title: 100_percent_d0_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d0_rep2.3


title: Overexpression of SOX17, TFAP2C, BLIMP1, clone_4; day4, MS151Y102

status: Public on Feb 15 2021

type: SRA

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C, BLIMP1 series, clone 4, harvested at day4, BT-sorted

library_source: transcriptomic

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the human genomeGRCh38.p2 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels (RPM) by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and GRC38.p2 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Expression levels (read counts per gene) were also estimated with HTSeq v0.9.1.
Genome_build: GRCh38.p2
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include gene name, entrez_id and read count for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: day4, from 585B1 hiPSC BTAG reporter line

growth_protocol: 585B1 hiPSCs (XY) was cultured with AK03N medium on iMatrix coated plate as reported previously (Sasaki and Yokobayashi et al., 2015; Kojima et al., 2017).

extract_protocol:
The cells were pelleted down and snap frozen until use.  RNA samples were extracted with RNeasy kit following manufacturer's protocol.
For 3'-seq analysis, cDNA synthesis / amplification from RNA samples and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60].

treatment_protocol:
The iMeLC induction was induced from iPSC cultured in above condition, passaged to fibronectin coated plate with Activin A (50 ng/ml), CHIR99021 (3µM) and Y27632 (10µM) in GMEM containing 15% KSR, and cultured for 44 to 48 hours.
Above iMeLCs were then dissociated and replated to low-adherent V-bottom plates to form aggregates with SCF (100 ng/ml), EGF (50 ng/ml), LIF(1000U/ml), Y27632 (10µM) and BMP4 (200 ng/mL) or Dox (1.0 µg/mL) in GMEM containing 15% KSR, until the harvest day.
For day 77 samples, BTAG positive cells were aggregated with mouse female E12.5 gonadal somatic cells and maintained at air-liquid interphase culture in MEMalpha with 10% FBS.

tag: cell line

value: 585B1 hiPSCs

tag: sampled time point

tag: reporter transgene

value: Blimp1-tdTomato, TFAP2C-EGFP

tag: other transgenes

value: rtTA; tetO-SOX17; tetO-TFAP2C; tetO-BLIMP1

tag: treatment

value: Dox


title: Overexpression of SOX17, TFAP2C, BLIMP1, clone_4; day2, MS151Y099

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C, BLIMP1 series, clone 4, harvested at day2, BT-sorted

source_name: day2, from 585B1 hiPSC BTAG reporter line


title: 85_percent_d8_rep2_Hsap_Mmul_Chimera

city: Boston

first: Jared

last: Brown

state: MA

address: Mailtop CLS11007, 450 Brookline Ave

department: Data Science

country: USA

institute: Dana Farber Cancer Institute

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d8_rep2

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts.
Sequencing reads were mapped to chimera transcriptome using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: A joint hg19/mm10 transcriptome reference was built by appending hg19 or mm10 respectively to the chromosome sequences and gene symbols. Tagging the gene symbols with the ID of the reference genome ensured easy decomposition of the resulting expression estimates into mouse and human subsets.
Supplementary_files_format_and_content: collated rsem output into tab files, expected counts (ec), transcripts per million (tpm's), and fragments per kilobase million (fpkm)

organism:
Homo sapiens
Mus musculus

source_name: Co-cultured human and mouse pluripotent stem cell-derived neural cells

growth_protocol: All cells were differentiated in vitro in DF3S (DMEM/F12, 64 mg/L L-ascorbic acid phosphate Mg salt, 0.014 mg/L sodium selenite, 1,743 mg/L sodium bicarbonate; Thermo Fisher Scientific, USA) + N2 and B27 Supplements (Thermo Fisher Scientific, USA) + 100ng/mL Noggin (R&D Systems, USA) on matrigel-coated multiwell culture plates.

extract_protocol:
Total RNA was then purified from 350 µL RLT-Plus Buffer using RNeasy Plus 96 and Micro Kits (Qiagen, Netherlands) and quantitated with the Quant-iT RNA Assay Kit (Thermo Fisher Scientific, USA).  RNA was diluted to one hundred nanograms for input.
The Ligation-Mediated Sequencing (LM-Seq) protocol was used to prepare and index all cDNA libraries (Hou et al 2015). Final cDNA libraries were quantitated with the Quant-iT PicoGreen Assay Kit (Thermofisher, Waltham, Massachusetts).
Twenty-five to forty-eight uniquely indexed samples were pooled per lane on an Illumina HiSeq 2500 with a single 51 base pair read and a 10 base pair index read.

treatment_protocol: For RNA sample collection, samples were washed with 1XPBS (Thermo Fisher Scientific, USA) and lysed in 700 µL RLT-PLUS buffer (Qiagen, USA), and stored at -80C until further processing.

tag: tissue composition

value: Homo Sapiens/Mus Musculus Chimera

tag: cell type

tag: growth time (days)

tag: mixing day

tag: mixing percent human

tag: biological replicate number

value: Neural induction medium (see protocols section below)


title: Overexpression of SOX17, TFAP2C, BLIMP1, clone_4; iPSC, MS151Y096

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C, BLIMP1 series, clone 4, harvested at iPSC, non-sorted

source_name: iPSC, from 585B1 hiPSC BTAG reporter line

value: iPSC


title: 100_percent_d0_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d0_rep2.2

value: Homo sapiens cells only

value: pluripotent stem cell-derived neural cells


title: 85_percent_d7_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d7_rep2.2


title: 85_percent_d7_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d7_rep2.3


title: Overexpression of SOX17, TFAP2C, clone_28; day2, MS155Y62

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 28, harvested at day2, BT-sorted

value: rtTA; tetO-SOX17; tetO-TFAP2C


title: 100_percent_d0_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d0_rep2.1


title: 85_percent_d7_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d7_rep2.1


title: Overexpression of SOX17, TFAP2C, clone_2; day2, MS155Y61

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 2, harvested at day2, BT-sorted


title: 85_percent_d6_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d6_rep2.3


title: 85_percent_d7_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d7_rep2


title: Overexpression of SOX17, TFAP2C, clone_28; day1, MS155Y60

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 28, harvested at day1, BT-sorted

source_name: day1, from 585B1 hiPSC BTAG reporter line


title: 100_percent_d0_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d0_rep2


title: 85_percent_d10_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d10_rep2.2


title: Overexpression of SOX17, TFAP2C, BLIMP1, clone_4; day4, MS151Y103

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C, BLIMP1 series, clone 4, harvested at day4, BTAG-sorted

tag: pgclcs induced

value: Yes


title: 85_percent_d6_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d6_rep2.1


title: 85_percent_d5_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d5_rep2.3


title: 85_percent_d6_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d6_rep2


title: Overexpression of SOX17, TFAP2C, clone_2; day1, MS155Y59

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 2, harvested at day1, BT-sorted


title: 100_percent_d1_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d1_rep2


title: 100_percent_d1_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d1_rep2.1


title: 85_percent_d5_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d5_rep2.2


title: 85_percent_d5_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d5_rep2


title: 0_percent_d42_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d42_rep2.3

value: Mus musculus cells only


title: 0_percent_d42_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d42_rep2.2


title: 0_percent_d42_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d42_rep2.1


title: 85_percent_d5_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d5_rep2.1


title: 0_percent_d42_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d42_rep2


title: 85_percent_d4_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d4_rep2.3


title: Overexpression of SOX17, TFAP2C, clone_28; iMeLC, MS155Y58

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 28, harvested at iMeLC, BT-sorted

source_name: iMeLC, from 585B1 hiPSC BTAG reporter line

value: iMeLC


title: Overexpression of SOX17, TFAP2C, clone_2; iMeLC, MS155Y57

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 2, harvested at iMeLC, BT-sorted


title: 85_percent_d4_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d4_rep2.2


title: Overexpression of SOX17, TFAP2C, clone_11; day2, MS151Y094

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 11, harvested at day2, BT-sorted


title: 85_percent_d6_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d6_rep2.2


title: 85_percent_d4_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d4_rep2.1


title: 0_percent_d40_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d40_rep2.3


title: 0_percent_d40_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d40_rep2.2


title: Overexpression of SOX17, TFAP2C, clone_2; day2, MS151Y093

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 2, harvested at day2, BT-sorted


title: 85_percent_d4_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d4_rep2


title: Overexpression of SOX17, TFAP2C, clone_11; day2, MS151Y092


title: 85_percent_d3_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d3_rep2.2


title: 85_percent_d3_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d3_rep2.1


title: 0_percent_d40_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d40_rep2.1


title: 85_percent_d3_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d3_rep2


title: 85_percent_d2_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d2_rep2.3


title: Overexpression of SOX17, TFAP2C, clone_2; day2, MS151Y091


title: 0_percent_d40_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d40_rep2


title: 85_percent_d2_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d2_rep2.2


title: 85_percent_d2_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d2_rep2.1


title: 85_percent_d2_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d2_rep2


title: 0_percent_d38_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d38_rep2.2


title: 85_percent_d1_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d1_rep2.3


title: 85_percent_d1_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d1_rep2.2


title: 0_percent_d38_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d38_rep2.1


title: 85_percent_d1_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d1_rep2.1


title: 85_percent_d1_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d1_rep2


title: Overexpression of SOX17, TFAP2C, clone_2; day2, MS151Y088

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 2, harvested at day2, BTAG-sorted

value: BMP+Dox


title: 85_percent_d3_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
85_percent_d3_rep2.3


title: 0_percent_d38_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d38_rep2


title: 10_percent_d42_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d42_rep2.3


title: 10_percent_d42_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d42_rep2.1


title: 0_percent_d36_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d36_rep2.3


title: 10_percent_d42_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d42_rep2


title: 0_percent_d36_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d36_rep2.1


title: 10_percent_d40_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d40_rep2.1


title: Overexpression of SOX17, TFAP2C, clone_11; iMeLC, MS151Y084

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 11, harvested at iMeLC, non-sorted


title: 10_percent_d40_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d40_rep2


title: Overexpression of SOX17, TFAP2C, clone_11; day2, MS151Y089

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 11, harvested at day2, BT-sorted


title: 0_percent_d36_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d36_rep2


title: 10_percent_d38_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d38_rep2.2


title: 10_percent_d38_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d38_rep2.3


title: 10_percent_d38_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d38_rep2.1


title: 0_percent_d34_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d34_rep2.3


title: Overexpression of SOX17, TFAP2C, clone_11; iPSC, MS151Y082

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 11, harvested at iPSC, non-sorted


title: Overexpression of SOX17, TFAP2C, clone_2; day2, MS151Y087

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 2, harvested at day2, BT-sorted


title: 10_percent_d38_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d38_rep2


title: 0_percent_d34_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d34_rep2.2


title: 10_percent_d36_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d36_rep2.3


title: 10_percent_d40_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d40_rep2.3


title: 10_percent_d36_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d36_rep2.2


title: 10_percent_d42_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d42_rep2.2


title: Overexpression of SOX17, TFAP2C, clone_11; day2, MS151Y090

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 11, harvested at day2, BTAG-sorted


title: Overexpression of SOX17, TFAP2C, clone_11; iMeLC, MS151Y086

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 11, harvested at iMeLC, non-sorted


title: Ctrl of Overexpression of SOX17, TFAP2C, GATA3, clone_BTAG; day77, MS192Y107

description: Transcriptome of amplified cDNA from PGCLC induction of  Ctrl of OE: SOX17, TFAP2C, GATA3 series, clone BTAG, harvested at day77, BTAG-sorted

source_name: day77, from 585B1 hiPSC BTAG reporter line

value: BMP


title: Overexpression of SOX17, TFAP2C, clone_2; iMeLC, MS151Y085

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 2, harvested at iMeLC, non-sorted


title: 10_percent_d36_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d36_rep2.1


title: 0_percent_d36_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d36_rep2.2


title: 10_percent_d36_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d36_rep2


title: 0_percent_d34_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d34_rep2.1


title: 10_percent_d34_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d34_rep2.3


title: Overexpression of SOX17, TFAP2C, clone_2; iPSC, MS151Y081

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: SOX17, TFAP2C series, clone 2, harvested at iPSC, non-sorted


title: 10_percent_d34_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d34_rep2.2


title: Ctrl of Overexpression of SOX17, TFAP2C, GATA3, clone_BTAG; day6, MS188Y91

description: Transcriptome of amplified cDNA from PGCLC induction of  Ctrl of OE: SOX17, TFAP2C, GATA3 series, clone BTAG, harvested at day6, BTAG-sorted

source_name: day6, from 585B1 hiPSC BTAG reporter line


title: Ctrl of GATA2/3 KO, clone_BTAG; day6, MS188Y131

description: Transcriptome of amplified cDNA from PGCLC induction of  Ctrl of GATA2/3 KO series, clone BTAG, harvested at day6, BTAG-sorted


title: 10_percent_d34_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d34_rep2.1


title: Overexpression of SOX17, TFAP2C, clone_2; iMeLC, MS151Y083


title: 10_percent_d32_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d32_rep2.3


title: 0_percent_d32_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d32_rep2.3


title: 10_percent_d34_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d34_rep2


title: 0_percent_d34_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d34_rep2


title: 0_percent_d32_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d32_rep2.2


title: 10_percent_d32_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d32_rep2.2


title: 10_percent_d30_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d30_rep2.3


title: 10_percent_d32_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d32_rep2.1


title: 0_percent_d32_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d32_rep2


title: 10_percent_d30_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d30_rep2.2


title: Ctrl of GATA2/3 KO, clone_BTAG; day2, MS188Y121

description: Transcriptome of amplified cDNA from PGCLC induction of  Ctrl of GATA2/3 KO series, clone BTAG, harvested at day2, BTAG-sorted


title: 0_percent_d32_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d32_rep2.1


title: 10_percent_d32_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d32_rep2


title: 10_percent_d30_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d30_rep2


title: Ctrl of GATA2/3 KO, clone_BTAG; day4, MS188Y111

description: Transcriptome of amplified cDNA from PGCLC induction of  Ctrl of GATA2/3 KO series, clone BTAG, harvested at day4, BTAG-sorted


title: 0_percent_d30_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d30_rep2.3


title: Ctrl of GATA2/3 KO, clone_BTAG; day6, MS188Y116

description: Transcriptome of amplified cDNA from PGCLC induction of  Ctrl of GATA2/3 KO series, clone BTAG, harvested at day6, BTAG-sorted


title: 10_percent_d28_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d28_rep2.3


title: 10_percent_d28_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d28_rep2.2


title: 0_percent_d30_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d30_rep2.2


title: Ctrl of GATA2/3 KO, clone_BTAG; day2, MS188Y106


title: 10_percent_d28_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d28_rep2.1


title: 0_percent_d30_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d30_rep2.1


title: Ctrl of GATA2/3 KO, clone_BTAG; day4, MS168Y29


title: Ctrl of GATA2/3 KO, clone_BTAG; day4, MS188Y126


title: Ctrl of GATA2/3 KO, clone_BTAG; day2, MS168Y19


title: 10_percent_d28_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d28_rep2


title: 10_percent_d26_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d26_rep2.3


title: 0_percent_d30_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d30_rep2


title: 10_percent_d26_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d26_rep2.2


title: Ctrl of GATA2/3 KO, clone_BTAG; iMeLC, MS168Y9

description: Transcriptome of amplified cDNA from PGCLC induction of  Ctrl of GATA2/3 KO series, clone BTAG, harvested at iMeLC, non-sorted


title: 10_percent_d26_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d26_rep2.1


title: 10_percent_d30_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d30_rep2.1


title: 0_percent_d28_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d28_rep2.3


title: 10_percent_d40_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d40_rep2.2


title: 10_percent_d26_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d26_rep2


title: 10_percent_d24_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d24_rep2.3


title: 10_percent_d24_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d24_rep2.2


title: GATA3 KO, clone_40; day6, MS188Y130

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 40, harvested at day6, BTAG-sorted


title: 0_percent_d28_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d28_rep2.1


title: 10_percent_d24_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d24_rep2.1


title: 0_percent_d28_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d28_rep2.2


title: GATA3 KO, clone_18; day6, MS188Y128

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 18, harvested at day6, BTAG-sorted


title: 10_percent_d22_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d22_rep2.3


title: 0_percent_d28_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d28_rep2


title: 10_percent_d22_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d22_rep2.2


title: GATA3 KO, clone_17; day6, MS188Y127

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 17, harvested at day6, BTAG-sorted


title: 10_percent_d22_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d22_rep2.1


title: 10_percent_d22_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d22_rep2


title: GATA3 KO, clone_40; day4, MS188Y125

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 40, harvested at day4, BTAG-sorted


title: 10_percent_d20_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d20_rep2.3


title: 10_percent_d20_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d20_rep2.2


title: GATA3 KO, clone_30; day4, MS188Y124

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 30, harvested at day4, BTAG-sorted


title: 0_percent_d26_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d26_rep2.2


title: 10_percent_d20_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d20_rep2.1


title: 0_percent_d26_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d26_rep2.1


title: 10_percent_d18_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d18_rep2.3


title: 10_percent_d20_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d20_rep2


title: 10_percent_d24_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d24_rep2


title: GATA3 KO, clone_18; day4, MS188Y123

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 18, harvested at day4, BTAG-sorted


title: GATA3 KO, clone_30; day6, MS188Y129

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 30, harvested at day6, BTAG-sorted


title: 10_percent_d18_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d18_rep2.1


title: 0_percent_d26_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d26_rep2


title: 10_percent_d18_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d18_rep2.2


title: GATA3 KO, clone_17; day4, MS188Y122

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 17, harvested at day4, BTAG-sorted


title: 10_percent_d18_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d18_rep2


title: 10_percent_d16_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d16_rep2.3


title: 10_percent_d16_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d16_rep2.2


title: GATA3 KO, clone_40; day2, MS188Y120

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 40, harvested at day2, BTAG-sorted


title: 0_percent_d24_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d24_rep2.2


title: 0_percent_d24_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d24_rep2.3


title: GATA3 KO, clone_30; day2, MS188Y119

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 30, harvested at day2, BTAG-sorted


title: 0_percent_d26_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d26_rep2.3


title: GATA3 KO, clone_18; day2, MS188Y118

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 18, harvested at day2, BTAG-sorted


title: 10_percent_d14_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d14_rep2.3


title: 0_percent_d24_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d24_rep2.1


title: 0_percent_d24_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d24_rep2


title: GATA3 KO, clone_17; day2, MS188Y117

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 17, harvested at day2, BTAG-sorted


title: 10_percent_d14_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d14_rep2.2


title: 0_percent_d22_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d22_rep2.3


title: 10_percent_d14_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d14_rep2


title: GATA3 KO, clone_40; day6, MS190Y115

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 40, harvested at day6, BTAG-sorted


title: 10_percent_d12_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d12_rep2.3


title: 0_percent_d22_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d22_rep2.2


title: 10_percent_d12_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d12_rep2.2


title: GATA3 KO, clone_30; day6, MS190Y114

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 30, harvested at day6, BTAG-sorted


title: 10_percent_d12_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d12_rep2.1


title: 10_percent_d12_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d12_rep2


title: 10_percent_d10_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d10_rep2.3


title: 0_percent_d22_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d22_rep2


title: 0_percent_d22_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d22_rep2.1


title: GATA3 KO, clone_18; day6, MS188Y113

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 18, harvested at day6, BTAG-sorted


title: 10_percent_d10_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d10_rep2.1


title: 10_percent_d16_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d16_rep2.1


title: 0_percent_d18_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d18_rep2.3


title: 10_percent_d16_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d16_rep2


title: GATA3 KO, clone_17; day6, MS188Y112

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 17, harvested at day6, BTAG-sorted


title: 10_percent_d8_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d8_rep2.3


title: 10_percent_d10_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d10_rep2


title: GATA3 KO, clone_40; day4, MS188Y110

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 40, harvested at day4, BTAG-sorted


title: 0_percent_d18_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d18_rep2.2


title: 10_percent_d8_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d8_rep2.2


title: GATA3 KO, clone_30; day4, MS192Y109

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 30, harvested at day4, BTAG-sorted


title: 10_percent_d8_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d8_rep2.1


title: 10_percent_d14_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d14_rep2.1


title: 10_percent_d8_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d8_rep2


title: 0_percent_d18_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d18_rep2.1


title: GATA3 KO, clone_18; day4, MS188Y108

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 18, harvested at day4, BTAG-sorted


title: 0_percent_d18_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d18_rep2


title: 10_percent_d7_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d7_rep2.3


title: 10_percent_d7_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d7_rep2.2


title: GATA3 KO, clone_17; day4, MS192Y108

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 17, harvested at day4, BTAG-sorted


title: 0_percent_d16_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d16_rep2.3


title: 10_percent_d6_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d6_rep2.3


title: 10_percent_d7_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d7_rep2.1


title: 10_percent_d7_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d7_rep2


title: 0_percent_d16_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d16_rep2.2


title: GATA3 KO, clone_30; day2, MS188Y104

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 30, harvested at day2, BTAG-sorted


title: GATA3 KO, clone_40; day2, MS188Y105

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 40, harvested at day2, BTAG-sorted


title: 10_percent_d6_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d6_rep2.2


title: 0_percent_d16_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d16_rep2.1


title: 10_percent_d6_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d6_rep2


title: 10_percent_d10_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d10_rep2.2


title: 10_percent_d5_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d5_rep2.2


title: GATA3 KO, clone_18; day2, MS188Y103

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 18, harvested at day2, BTAG-sorted


title: 0_percent_d16_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d16_rep2


title: 10_percent_d5_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d5_rep2.3


title: 10_percent_d4_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d4_rep2.3


title: 0_percent_d14_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d14_rep2.3


title: 10_percent_d6_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d6_rep2.1


title: GATA3 KO, clone_17; day2, MS188Y102

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 17, harvested at day2, BTAG-sorted


title: 0_percent_d14_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d14_rep2.2


title: 10_percent_d4_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d4_rep2.2


title: GATA3 KO, clone_18; day4, MS168Y51

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 18, harvested at day4, BTAG-sorted


title: 10_percent_d4_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d4_rep2.1


title: 0_percent_d14_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d14_rep2.1


title: GATA3 KO, clone_17; day4, MS168Y50

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 17, harvested at day4, BTAG-sorted


title: 10_percent_d4_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d4_rep2


title: 0_percent_d14_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d14_rep2


title: 0_percent_d12_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d12_rep2.3


title: GATA3 KO, clone_40; day2, MS168Y46

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 40, harvested at day2, BTAG-sorted


title: GATA3 KO, clone_18; day2, MS168Y45

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 18, harvested at day2, BTAG-sorted


title: 10_percent_d3_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d3_rep2.1


title: 10_percent_d3_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d3_rep2


title: 0_percent_d12_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d12_rep2.2


title: 10_percent_d3_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d3_rep2.2


title: 10_percent_d2_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d2_rep2.3


title: 0_percent_d12_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d12_rep2.1


title: 10_percent_d2_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d2_rep2.2


title: 10_percent_d5_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d5_rep2.1


title: GATA3 KO, clone_40; day4, MS168Y52

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 40, harvested at day4, BTAG-sorted


title: 10_percent_d2_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d2_rep2.1


title: GATA3 KO, clone_17; day2, MS168Y44

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 17, harvested at day2, BTAG-sorted


title: 10_percent_d5_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d5_rep2


title: 10_percent_d2_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d2_rep2


title: GATA3 KO, clone_40; iMeLC, MS168Y40

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 40, harvested at iMeLC, non-sorted


title: 10_percent_d1_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d1_rep2.3


title: 0_percent_d12_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d12_rep2


title: 10_percent_d1_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d1_rep2.2


title: GATA3 KO, clone_18; iMeLC, MS168Y39

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 18, harvested at iMeLC, non-sorted


title: 10_percent_d3_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d3_rep2.3


title: 0_percent_d10_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d10_rep2.3


title: 10_percent_d1_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d1_rep2


title: 0_percent_d10_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d10_rep2.2


title: 85_percent_d42_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d42


title: 85_percent_d42.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d42.1


title: GATA3 KO, clone_30; day4, MS168Y28

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 30, harvested at day4, BTAG-sorted


title: GATA3 KO, clone_30; day2, MS168Y18

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 30, harvested at day2, BTAG-sorted


title: 85_percent_d40_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d40


title: 85_percent_d38.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d38.1


title: 0_percent_d10_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d10_rep2


title: 85_percent_d38_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d38


title: 0_percent_d10_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d10_rep2.1


title: 0_percent_d8_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d8_rep2.3


title: GATA2 KO, clone_12; day4, MS168Y27

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA2 KO series, clone 12, harvested at day4, BTAG-sorted


title: 0_percent_d38_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d38_rep2.3


title: GATA3 KO, clone_30; iMeLC, MS168Y8

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 30, harvested at iMeLC, non-sorted


title: 10_percent_d1_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
10_percent_d1_rep2.1


title: 0_percent_d8_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d8_rep2.1


title: 85_percent_d36_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d36


title: 85_percent_d36.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d36.1


title: 85_percent_d32.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d32.1


title: 0_percent_d8_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d8_rep2.2


title: 85_percent_d40.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d40.1


title: GATA2 KO, clone_6; day4, MS168Y26

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA2 KO series, clone 6, harvested at day4, BTAG-sorted


title: GATA2 KO, clone_1; day4, MS168Y25

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA2 KO series, clone 1, harvested at day4, BTAG-sorted


title: GATA3 KO, clone_17; iMeLC, MS168Y38

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA3 KO series, clone 17, harvested at iMeLC, non-sorted


title: 85_percent_d32_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d32


title: 85_percent_d30_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d30


title: 0_percent_d8_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d8_rep2


title: 85_percent_d30.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d30.1


title: 0_percent_d7_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d7_rep2.3


title: 85_percent_d28.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d28.1


title: GATA2 KO, clone_12; day2, MS168Y17

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA2 KO series, clone 12, harvested at day2, BTAG-sorted


title: 85_percent_d28_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d28


title: GATA2 KO, clone_6; day2, MS168Y16

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA2 KO series, clone 6, harvested at day2, BTAG-sorted


title: 0_percent_d7_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d7_rep2.2


title: 0_percent_d7_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d7_rep2.1


title: 85_percent_d34.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d34.1


title: GATA2 KO, clone_1; day2, MS168Y15

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA2 KO series, clone 1, harvested at day2, BTAG-sorted


title: 85_percent_d24.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d24.1


title: 85_percent_d26_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d26


title: 85_percent_d34_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d34


title: 85_percent_d22.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d22.1


title: 0_percent_d7_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d7_rep2


title: 85_percent_d24_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d24


title: 0_percent_d6_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d6_rep2.3


title: 85_percent_d20.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d20.1


title: 85_percent_d20_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d20


title: 85_percent_d18_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d18


title: GATA2 KO, clone_1; iMeLC, MS168Y5

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA2 KO series, clone 1, harvested at iMeLC, non-sorted


title: 85_percent_d18.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d18.1


title: 0_percent_d6_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d6_rep2.2


title: GATA2 KO, clone_6; iMeLC, MS168Y6

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA2 KO series, clone 6, harvested at iMeLC, non-sorted


title: Overexpression of TFAP2C, BLIMP1, clone_2; day2, MS152Y49

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: TFAP2C, BLIMP1 series, clone 2, harvested at day2, BT-sorted

value: rtTA; tetO-TFAP2C; tetO-BLIMP1


title: 85_percent_d22_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d22


title: 0_percent_d6_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d6_rep2.1


title: 85_percent_d14_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d14


title: 85_percent_d16_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d16


title: 0_percent_d6_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d6_rep2


title: 85_percent_d26.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d26.1


title: 85_percent_d12.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d12.1


title: Overexpression of TFAP2C, BLIMP1, clone_2; iMeLC, MS151Y123

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: TFAP2C, BLIMP1 series, clone 2, harvested at iMeLC, non-sorted


title: 0_percent_d5_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d5_rep2.3


title: 85_percent_d12_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d12


title: 85_percent_d10.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d10.1


title: 0_percent_d5_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d5_rep2.2


title: Overexpression of TFAP2C, BLIMP1, clone_2; day4, MS151Y119

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: TFAP2C, BLIMP1 series, clone 2, harvested at day4, BT-sorted


title: 85_percent_d14.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d14.1


title: 85_percent_d8.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d8.1


title: 0_percent_d5_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d5_rep2.1


title: Overexpression of TFAP2C, BLIMP1, clone_2; day2, MS151Y116

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: TFAP2C, BLIMP1 series, clone 2, harvested at day2, BT-sorted


title: 85_percent_d10_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d10


title: 85_percent_d16.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d16.1


title: 85_percent_d7.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d7.1


title: 85_percent_d8_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d8


title: 0_percent_d5_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d5_rep2


title: 85_percent_d7_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d7


title: Overexpression of TFAP2C, BLIMP1, clone_2; day1, MS151Y113

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: TFAP2C, BLIMP1 series, clone 2, harvested at day1, non-sorted


title: Overexpression of TFAP2C, BLIMP1, clone_2; iMeLC, MS151Y110

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: TFAP2C, BLIMP1 series, clone 2, harvested at iMeLC, non-sorted


title: 85_percent_d6.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d6.1


title: Overexpression of TFAP2C, BLIMP1, clone_2; day1, MS151Y126


title: 0_percent_d4_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d4_rep2.3


title: Overexpression of TFAP2C, BLIMP1, clone_2; iPSC, MS151Y107

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: TFAP2C, BLIMP1 series, clone 2, harvested at iPSC, non-sorted


title: 85_percent_d5.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d5.1


title: 0_percent_d4_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d4_rep2.2


title: 85_percent_d5_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d5


title: Overexpression of TFAP2C, BLIMP1, clone_2; day4, MS151Y101

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: TFAP2C, BLIMP1 series, clone 2, harvested at day4, BT-sorted


title: 85_percent_d4.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d4.1


title: 85_percent_d4_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d4


title: 0_percent_d4_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d4_rep2.1


title: 85_percent_d3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d3.1


title: Overexpression of TFAP2C, BLIMP1, clone_2; day2, MS151Y098

description: Transcriptome of amplified cDNA from PGCLC induction of Dox-inducible OE: TFAP2C, BLIMP1 series, clone 2, harvested at day2, BT-sorted


title: 85_percent_d3_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d3


title: 0_percent_d3_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d3_rep2.3


title: 0_percent_d3_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d3_rep2.2


title: RPE1 cells, RB26_plus_dox_replicate_2

city: Columbus

first: Wayne

last: Miles

state: OH

address: 460 West 12th Avenue

department: Molecular Genetics

institute: The Ohio State University

data_processing:
The RNA- seq was conducted on the Hi-SEQ at the MGH Cancer Center using Nextseq 500 High output v2 kit (Illumina).
Raw sequencing data demultiplexed using flexbar
Files containing RNA sequencing reads were adaptor- and quality-trimmed using TrimGalore-0.6.0
Bowtie2 (version 2.2.9) was used to removing contaminating reads from ribosomal RNA and transfer RNA
The trimmed and contamination-filtered reads were mapped to the hg38 genome (GENCODE Release 31) using STAR aligner version 2.5.2a and a counts matrix was obtained using the ‘GeneCounts’ option
Genome_build: hg38
Supplementary_files_format_and_content: .txt files with raw counts for each sample and a .txt file with FPKMs for each sample

source_name: RPE1 cells

growth_protocol: RPE1 cells were grown DMEM containing 5% (tetracycline free) FBS and Glutamine under standard culturing conditions.

extract_protocol:
Total RNA from cells was generated using the TruSeq Stranded Total RNA kit with Ribo Zero Gold kit (Illumina). The RNA was then purified using the Agencourt RNAclean XP kit (Beckman Culter).
cDNA was generated using Superscript II (Life Technologies). The quality of the library was measured using the high sensitivity D1000 reagents and screen tape from Agilent. The RNA- seq was conducted on the Hi-SEQ at the MGH Cancer Center using Nextseq 500 High output v2 kit (Illumina).

treatment_protocol: RB depletion cells were grown in the media described above supplemented with 4ug/ml of Doxycycline for 3 days before being split and grown in new DOX-supplemented DMEM/FBS for a further 3 days. Non-DOX treated cells were grown using the same protocol without the addition of DOX.

tag: shirna

tag: dox

value: DOX+


title: 85_percent_d2_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d2


title: 0_percent_d3_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d3_rep2.1


title: Overexpression of TFAP2C, BLIMP1, clone_2; iPSC, MS151Y095

value: 585B1 hiPSCs


title: 85_percent_d1.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d1.1


title: 85_percent_d1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d1


title: 10_percent_d42_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d42


title: 10_percent_d40.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d40.1


title: GATA2 KO, clone_12; iMeLC, MS168Y7

description: Transcriptome of amplified cDNA from PGCLC induction of  GATA2 KO series, clone 12, harvested at iMeLC, non-sorted

value: Blimp1-tdTomato, TFAP2C-EGFP


title: 0_percent_d3_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d3_rep2


title: 85_percent_d6_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d6


title: RPE1 cells, RB26_minus_dox_replicate_1

value: DOX-


title: 10_percent_d40_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d40


title: 10_percent_d38.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d38.1


title: 10_percent_d38_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d38


title: 0_percent_d4_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d4_rep2


title: 85_percent_d2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
85_percent_d2.1


title: RPE1 cells, RB26_minus_dox_replicate_2


title: 10_percent_d42.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d42.1


title: RPE1 cells, RB25_plus_dox_replicate_2


title: 0_percent_d2_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d2_rep2.1


title: 10_percent_d34.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d34.1


title: RPE1 cells, RB26_plus_dox_replicate_1


title: RPE1 cells, RB25_plus_dox_replicate_1


title: 10_percent_d34_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d34


title: RPE1 cells, RB25_minus_dox_replicate_2


title: 10_percent_d32.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d32.1


title: 10_percent_d30_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d30


title: 10_percent_d30.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d30.1


title: 10_percent_d32_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d32


title: 0_percent_d1_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d1_rep2.3


title: 0_percent_d1_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d1_rep2.2


title: 0_percent_d2_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d2_rep2.3


title: 0_percent_d2_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d2_rep2


title: RPE1 cells, RB25_minus_dox_replicate_1


title: 10_percent_d36.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d36.1


title: 10_percent_d28.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d28.1


title: 10_percent_d28_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d28


title: 10_percent_d26.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d26.1


title: 0_percent_d2_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d2_rep2.2


title: 10_percent_d36_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d36


title: 10_percent_d26_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d26


title: 0_percent_d1_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d1_rep2


title: 10_percent_d24_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d24


title: IFNAR1 wild type, replicate 4

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: IFNAR1 wild type, replicate 4

data_processing:
RNA-seq data was aligned using bowtie2 against mm10 version of the mouse genome and RSEM v1.2.31 software was used to estimate raw read counts using transcriptome information from Ensemble v84 set
DESeq2 was used to estimate significance of differential expression between groups
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene as estimated by RSEM

organism: Mus musculus

source_name: PMN-MDSC cells

extract_protocol:
Total RNA was extracted from 1-2 million PMN-MDSC using the Direct-zol RNA Miniprep (Zymo Research, Irvine, CA). RNA quantity was determined using the Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA) and the quality was validated using the TapeStation RNA ScreenTape (Agilent, Santa Clara, CA).
75 ng of DNAse I treated, total RNA was used to prepare library for Illumina Sequencing using the Quant-Seq 3’mRNA-Seq Library Preparation Kit (Lexogen, Vienna, Austria)

value: wild type

tag: replicate


title: IFNAR1 mutant, replicate 1

description: IFNAR1 mutant, replicate 1

value: mutant


title: 10_percent_d22.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d22.1

value: Homo Sapiens/Mus Musculus Chimera

value: Neural induction medium (see protocols section below)


title: 0_percent_d0_rep2.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d0_rep2.3


title: IFNAR1 wild type, replicate 3

description: IFNAR1 wild type, replicate 3


title: 10_percent_d22_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d22


title: 10_percent_d20.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d20.1


title: 0_percent_d0_rep2.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d0_rep2.2


title: IFNAR1 wild type, replicate 1

description: IFNAR1 wild type, replicate 1


title: IFNAR1 wild type, replicate 2

description: IFNAR1 wild type, replicate 2


title: 10_percent_d20_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d20


title: 10_percent_d18.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d18.1


title: 10_percent_d16.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d16.1


title: 10_percent_d18_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d18


title: 10_percent_d16_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d16


title: 0_percent_d1_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d1_rep2.1


title: 100_percent_d42_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d42

value: Homo sapiens cells only


title: 10_percent_d24.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d24.1

value: pluripotent stem cell-derived neural cells


title: LCL_461_B958

city: Durham

first: Elliott

middle: Daniel

last: SoRelle

state: NC

address: 130 Research Drive (CARL Building)

department: Molecular Genetics & Microbiology

institute: Duke University

description: total polyA mRNA (single cell, host and viral)

data_processing:
[base-calling]  Illumina HiSeq 3000/4000
[alignment]  cellranger v.2.0.0 (mkfastq); alignment was performed against the human genome (hg38) concatenated with the type 1 EBV genome (NC_007605) as an extra chromosome to capture viral transcripts
[qc filtering]  Seurat  v.3.1.5 (R); filtered out cells with <200 or >65000 unique RNA molecules and cells with >5% mitochondrial gene expression.
[normalization]  Seurat  v.3.1.5 (R)
[cell cycle marker regression]  Seurat  v.3.1.5 (R)
[scaling and feature selection]  Seurat  v.3.1.5 (R)
[PCA, dimensional reduction, and visualization]  Seurat  v.3.1.5 (R)
Supplementary_files_format_and_content: TSV, MTX

organism:
Homo sapiens
human gammaherpesvirus 4

source_name: primary B cells (EBV-infected)

growth_protocol: Primary human B cells were isolated from whole blood by Ficoll gradient. CD19+ B cells were isolated from purified PBMCs by magnetic separation. Purified B cells were infected in bulk by incubation with viral supernatnants prepared from stimulated B95-8 Z-HT or M81 cells. Viral supernatants were incubated with primary B cells for 1 hr at 37 degrees C with 5% CO2. Cells were rinsed in 1x PBS after infection and cultured in RPMI 1640 media with 15% fetal calf serum (R15). Prior to single cell preparation, outgrown LCLs were cultured in RPMI 1640 media with 10% fetal calf serum (R10) supplemented with 2 mM L-glutamine, 100 U/mL penicillin, 100 ug/mL streptomycin, and 0.5 ug.mL cyclosporine A.

extract_protocol:
Each of the three samples was prepared separetly using the 10x Genomics Chromium controller
Standard library construction as specified by the manufacturer's protocols (v2 chemistry)
capture and single-cell indexing of total polyA mRNA

treatment_protocol: No additional treatments were applied after primary cell infection and culture

value: B lymphocyte

tag: donor

tag: viral strain (transformant)


title: WT mEpiSCs replicate 2

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were trimmed with TrimGalore software (flags --stringency 3 --paired)
Trimmed reads were aligned to GRCm38 genome using STAR aligner (flags --runThreadN 64 --genomeLoad).
Counts were estimated using HTSeq-count (flags -q -f bam -r pos -s no -t exon -i gene_name).
Genome_build: GRCn38
Supplementary_files_format_and_content: HTSeq counts

molecule: polyA RNA

source_name: Epiblast stem cells

growth_protocol: mESCs were grown in 2i/LIF conditions, and mEpiSCs were grown in FGF/Activin A conditions

extract_protocol:
Total RNA was extracted using the TRIzol-based RNA MiniPrep kit (Zymo Research).
mRNA was purified using Poly-A Dynabeads mRNA DIRECT Kit (Invitrogen) and mRNA then was utilized for RNA-Seq by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s instruction.

tag: genotype

value: WT

tag: growth protocol

value: DMEM-F12 with HEPES (Sigma; D6421), N2 supplement (in-house made), 5 ml B27 supplement (in-house made), 2mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Invitrogen), 5 mg/ml BSA (Sigma), with 12 ng/ml recombinant human bFGF (Peprotech) and 20 ng/ml recombinant Activin A (Peprotech)


title: LCL_777_M81


title: IFNAR1 mutant, replicate 2

description: IFNAR1 mutant, replicate 2


title: 10_percent_d14.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d14.1


title: 0_percent_d0_rep2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d0_rep2

value: Mus musculus cells only


title: 100_percent_d40_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d40


title: LCL_777_B958


title: WT mESCs replicate 2

source_name: Embryonic stem cells

value: 500 mL [1:1] Neurobasal (ThermoFisher; 21103049) and DMEM-F12 with HEPES (Sigma; D6421), N2 supplement (in-house made), 5 ml B27 supplement (in-house made), 2mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Invitrogen), 5 mg/ml BSA (Sigma), 10 ng/ml recombinant human LIF (in-house made), 3μM CHIR99021 (Axon Medchem; HY10182) and 1μM PD0325901 (Axon Medchem; HY10254)


title: 100_percent_d38_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d38


title: 0_percent_d0_rep2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d0_rep2.1


title: WT mEpiSCs replicate 1


title: 10_percent_d12.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d12.1


title: 100_percent_d36_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d36


title: WT mESCs replicate 1


title: mouse_huT-cells_h7

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling with NextSeq Control/RTA v2 and FASTQ file generation with bcl2fastq v2.20.0.422
Adapter clipping and trimming with cutadapt 2.5 with default parameters. In addition, Cutadapt was given the –nextseq-trim=20 switch to handle two color sequencing chemistry and reads that were trimmed to length 0 were discarded.
Computational deconvolution of mouse and human reads in the xenograft sequence data was done using the tool XenofilteR
Mapping to RefSeq GRCm38.p6 Mouse genome with STAR version 2.7.2b and raw read counting with featureCounts v 1.6.4 using the RefSeq annotation.
Differential Expression analysis with DESeq2_1.22.2
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: CSV: Raw read table

extract_protocol: RNA was purified using the RNeasy Plus Micro Kit (Qiagen ID: 74034)

treatment_protocol: myocardial tissue (apical region) was collected fromNSG-DR1 hearts left untreated (control) or transferred with human CD4+ T cells, 6 weeks after transfer.Tissue was maintained in RNAlater solution for 24h at 4°C before and RNA was purified using the RNAeasy Plus Micro Kit (ID: 74034)

tag: strain

value: human CD4+ T cell transfer

tag: tissue

value: heart


title: 10_percent_d12_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d12

tag: treatment


title: mouse_huT-cells_h45


title: 10_percent_d10_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d10

tag: tissue composition


title: 10_percent_d14_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d14

tag: cell type


title: IFNAR1 mutant, replicate 3

description: IFNAR1 mutant, replicate 3


title: mouse_ctrl_h4

value: control


title: 100_percent_d30.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d30.1

tag: growth time (days)


title: third series, GS5 day 3 _1

type: RNA

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Gene expression of exponentially growing GS5 fibroblasts, day 3 after 1× 4 Gy

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human  U133 Plus 2.0 Array-type from Affymetrix. A Custom CDF Version 24 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: skin fibroblasts GS5, exp. growth

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: AmnioMax C-100 basal medium with 7.5% AmnioMax supplement and 7.5% fetal calf serum, 2 mM glutamine plus penicillin/streptomycin

extract_protocol: Total RNA was prepared using Trizol (Gibco) followed by additional purification using the RNeasy Mini Kit (Qiagen)

treatment_protocol: Irradiation with 6 MV X-rays given asa  single dose of 4 Gy or fractions of 4 Gy/fraction.

tag: dosis[gy]

value: 4 Gy

tag: post-ir[day]

value: day 3 after 4 Gy


title: 10_percent_d8_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d8

tag: mixing day

tag: mixing percent human

tag: biological replicate number


title: mouse_huT_cells_h1


title: 10_percent_d10.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d10.1


title: 100_percent_d32_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d32


title: 100_percent_d28.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d28.1


title: 100_percent_d30_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d30


title: 10_percent_d7.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d7.1


title: third series, GS5 ctr. _2

description: Gene expression of exponentially growing GS5 fibroblasts

value: 0 Gy

value: day 1 after sham IR


title: 100_percent_d34_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d34


title: mouse_ctrl_h3


title: third series, GS3 day 3 _5

description: Gene expression of exponentially growing GS3 fibroblasts, day 3 after 1× 4 Gy

source_name: skin fibroblasts GS3, exp. growth


title: third series, GS4 day 3 _3

description: Gene expression of exponentially growing GS4 fibroblasts, day 3 after 1× 4 Gy

source_name: skin fibroblasts GS4, exp. growth


title: 10_percent_d7_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d7


title: mouse_ctrl_h2


title: third series, GS3 ctr. _6

description: Gene expression of exponentially growing GS3 fibroblasts


title: 100_percent_d28_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d28


title: mouse_ctrl_h1


title: 10_percent_d8.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d8.1


title: 100_percent_d26.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d26.1


title: 10_percent_d6.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d6.1


title: MaeaCsf1r-Cre HSC rep3

city: Bronx

first: Paul

last: Frenette

state: NY

address: 1301 Morris Park Avenue , Room 101

department: Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research

institute: Albert Einstein College of Medicine

data_processing:
Library adaptor sequences were trimmed using trim galore ( https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ )
Then reads were aligned to the mouse genome (mm10) using Spliced Transcripts Alignment to a Reference (STAR 2.5.3a)
Aligned reads were then quantified to transcriptome (mm10 - Ensembl Transcripts release 83), normalized and differentially expressed genes were identified using Partek Flow
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file contains gene counts for individual samples generated by Partek Flow

source_name: bone marrow

extract_protocol:
Total RNA from ~2000 sorted HSCs was extracted using the RNAeasy Plus Micro kit (Qiagen), and assessed for integrity and purity using an Aligent 2100 Bioanalyzer (Agilent Technologies).
Complementary DNA libraries were then generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) and the Nextera XT DNA Sample preparation Kit (Illumina).

tag: age

value: adult

value: bone marrow

value: Haematopoietic stem cells


title: MaeaCsf1r-Cre HSC rep2


title: 100_percent_d24_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d24

value: Homo sapiens cells only

value: Neural induction medium (see protocols section below)


title: 10_percent_d5.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d5.1

value: Homo Sapiens/Mus Musculus Chimera

value: pluripotent stem cell-derived neural cells


title: MaeaCsf1r-Cre HSC rep1


title: Aarhus protocol, IR, rep. 2

description: Gene expression of confluent GS4 fibroblasts after 3×Gy

source_name: skin fibroblasts GS4, confluent

value: day 2 after 1st IR, 2h after last


title: 10_percent_d6_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d6


title: third series, GS4 ctr. _4

description: Gene expression of exponentially growing GS4 fibroblasts


title: 100_percent_d26_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d26


title: Aarhus protocol, ctr., rep. 1 [H791]

description: Gene expression of confluent GS4 fibroblasts

value: 0Gy, control for 3×4Gy

value: day 2 after first, 2h after last sham IR


title: 100_percent_d22.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d22.1


title: Control HSC rep3


title: Control HSC rep2


title: Control HSC rep1


title: 10_percent_d4_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d4


title: 10_percent_d4.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d4.1


title: 100_percent_d20.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d20.1


title: day 2, rep. 2

description: Gene expression of exponentially growing GS4 fibroblasts, day 2 after 1× 4 Gy

value: day 2 after 4 Gy


title: 0_percent_d42.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d42.1

value: Mus musculus cells only


title: 100_percent_d24.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d24.1


title: 10_percent_d3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d3.1


title: control, rep.2


title: 100_percent_d20_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d20


title: day 3, rep. 2

description: Gene expression of exponentially growing GS4 fibroblasts, day 3 after 1× 4 Gy


title: 10_percent_d5_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d5


title: 0_percent_d42_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d42


title: Aarhus protocol, IR, rep. 1

description: Gene expression of confluent GS4 fibroblasts after 3×Gy


title: 10_percent_d3_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d3


title: 100_percent_d18.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d18.1


title: Aarhus protocol, ctr., rep. 1 [H667]


title: 10_percent_d2_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d2


title: 100_percent_d22_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d22


title: 10_percent_d2.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d2.1


title: 0_percent_d40_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d40


title: day 5 after first of two fractions (d0, d3), rep 1

description: Gene expression of exponentially growing GS4 fibroblasts, day 5 after first of 2× 4 Gy

value: day 5 after first IR, day 2 after  last IR


title: 0_percent_d38.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d38.1


title: 100_percent_d18_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d18


title: 10_percent_d1.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d1.1


title: day 3, rep. 1


title: 100_percent_d14.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d14.1


title: 10_percent_d1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
10_percent_d1


title: day 5, rep. 2

description: Gene expression of exponentially growing GS4 fibroblasts, day 5 after 1× 4 Gy

value: day 5 after 4 Gy


title: 0_percent_d36.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d36.1


title: 100_percent_d14_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d14


title: 0_percent_d36_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d36


title: 100_percent_d12.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d12.1


title: 100_percent_d12_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d12


title: 0_percent_d34_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d34


title: COS_2_17

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

data_processing:
base calling and demultiplexed with bcl2fastq
Sequencing quality was assessed with FastQC (v0.11.8)
Trimming of adapters and low quality bases with Trimmomatic (v0.39)
Trimmed reads were aligned to the Ensembl rhesus macaque reference genome (Mmul_10) with STAR (v2.7.0) using default parameters
Gene counts were obtained via STAR with the "--quantMode GeneCounts" parameter and Ensembl annotation (Mmul_10.99)
Genome_build: Mmul_10
Supplementary_files_format_and_content: tab delimited text file containing the raw counts for each gene (Ensembl Gene ID) in each sample

organism: Macaca mulatta

source_name: Blastocysts

growth_protocol: After IVF for 14-16 hr, oocytes were stripped of excess sperm by pipetting and visually assessed for fertilization; i.e., the presence of two pronuclei and/or two polar bodies. The zygotes were cultured for 6-8 days till they reached the blastocyst stage of development in 100 μL of one-step commercial medium supplemented with 10% serum protein (LifeGlobal, Guildford, CT) under mineral oil (Sage™, Trumbull, CT) at 37°C with 6% CO2, 5% O2

extract_protocol:
RNA was extracted from the blastocysts and cDNA prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (TakaraBio, Shiga, Japan) and the amplified cDNA was purified using the Agencourt AMPure XP Kit (Beckman Coulter, Brea, CA), both according to manufacturer’s instructions. cDNA was then sheared to approximately 250 base pairs in length using a Covaris M220 sonicator.
Sheared cDNA was resuspended in Tru-seq Resuspension Buffer and libraries prepared using a Tru-Seq Nano kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, except that 16 cycles of amplification were performed to account for the low input samples. Fragment size was measured using a Fragment Analyzer 5200 and samples quantified with qPCR and pooled at equimolar concentration. Multiplexed samples were sequenced across seven lanes of a single-read, 75 cycle run on an Illumina HiSeq 4000 sequencer.

treatment_protocol: Blastocysts were collected and incubated in EmbryoMax Acidic Tyrode’s Solution EMD Millipore, Burlington MA) for ~30 seconds for removal of the zona pellucida. These zona free blastocysts were then transferred to the extraction buffer of the ARCTURUS PicoPure RNA Isolation Kit (ThermoFisher Scientific KIT0204, Waltham, MA) and frozen at -80oC until RNA isolation.

tag: diet

value: Western Style Diet

tag: morphology durign development

value: Non-fragmented, non-multipolar


title: COS_2_15


title: 0_percent_d34.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d34.1

source_name: Co-cultured human and mouse pluripotent stem cell-derived neural cells


title: COS_2_16


title: COS_2_18

value: Fragmented, non-multipolar


title: VH_hp_1m_sample4

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

country: Italy

institute: European Brain Research Institute

hyb_protocol: Hybridizations were performed at 55°C for 20 h in a rotating oven. The hybridized microarrays were disassembled at room temperature in Agilent Gene Expression Wash Buffer 1. After the disassembly, the microarrays were washed in Gene expression Buffer 1 for five minutes at room temperature, followed by washing with Gene Expression Wash Buffer 2 for five minutes at 37°C. The microarrays were then treated with Acetonitrile for five minutes at room temperature.

scan_protocol: Post-hybridization image acquisition was accomplished using the Agilent Scanner G2564B. Data extraction from the 20 bits TIFF images was accomplished by Agilent Feature Extraction (FE)  ver 10.7  software using the standard Agilent one-color microRNA gene expression extraction protocol (ver  miRNA_107_Sep09 ).

data_processing: Data analyses pre-processing was performed using the proprietary Agilent GeneSpring GX software. Samples were normalized by the software to the 75th percentile in Log2 scale. The “gTotalGeneSignal” column of raw data files has been background subtracted and outlier rejected and is appropriate for use as the measured intensity for each miRNA gene without further manipulation. “gTotalGeneSignal” has then been summarized by gene symbol and the final normalized aggregated expression data in Log2 scale are provide in the  *GeneView.txt files. Differential espressed miRNAs have been selected by R-Bioconductor using a combination of two thresholds: |Log2 fold change| >1.0 and 1-tail heteroscedastic t-test p-value <0.05.

source_name: hippocampus

label_protocol: All the experimental steps involving the labelling, hybridization and washings of the samples were done following the Agilent protocol (http://chem.agilent.com). The Small RNA kit was used for separation and quantification of miRNA. One-color miRNA expression was performed according to the Agilent procedure, version 1.5, December 2007 (http://www.chem.agilent.com). Labeled miRNAs were obtained from 100 ng of total RNA through the ligation of a 5′-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) group at the 3′-end of each miRNA. To enhance the T4 RNA-ligase (Ambion) efficiency, we had previously treated total RNA with alkaline phosphatase (TaKaRa) at 37°C for 30 min. Labeled miRNAs were purified on chromatography columns (Micro Biospin 6, Biorad Laboratories) and then hybridized on a microarray. Each slide contained 8 identical microarrays with probes for 567 mouse and 73 mouse viral miRNAs.

growth_protocol: AD11 transgenic mice (Ruberti et al., 2000) express a recombinant version of the monoclonal antibody mAb alfaD11 that specifically recognizes and neutralizes NGF (Cattaneo et al., 1988; Covaceuszach et al., 2008). The AD11-VH controls are transgenic mice where only the heavy chain of the transgenic antibody is expressed, while in AD11 mice express the whole functional antibody (heavy + light chain). AD11-VH mice were used as transgenic control mice, since they are consistently negative with respect to all the neurodegeneration markers. Each AD11 or AD11-VH mouse was individually tested by transgene genotyping.  Mice were kept under a 12 hours dark to light cycle, with food and water ad libitum. Experiments were performed according to the European law for laboratory animal welfare and experimentation.

extract_protocol: Hippocampus of the right hemisphere was dissected from the brains of freshly sacrificed mice. Total RNA was isolated from these brain areas using Trizol (Invitrogen) and DNAse treated by Qiagen columns. Quality and integrity of each sample was checked using the Agilent BioAnalyzer 2100 (Agilent RNA 6000 nano kit): only samples that showed a ratio of absorbance 1.8< OD260/OD280 <2.0 and OD260/OD230 >2.0 were selected samples with a RNA Integrity Number (RIN) index higher than 8.0 .

treatment_protocol: The moce did not undergo any treatment before tissue extraction.

value: brain

tag: transgenic

value: anti-NGF antibody, only heavy chain

tag: Sex

value: female

value: 1 month


title: VH_hp_1m_sample3


title: VH_hp_1m_sample2


title: 100_percent_d16_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d16

value: Homo sapiens cells only

value: Neural induction medium (see protocols section below)


title: 0_percent_d38_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d38

value: pluripotent stem cell-derived neural cells


title: control, rep.1

description: Gene expression of exponentially growing GS4 fibroblasts

value: day 1 after sham IR


title: COS_2_14


title: 0_percent_d32.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d32.1


title: 100_percent_d10.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d10.1


title: VH_hp_1m_sample1


title: 100_percent_d8.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d8.1


title: day 2, rep. 1

description: Gene expression of exponentially growing GS4 fibroblasts, day 2 after 1× 4 Gy


title: AD11_hp_1m_sample4

value: anti-NGF antibody, heavy+light chain


title: 100_percent_d10_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d10


title: AD11_hp_1m_sample2


title: 0_percent_d32_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d32


title: 100_percent_d8_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d8


title: AD11_hp_1m_sample3


title: 0_percent_d40.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d40.1


title: COS_2_11


title: COS_2_10


title: 100_percent_d7.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d7.1


title: 100_percent_d7_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d7


title: cisplatin-treated_rat2

data_processing:
Trimming with preprocessReads from the systemPipeR package in R (Parameter: cutoff=20, low_quality_rate=0.4, batchsize=100000)
Aligment:tophat v2.1.1 bowtie v2.2.9 Parameter: -g 1 --segment-length 25 -i 30 -I  3000 Genome RN6
Read Counts: summarizeOverlaps from the GenomicsAlignments package in R Parameter: mode=Union, ignore.strand=TRUE, inter.feature=FALSE, singleEnd=TRUE
RPKM Normalization with the returnRPKM function from systemPipeR package in R
Genome_build: RN6
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

source_name: left kidney

growth_protocol: Male Sprague Dawley (SD) rats (250g) were purchased from Janvier Labs (Le Genest Saint Isle, France). Experiment started after 2 weeks of acclimatization. The animals had free access to pelleted standard rat chow (rat/mouse maintenance V1534-0001, Ssniff, Soest, Germany) and water in a temperature- and humidity- controlled facility (22°C, 55+/-5% rel. Hum.) with 12h light/12h dark cycle.

extract_protocol:
fresh left kidney was collected and snap frozen
RNA libraries were prepared for sequencing using standard BGISEQ protocols

treatment_protocol: Rats were treated with a single intraperioteneal dose of cisplatin (7mg/kgBW). 15 days after animals were sacrificed and the left kidney was collected from gene expression profiling

value: Sprague Dawley

value: Saline

value: full kidney


title: COS_2_9


title: day 5, rep. 1

description: Gene expression of exponentially growing GS4 fibroblasts, day 5 after 1× 4 Gy


title: 0_percent_d28_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d28

value: Mus musculus cells only


title: 0_percent_d28.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d28.1


title: COS_2_8


title: cisplatin-treated_rat1


title: COS_2_12


title: COS_2_7


title: cisplatin-treated_rat3


title: 100_percent_d6.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
100_percent_d6.1


title: 0_percent_d30.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d30.1


title: 0_percent_d26.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_441.ec.tab
genes_441.tpm.tab
0_percent_d26.1


title: AD11_hp_1m_sample1