241+ biological rep 1 technical rep 1


title: SYC117

value: glioblastoma tissues


title: MCF-7 ChIP-seq HDAC6 PRL+ ACY241- biological rep 2 technical rep 2

value: 30 minutes 250 ng/mL prolactin, 120 minutes 0.1% DMSO


title: Group3: 4T1 Clone#3 rep3 (miR-204-5p)

city: Seoul

first: Boksil

last: Hong

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University of Hopsital

data_processing:
Reads were aligned them to the Mus musculus (mm10) using Tophat v2.0.13 with Bowtie v2.2.3 algorithm to perform the alignment from McMillan KS et al., Bioinformatics, 2009.
Transcript assembly and abundance estimation using Cufflinks v2.2.1 with a protocol from Trapnel C at al., Nature Biotechnology, 2010 (‘--max-bundle-frags 50000000’ options to correct sequence expression count bias and the ‘-G’ option for making the best use of known gene annotation information).
The transcript-level relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks. Gene-level relative abundances were calculated as the sum of FPKMs of transcripts in the gene.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with FPKM; data2.xlsx contains statistical analysis

source_name: Murine breast cancer cells

growth_protocol: 4T1 was cultured in RPMI 1640 or Dulbecco’s modified essential medium (Hyclone, Logan, USA) supplemented with 10% FBS and antibiotics/antimycotic, respectively.

extract_protocol:
Total RNA from 4T1 overexpressing miR-204-5p or control was purified using TRIzol reagent (Thermofisher, USA).
A TruSeq RNA library preparation kit (Illumina, San Diego, CA, USA) was used according to the anufacturer’s instructions. The protocol consisted of polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100-nt paired-end sequencing by Illumina HiSeq2500

treatment_protocol: Control or overexpression plasmids for miR-204-5p (Genolution Pharmarceuticals, Seoul, Korea) were transfected to 4T1 using Lipofectamine 3000 (Invitrogen, USA) according to the manufacturer’s instruction and stable clones expressing miR-204-5p were selected using 100 mg/ml Zeoicin, respectively

tag: genotype/variation

value: miR-204-5p overexpression (average 525-fold increase than control)

value: breast cancer cells


title: MCF-7 ChIP-seq HDAC6 PRL+ ACY241+ biological rep 1 technical rep 1


title: Group3: 4T1 Clone#3 rep2 (miR-204-5p)


title: NKTnonFH_rep2

description:
004_RSS96_IsEn16
all_counts.tsv

tag: strain

value: Female

value: B CXCR5- PD-1-


title: MCF-7 ChIP-seq HDAC6 PRL+ ACY241- biological rep 2 technical rep 1

tag: cell type

value: HDAC6 Cell Signaling Technology #7558


title: SYC116


title: MCF-7 ChIP-seq HDAC6 PRL+ ACY241- biological rep 1 technical rep 2

tag: chip antibody


title: NKTFH_rep1

description:
001_RSS96_IsEn16
all_counts.tsv


title: Group2: 4T1 Clone#2 rep3 (miR-204-5p)

value: miR-204-5p overexpression (average 150-fold increase than control)

tag: cell line


title: NKT2_spleen_rep1

description:
002_2_S2_NKT_61417_200_IsEn12_B1
all_counts.tsv


title: NKTnonFH_rep1

description:
002_RSS96_IsEn16
all_counts.tsv


title: Group3: 4T1 Clone#3 rep1 (miR-204-5p)


title: NKTnonFH_rep4

description:
008_RSS96_IsEn16
all_counts.tsv


title: SYC115


title: ApoE shRNA mice with FC

description: processed data file: mice APOE shRNA with fc.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0
Reads Count for each gene in each sample was counted by HTSeq v0.6.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt files include normalized abundance measurements for each group

source_name: mice hippocampus ApoE knockdown with FC treatment

growth_protocol: Standard protocol for primary neuron culture for RNA-seq

extract_protocol:
Total RNA was extracted by Trizol.Total amount of 2 μg RNA per sample was used as input material for the RNA   sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA   Library  Prep  Kit  for  Illumina following the manufacturer’s   recommendations  and  index  codes  were  added  to  attribute  sequences  to  each  sample
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: brain

tag: tissue/cell type

value: mice hippocampus


title: NKT1_spleen_rep1

description:
001_1_S1_NKT_61417_200_IsEn12_A1
all_counts.tsv

value: A / CXCR3+ICOS-CD122+SDC1-IL-17RB-


title: Group2: 4T1 Clone#2 rep2 (miR-204-5p)


title: MCF-7 ChIP-seq HDAC6 PRL- ACY241+ biological rep 1 technical rep 2

tag: treatment


title: control shRNA mice with FC

source_name: mice hippocampus control with FC treatment


title: SYC114

tag: patient gender

tag: patient age

tag: idh1 status


title: MCF-7 ChIP-seq HDAC6 PRL+ ACY241- biological rep 1 technical rep 1


title: MCF-7 ChIP-seq HDAC6 PRL- ACY241- biological rep 2 technical rep 2

value: 120 minutes 0.1% DMSO


title: Group2: 4T1 Clone#2 rep1 (miR-204-5p)


title: NKT2_spleen_rep3

description:
033_33_S2_NKT_80817_200_IsEn12_A5
all_counts.tsv


title: SYC113

tag: tissue type


title: control shRNA mice without FC

source_name: mice hippocampus control without FC treatment


title: MCF-7 ChIP-seq HDAC6 PRL- ACY241- biological rep 2 technical rep 1


title: Group1: 4T1 Control rep3

value: control


title: SYC111

value: Mut


title: ApoE particle treatment rep1

description: processed data file: ApoE particle treatment.txt

source_name: ApoE particle treatment

value: primary neurons


title: MCF-7 ChIP-seq HDAC6 PRL- ACY241- biological rep 1 technical rep 2

value: ER+ breast cancer cells derived from pleural effusion of pt with breast adenocarcinoma


title: SYC110

value: Male

value: WT


title: Group1: 4T1 Control rep2


title: MCF-7 ChIP-seq HDAC6 PRL- ACY241- biological rep 1 technical rep 1


title: ApoE particle control rep1

source_name: ApoE particle treatment control


title: ApoE particle control rep2